diff --git a/.travis.yml b/.travis.yml index ba541f63f8..6dbefbd97c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -42,7 +42,7 @@ install: echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}; } - travis_retry inst script: -- python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest --with-doctest-ignore-unicode --with-cov --cover-package nipype --logging-level=DEBUG --verbosity=3 +- py.test --doctest-modules --cov=nipype nipype after_success: - bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests deploy: diff --git a/Makefile b/Makefile index 977e723ebb..f7bfffcd6c 100644 --- a/Makefile +++ b/Makefile @@ -5,7 +5,7 @@ PYTHON ?= python NOSETESTS=`which nosetests` -.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-doc test-coverage test html specs check-before-commit check +.PHONY: zipdoc sdist egg upload_to_pypi trailing-spaces clean-pyc clean-so clean-build clean-ctags clean in inplace test-code test-coverage test html specs check-before-commit check zipdoc: html zip documentation.zip doc/_build/html @@ -56,16 +56,11 @@ inplace: $(PYTHON) setup.py build_ext -i test-code: in - python -W once:FSL:UserWarning:nipype $(NOSETESTS) --with-doctest --with-doctest-ignore-unicode --logging-level=DEBUG --verbosity=3 nipype - -test-doc: - $(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --doctest-tests --doctest-extension=rst \ - --doctest-fixtures=_fixture doc/ + py.test --doctest-module nipype test-coverage: clean-tests in - $(NOSETESTS) -s --with-doctest --with-doctest-ignore-unicode --with-coverage --cover-package=nipype \ - --config=.coveragerc - + py.test --doctest-modules --cov-config .coveragerc --cov=nipype nipype + test: tests # just another name tests: clean test-code diff --git a/circle.yml b/circle.yml index 24af7cdd46..03032c988f 100644 --- a/circle.yml +++ b/circle.yml @@ -20,7 +20,7 @@ dependencies: - sudo apt-get -y update && sudo apt-get install -y wget bzip2 override: - - mkdir -p ~/examples ~/scratch/nose ~/scratch/logs + - mkdir -p ~/examples ~/scratch/pytest ~/scratch/logs - if [[ ! -d ~/examples/nipype-tutorial ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-tutorial.tar.bz2 "${DATA_NIPYPE_TUTORIAL_URL}" && tar xjf nipype-tutorial.tar.bz2 -C ~/examples/; fi - if [[ ! -d ~/examples/nipype-fsl_course_data ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O nipype-fsl_course_data.tar.gz "${DATA_NIPYPE_FSL_COURSE}" && tar xzf nipype-fsl_course_data.tar.gz -C ~/examples/; fi - if [[ ! -d ~/examples/feeds ]]; then wget --retry-connrefused --waitretry=5 --read-timeout=20 --timeout=15 -t 0 -q -O fsl-5.0.9-feeds.tar.gz "${DATA_NIPYPE_FSL_FEEDS}" && tar xzf fsl-5.0.9-feeds.tar.gz -C ~/examples/; fi @@ -35,10 +35,10 @@ dependencies: test: override: - docker run -v /etc/localtime:/etc/localtime:ro -v ~/scratch:/scratch -w /root/src/nipype/doc nipype/nipype_test:py35 /usr/bin/run_builddocs.sh - - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -e TRAVIS_PYTHON_VERSION="3.5" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_nosetests.sh py35 : + - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py35 /usr/bin/run_pytests.sh py35 : + timeout: 2600 + - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_pytests.sh py27 : timeout: 2600 - - docker run -v /etc/localtime:/etc/localtime:ro -e FSL_COURSE_DATA="/root/examples/nipype-fsl_course_data" -e TRAVIS_PYTHON_VERSION="2.7" -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /root/src/nipype nipype/nipype_test:py27 /usr/bin/run_nosetests.sh py27 : - timeout: 5200 - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow3d : timeout: 1600 - docker run -v /etc/localtime:/etc/localtime:ro -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh test_spm Linear /root/examples/ workflow4d : @@ -56,8 +56,8 @@ test: post: - bash docker/circleci/teardown.sh - - for xml_f in ${CIRCLE_TEST_REPORTS}/nose/coverage*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests; done - - for xml_f in ${CIRCLE_TEST_REPORTS}/nose/smoketest*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests; done + - for xml_f in ${CIRCLE_TEST_REPORTS}/pytest/coverage*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F unittests; done + - for xml_f in ${CIRCLE_TEST_REPORTS}/pytest/smoketest*.xml; do bash <(curl -s https://codecov.io/bash) -f $xml_f -t ac172a50-8e66-42e5-8822-5373fcf54686 -F smoketests; done general: artifacts: diff --git a/doc/devel/testing_nipype.rst b/doc/devel/testing_nipype.rst index 61fd877fbc..099539260e 100644 --- a/doc/devel/testing_nipype.rst +++ b/doc/devel/testing_nipype.rst @@ -40,7 +40,7 @@ or:: Test implementation ------------------- -Nipype testing framework is built upon `nose `_. +Nipype testing framework is built upon `pytest `_. By the time these guidelines are written, Nipype implements 17638 tests. After installation in developer mode, the tests can be run with the @@ -50,20 +50,18 @@ following simple command at the root folder of the project :: If ``make`` is not installed in the system, it is possible to run the tests using:: - python -W once:FSL:UserWarning:nipype `which nosetests` --with-doctest \ - --with-doctest-ignore-unicode --logging-level=DEBUG --verbosity=3 nipype + py.test --doctest-modules --cov=nipype nipype -A successful test run should complete in a few minutes and end with +A successful test run should complete in 10-30 minutes and end with something like:: ---------------------------------------------------------------------- - Ran 17922 tests in 107.254s + 2445 passed, 41 skipped, 7 xfailed in 1277.66 seconds - OK (SKIP=27) -All tests should pass (unless you're missing a dependency). If the ``SUBJECTS_DIR``` +No test should fail (unless you're missing a dependency). If the ``SUBJECTS_DIR``` environment variable is not set, some FreeSurfer related tests will fail. If any of the tests failed, please report them on our `bug tracker `_. @@ -90,6 +88,11 @@ Some tests in Nipype make use of some images distributed within the `FSL course To enable the tests depending on these data, just unpack the targz file and set the :code:`FSL_COURSE_DATA` environment variable to point to that folder. +Xfail tests +~~~~~~~~~~ + +Some tests are expect to fail until the code will be changed or for other reasons. + Avoiding any MATLAB calls from testing ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -115,7 +118,7 @@ Nipype is as easy as follows:: -v ~/examples:/root/examples:ro \ -v ~/scratch:/scratch \ -w /root/src/nipype \ - nipype/nipype_test:py27 /usr/bin/run_nosetests.sh + nipype/nipype_test:py27 /usr/bin/run_pytest.sh For running nipype in Python 3.5:: @@ -126,4 +129,4 @@ For running nipype in Python 3.5:: -v ~/examples:/root/examples:ro \ -v ~/scratch:/scratch \ -w /root/src/nipype \ - nipype/nipype_test:py35 /usr/bin/run_nosetests.sh + nipype/nipype_test:py35 /usr/bin/run_pytest.sh diff --git a/docker/circleci/run_nosetests.sh b/docker/circleci/run_pytests.sh similarity index 60% rename from docker/circleci/run_nosetests.sh rename to docker/circleci/run_pytests.sh index 9e912e20de..70f4b44ce6 100644 --- a/docker/circleci/run_nosetests.sh +++ b/docker/circleci/run_pytests.sh @@ -6,7 +6,7 @@ set -u PYTHON_VERSION=$( python -c "import sys; print('{}{}'.format(sys.version_info[0], sys.version_info[1]))" ) # Create necessary directories -mkdir -p /scratch/nose /scratch/crashfiles /scratch/logs/py${PYTHON_VERSION} +mkdir -p /scratch/pytest /scratch/crashfiles /scratch/logs/py${PYTHON_VERSION} # Create a nipype config file mkdir -p /root/.nipype @@ -20,17 +20,18 @@ if [[ "${PYTHON_VERSION}" -lt "30" ]]; then echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg fi -# Run tests +# Run tests using pytest cd /root/src/nipype/ make clean -nosetests -s nipype -c /root/src/nipype/.noserc --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}.xml" +py.test --doctest-modules --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}.xml --cov=nipype nipype + # Workaround: run here the profiler tests in python 3 if [[ "${PYTHON_VERSION}" -ge "30" ]]; then echo '[execution]' >> /root/.nipype/nipype.cfg echo 'profile_runtime = true' >> /root/.nipype/nipype.cfg - nosetests nipype/interfaces/tests/test_runtime_profiler.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_profiler.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_profiler.xml" - nosetests nipype/pipeline/plugins/tests/test_multiproc*.py --xunit-file="/scratch/nosetests_py${PYTHON_VERSION}_multiproc.xml" --cover-xml-file="/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml" + py.test --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}_profiler.xml --cov=nipype nipype/interfaces/tests/test_runtime_profiler.py + py.test --cov-report xml:/scratch/coverage_py${PYTHON_VERSION}_multiproc.xml --cov=nipype nipype/pipeline/plugins/tests/test_multiproc*.py fi # Copy crashfiles to scratch diff --git a/docker/circleci/teardown.sh b/docker/circleci/teardown.sh index c7ef852f5c..3b87a3c85c 100644 --- a/docker/circleci/teardown.sh +++ b/docker/circleci/teardown.sh @@ -6,8 +6,8 @@ set -u set -e -mkdir -p ${CIRCLE_TEST_REPORTS}/nose -sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/nose +mkdir -p ${CIRCLE_TEST_REPORTS}/pytest +sudo mv ~/scratch/*.xml ${CIRCLE_TEST_REPORTS}/pytest mkdir -p ~/docs sudo mv ~/scratch/docs/* ~/docs/ mkdir -p ~/logs diff --git a/docker/nipype_test/Dockerfile_base b/docker/nipype_test/Dockerfile_base index 4e242c5f6b..e2cebd02f0 100644 --- a/docker/nipype_test/Dockerfile_base +++ b/docker/nipype_test/Dockerfile_base @@ -122,6 +122,6 @@ RUN conda config --add channels conda-forge && \ nitime \ dipy \ pandas && \ - pip install nose-cov doctest-ignore-unicode configparser + pip install configparser CMD ["/bin/bash"] diff --git a/docker/nipype_test/Dockerfile_py27 b/docker/nipype_test/Dockerfile_py27 index d648771b6f..dc464b9e15 100644 --- a/docker/nipype_test/Dockerfile_py27 +++ b/docker/nipype_test/Dockerfile_py27 @@ -32,7 +32,7 @@ MAINTAINER The nipype developers https://github.com/nipy/nipype # Downgrade python to 2.7 RUN conda update -y conda && \ conda update --all -y python=2.7 && \ - pip install nose-cov doctest-ignore-unicode configparser + pip install configparser COPY docker/circleci/run_* /usr/bin/ RUN chmod +x /usr/bin/run_* diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py index 89a52b8abe..d3c8926497 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVColumn.py +++ b/nipype/algorithms/tests/test_auto_AddCSVColumn.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import AddCSVColumn @@ -15,7 +14,7 @@ def test_AddCSVColumn_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVColumn_outputs(): @@ -25,4 +24,4 @@ def test_AddCSVColumn_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index eaac3370c9..2477f30e1e 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import AddCSVRow @@ -16,7 +15,7 @@ def test_AddCSVRow_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AddCSVRow_outputs(): @@ -26,4 +25,4 @@ def test_AddCSVRow_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_AddNoise.py b/nipype/algorithms/tests/test_auto_AddNoise.py index 50aa563ce0..b7b9536c2a 100644 --- a/nipype/algorithms/tests/test_auto_AddNoise.py +++ b/nipype/algorithms/tests/test_auto_AddNoise.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import AddNoise @@ -21,7 +20,7 @@ def test_AddNoise_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AddNoise_outputs(): @@ -31,4 +30,4 @@ def test_AddNoise_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 03bb917e8b..da0edf3fb6 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..rapidart import ArtifactDetect @@ -49,7 +48,7 @@ def test_ArtifactDetect_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ArtifactDetect_outputs(): @@ -65,4 +64,4 @@ def test_ArtifactDetect_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py index 62a7b67b0c..52c31e5414 100644 --- a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py +++ b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import CalculateNormalizedMoments @@ -13,7 +12,7 @@ def test_CalculateNormalizedMoments_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CalculateNormalizedMoments_outputs(): @@ -23,4 +22,4 @@ def test_CalculateNormalizedMoments_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_ComputeDVARS.py b/nipype/algorithms/tests/test_auto_ComputeDVARS.py index 54050a9986..3d62e3f517 100644 --- a/nipype/algorithms/tests/test_auto_ComputeDVARS.py +++ b/nipype/algorithms/tests/test_auto_ComputeDVARS.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..confounds import ComputeDVARS @@ -35,7 +34,7 @@ def test_ComputeDVARS_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeDVARS_outputs(): @@ -54,4 +53,4 @@ def test_ComputeDVARS_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index e0a2d5f85c..4c524adce0 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..mesh import ComputeMeshWarp @@ -24,7 +23,7 @@ def test_ComputeMeshWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMeshWarp_outputs(): @@ -36,4 +35,4 @@ def test_ComputeMeshWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index 0e12142783..fab4362e3e 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import CreateNifti @@ -17,7 +16,7 @@ def test_CreateNifti_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CreateNifti_outputs(): @@ -27,4 +26,4 @@ def test_CreateNifti_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 4e5da64ba9..3404b1454b 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import Distance @@ -19,7 +18,7 @@ def test_Distance_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Distance_outputs(): @@ -32,4 +31,4 @@ def test_Distance_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py index 98450d8a64..bd4afa89d0 100644 --- a/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py +++ b/nipype/algorithms/tests/test_auto_FramewiseDisplacement.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..confounds import FramewiseDisplacement @@ -29,7 +28,7 @@ def test_FramewiseDisplacement_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FramewiseDisplacement_outputs(): @@ -41,4 +40,4 @@ def test_FramewiseDisplacement_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index dbc0c02474..f94f76ae32 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import FuzzyOverlap @@ -20,7 +19,7 @@ def test_FuzzyOverlap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FuzzyOverlap_outputs(): @@ -34,4 +33,4 @@ def test_FuzzyOverlap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index b77e6dfbd5..48bda3f74b 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import Gunzip @@ -14,7 +13,7 @@ def test_Gunzip_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Gunzip_outputs(): @@ -24,4 +23,4 @@ def test_Gunzip_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index 76b70b3369..568aebd68b 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..icc import ICC @@ -16,7 +15,7 @@ def test_ICC_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ICC_outputs(): @@ -28,4 +27,4 @@ def test_ICC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py index 1382385dc3..900cd3dd19 100644 --- a/nipype/algorithms/tests/test_auto_Matlab2CSV.py +++ b/nipype/algorithms/tests/test_auto_Matlab2CSV.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import Matlab2CSV @@ -13,7 +12,7 @@ def test_Matlab2CSV_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Matlab2CSV_outputs(): @@ -23,4 +22,4 @@ def test_Matlab2CSV_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py index 4d2d896db3..3d6d19e117 100644 --- a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py +++ b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import MergeCSVFiles @@ -19,7 +18,7 @@ def test_MergeCSVFiles_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MergeCSVFiles_outputs(): @@ -29,4 +28,4 @@ def test_MergeCSVFiles_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_MergeROIs.py b/nipype/algorithms/tests/test_auto_MergeROIs.py index 83eed3a4d4..8bbb37163c 100644 --- a/nipype/algorithms/tests/test_auto_MergeROIs.py +++ b/nipype/algorithms/tests/test_auto_MergeROIs.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import MergeROIs @@ -12,7 +11,7 @@ def test_MergeROIs_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MergeROIs_outputs(): @@ -22,4 +21,4 @@ def test_MergeROIs_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index dfd4c5bd63..bab79c3c14 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..mesh import MeshWarpMaths @@ -23,7 +22,7 @@ def test_MeshWarpMaths_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MeshWarpMaths_outputs(): @@ -34,4 +33,4 @@ def test_MeshWarpMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py index fb8c5ca876..ebdf824165 100644 --- a/nipype/algorithms/tests/test_auto_ModifyAffine.py +++ b/nipype/algorithms/tests/test_auto_ModifyAffine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import ModifyAffine @@ -16,7 +15,7 @@ def test_ModifyAffine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ModifyAffine_outputs(): @@ -26,4 +25,4 @@ def test_ModifyAffine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py index c2595baa72..148021fb74 100644 --- a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py +++ b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import NormalizeProbabilityMapSet @@ -11,7 +10,7 @@ def test_NormalizeProbabilityMapSet_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NormalizeProbabilityMapSet_outputs(): @@ -21,4 +20,4 @@ def test_NormalizeProbabilityMapSet_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index 0a30a382c9..87ac4cc6c0 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..mesh import P2PDistance @@ -24,7 +23,7 @@ def test_P2PDistance_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_P2PDistance_outputs(): @@ -36,4 +35,4 @@ def test_P2PDistance_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index 27aaac7d41..27b1a8a568 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import PickAtlas @@ -21,7 +20,7 @@ def test_PickAtlas_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PickAtlas_outputs(): @@ -31,4 +30,4 @@ def test_PickAtlas_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index 109933677c..c60c1bdc51 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..metrics import Similarity @@ -20,7 +19,7 @@ def test_Similarity_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Similarity_outputs(): @@ -30,4 +29,4 @@ def test_Similarity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py index ff46592c11..1f1dafcafb 100644 --- a/nipype/algorithms/tests/test_auto_SimpleThreshold.py +++ b/nipype/algorithms/tests/test_auto_SimpleThreshold.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import SimpleThreshold @@ -16,7 +15,7 @@ def test_SimpleThreshold_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SimpleThreshold_outputs(): @@ -26,4 +25,4 @@ def test_SimpleThreshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py index aac457a283..e850699315 100644 --- a/nipype/algorithms/tests/test_auto_SpecifyModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifyModel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..modelgen import SpecifyModel @@ -31,7 +30,7 @@ def test_SpecifyModel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SpecifyModel_outputs(): @@ -41,4 +40,4 @@ def test_SpecifyModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py index 6232ea0f11..892d9441ce 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..modelgen import SpecifySPMModel @@ -35,7 +34,7 @@ def test_SpecifySPMModel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SpecifySPMModel_outputs(): @@ -45,4 +44,4 @@ def test_SpecifySPMModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index 06fa7dad34..fcf8a3f358 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..modelgen import SpecifySparseModel @@ -45,7 +44,7 @@ def test_SpecifySparseModel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SpecifySparseModel_outputs(): @@ -57,4 +56,4 @@ def test_SpecifySparseModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_SplitROIs.py b/nipype/algorithms/tests/test_auto_SplitROIs.py index cd23a51468..f9c76b0d82 100644 --- a/nipype/algorithms/tests/test_auto_SplitROIs.py +++ b/nipype/algorithms/tests/test_auto_SplitROIs.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..misc import SplitROIs @@ -13,7 +12,7 @@ def test_SplitROIs_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SplitROIs_outputs(): @@ -25,4 +24,4 @@ def test_SplitROIs_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index f1b786aa8e..93d736b307 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..rapidart import StimulusCorrelation @@ -20,7 +19,7 @@ def test_StimulusCorrelation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_StimulusCorrelation_outputs(): @@ -30,4 +29,4 @@ def test_StimulusCorrelation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_TCompCor.py b/nipype/algorithms/tests/test_auto_TCompCor.py index 801aee89a6..6592187eb8 100644 --- a/nipype/algorithms/tests/test_auto_TCompCor.py +++ b/nipype/algorithms/tests/test_auto_TCompCor.py @@ -1,11 +1,11 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..confounds import TCompCor def test_TCompCor_inputs(): input_map = dict(components_file=dict(usedefault=True, ), + header=dict(), ignore_exception=dict(nohash=True, usedefault=True, ), @@ -25,7 +25,7 @@ def test_TCompCor_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TCompCor_outputs(): @@ -35,4 +35,4 @@ def test_TCompCor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py index 3dd8ac6d2a..6dbc4105a3 100644 --- a/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py +++ b/nipype/algorithms/tests/test_auto_TVTKBaseInterface.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..mesh import TVTKBaseInterface @@ -12,5 +11,5 @@ def test_TVTKBaseInterface_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index 741b9f0c60..78caf976ea 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..mesh import WarpPoints @@ -24,7 +23,7 @@ def test_WarpPoints_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): @@ -34,4 +33,4 @@ def test_WarpPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/algorithms/tests/test_compcor.py b/nipype/algorithms/tests/test_compcor.py index bbc3bc243c..1d582b7404 100644 --- a/nipype/algorithms/tests/test_compcor.py +++ b/nipype/algorithms/tests/test_compcor.py @@ -1,27 +1,26 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: import os -import tempfile -import shutil -import unittest import nibabel as nb import numpy as np -from ...testing import assert_equal, assert_true, utils, assert_in +import pytest +from ...testing import utils from ..confounds import CompCor, TCompCor, ACompCor -class TestCompCor(unittest.TestCase): + +class TestCompCor(): ''' Note: Tests currently do a poor job of testing functionality ''' filenames = {'functionalnii': 'compcorfunc.nii', 'masknii': 'compcormask.nii', 'components_file': None} - - def setUp(self): + + @pytest.fixture(autouse=True) + def setup_class(self, tmpdir): # setup - self.orig_dir = os.getcwd() - self.temp_dir = tempfile.mkdtemp() + self.temp_dir = str(tmpdir) os.chdir(self.temp_dir) noise = np.fromfunction(self.fake_noise_fun, self.fake_data.shape) self.realigned_file = utils.save_toy_nii(self.fake_data + noise, @@ -45,6 +44,7 @@ def test_compcor(self): components_file='acc_components_file'), expected_components, 'aCompCor') + def test_tcompcor(self): ccinterface = TCompCor(realigned_file=self.realigned_file, percentile_threshold=0.75) self.run_cc(ccinterface, [['-0.1114536190', '-0.4632908609'], @@ -59,7 +59,7 @@ def test_tcompcor_no_percentile(self): mask = nb.load('mask.nii').get_data() num_nonmasked_voxels = np.count_nonzero(mask) - assert_equal(num_nonmasked_voxels, 1) + assert num_nonmasked_voxels == 1 def test_compcor_no_regress_poly(self): self.run_cc(CompCor(realigned_file=self.realigned_file, mask_file=self.mask_file, @@ -74,7 +74,7 @@ def test_tcompcor_asymmetric_dim(self): asymmetric_data = utils.save_toy_nii(np.zeros(asymmetric_shape), 'asymmetric.nii') TCompCor(realigned_file=asymmetric_data).run() - self.assertEqual(nb.load('mask.nii').get_data().shape, asymmetric_shape[:3]) + assert nb.load('mask.nii').get_data().shape == asymmetric_shape[:3] def test_compcor_bad_input_shapes(self): shape_less_than = (1, 2, 2, 5) # dim 0 is < dim 0 of self.mask_file (2) @@ -83,13 +83,13 @@ def test_compcor_bad_input_shapes(self): for data_shape in (shape_less_than, shape_more_than): data_file = utils.save_toy_nii(np.zeros(data_shape), 'temp.nii') interface = CompCor(realigned_file=data_file, mask_file=self.mask_file) - self.assertRaisesRegexp(ValueError, "dimensions", interface.run) + with pytest.raises_regexp(ValueError, "dimensions"): interface.run() def test_tcompcor_bad_input_dim(self): bad_dims = (2, 2, 2) data_file = utils.save_toy_nii(np.zeros(bad_dims), 'temp.nii') interface = TCompCor(realigned_file=data_file) - self.assertRaisesRegexp(ValueError, '4-D', interface.run) + with pytest.raises_regexp(ValueError, '4-D'): interface.run() def run_cc(self, ccinterface, expected_components, expected_header='CompCor'): # run @@ -97,10 +97,10 @@ def run_cc(self, ccinterface, expected_components, expected_header='CompCor'): # assert expected_file = ccinterface._list_outputs()['components_file'] - assert_equal(ccresult.outputs.components_file, expected_file) - assert_true(os.path.exists(expected_file)) - assert_true(os.path.getsize(expected_file) > 0) - assert_equal(ccinterface.inputs.num_components, 6) + assert ccresult.outputs.components_file == expected_file + assert os.path.exists(expected_file) + assert os.path.getsize(expected_file) > 0 + assert ccinterface.inputs.num_components == 6 with open(ccresult.outputs.components_file, 'r') as components_file: expected_n_components = min(ccinterface.inputs.num_components, self.fake_data.shape[3]) @@ -110,21 +110,19 @@ def run_cc(self, ccinterface, expected_components, expected_header='CompCor'): header = components_data.pop(0) # the first item will be '#', we can throw it out expected_header = [expected_header + str(i) for i in range(expected_n_components)] for i, heading in enumerate(header): - assert_in(expected_header[i], heading) + assert expected_header[i] in heading num_got_timepoints = len(components_data) - assert_equal(num_got_timepoints, self.fake_data.shape[3]) + assert num_got_timepoints == self.fake_data.shape[3] for index, timepoint in enumerate(components_data): - assert_true(len(timepoint) == ccinterface.inputs.num_components - or len(timepoint) == self.fake_data.shape[3]) - assert_equal(timepoint[:2], expected_components[index]) + assert (len(timepoint) == ccinterface.inputs.num_components + or len(timepoint) == self.fake_data.shape[3]) + assert timepoint[:2] == expected_components[index] return ccresult - def tearDown(self): - os.chdir(self.orig_dir) - shutil.rmtree(self.temp_dir) - def fake_noise_fun(self, i, j, l, m): + @staticmethod + def fake_noise_fun(i, j, l, m): return m*i + l - j fake_data = np.array([[[[8, 5, 3, 8, 0], diff --git a/nipype/algorithms/tests/test_confounds.py b/nipype/algorithms/tests/test_confounds.py index 2a32f6c156..a1d6ec9557 100644 --- a/nipype/algorithms/tests/test_confounds.py +++ b/nipype/algorithms/tests/test_confounds.py @@ -1,12 +1,11 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- import os -from tempfile import mkdtemp -from shutil import rmtree from io import open -from nipype.testing import (assert_equal, example_data, skipif, assert_true, assert_in) +import pytest +from nipype.testing import example_data from nipype.algorithms.confounds import FramewiseDisplacement, ComputeDVARS import numpy as np @@ -19,8 +18,8 @@ pass -def test_fd(): - tempdir = mkdtemp() +def test_fd(tmpdir): + tempdir = str(tmpdir) ground_truth = np.loadtxt(example_data('fsl_motion_outliers_fd.txt')) fdisplacement = FramewiseDisplacement(in_plots=example_data('fsl_mcflirt_movpar.txt'), out_file=tempdir + '/fd.txt') @@ -28,29 +27,21 @@ def test_fd(): with open(res.outputs.out_file) as all_lines: for line in all_lines: - yield assert_in, 'FramewiseDisplacement', line + assert 'FramewiseDisplacement' in line break - yield assert_true, np.allclose(ground_truth, np.loadtxt(res.outputs.out_file, skiprows=1), atol=.16) - yield assert_true, np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-2 + assert np.allclose(ground_truth, np.loadtxt(res.outputs.out_file, skiprows=1), atol=.16) + assert np.abs(ground_truth.mean() - res.outputs.fd_average) < 1e-2 - rmtree(tempdir) -@skipif(nonitime) -def test_dvars(): - tempdir = mkdtemp() +@pytest.mark.skipif(nonitime, reason="nitime is not installed") +def test_dvars(tmpdir): ground_truth = np.loadtxt(example_data('ds003_sub-01_mc.DVARS')) dvars = ComputeDVARS(in_file=example_data('ds003_sub-01_mc.nii.gz'), in_mask=example_data('ds003_sub-01_mc_brainmask.nii.gz'), save_all=True) - - origdir = os.getcwd() - os.chdir(tempdir) - + os.chdir(str(tmpdir)) res = dvars.run() dv1 = np.loadtxt(res.outputs.out_std) - yield assert_equal, (np.abs(dv1 - ground_truth).sum()/ len(dv1)) < 0.05, True - - os.chdir(origdir) - rmtree(tempdir) + assert (np.abs(dv1 - ground_truth).sum()/ len(dv1)) < 0.05 diff --git a/nipype/algorithms/tests/test_errormap.py b/nipype/algorithms/tests/test_errormap.py index 361646add0..a86c932ca4 100644 --- a/nipype/algorithms/tests/test_errormap.py +++ b/nipype/algorithms/tests/test_errormap.py @@ -1,17 +1,17 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -from nipype.testing import (assert_equal, example_data) +import pytest +from nipype.testing import example_data from nipype.algorithms.metrics import ErrorMap import nibabel as nib import numpy as np -from tempfile import mkdtemp import os -def test_errormap(): +def test_errormap(tmpdir): - tempdir = mkdtemp() + tempdir = str(tmpdir) # Single-Spectual # Make two fake 2*2*2 voxel volumes volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]]) # John von Neumann's birthday @@ -32,22 +32,22 @@ def test_errormap(): errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz') errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz') result = errmap.run() - yield assert_equal, result.outputs.distance, 1.125 + assert result.outputs.distance == 1.125 # Square metric errmap.inputs.metric = 'sqeuclidean' result = errmap.run() - yield assert_equal, result.outputs.distance, 1.125 + assert result.outputs.distance == 1.125 # Linear metric errmap.inputs.metric = 'euclidean' result = errmap.run() - yield assert_equal, result.outputs.distance, 0.875 + assert result.outputs.distance == 0.875 # Masked errmap.inputs.mask = os.path.join(tempdir, 'mask.nii.gz') result = errmap.run() - yield assert_equal, result.outputs.distance, 1.0 + assert result.outputs.distance == 1.0 # Multi-Spectual volume3 = np.array([[[1.0, 6.0], [0.0, 3.0]], [[1.0, 9.0], [3.0, 6.0]]]) # Raymond Vahan Damadian's birthday @@ -69,8 +69,8 @@ def test_errormap(): errmap.inputs.in_ref = os.path.join(tempdir, 'alan-ray.nii.gz') errmap.inputs.metric = 'sqeuclidean' result = errmap.run() - yield assert_equal, result.outputs.distance, 5.5 + assert result.outputs.distance == 5.5 errmap.inputs.metric = 'euclidean' result = errmap.run() - yield assert_equal, result.outputs.distance, np.float32(1.25 * (2**0.5)) + assert result.outputs.distance == np.float32(1.25 * (2**0.5)) diff --git a/nipype/algorithms/tests/test_icc_anova.py b/nipype/algorithms/tests/test_icc_anova.py index 8b0262848b..8177c89940 100644 --- a/nipype/algorithms/tests/test_icc_anova.py +++ b/nipype/algorithms/tests/test_icc_anova.py @@ -1,7 +1,6 @@ # -*- coding: utf-8 -*- from __future__ import division import numpy as np -from nipype.testing import assert_equal from nipype.algorithms.icc import ICC_rep_anova @@ -17,7 +16,7 @@ def test_ICC_rep_anova(): icc, r_var, e_var, _, dfc, dfe = ICC_rep_anova(Y) # see table 4 - yield assert_equal, round(icc, 2), 0.71 - yield assert_equal, dfc, 3 - yield assert_equal, dfe, 15 - yield assert_equal, r_var / (r_var + e_var), icc + assert round(icc, 2) == 0.71 + assert dfc == 3 + assert dfe == 15 + assert r_var / (r_var + e_var) == icc diff --git a/nipype/algorithms/tests/test_mesh_ops.py b/nipype/algorithms/tests/test_mesh_ops.py index 03091ed264..32f59e8f04 100644 --- a/nipype/algorithms/tests/test_mesh_ops.py +++ b/nipype/algorithms/tests/test_mesh_ops.py @@ -4,101 +4,86 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: import os -from shutil import rmtree -from tempfile import mkdtemp -from nipype.testing import (assert_equal, assert_raises, skipif, - assert_almost_equal, example_data) +import pytest +import nipype.testing as npt +from nipype.testing import example_data import numpy as np from nipype.algorithms import mesh as m from ...interfaces import vtkbase as VTKInfo -def test_ident_distances(): - tempdir = mkdtemp() - curdir = os.getcwd() +@pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed") +def test_ident_distances(tmpdir): + tempdir = str(tmpdir) os.chdir(tempdir) - if VTKInfo.no_tvtk(): - yield assert_raises, ImportError, m.ComputeMeshWarp - else: - in_surf = example_data('surf01.vtk') - dist_ident = m.ComputeMeshWarp() - dist_ident.inputs.surface1 = in_surf - dist_ident.inputs.surface2 = in_surf - dist_ident.inputs.out_file = os.path.join(tempdir, 'distance.npy') - res = dist_ident.run() - yield assert_equal, res.outputs.distance, 0.0 - - dist_ident.inputs.weighting = 'area' - res = dist_ident.run() - yield assert_equal, res.outputs.distance, 0.0 - - os.chdir(curdir) - rmtree(tempdir) - - -def test_trans_distances(): - tempdir = mkdtemp() - curdir = os.getcwd() + in_surf = example_data('surf01.vtk') + dist_ident = m.ComputeMeshWarp() + dist_ident.inputs.surface1 = in_surf + dist_ident.inputs.surface2 = in_surf + dist_ident.inputs.out_file = os.path.join(tempdir, 'distance.npy') + res = dist_ident.run() + assert res.outputs.distance == 0.0 + + dist_ident.inputs.weighting = 'area' + res = dist_ident.run() + assert res.outputs.distance == 0.0 + + +@pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed") +def test_trans_distances(tmpdir): + tempdir = str(tmpdir) os.chdir(tempdir) + + from ...interfaces.vtkbase import tvtk + + in_surf = example_data('surf01.vtk') + warped_surf = os.path.join(tempdir, 'warped.vtk') + + inc = np.array([0.7, 0.3, -0.2]) + + r1 = tvtk.PolyDataReader(file_name=in_surf) + vtk1 = VTKInfo.vtk_output(r1) + r1.update() + vtk1.points = np.array(vtk1.points) + inc + + writer = tvtk.PolyDataWriter(file_name=warped_surf) + VTKInfo.configure_input_data(writer, vtk1) + writer.write() + + dist = m.ComputeMeshWarp() + dist.inputs.surface1 = in_surf + dist.inputs.surface2 = warped_surf + dist.inputs.out_file = os.path.join(tempdir, 'distance.npy') + res = dist.run() + npt.assert_almost_equal(res.outputs.distance, np.linalg.norm(inc), 4) + dist.inputs.weighting = 'area' + res = dist.run() + npt.assert_almost_equal(res.outputs.distance, np.linalg.norm(inc), 4) + + +@pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed") +def test_warppoints(tmpdir): + os.chdir(str(tmpdir)) - if VTKInfo.no_tvtk(): - yield assert_raises, ImportError, m.ComputeMeshWarp - else: - from ...interfaces.vtkbase import tvtk - - in_surf = example_data('surf01.vtk') - warped_surf = os.path.join(tempdir, 'warped.vtk') - - inc = np.array([0.7, 0.3, -0.2]) - - r1 = tvtk.PolyDataReader(file_name=in_surf) - vtk1 = VTKInfo.vtk_output(r1) - r1.update() - vtk1.points = np.array(vtk1.points) + inc - - writer = tvtk.PolyDataWriter(file_name=warped_surf) - VTKInfo.configure_input_data(writer, vtk1) - writer.write() - - dist = m.ComputeMeshWarp() - dist.inputs.surface1 = in_surf - dist.inputs.surface2 = warped_surf - dist.inputs.out_file = os.path.join(tempdir, 'distance.npy') - res = dist.run() - yield assert_almost_equal, res.outputs.distance, np.linalg.norm(inc), 4 - dist.inputs.weighting = 'area' - res = dist.run() - yield assert_almost_equal, res.outputs.distance, np.linalg.norm(inc), 4 - - os.chdir(curdir) - rmtree(tempdir) - + # TODO: include regression tests for when tvtk is installed -def test_warppoints(): - tempdir = mkdtemp() - curdir = os.getcwd() - os.chdir(tempdir) - if VTKInfo.no_tvtk(): - yield assert_raises, ImportError, m.WarpPoints +@pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed") +def test_meshwarpmaths(tmpdir): + os.chdir(str(tmpdir)) # TODO: include regression tests for when tvtk is installed - os.chdir(curdir) - rmtree(tempdir) +@pytest.mark.skipif(not VTKInfo.no_tvtk(), reason="tvtk is installed") +def test_importerror(): + with pytest.raises(ImportError): + m.ComputeMeshWarp() -def test_meshwarpmaths(): - tempdir = mkdtemp() - curdir = os.getcwd() - os.chdir(tempdir) - - if VTKInfo.no_tvtk(): - yield assert_raises, ImportError, m.MeshWarpMaths - - # TODO: include regression tests for when tvtk is installed + with pytest.raises(ImportError): + m.WarpPoints() - os.chdir(curdir) - rmtree(tempdir) + with pytest.raises(ImportError): + m.MeshWarpMaths() diff --git a/nipype/algorithms/tests/test_modelgen.py b/nipype/algorithms/tests/test_modelgen.py index 72aa0eb845..9359c6e665 100644 --- a/nipype/algorithms/tests/test_modelgen.py +++ b/nipype/algorithms/tests/test_modelgen.py @@ -5,21 +5,19 @@ from copy import deepcopy import os -from shutil import rmtree -from tempfile import mkdtemp from nibabel import Nifti1Image import numpy as np -from nipype.testing import (assert_equal, - assert_raises, assert_almost_equal) +import pytest +import numpy.testing as npt from nipype.interfaces.base import Bunch, TraitError from nipype.algorithms.modelgen import (SpecifyModel, SpecifySparseModel, SpecifySPMModel) -def test_modelgen1(): - tempdir = mkdtemp() +def test_modelgen1(tmpdir): + tempdir = str(tmpdir) filename1 = os.path.join(tempdir, 'test1.nii') filename2 = os.path.join(tempdir, 'test2.nii') Nifti1Image(np.random.rand(10, 10, 10, 200), np.eye(4)).to_filename(filename1) @@ -27,7 +25,7 @@ def test_modelgen1(): s = SpecifyModel() s.inputs.input_units = 'scans' set_output_units = lambda: setattr(s.inputs, 'output_units', 'scans') - yield assert_raises, TraitError, set_output_units + with pytest.raises(TraitError): set_output_units() s.inputs.functional_runs = [filename1, filename2] s.inputs.time_repetition = 6 s.inputs.high_pass_filter_cutoff = 128. @@ -37,39 +35,39 @@ def test_modelgen1(): pmod=None, regressors=None, regressor_names=None, tmod=None)] s.inputs.subject_info = info res = s.run() - yield assert_equal, len(res.outputs.session_info), 2 - yield assert_equal, len(res.outputs.session_info[0]['regress']), 0 - yield assert_equal, len(res.outputs.session_info[0]['cond']), 1 - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([12, 300, 600, 1080]) + assert len(res.outputs.session_info) == 2 + assert len(res.outputs.session_info[0]['regress']) == 0 + assert len(res.outputs.session_info[0]['cond']) == 1 + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([12, 300, 600, 1080])) info = [Bunch(conditions=['cond1'], onsets=[[2]], durations=[[1]]), Bunch(conditions=['cond1'], onsets=[[3]], durations=[[1]])] s.inputs.subject_info = deepcopy(info) res = s.run() - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([6.]) - yield assert_almost_equal, np.array(res.outputs.session_info[1]['cond'][0]['duration']), np.array([6.]) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([6.])) + npt.assert_almost_equal(np.array(res.outputs.session_info[1]['cond'][0]['duration']), np.array([6.])) info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]]), Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2, 4]], durations=[[1, 1], [1, 1]])] s.inputs.subject_info = deepcopy(info) s.inputs.input_units = 'scans' res = s.run() - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([6., 6.]) - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([6., ]) - yield assert_almost_equal, np.array(res.outputs.session_info[1]['cond'][1]['duration']), np.array([6., 6.]) - rmtree(tempdir) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([6., 6.])) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([6., ])) + npt.assert_almost_equal(np.array(res.outputs.session_info[1]['cond'][1]['duration']), np.array([6., 6.])) -def test_modelgen_spm_concat(): - tempdir = mkdtemp() +def test_modelgen_spm_concat(tmpdir): + tempdir = str(tmpdir) filename1 = os.path.join(tempdir, 'test1.nii') filename2 = os.path.join(tempdir, 'test2.nii') Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename1) Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename2) + # Test case when only one duration is passed, as being the same for all onsets. s = SpecifySPMModel() s.inputs.input_units = 'secs' s.inputs.concatenate_runs = True setattr(s.inputs, 'output_units', 'secs') - yield assert_equal, s.inputs.output_units, 'secs' + assert s.inputs.output_units == 'secs' s.inputs.functional_runs = [filename1, filename2] s.inputs.time_repetition = 6 s.inputs.high_pass_filter_cutoff = 128. @@ -77,24 +75,27 @@ def test_modelgen_spm_concat(): Bunch(conditions=['cond1'], onsets=[[30, 40, 100, 150]], durations=[[1]])] s.inputs.subject_info = deepcopy(info) res = s.run() - yield assert_equal, len(res.outputs.session_info), 1 - yield assert_equal, len(res.outputs.session_info[0]['regress']), 1 - yield assert_equal, np.sum(res.outputs.session_info[0]['regress'][0]['val']), 30 - yield assert_equal, len(res.outputs.session_info[0]['cond']), 1 - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0]) - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1., 1., 1., 1., 1., 1., 1.]) + assert len(res.outputs.session_info) == 1 + assert len(res.outputs.session_info[0]['regress']) == 1 + assert np.sum(res.outputs.session_info[0]['regress'][0]['val']) == 30 + assert len(res.outputs.session_info[0]['cond']) == 1 + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0])) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1., 1., 1., 1., 1., 1., 1.])) + # Test case of scans as output units instead of seconds setattr(s.inputs, 'output_units', 'scans') - yield assert_equal, s.inputs.output_units, 'scans' + assert s.inputs.output_units == 'scans' s.inputs.subject_info = deepcopy(info) res = s.run() - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0]) / 6 + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0, 210.0, 220.0, 280.0, 330.0]) / 6) + # Test case for no concatenation with seconds as output units s.inputs.concatenate_runs = False s.inputs.subject_info = deepcopy(info) s.inputs.output_units = 'secs' res = s.run() - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0]) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['onset']), np.array([2.0, 50.0, 100.0, 170.0])) + # Test case for variable number of events in separate runs, sometimes unique. filename3 = os.path.join(tempdir, 'test3.nii') Nifti1Image(np.random.rand(10, 10, 10, 30), np.eye(4)).to_filename(filename3) @@ -104,10 +105,11 @@ def test_modelgen_spm_concat(): Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]])] s.inputs.subject_info = deepcopy(info) res = s.run() - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1.]) - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1., ]) - yield assert_almost_equal, np.array(res.outputs.session_info[1]['cond'][1]['duration']), np.array([1., 1.]) - yield assert_almost_equal, np.array(res.outputs.session_info[2]['cond'][1]['duration']), np.array([1., ]) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1.])) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1., ])) + npt.assert_almost_equal(np.array(res.outputs.session_info[1]['cond'][1]['duration']), np.array([1., 1.])) + npt.assert_almost_equal(np.array(res.outputs.session_info[2]['cond'][1]['duration']), np.array([1., ])) + # Test case for variable number of events in concatenated runs, sometimes unique. s.inputs.concatenate_runs = True info = [Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]]), @@ -115,13 +117,12 @@ def test_modelgen_spm_concat(): Bunch(conditions=['cond1', 'cond2'], onsets=[[2, 3], [2]], durations=[[1, 1], [1]])] s.inputs.subject_info = deepcopy(info) res = s.run() - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1., 1., 1., 1., 1.]) - yield assert_almost_equal, np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1., 1., 1., 1.]) - rmtree(tempdir) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][0]['duration']), np.array([1., 1., 1., 1., 1., 1.])) + npt.assert_almost_equal(np.array(res.outputs.session_info[0]['cond'][1]['duration']), np.array([1., 1., 1., 1.])) -def test_modelgen_sparse(): - tempdir = mkdtemp() +def test_modelgen_sparse(tmpdir): + tempdir = str(tmpdir) filename1 = os.path.join(tempdir, 'test1.nii') filename2 = os.path.join(tempdir, 'test2.nii') Nifti1Image(np.random.rand(10, 10, 10, 50), np.eye(4)).to_filename(filename1) @@ -137,19 +138,22 @@ def test_modelgen_sparse(): s.inputs.time_acquisition = 2 s.inputs.high_pass_filter_cutoff = np.inf res = s.run() - yield assert_equal, len(res.outputs.session_info), 2 - yield assert_equal, len(res.outputs.session_info[0]['regress']), 1 - yield assert_equal, len(res.outputs.session_info[0]['cond']), 0 + assert len(res.outputs.session_info) == 2 + assert len(res.outputs.session_info[0]['regress']) == 1 + assert len(res.outputs.session_info[0]['cond']) == 0 + s.inputs.stimuli_as_impulses = False res = s.run() - yield assert_equal, res.outputs.session_info[0]['regress'][0]['val'][0], 1.0 + assert res.outputs.session_info[0]['regress'][0]['val'][0] == 1.0 + s.inputs.model_hrf = True res = s.run() - yield assert_almost_equal, res.outputs.session_info[0]['regress'][0]['val'][0], 0.016675298129743384 - yield assert_equal, len(res.outputs.session_info[0]['regress']), 1 + npt.assert_almost_equal(res.outputs.session_info[0]['regress'][0]['val'][0], 0.016675298129743384) + assert len(res.outputs.session_info[0]['regress']) == 1 s.inputs.use_temporal_deriv = True res = s.run() - yield assert_equal, len(res.outputs.session_info[0]['regress']), 2 - yield assert_almost_equal, res.outputs.session_info[0]['regress'][0]['val'][0], 0.016675298129743384 - yield assert_almost_equal, res.outputs.session_info[1]['regress'][1]['val'][5], 0.007671459162258378 - rmtree(tempdir) + + assert len(res.outputs.session_info[0]['regress']) == 2 + npt.assert_almost_equal(res.outputs.session_info[0]['regress'][0]['val'][0], 0.016675298129743384) + npt.assert_almost_equal(res.outputs.session_info[1]['regress'][1]['val'][5], 0.007671459162258378) + diff --git a/nipype/algorithms/tests/test_moments.py b/nipype/algorithms/tests/test_moments.py index 3c7b0b46ce..12de44750a 100644 --- a/nipype/algorithms/tests/test_moments.py +++ b/nipype/algorithms/tests/test_moments.py @@ -1,6 +1,5 @@ # -*- coding: utf-8 -*- import numpy as np -from nipype.testing import assert_true import tempfile from nipype.algorithms.misc import calc_moments @@ -131,9 +130,9 @@ def test_skew(): f.write(data) f.flush() skewness = calc_moments(f.name, 3) - yield assert_true, np.allclose(skewness, np.array( - [-0.23418937314622, 0.2946365564954823, -0.05781002053540932, - -0.3512508282578762, - - 0.07035664150233077, - - 0.01935867699166935, - 0.00483863369427428, 0.21879460029850167])) + assert np.allclose(skewness, np.array( + [-0.23418937314622, 0.2946365564954823, -0.05781002053540932, + -0.3512508282578762, - + 0.07035664150233077, - + 0.01935867699166935, + 0.00483863369427428, 0.21879460029850167])) diff --git a/nipype/algorithms/tests/test_normalize_tpms.py b/nipype/algorithms/tests/test_normalize_tpms.py index d612ce2708..907c1d9619 100644 --- a/nipype/algorithms/tests/test_normalize_tpms.py +++ b/nipype/algorithms/tests/test_normalize_tpms.py @@ -5,11 +5,9 @@ from builtins import range import os -from shutil import rmtree -from tempfile import mkdtemp -from nipype.testing import (assert_equal, assert_raises, - assert_almost_equal, example_data) +import pytest +from nipype.testing import example_data import numpy as np import nibabel as nb @@ -18,8 +16,8 @@ from nipype.algorithms.misc import normalize_tpms -def test_normalize_tpms(): - tempdir = mkdtemp() +def test_normalize_tpms(tmpdir): + tempdir = str(tmpdir) in_mask = example_data('tpms_msk.nii.gz') mskdata = nb.load(in_mask).get_data() @@ -49,9 +47,8 @@ def test_normalize_tpms(): for i, tstfname in enumerate(out_files): normdata = nb.load(tstfname).get_data() sumdata += normdata - yield assert_equal, np.all(normdata[mskdata == 0] == 0), True - yield assert_equal, np.allclose(normdata, mapdata[i]), True + assert np.all(normdata[mskdata == 0] == 0) + assert np.allclose(normdata, mapdata[i]) - yield assert_equal, np.allclose(sumdata[sumdata > 0.0], 1.0), True + assert np.allclose(sumdata[sumdata > 0.0], 1.0) - rmtree(tempdir) diff --git a/nipype/algorithms/tests/test_overlap.py b/nipype/algorithms/tests/test_overlap.py index f7f9f9df29..d4b32ef38d 100644 --- a/nipype/algorithms/tests/test_overlap.py +++ b/nipype/algorithms/tests/test_overlap.py @@ -4,48 +4,41 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: import os -from shutil import rmtree -from tempfile import mkdtemp from nipype.testing import (example_data) import numpy as np -def test_overlap(): +def test_overlap(tmpdir): from nipype.algorithms.metrics import Overlap def check_close(val1, val2): import numpy.testing as npt return npt.assert_almost_equal(val1, val2, decimal=3) - tempdir = mkdtemp() in1 = example_data('segmentation0.nii.gz') in2 = example_data('segmentation1.nii.gz') - cwd = os.getcwd() - os.chdir(tempdir) + os.chdir(str(tmpdir)) overlap = Overlap() overlap.inputs.volume1 = in1 overlap.inputs.volume2 = in1 res = overlap.run() - yield check_close, res.outputs.jaccard, 1.0 + check_close(res.outputs.jaccard, 1.0) + overlap = Overlap() overlap.inputs.volume1 = in1 overlap.inputs.volume2 = in2 res = overlap.run() - - yield check_close, res.outputs.jaccard, 0.99705 + check_close(res.outputs.jaccard, 0.99705) overlap = Overlap() overlap.inputs.volume1 = in1 overlap.inputs.volume2 = in2 overlap.inputs.vol_units = 'mm' res = overlap.run() + check_close(res.outputs.jaccard, 0.99705) + check_close(res.outputs.roi_voldiff, + np.array([0.0063086, -0.0025506, 0.0])) - yield check_close, res.outputs.jaccard, 0.99705 - yield (check_close, res.outputs.roi_voldiff, - np.array([0.0063086, -0.0025506, 0.0])) - - os.chdir(cwd) - rmtree(tempdir) diff --git a/nipype/algorithms/tests/test_rapidart.py b/nipype/algorithms/tests/test_rapidart.py index a75745cda5..69e6334448 100644 --- a/nipype/algorithms/tests/test_rapidart.py +++ b/nipype/algorithms/tests/test_rapidart.py @@ -5,16 +5,15 @@ import numpy as np -from ...testing import (assert_equal, assert_false, assert_true, - assert_almost_equal) +import numpy.testing as npt from .. import rapidart as ra from ...interfaces.base import Bunch def test_ad_init(): ad = ra.ArtifactDetect(use_differences=[True, False]) - yield assert_true, ad.inputs.use_differences[0] - yield assert_false, ad.inputs.use_differences[1] + assert ad.inputs.use_differences[0] + assert not ad.inputs.use_differences[1] def test_ad_output_filenames(): @@ -23,39 +22,39 @@ def test_ad_output_filenames(): f = 'motion.nii' (outlierfile, intensityfile, statsfile, normfile, plotfile, displacementfile, maskfile) = ad._get_output_filenames(f, outputdir) - yield assert_equal, outlierfile, '/tmp/art.motion_outliers.txt' - yield assert_equal, intensityfile, '/tmp/global_intensity.motion.txt' - yield assert_equal, statsfile, '/tmp/stats.motion.txt' - yield assert_equal, normfile, '/tmp/norm.motion.txt' - yield assert_equal, plotfile, '/tmp/plot.motion.png' - yield assert_equal, displacementfile, '/tmp/disp.motion.nii' - yield assert_equal, maskfile, '/tmp/mask.motion.nii' + assert outlierfile == '/tmp/art.motion_outliers.txt' + assert intensityfile == '/tmp/global_intensity.motion.txt' + assert statsfile == '/tmp/stats.motion.txt' + assert normfile == '/tmp/norm.motion.txt' + assert plotfile == '/tmp/plot.motion.png' + assert displacementfile == '/tmp/disp.motion.nii' + assert maskfile == '/tmp/mask.motion.nii' def test_ad_get_affine_matrix(): matrix = ra._get_affine_matrix(np.array([0]), 'SPM') - yield assert_equal, matrix, np.eye(4) + npt.assert_equal(matrix, np.eye(4)) # test translation params = [1, 2, 3] matrix = ra._get_affine_matrix(params, 'SPM') out = np.eye(4) out[0:3, 3] = params - yield assert_equal, matrix, out + npt.assert_equal(matrix, out) # test rotation params = np.array([0, 0, 0, np.pi / 2, np.pi / 2, np.pi / 2]) matrix = ra._get_affine_matrix(params, 'SPM') out = np.array([0, 0, 1, 0, 0, -1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1]).reshape((4, 4)) - yield assert_almost_equal, matrix, out + npt.assert_almost_equal(matrix, out) # test scaling params = np.array([0, 0, 0, 0, 0, 0, 1, 2, 3]) matrix = ra._get_affine_matrix(params, 'SPM') out = np.array([1, 0, 0, 0, 0, 2, 0, 0, 0, 0, 3, 0, 0, 0, 0, 1]).reshape((4, 4)) - yield assert_equal, matrix, out + npt.assert_equal(matrix, out) # test shear params = np.array([0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 3]) matrix = ra._get_affine_matrix(params, 'SPM') out = np.array([1, 1, 2, 0, 0, 1, 3, 0, 0, 0, 1, 0, 0, 0, 0, 1]).reshape((4, 4)) - yield assert_equal, matrix, out + npt.assert_equal(matrix, out) def test_ad_get_norm(): @@ -63,14 +62,14 @@ def test_ad_get_norm(): np.pi / 4, 0, 0, 0, -np.pi / 4, -np.pi / 4, -np.pi / 4]).reshape((3, 6)) norm, _ = ra._calc_norm(params, False, 'SPM') - yield assert_almost_equal, norm, np.array([18.86436316, 37.74610158, 31.29780829]) + npt.assert_almost_equal(norm, np.array([18.86436316, 37.74610158, 31.29780829])) norm, _ = ra._calc_norm(params, True, 'SPM') - yield assert_almost_equal, norm, np.array([0., 143.72192614, 173.92527131]) + npt.assert_almost_equal(norm, np.array([0., 143.72192614, 173.92527131])) def test_sc_init(): sc = ra.StimulusCorrelation(concatenated_design=True) - yield assert_true, sc.inputs.concatenated_design + assert sc.inputs.concatenated_design def test_sc_populate_inputs(): @@ -79,7 +78,7 @@ def test_sc_populate_inputs(): intensity_values=None, spm_mat_file=None, concatenated_design=None) - yield assert_equal, set(sc.inputs.__dict__.keys()), set(inputs.__dict__.keys()) + assert set(sc.inputs.__dict__.keys()) == set(inputs.__dict__.keys()) def test_sc_output_filenames(): @@ -87,4 +86,4 @@ def test_sc_output_filenames(): outputdir = '/tmp' f = 'motion.nii' corrfile = sc._get_output_filenames(f, outputdir) - yield assert_equal, corrfile, '/tmp/qa.motion_stimcorr.txt' + assert corrfile == '/tmp/qa.motion_stimcorr.txt' diff --git a/nipype/algorithms/tests/test_splitmerge.py b/nipype/algorithms/tests/test_splitmerge.py index 89af22afe7..46cd05f995 100644 --- a/nipype/algorithms/tests/test_splitmerge.py +++ b/nipype/algorithms/tests/test_splitmerge.py @@ -1,29 +1,25 @@ #!/usr/bin/env python # -*- coding: utf-8 -*- -from shutil import rmtree -from tempfile import mkdtemp -from nipype.testing import (assert_equal, example_data) +from nipype.testing import example_data -def test_split_and_merge(): +def test_split_and_merge(tmpdir): import numpy as np import nibabel as nb import os.path as op import os - cwd = os.getcwd() from nipype.algorithms.misc import split_rois, merge_rois - tmpdir = mkdtemp() in_mask = example_data('tpms_msk.nii.gz') - dwfile = op.join(tmpdir, 'dwi.nii.gz') + dwfile = op.join(str(tmpdir), 'dwi.nii.gz') mskdata = nb.load(in_mask).get_data() aff = nb.load(in_mask).affine dwshape = (mskdata.shape[0], mskdata.shape[1], mskdata.shape[2], 6) dwdata = np.random.normal(size=dwshape) - os.chdir(tmpdir) + os.chdir(str(tmpdir)) nb.Nifti1Image(dwdata.astype(np.float32), aff, None).to_filename(dwfile) @@ -32,7 +28,5 @@ def test_split_and_merge(): dwmerged = nb.load(merged).get_data() dwmasked = dwdata * mskdata[:, :, :, np.newaxis] - os.chdir(cwd) - rmtree(tmpdir) - yield assert_equal, np.allclose(dwmasked, dwmerged), True + assert np.allclose(dwmasked, dwmerged) diff --git a/nipype/algorithms/tests/test_tsnr.py b/nipype/algorithms/tests/test_tsnr.py index 98af1d4dd5..7b44979da8 100644 --- a/nipype/algorithms/tests/test_tsnr.py +++ b/nipype/algorithms/tests/test_tsnr.py @@ -1,19 +1,19 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -from ...testing import (assert_equal, assert_almost_equal, assert_in, utils) +from ...testing import utils from ..confounds import TSNR from .. import misc -import unittest +import pytest +import numpy.testing as npt import mock import nibabel as nb import numpy as np import os -import tempfile -import shutil -class TestTSNR(unittest.TestCase): + +class TestTSNR(): ''' Note: Tests currently do a poor job of testing functionality ''' in_filenames = { @@ -27,10 +27,10 @@ class TestTSNR(unittest.TestCase): 'tsnr_file': 'tsnr.nii.gz' } - def setUp(self): + @pytest.fixture(autouse=True) + def setup_class(self, tmpdir): # setup temp folder - self.orig_dir = os.getcwd() - self.temp_dir = tempfile.mkdtemp() + self.temp_dir = str(tmpdir) os.chdir(self.temp_dir) utils.save_toy_nii(self.fake_data, self.in_filenames['in_file']) @@ -92,11 +92,11 @@ def test_warning(self, mock_warn): misc.TSNR(in_file=self.in_filenames['in_file']) # assert - assert_in(True, [args[0].count('confounds') > 0 for _, args, _ in mock_warn.mock_calls]) + assert True in [args[0].count('confounds') > 0 for _, args, _ in mock_warn.mock_calls] def assert_expected_outputs_poly(self, tsnrresult, expected_ranges): - assert_equal(os.path.basename(tsnrresult.outputs.detrended_file), - self.out_filenames['detrended_file']) + assert os.path.basename(tsnrresult.outputs.detrended_file) == \ + self.out_filenames['detrended_file'] self.assert_expected_outputs(tsnrresult, expected_ranges) def assert_expected_outputs(self, tsnrresult, expected_ranges): @@ -104,22 +104,19 @@ def assert_expected_outputs(self, tsnrresult, expected_ranges): self.assert_unchanged(expected_ranges) def assert_default_outputs(self, outputs): - assert_equal(os.path.basename(outputs.mean_file), - self.out_filenames['mean_file']) - assert_equal(os.path.basename(outputs.stddev_file), - self.out_filenames['stddev_file']) - assert_equal(os.path.basename(outputs.tsnr_file), - self.out_filenames['tsnr_file']) + assert os.path.basename(outputs.mean_file) == \ + self.out_filenames['mean_file'] + assert os.path.basename(outputs.stddev_file) == \ + self.out_filenames['stddev_file'] + assert os.path.basename(outputs.tsnr_file) == \ + self.out_filenames['tsnr_file'] def assert_unchanged(self, expected_ranges): for key, (min_, max_) in expected_ranges.items(): data = np.asarray(nb.load(self.out_filenames[key])._data) - assert_almost_equal(np.amin(data), min_, decimal=1) - assert_almost_equal(np.amax(data), max_, decimal=1) + npt.assert_almost_equal(np.amin(data), min_, decimal=1) + npt.assert_almost_equal(np.amax(data), max_, decimal=1) - def tearDown(self): - os.chdir(self.orig_dir) - shutil.rmtree(self.temp_dir) fake_data = np.array([[[[2, 4, 3, 9, 1], [3, 6, 4, 7, 4]], diff --git a/nipype/caching/tests/test_memory.py b/nipype/caching/tests/test_memory.py index d32b3cd8aa..d2968ae3f2 100644 --- a/nipype/caching/tests/test_memory.py +++ b/nipype/caching/tests/test_memory.py @@ -2,13 +2,8 @@ """ Test the nipype interface caching mechanism """ -from tempfile import mkdtemp -from shutil import rmtree - -from nose.tools import assert_equal - from .. import Memory -from ...pipeline.engine.tests.test_engine import TestInterface +from ...pipeline.engine.tests.test_engine import EngineTestInterface from ... import config config.set_default_config() @@ -16,7 +11,7 @@ nb_runs = 0 -class SideEffectInterface(TestInterface): +class SideEffectInterface(EngineTestInterface): def _run_interface(self, runtime): global nb_runs @@ -25,29 +20,24 @@ def _run_interface(self, runtime): return runtime -def test_caching(): - temp_dir = mkdtemp(prefix='test_memory_') +def test_caching(tmpdir): old_rerun = config.get('execution', 'stop_on_first_rerun') try: # Prevent rerun to check that evaluation is computed only once config.set('execution', 'stop_on_first_rerun', 'true') - mem = Memory(temp_dir) + mem = Memory(str(tmpdir)) first_nb_run = nb_runs results = mem.cache(SideEffectInterface)(input1=2, input2=1) - assert_equal(nb_runs, first_nb_run + 1) - assert_equal(results.outputs.output1, [1, 2]) + assert nb_runs == first_nb_run + 1 + assert results.outputs.output1 == [1, 2] results = mem.cache(SideEffectInterface)(input1=2, input2=1) # Check that the node hasn't been rerun - assert_equal(nb_runs, first_nb_run + 1) - assert_equal(results.outputs.output1, [1, 2]) + assert nb_runs == first_nb_run + 1 + assert results.outputs.output1 == [1, 2] results = mem.cache(SideEffectInterface)(input1=1, input2=1) # Check that the node hasn been rerun - assert_equal(nb_runs, first_nb_run + 2) - assert_equal(results.outputs.output1, [1, 1]) + assert nb_runs == first_nb_run + 2 + assert results.outputs.output1 == [1, 1] finally: - rmtree(temp_dir) config.set('execution', 'stop_on_first_rerun', old_rerun) - -if __name__ == '__main__': - test_caching() diff --git a/nipype/fixes/numpy/testing/nosetester.py b/nipype/fixes/numpy/testing/nosetester.py index e6b7e10a2e..314e58a907 100644 --- a/nipype/fixes/numpy/testing/nosetester.py +++ b/nipype/fixes/numpy/testing/nosetester.py @@ -23,7 +23,8 @@ def get_package_name(filepath): Examples -------- - >>> np.testing.nosetester.get_package_name('nonsense') # doctest: +IGNORE_UNICODE + >>> import numpy as np + >>> np.testing.nosetester.get_package_name('nonsense') # doctest: +ALLOW_UNICODE 'numpy' """ diff --git a/nipype/info.py b/nipype/info.py index 024ddc57f4..ec60053b3e 100644 --- a/nipype/info.py +++ b/nipype/info.py @@ -108,7 +108,7 @@ def get_nipype_gitversion(): SCIPY_MIN_VERSION = '0.11' TRAITS_MIN_VERSION = '4.3' DATEUTIL_MIN_VERSION = '1.5' -NOSE_MIN_VERSION = '1.2' +PYTEST_MIN_VERSION = '3.0' FUTURE_MIN_VERSION = '0.15.2' SIMPLEJSON_MIN_VERSION = '3.8.0' PROV_MIN_VERSION = '1.4.0' @@ -149,17 +149,18 @@ def get_nipype_gitversion(): ] TESTS_REQUIRES = [ - 'nose>=%s' % NOSE_MIN_VERSION, + 'pytest>=%s' % PYTEST_MIN_VERSION, + 'pytest-raisesregexp', + 'pytest-cov', 'mock', 'codecov', - 'doctest-ignore-unicode', 'dipy', 'nipy', 'matplotlib' ] EXTRA_REQUIRES = { - 'doc': ['Sphinx>=0.3', 'matplotlib', 'pydotplus', 'doctest-ignore-unicode'], + 'doc': ['Sphinx>=0.3', 'matplotlib', 'pydotplus'], 'tests': TESTS_REQUIRES, 'fmri': ['nitime', 'nilearn', 'dipy', 'nipy', 'matplotlib'], 'profiler': ['psutil'], diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index 0ade11c94a..19fe073ac5 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -268,7 +268,7 @@ class Allineate(AFNICommand): >>> allineate.inputs.in_file = 'functional.nii' >>> allineate.inputs.out_file = 'functional_allineate.nii' >>> allineate.inputs.in_matrix = 'cmatrix.mat' - >>> allineate.cmdline # doctest: +IGNORE_UNICODE + >>> allineate.cmdline # doctest: +ALLOW_UNICODE '3dAllineate -1Dmatrix_apply cmatrix.mat -prefix functional_allineate.nii -source functional.nii' >>> res = allineate.run() # doctest: +SKIP @@ -354,7 +354,7 @@ class AutoTcorrelate(AFNICommand): >>> corr.inputs.eta2 = True >>> corr.inputs.mask = 'mask.nii' >>> corr.inputs.mask_only_targets = True - >>> corr.cmdline # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> corr.cmdline # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE +ALLOW_UNICODE '3dAutoTcorrelate -eta2 -mask mask.nii -mask_only_targets -prefix functional_similarity_matrix.1D -polort -1 functional.nii' >>> res = corr.run() # doctest: +SKIP """ @@ -422,7 +422,7 @@ class Automask(AFNICommand): >>> automask.inputs.in_file = 'functional.nii' >>> automask.inputs.dilate = 1 >>> automask.inputs.outputtype = 'NIFTI' - >>> automask.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> automask.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dAutomask -apply_prefix functional_masked.nii -dilate 1 -prefix functional_mask.nii functional.nii' >>> res = automask.run() # doctest: +SKIP @@ -531,7 +531,7 @@ class Bandpass(AFNICommand): >>> bandpass.inputs.in_file = 'functional.nii' >>> bandpass.inputs.highpass = 0.005 >>> bandpass.inputs.lowpass = 0.1 - >>> bandpass.cmdline # doctest: +IGNORE_UNICODE + >>> bandpass.cmdline # doctest: +ALLOW_UNICODE '3dBandpass -prefix functional_bp 0.005000 0.100000 functional.nii' >>> res = bandpass.run() # doctest: +SKIP @@ -599,7 +599,7 @@ class BlurInMask(AFNICommand): >>> bim.inputs.in_file = 'functional.nii' >>> bim.inputs.mask = 'mask.nii' >>> bim.inputs.fwhm = 5.0 - >>> bim.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> bim.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dBlurInMask -input functional.nii -FWHM 5.000000 -mask mask.nii -prefix functional_blur' >>> res = bim.run() # doctest: +SKIP @@ -650,7 +650,7 @@ class BlurToFWHM(AFNICommand): >>> blur = afni.preprocess.BlurToFWHM() >>> blur.inputs.in_file = 'epi.nii' >>> blur.inputs.fwhm = 2.5 - >>> blur.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> blur.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dBlurToFWHM -FWHM 2.500000 -input epi.nii -prefix epi_afni' >>> res = blur.run() # doctest: +SKIP @@ -701,7 +701,7 @@ class ClipLevel(AFNICommandBase): >>> from nipype.interfaces.afni import preprocess >>> cliplevel = preprocess.ClipLevel() >>> cliplevel.inputs.in_file = 'anatomical.nii' - >>> cliplevel.cmdline # doctest: +IGNORE_UNICODE + >>> cliplevel.cmdline # doctest: +ALLOW_UNICODE '3dClipLevel anatomical.nii' >>> res = cliplevel.run() # doctest: +SKIP @@ -784,7 +784,7 @@ class DegreeCentrality(AFNICommand): >>> degree.inputs.mask = 'mask.nii' >>> degree.inputs.sparsity = 1 # keep the top one percent of connections >>> degree.inputs.out_file = 'out.nii' - >>> degree.cmdline # doctest: +IGNORE_UNICODE + >>> degree.cmdline # doctest: +ALLOW_UNICODE '3dDegreeCentrality -mask mask.nii -prefix out.nii -sparsity 1.000000 functional.nii' >>> res = degree.run() # doctest: +SKIP @@ -834,7 +834,7 @@ class Despike(AFNICommand): >>> from nipype.interfaces import afni >>> despike = afni.Despike() >>> despike.inputs.in_file = 'functional.nii' - >>> despike.cmdline # doctest: +IGNORE_UNICODE + >>> despike.cmdline # doctest: +ALLOW_UNICODE '3dDespike -prefix functional_despike functional.nii' >>> res = despike.run() # doctest: +SKIP @@ -875,7 +875,7 @@ class Detrend(AFNICommand): >>> detrend.inputs.in_file = 'functional.nii' >>> detrend.inputs.args = '-polort 2' >>> detrend.inputs.outputtype = 'AFNI' - >>> detrend.cmdline # doctest: +IGNORE_UNICODE + >>> detrend.cmdline # doctest: +ALLOW_UNICODE '3dDetrend -polort 2 -prefix functional_detrend functional.nii' >>> res = detrend.run() # doctest: +SKIP @@ -947,7 +947,7 @@ class ECM(AFNICommand): >>> ecm.inputs.mask = 'mask.nii' >>> ecm.inputs.sparsity = 0.1 # keep top 0.1% of connections >>> ecm.inputs.out_file = 'out.nii' - >>> ecm.cmdline # doctest: +IGNORE_UNICODE + >>> ecm.cmdline # doctest: +ALLOW_UNICODE '3dECM -mask mask.nii -prefix out.nii -sparsity 0.100000 functional.nii' >>> res = ecm.run() # doctest: +SKIP @@ -1004,7 +1004,7 @@ class Fim(AFNICommand): >>> fim.inputs.out_file = 'functional_corr.nii' >>> fim.inputs.out = 'Correlation' >>> fim.inputs.fim_thr = 0.0009 - >>> fim.cmdline # doctest: +IGNORE_UNICODE + >>> fim.cmdline # doctest: +ALLOW_UNICODE '3dfim+ -input functional.nii -ideal_file seed.1D -fim_thr 0.000900 -out Correlation -bucket functional_corr.nii' >>> res = fim.run() # doctest: +SKIP @@ -1058,7 +1058,7 @@ class Fourier(AFNICommand): >>> fourier.inputs.retrend = True >>> fourier.inputs.highpass = 0.005 >>> fourier.inputs.lowpass = 0.1 - >>> fourier.cmdline # doctest: +IGNORE_UNICODE + >>> fourier.cmdline # doctest: +ALLOW_UNICODE '3dFourier -highpass 0.005000 -lowpass 0.100000 -prefix functional_fourier -retrend functional.nii' >>> res = fourier.run() # doctest: +SKIP @@ -1131,7 +1131,7 @@ class Hist(AFNICommandBase): >>> from nipype.interfaces import afni >>> hist = afni.Hist() >>> hist.inputs.in_file = 'functional.nii' - >>> hist.cmdline # doctest: +IGNORE_UNICODE + >>> hist.cmdline # doctest: +ALLOW_UNICODE '3dHist -input functional.nii -prefix functional_hist' >>> res = hist.run() # doctest: +SKIP @@ -1195,7 +1195,7 @@ class LFCD(AFNICommand): >>> lfcd.inputs.mask = 'mask.nii' >>> lfcd.inputs.thresh = 0.8 # keep all connections with corr >= 0.8 >>> lfcd.inputs.out_file = 'out.nii' - >>> lfcd.cmdline # doctest: +IGNORE_UNICODE + >>> lfcd.cmdline # doctest: +ALLOW_UNICODE '3dLFCD -mask mask.nii -prefix out.nii -thresh 0.800000 functional.nii' >>> res = lfcd.run() # doctest: +SKIP """ @@ -1246,7 +1246,7 @@ class Maskave(AFNICommand): >>> maskave.inputs.in_file = 'functional.nii' >>> maskave.inputs.mask= 'seed_mask.nii' >>> maskave.inputs.quiet= True - >>> maskave.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> maskave.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dmaskave -mask seed_mask.nii -quiet functional.nii > functional_maskave.1D' >>> res = maskave.run() # doctest: +SKIP @@ -1314,7 +1314,7 @@ class Means(AFNICommand): >>> means.inputs.in_file_a = 'im1.nii' >>> means.inputs.in_file_b = 'im2.nii' >>> means.inputs.out_file = 'output.nii' - >>> means.cmdline # doctest: +IGNORE_UNICODE + >>> means.cmdline # doctest: +ALLOW_UNICODE '3dMean im1.nii im2.nii -prefix output.nii' >>> res = means.run() # doctest: +SKIP @@ -1421,7 +1421,7 @@ class OutlierCount(CommandLine): >>> from nipype.interfaces import afni >>> toutcount = afni.OutlierCount() >>> toutcount.inputs.in_file = 'functional.nii' - >>> toutcount.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> toutcount.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dToutcount functional.nii > functional_outliers' >>> res = toutcount.run() # doctest: +SKIP @@ -1520,7 +1520,7 @@ class QualityIndex(CommandLine): >>> from nipype.interfaces import afni >>> tqual = afni.QualityIndex() >>> tqual.inputs.in_file = 'functional.nii' - >>> tqual.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> tqual.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dTqual functional.nii > functional_tqual' >>> res = tqual.run() # doctest: +SKIP @@ -1580,7 +1580,7 @@ class ROIStats(AFNICommandBase): >>> roistats.inputs.in_file = 'functional.nii' >>> roistats.inputs.mask = 'skeleton_mask.nii.gz' >>> roistats.inputs.quiet = True - >>> roistats.cmdline # doctest: +IGNORE_UNICODE + >>> roistats.cmdline # doctest: +ALLOW_UNICODE '3dROIstats -quiet -mask skeleton_mask.nii.gz functional.nii' >>> res = roistats.run() # doctest: +SKIP @@ -1674,7 +1674,7 @@ class Retroicor(AFNICommand): >>> ret.inputs.card = 'mask.1D' >>> ret.inputs.resp = 'resp.1D' >>> ret.inputs.outputtype = 'NIFTI' - >>> ret.cmdline # doctest: +IGNORE_UNICODE + >>> ret.cmdline # doctest: +ALLOW_UNICODE '3dretroicor -prefix functional_retroicor.nii -resp resp.1D -card mask.1D functional.nii' >>> res = ret.run() # doctest: +SKIP @@ -1757,7 +1757,7 @@ class Seg(AFNICommandBase): >>> seg = preprocess.Seg() >>> seg.inputs.in_file = 'structural.nii' >>> seg.inputs.mask = 'AUTO' - >>> seg.cmdline # doctest: +IGNORE_UNICODE + >>> seg.cmdline # doctest: +ALLOW_UNICODE '3dSeg -mask AUTO -anat structural.nii' >>> res = seg.run() # doctest: +SKIP @@ -1813,7 +1813,7 @@ class SkullStrip(AFNICommand): >>> skullstrip = afni.SkullStrip() >>> skullstrip.inputs.in_file = 'functional.nii' >>> skullstrip.inputs.args = '-o_ply' - >>> skullstrip.cmdline # doctest: +IGNORE_UNICODE + >>> skullstrip.cmdline # doctest: +ALLOW_UNICODE '3dSkullStrip -input functional.nii -o_ply -prefix functional_skullstrip' >>> res = skullstrip.run() # doctest: +SKIP @@ -1891,7 +1891,7 @@ class TCorr1D(AFNICommand): >>> tcorr1D = afni.TCorr1D() >>> tcorr1D.inputs.xset= 'u_rc1s1_Template.nii' >>> tcorr1D.inputs.y_1d = 'seed.1D' - >>> tcorr1D.cmdline # doctest: +IGNORE_UNICODE + >>> tcorr1D.cmdline # doctest: +ALLOW_UNICODE '3dTcorr1D -prefix u_rc1s1_Template_correlation.nii.gz u_rc1s1_Template.nii seed.1D' >>> res = tcorr1D.run() # doctest: +SKIP @@ -2033,7 +2033,7 @@ class TCorrMap(AFNICommand): >>> tcm.inputs.in_file = 'functional.nii' >>> tcm.inputs.mask = 'mask.nii' >>> tcm.mean_file = 'functional_meancorr.nii' - >>> tcm.cmdline # doctest: +IGNORE_UNICODE +SKIP + >>> tcm.cmdline # doctest: +ALLOW_UNICODE +SKIP '3dTcorrMap -input functional.nii -mask mask.nii -Mean functional_meancorr.nii' >>> res = tcm.run() # doctest: +SKIP @@ -2101,7 +2101,7 @@ class TCorrelate(AFNICommand): >>> tcorrelate.inputs.out_file = 'functional_tcorrelate.nii.gz' >>> tcorrelate.inputs.polort = -1 >>> tcorrelate.inputs.pearson = True - >>> tcorrelate.cmdline # doctest: +IGNORE_UNICODE + >>> tcorrelate.cmdline # doctest: +ALLOW_UNICODE '3dTcorrelate -prefix functional_tcorrelate.nii.gz -pearson -polort -1 u_rc1s1_Template.nii u_rc1s2_Template.nii' >>> res = tcarrelate.run() # doctest: +SKIP @@ -2172,7 +2172,7 @@ class TShift(AFNICommand): >>> tshift.inputs.in_file = 'functional.nii' >>> tshift.inputs.tpattern = 'alt+z' >>> tshift.inputs.tzero = 0.0 - >>> tshift.cmdline # doctest: +IGNORE_UNICODE + >>> tshift.cmdline # doctest: +ALLOW_UNICODE '3dTshift -prefix functional_tshift -tpattern alt+z -tzero 0.0 functional.nii' >>> res = tshift.run() # doctest: +SKIP @@ -2264,7 +2264,7 @@ class Volreg(AFNICommand): >>> volreg.inputs.args = '-Fourier -twopass' >>> volreg.inputs.zpad = 4 >>> volreg.inputs.outputtype = 'NIFTI' - >>> volreg.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> volreg.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dvolreg -Fourier -twopass -1Dfile functional.1D -1Dmatrix_save functional.aff12.1D -prefix functional_volreg.nii -zpad 4 -maxdisp1D functional_md.1D functional.nii' >>> res = volreg.run() # doctest: +SKIP @@ -2331,7 +2331,7 @@ class Warp(AFNICommand): >>> warp.inputs.in_file = 'structural.nii' >>> warp.inputs.deoblique = True >>> warp.inputs.out_file = 'trans.nii.gz' - >>> warp.cmdline # doctest: +IGNORE_UNICODE + >>> warp.cmdline # doctest: +ALLOW_UNICODE '3dWarp -deoblique -prefix trans.nii.gz structural.nii' >>> res = warp.run() # doctest: +SKIP @@ -2339,7 +2339,7 @@ class Warp(AFNICommand): >>> warp_2.inputs.in_file = 'structural.nii' >>> warp_2.inputs.newgrid = 1.0 >>> warp_2.inputs.out_file = 'trans.nii.gz' - >>> warp_2.cmdline # doctest: +IGNORE_UNICODE + >>> warp_2.cmdline # doctest: +ALLOW_UNICODE '3dWarp -newgrid 1.000000 -prefix trans.nii.gz structural.nii' >>> res = warp_2.run() # doctest: +SKIP diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index 82774d69f4..b4da361993 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import AFNICommand @@ -24,5 +23,5 @@ def test_AFNICommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py index 9052c5345a..7f9fcce12a 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommandBase.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import AFNICommandBase @@ -19,5 +18,5 @@ def test_AFNICommandBase_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 7bb382cb5e..807a9d6f6a 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import AFNItoNIFTI @@ -40,7 +39,7 @@ def test_AFNItoNIFTI_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AFNItoNIFTI_outputs(): @@ -50,4 +49,4 @@ def test_AFNItoNIFTI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 27a1cc5dae..b84748e0e8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Allineate @@ -109,7 +108,7 @@ def test_Allineate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Allineate_outputs(): @@ -120,4 +119,4 @@ def test_Allineate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index 31216252a4..de7c12cc3c 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import AutoTcorrelate @@ -41,7 +40,7 @@ def test_AutoTcorrelate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AutoTcorrelate_outputs(): @@ -51,4 +50,4 @@ def test_AutoTcorrelate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index a994c9a293..6ee23e811f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Autobox @@ -31,7 +30,7 @@ def test_Autobox_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Autobox_outputs(): @@ -47,4 +46,4 @@ def test_Autobox_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index 5ee4b08162..f0c73e2c7e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Automask @@ -39,7 +38,7 @@ def test_Automask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Automask_outputs(): @@ -50,4 +49,4 @@ def test_Automask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index 519d8fd501..a482421df5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Bandpass @@ -64,7 +63,7 @@ def test_Bandpass_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Bandpass_outputs(): @@ -74,4 +73,4 @@ def test_Bandpass_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index 276cf8a81f..0145146861 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import BlurInMask @@ -46,7 +45,7 @@ def test_BlurInMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BlurInMask_outputs(): @@ -56,4 +55,4 @@ def test_BlurInMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py index b0c965dc07..9ebab4f107 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurToFWHM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import BlurToFWHM @@ -37,7 +36,7 @@ def test_BlurToFWHM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BlurToFWHM_outputs(): @@ -47,4 +46,4 @@ def test_BlurToFWHM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index 739663ab3e..0a776a693e 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import BrickStat @@ -29,7 +28,7 @@ def test_BrickStat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BrickStat_outputs(): @@ -39,4 +38,4 @@ def test_BrickStat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index 80f0442c1c..f98d81c084 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Calc @@ -45,7 +44,7 @@ def test_Calc_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): @@ -55,4 +54,4 @@ def test_Calc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py index f6e5ae3e98..4e807fbf29 100644 --- a/nipype/interfaces/afni/tests/test_auto_ClipLevel.py +++ b/nipype/interfaces/afni/tests/test_auto_ClipLevel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ClipLevel @@ -34,7 +33,7 @@ def test_ClipLevel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ClipLevel_outputs(): @@ -44,4 +43,4 @@ def test_ClipLevel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index bc83efde94..bc93648094 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Copy @@ -30,7 +29,7 @@ def test_Copy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): @@ -40,4 +39,4 @@ def test_Copy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py index 9b5d16b094..312e12e550 100644 --- a/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py +++ b/nipype/interfaces/afni/tests/test_auto_DegreeCentrality.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import DegreeCentrality @@ -43,7 +42,7 @@ def test_DegreeCentrality_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DegreeCentrality_outputs(): @@ -54,4 +53,4 @@ def test_DegreeCentrality_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index 0e8c5876f9..9a0b3fac60 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Despike @@ -29,7 +28,7 @@ def test_Despike_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Despike_outputs(): @@ -39,4 +38,4 @@ def test_Despike_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 2fd8bf3d6f..27a4169755 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Detrend @@ -29,7 +28,7 @@ def test_Detrend_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Detrend_outputs(): @@ -39,4 +38,4 @@ def test_Detrend_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_ECM.py b/nipype/interfaces/afni/tests/test_auto_ECM.py index 1171db8d4a..b517a288f0 100644 --- a/nipype/interfaces/afni/tests/test_auto_ECM.py +++ b/nipype/interfaces/afni/tests/test_auto_ECM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ECM @@ -55,7 +54,7 @@ def test_ECM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ECM_outputs(): @@ -65,4 +64,4 @@ def test_ECM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 7bbbaa78a5..ec45e7aa6b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Eval @@ -47,7 +46,7 @@ def test_Eval_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Eval_outputs(): @@ -57,4 +56,4 @@ def test_Eval_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_FWHMx.py b/nipype/interfaces/afni/tests/test_auto_FWHMx.py index 267f88db4e..9bd42d596f 100644 --- a/nipype/interfaces/afni/tests/test_auto_FWHMx.py +++ b/nipype/interfaces/afni/tests/test_auto_FWHMx.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import FWHMx @@ -65,7 +64,7 @@ def test_FWHMx_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FWHMx_outputs(): @@ -80,4 +79,4 @@ def test_FWHMx_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index bc139aac34..de1be3112d 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Fim @@ -39,7 +38,7 @@ def test_Fim_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Fim_outputs(): @@ -49,4 +48,4 @@ def test_Fim_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 6d8e42b1cd..793deb0c54 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Fourier @@ -37,7 +36,7 @@ def test_Fourier_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Fourier_outputs(): @@ -47,4 +46,4 @@ def test_Fourier_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Hist.py b/nipype/interfaces/afni/tests/test_auto_Hist.py index d5c69116b0..116628e8bb 100644 --- a/nipype/interfaces/afni/tests/test_auto_Hist.py +++ b/nipype/interfaces/afni/tests/test_auto_Hist.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Hist @@ -48,7 +47,7 @@ def test_Hist_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Hist_outputs(): @@ -59,4 +58,4 @@ def test_Hist_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_LFCD.py b/nipype/interfaces/afni/tests/test_auto_LFCD.py index ff53651d79..195bdff1bf 100644 --- a/nipype/interfaces/afni/tests/test_auto_LFCD.py +++ b/nipype/interfaces/afni/tests/test_auto_LFCD.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import LFCD @@ -39,7 +38,7 @@ def test_LFCD_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_LFCD_outputs(): @@ -49,4 +48,4 @@ def test_LFCD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_MaskTool.py b/nipype/interfaces/afni/tests/test_auto_MaskTool.py index 14a35c9492..3f63892ef3 100644 --- a/nipype/interfaces/afni/tests/test_auto_MaskTool.py +++ b/nipype/interfaces/afni/tests/test_auto_MaskTool.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MaskTool @@ -49,7 +48,7 @@ def test_MaskTool_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MaskTool_outputs(): @@ -59,4 +58,4 @@ def test_MaskTool_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index dbff513cc8..590c14cb0b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Maskave @@ -37,7 +36,7 @@ def test_Maskave_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Maskave_outputs(): @@ -47,4 +46,4 @@ def test_Maskave_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index de764464b5..c60128e21b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Means @@ -47,7 +46,7 @@ def test_Means_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Means_outputs(): @@ -57,4 +56,4 @@ def test_Means_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index 100a397862..2f05c733ae 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Merge @@ -34,7 +33,7 @@ def test_Merge_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): @@ -44,4 +43,4 @@ def test_Merge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Notes.py b/nipype/interfaces/afni/tests/test_auto_Notes.py index 8f783fdae9..b2f7770842 100644 --- a/nipype/interfaces/afni/tests/test_auto_Notes.py +++ b/nipype/interfaces/afni/tests/test_auto_Notes.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Notes @@ -39,7 +38,7 @@ def test_Notes_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Notes_outputs(): @@ -49,4 +48,4 @@ def test_Notes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py index f2d7c63846..350c6de42e 100644 --- a/nipype/interfaces/afni/tests/test_auto_OutlierCount.py +++ b/nipype/interfaces/afni/tests/test_auto_OutlierCount.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import OutlierCount @@ -61,7 +60,7 @@ def test_OutlierCount_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_OutlierCount_outputs(): @@ -77,4 +76,4 @@ def test_OutlierCount_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py index cb41475a18..a483f727fe 100644 --- a/nipype/interfaces/afni/tests/test_auto_QualityIndex.py +++ b/nipype/interfaces/afni/tests/test_auto_QualityIndex.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import QualityIndex @@ -51,7 +50,7 @@ def test_QualityIndex_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_QualityIndex_outputs(): @@ -61,4 +60,4 @@ def test_QualityIndex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index 447b5000f6..3ba34a2bff 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ROIStats @@ -34,7 +33,7 @@ def test_ROIStats_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ROIStats_outputs(): @@ -44,4 +43,4 @@ def test_ROIStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index 16a97fb139..a30bdb0e6c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Refit @@ -40,7 +39,7 @@ def test_Refit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Refit_outputs(): @@ -50,4 +49,4 @@ def test_Refit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index b41f33a7ae..260a4a7671 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Resample @@ -37,7 +36,7 @@ def test_Resample_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): @@ -47,4 +46,4 @@ def test_Resample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index e80c138b7d..740b2f478e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Retroicor @@ -50,7 +49,7 @@ def test_Retroicor_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Retroicor_outputs(): @@ -60,4 +59,4 @@ def test_Retroicor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index a1566c59f7..27ef1eb291 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..svm import SVMTest @@ -41,7 +40,7 @@ def test_SVMTest_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SVMTest_outputs(): @@ -51,4 +50,4 @@ def test_SVMTest_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index eb13dcb531..487824e7c3 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..svm import SVMTrain @@ -60,7 +59,7 @@ def test_SVMTrain_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SVMTrain_outputs(): @@ -72,4 +71,4 @@ def test_SVMTrain_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Seg.py b/nipype/interfaces/afni/tests/test_auto_Seg.py index 753e2b04fb..7258618e2d 100644 --- a/nipype/interfaces/afni/tests/test_auto_Seg.py +++ b/nipype/interfaces/afni/tests/test_auto_Seg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Seg @@ -46,7 +45,7 @@ def test_Seg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Seg_outputs(): @@ -56,4 +55,4 @@ def test_Seg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index 12449c331f..1db2f5cdfd 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SkullStrip @@ -29,7 +28,7 @@ def test_SkullStrip_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SkullStrip_outputs(): @@ -39,4 +38,4 @@ def test_SkullStrip_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 756cc83ed9..2d8deeb051 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import TCat @@ -32,7 +31,7 @@ def test_TCat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TCat_outputs(): @@ -42,4 +41,4 @@ def test_TCat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index f374ce8a19..94f269fce6 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import TCorr1D @@ -50,7 +49,7 @@ def test_TCorr1D_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TCorr1D_outputs(): @@ -60,4 +59,4 @@ def test_TCorr1D_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index 45edca85c5..44ec6cddcb 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import TCorrMap @@ -105,7 +104,7 @@ def test_TCorrMap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TCorrMap_outputs(): @@ -127,4 +126,4 @@ def test_TCorrMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index af4c6c6f77..0e30676f92 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import TCorrelate @@ -38,7 +37,7 @@ def test_TCorrelate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TCorrelate_outputs(): @@ -48,4 +47,4 @@ def test_TCorrelate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index fca649bca3..8c85b1c3bc 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import TShift @@ -47,7 +46,7 @@ def test_TShift_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TShift_outputs(): @@ -57,4 +56,4 @@ def test_TShift_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index ce179f5e29..6151aa92fa 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import TStat @@ -33,7 +32,7 @@ def test_TStat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TStat_outputs(): @@ -43,4 +42,4 @@ def test_TStat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 27eba788a9..dbb2316c54 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import To3D @@ -38,7 +37,7 @@ def test_To3D_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_To3D_outputs(): @@ -48,4 +47,4 @@ def test_To3D_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index f97afe6366..d3a9e13616 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Volreg @@ -57,7 +56,7 @@ def test_Volreg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Volreg_outputs(): @@ -70,4 +69,4 @@ def test_Volreg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index c749d7fade..14e197a83f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Warp @@ -45,7 +44,7 @@ def test_Warp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Warp_outputs(): @@ -55,4 +54,4 @@ def test_Warp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index 95b3cc4dc6..6861e79211 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ZCutUp @@ -31,7 +30,7 @@ def test_ZCutUp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ZCutUp_outputs(): @@ -41,4 +40,4 @@ def test_ZCutUp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/afni/utils.py b/nipype/interfaces/afni/utils.py index ac53c3a458..94a9378c2a 100644 --- a/nipype/interfaces/afni/utils.py +++ b/nipype/interfaces/afni/utils.py @@ -83,7 +83,7 @@ class AFNItoNIFTI(AFNICommand): >>> a2n = afni.AFNItoNIFTI() >>> a2n.inputs.in_file = 'afni_output.3D' >>> a2n.inputs.out_file = 'afni_output.nii' - >>> a2n.cmdline # doctest: +IGNORE_UNICODE + >>> a2n.cmdline # doctest: +ALLOW_UNICODE '3dAFNItoNIFTI -prefix afni_output.nii afni_output.3D' >>> res = a2n.run() # doctest: +SKIP @@ -150,7 +150,7 @@ class Autobox(AFNICommand): >>> abox = afni.Autobox() >>> abox.inputs.in_file = 'structural.nii' >>> abox.inputs.padding = 5 - >>> abox.cmdline # doctest: +IGNORE_UNICODE + >>> abox.cmdline # doctest: +ALLOW_UNICODE '3dAutobox -input structural.nii -prefix structural_generated -npad 5' >>> res = abox.run() # doctest: +SKIP @@ -219,7 +219,7 @@ class BrickStat(AFNICommandBase): >>> brickstat.inputs.in_file = 'functional.nii' >>> brickstat.inputs.mask = 'skeleton_mask.nii.gz' >>> brickstat.inputs.min = True - >>> brickstat.cmdline # doctest: +IGNORE_UNICODE + >>> brickstat.cmdline # doctest: +ALLOW_UNICODE '3dBrickStat -min -mask skeleton_mask.nii.gz functional.nii' >>> res = brickstat.run() # doctest: +SKIP @@ -313,7 +313,7 @@ class Calc(AFNICommand): >>> calc.inputs.expr='a*b' >>> calc.inputs.out_file = 'functional_calc.nii.gz' >>> calc.inputs.outputtype = 'NIFTI' - >>> calc.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> calc.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '3dcalc -a functional.nii -b functional2.nii -expr "a*b" -prefix functional_calc.nii.gz' >>> res = calc.run() # doctest: +SKIP @@ -370,26 +370,26 @@ class Copy(AFNICommand): >>> from nipype.interfaces import afni >>> copy3d = afni.Copy() >>> copy3d.inputs.in_file = 'functional.nii' - >>> copy3d.cmdline # doctest: +IGNORE_UNICODE + >>> copy3d.cmdline # doctest: +ALLOW_UNICODE '3dcopy functional.nii functional_copy' >>> res = copy3d.run() # doctest: +SKIP >>> from copy import deepcopy >>> copy3d_2 = deepcopy(copy3d) >>> copy3d_2.inputs.outputtype = 'NIFTI' - >>> copy3d_2.cmdline # doctest: +IGNORE_UNICODE + >>> copy3d_2.cmdline # doctest: +ALLOW_UNICODE '3dcopy functional.nii functional_copy.nii' >>> res = copy3d_2.run() # doctest: +SKIP >>> copy3d_3 = deepcopy(copy3d) >>> copy3d_3.inputs.outputtype = 'NIFTI_GZ' - >>> copy3d_3.cmdline # doctest: +IGNORE_UNICODE + >>> copy3d_3.cmdline # doctest: +ALLOW_UNICODE '3dcopy functional.nii functional_copy.nii.gz' >>> res = copy3d_3.run() # doctest: +SKIP >>> copy3d_4 = deepcopy(copy3d) >>> copy3d_4.inputs.out_file = 'new_func.nii' - >>> copy3d_4.cmdline # doctest: +IGNORE_UNICODE + >>> copy3d_4.cmdline # doctest: +ALLOW_UNICODE '3dcopy functional.nii new_func.nii' >>> res = copy3d_4.run() # doctest: +SKIP @@ -460,7 +460,7 @@ class Eval(AFNICommand): >>> eval.inputs.expr = 'a*b' >>> eval.inputs.out1D = True >>> eval.inputs.out_file = 'data_calc.1D' - >>> eval.cmdline # doctest: +IGNORE_UNICODE + >>> eval.cmdline # doctest: +ALLOW_UNICODE '1deval -a seed.1D -b resp.1D -expr "a*b" -1D -prefix data_calc.1D' >>> res = eval.run() # doctest: +SKIP @@ -611,7 +611,7 @@ class FWHMx(AFNICommandBase): >>> from nipype.interfaces import afni >>> fwhm = afni.FWHMx() >>> fwhm.inputs.in_file = 'functional.nii' - >>> fwhm.cmdline # doctest: +IGNORE_UNICODE + >>> fwhm.cmdline # doctest: +ALLOW_UNICODE '3dFWHMx -input functional.nii -out functional_subbricks.out > functional_fwhmx.out' >>> res = fwhm.run() # doctest: +SKIP @@ -828,7 +828,7 @@ class MaskTool(AFNICommand): >>> masktool = afni.MaskTool() >>> masktool.inputs.in_file = 'functional.nii' >>> masktool.inputs.outputtype = 'NIFTI' - >>> masktool.cmdline # doctest: +IGNORE_UNICODE + >>> masktool.cmdline # doctest: +ALLOW_UNICODE '3dmask_tool -prefix functional_mask.nii -input functional.nii' >>> res = automask.run() # doctest: +SKIP @@ -877,7 +877,7 @@ class Merge(AFNICommand): >>> merge.inputs.blurfwhm = 4 >>> merge.inputs.doall = True >>> merge.inputs.out_file = 'e7.nii' - >>> merge.cmdline # doctest: +IGNORE_UNICODE + >>> merge.cmdline # doctest: +ALLOW_UNICODE '3dmerge -1blur_fwhm 4 -doall -prefix e7.nii functional.nii functional2.nii' >>> res = merge.run() # doctest: +SKIP @@ -932,7 +932,7 @@ class Notes(CommandLine): >>> notes.inputs.in_file = 'functional.HEAD' >>> notes.inputs.add = 'This note is added.' >>> notes.inputs.add_history = 'This note is added to history.' - >>> notes.cmdline # doctest: +IGNORE_UNICODE + >>> notes.cmdline # doctest: +ALLOW_UNICODE '3dNotes -a "This note is added." -h "This note is added to history." functional.HEAD' >>> res = notes.run() # doctest: +SKIP """ @@ -996,7 +996,7 @@ class Refit(AFNICommandBase): >>> refit = afni.Refit() >>> refit.inputs.in_file = 'structural.nii' >>> refit.inputs.deoblique = True - >>> refit.cmdline # doctest: +IGNORE_UNICODE + >>> refit.cmdline # doctest: +ALLOW_UNICODE '3drefit -deoblique structural.nii' >>> res = refit.run() # doctest: +SKIP @@ -1057,7 +1057,7 @@ class Resample(AFNICommand): >>> resample.inputs.in_file = 'functional.nii' >>> resample.inputs.orientation= 'RPI' >>> resample.inputs.outputtype = 'NIFTI' - >>> resample.cmdline # doctest: +IGNORE_UNICODE + >>> resample.cmdline # doctest: +ALLOW_UNICODE '3dresample -orient RPI -prefix functional_resample.nii -inset functional.nii' >>> res = resample.run() # doctest: +SKIP @@ -1110,7 +1110,7 @@ class TCat(AFNICommand): >>> tcat.inputs.in_files = ['functional.nii', 'functional2.nii'] >>> tcat.inputs.out_file= 'functional_tcat.nii' >>> tcat.inputs.rlt = '+' - >>> tcat.cmdline # doctest: +IGNORE_UNICODE +NORMALIZE_WHITESPACE + >>> tcat.cmdline # doctest: +ALLOW_UNICODE +NORMALIZE_WHITESPACE '3dTcat -rlt+ -prefix functional_tcat.nii functional.nii functional2.nii' >>> res = tcat.run() # doctest: +SKIP @@ -1157,7 +1157,7 @@ class TStat(AFNICommand): >>> tstat.inputs.in_file = 'functional.nii' >>> tstat.inputs.args = '-mean' >>> tstat.inputs.out_file = 'stats' - >>> tstat.cmdline # doctest: +IGNORE_UNICODE + >>> tstat.cmdline # doctest: +ALLOW_UNICODE '3dTstat -mean -prefix stats functional.nii' >>> res = tstat.run() # doctest: +SKIP @@ -1219,7 +1219,7 @@ class To3D(AFNICommand): >>> to3d.inputs.in_folder = '.' >>> to3d.inputs.out_file = 'dicomdir.nii' >>> to3d.inputs.filetype = 'anat' - >>> to3d.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> to3d.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'to3d -datum float -anat -prefix dicomdir.nii ./*.dcm' >>> res = to3d.run() # doctest: +SKIP @@ -1262,7 +1262,7 @@ class ZCutUp(AFNICommand): >>> zcutup.inputs.in_file = 'functional.nii' >>> zcutup.inputs.out_file = 'functional_zcutup.nii' >>> zcutup.inputs.keep= '0 10' - >>> zcutup.cmdline # doctest: +IGNORE_UNICODE + >>> zcutup.cmdline # doctest: +ALLOW_UNICODE '3dZcutup -keep 0 10 -prefix functional_zcutup.nii functional.nii' >>> res = zcutup.run() # doctest: +SKIP diff --git a/nipype/interfaces/ants/legacy.py b/nipype/interfaces/ants/legacy.py index 677abedaab..3019f27c22 100644 --- a/nipype/interfaces/ants/legacy.py +++ b/nipype/interfaces/ants/legacy.py @@ -86,7 +86,7 @@ class antsIntroduction(ANTSCommand): >>> warp.inputs.reference_image = 'Template_6.nii' >>> warp.inputs.input_image = 'structural.nii' >>> warp.inputs.max_iterations = [30,90,20] - >>> warp.cmdline # doctest: +IGNORE_UNICODE + >>> warp.cmdline # doctest: +ALLOW_UNICODE 'antsIntroduction.sh -d 3 -i structural.nii -m 30x90x20 -o ants_ -r Template_6.nii -t GR' """ @@ -204,7 +204,7 @@ class buildtemplateparallel(ANTSCommand): >>> tmpl = buildtemplateparallel() >>> tmpl.inputs.in_files = ['T1.nii', 'structural.nii'] >>> tmpl.inputs.max_iterations = [30, 90, 20] - >>> tmpl.cmdline # doctest: +IGNORE_UNICODE + >>> tmpl.cmdline # doctest: +ALLOW_UNICODE 'buildtemplateparallel.sh -d 3 -i 4 -m 30x90x20 -o antsTMPL_ -c 0 -t GR T1.nii structural.nii' """ diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index fcc60b2f4f..91a6d2a557 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -120,7 +120,7 @@ class ANTS(ANTSCommand): >>> ants.inputs.regularization_gradient_field_sigma = 3 >>> ants.inputs.regularization_deformation_field_sigma = 0 >>> ants.inputs.number_of_affine_iterations = [10000,10000,10000,10000,10000] - >>> ants.cmdline # doctest: +IGNORE_UNICODE + >>> ants.cmdline # doctest: +ALLOW_UNICODE 'ANTS 3 --MI-option 32x16000 --image-metric CC[ T1.nii, resting.nii, 1, 5 ] --number-of-affine-iterations \ 10000x10000x10000x10000x10000 --number-of-iterations 50x35x15 --output-naming MY --regularization Gauss[3.0,0.0] \ --transformation-model SyN[0.25] --use-Histogram-Matching 1' @@ -428,7 +428,7 @@ class Registration(ANTSCommand): >>> reg.inputs.use_estimate_learning_rate_once = [True, True] >>> reg.inputs.use_histogram_matching = [True, True] # This is the default >>> reg.inputs.output_warped_image = 'output_warped_image.nii.gz' - >>> reg.cmdline # doctest: +IGNORE_UNICODE + >>> reg.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 0 ] \ --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ @@ -442,7 +442,7 @@ class Registration(ANTSCommand): >>> reg.inputs.invert_initial_moving_transform = True >>> reg1 = copy.deepcopy(reg) >>> reg1.inputs.winsorize_lower_quantile = 0.025 - >>> reg1.cmdline # doctest: +IGNORE_UNICODE + >>> reg1.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ @@ -455,7 +455,7 @@ class Registration(ANTSCommand): >>> reg2 = copy.deepcopy(reg) >>> reg2.inputs.winsorize_upper_quantile = 0.975 - >>> reg2.cmdline # doctest: +IGNORE_UNICODE + >>> reg2.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ @@ -468,7 +468,7 @@ class Registration(ANTSCommand): >>> reg3 = copy.deepcopy(reg) >>> reg3.inputs.winsorize_lower_quantile = 0.025 >>> reg3.inputs.winsorize_upper_quantile = 0.975 - >>> reg3.cmdline # doctest: +IGNORE_UNICODE + >>> reg3.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ @@ -480,7 +480,7 @@ class Registration(ANTSCommand): >>> reg3a = copy.deepcopy(reg) >>> reg3a.inputs.float = True - >>> reg3a.cmdline # doctest: +IGNORE_UNICODE + >>> reg3a.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --float 1 \ --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear \ --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] \ @@ -493,7 +493,7 @@ class Registration(ANTSCommand): >>> reg3b = copy.deepcopy(reg) >>> reg3b.inputs.float = False - >>> reg3b.cmdline # doctest: +IGNORE_UNICODE + >>> reg3b.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --float 0 \ --initial-moving-transform [ trans.mat, 1 ] --initialize-transforms-per-stage 0 --interpolation Linear \ --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] \ @@ -511,7 +511,7 @@ class Registration(ANTSCommand): >>> reg4.inputs.initialize_transforms_per_stage = True >>> reg4.inputs.collapse_output_transforms = True >>> outputs = reg4._list_outputs() - >>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE +ALLOW_UNICODE {'composite_transform': '.../nipype/testing/data/output_Composite.h5', 'forward_invert_flags': [], 'forward_transforms': [], @@ -521,7 +521,7 @@ class Registration(ANTSCommand): 'reverse_transforms': [], 'save_state': '.../nipype/testing/data/trans.mat', 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz'} - >>> reg4.cmdline # doctest: +IGNORE_UNICODE + >>> reg4.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 1 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 1 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --restore-state trans.mat --save-state trans.mat --transform Affine[ 2.0 ] \ @@ -536,7 +536,7 @@ class Registration(ANTSCommand): >>> reg4b = copy.deepcopy(reg4) >>> reg4b.inputs.write_composite_transform = False >>> outputs = reg4b._list_outputs() - >>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> pprint.pprint(outputs) # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE +ALLOW_UNICODE {'composite_transform': , 'forward_invert_flags': [False, False], 'forward_transforms': ['.../nipype/testing/data/output_0GenericAffine.mat', @@ -549,7 +549,7 @@ class Registration(ANTSCommand): 'save_state': '.../nipype/testing/data/trans.mat', 'warped_image': '.../nipype/testing/data/output_warped_image.nii.gz'} >>> reg4b.aggregate_outputs() # doctest: +SKIP - >>> reg4b.cmdline # doctest: +IGNORE_UNICODE + >>> reg4b.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 1 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 1 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --restore-state trans.mat --save-state trans.mat --transform Affine[ 2.0 ] \ @@ -569,7 +569,7 @@ class Registration(ANTSCommand): >>> reg5.inputs.radius_or_number_of_bins = [32, [32, 4] ] >>> reg5.inputs.sampling_strategy = ['Random', None] # use default strategy in second stage >>> reg5.inputs.sampling_percentage = [0.05, [0.05, 0.10]] - >>> reg5.cmdline # doctest: +IGNORE_UNICODE + >>> reg5.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ @@ -584,7 +584,7 @@ class Registration(ANTSCommand): >>> reg6 = copy.deepcopy(reg5) >>> reg6.inputs.fixed_image = ['fixed1.nii', 'fixed2.nii'] >>> reg6.inputs.moving_image = ['moving1.nii', 'moving2.nii'] - >>> reg6.cmdline # doctest: +IGNORE_UNICODE + >>> reg6.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ @@ -599,7 +599,7 @@ class Registration(ANTSCommand): >>> reg7a = copy.deepcopy(reg) >>> reg7a.inputs.interpolation = 'BSpline' >>> reg7a.inputs.interpolation_parameters = (3,) - >>> reg7a.cmdline # doctest: +IGNORE_UNICODE + >>> reg7a.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation BSpline[ 3 ] --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ @@ -613,7 +613,7 @@ class Registration(ANTSCommand): >>> reg7b = copy.deepcopy(reg) >>> reg7b.inputs.interpolation = 'Gaussian' >>> reg7b.inputs.interpolation_parameters = (1.0, 1.0) - >>> reg7b.cmdline # doctest: +IGNORE_UNICODE + >>> reg7b.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation Gaussian[ 1.0, 1.0 ] \ --output [ output_, output_warped_image.nii.gz ] --transform Affine[ 2.0 ] \ @@ -628,7 +628,7 @@ class Registration(ANTSCommand): >>> reg8 = copy.deepcopy(reg) >>> reg8.inputs.transforms = ['Affine', 'BSplineSyN'] >>> reg8.inputs.transform_parameters = [(2.0,), (0.25, 26, 0, 3)] - >>> reg8.cmdline # doctest: +IGNORE_UNICODE + >>> reg8.cmdline # doctest: +ALLOW_UNICODE 'antsRegistration --collapse-output-transforms 0 --dimensionality 3 --initial-moving-transform [ trans.mat, 1 ] \ --initialize-transforms-per-stage 0 --interpolation Linear --output [ output_, output_warped_image.nii.gz ] \ --transform Affine[ 2.0 ] --metric Mattes[ fixed1.nii, moving1.nii, 1, 32, Random, 0.05 ] \ diff --git a/nipype/interfaces/ants/resampling.py b/nipype/interfaces/ants/resampling.py index c879cc0d6f..39393dc0f0 100644 --- a/nipype/interfaces/ants/resampling.py +++ b/nipype/interfaces/ants/resampling.py @@ -63,7 +63,7 @@ class WarpTimeSeriesImageMultiTransform(ANTSCommand): >>> wtsimt.inputs.input_image = 'resting.nii' >>> wtsimt.inputs.reference_image = 'ants_deformed.nii.gz' >>> wtsimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt'] - >>> wtsimt.cmdline # doctest: +IGNORE_UNICODE + >>> wtsimt.cmdline # doctest: +ALLOW_UNICODE 'WarpTimeSeriesImageMultiTransform 4 resting.nii resting_wtsimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz \ ants_Affine.txt' @@ -159,7 +159,7 @@ class WarpImageMultiTransform(ANTSCommand): >>> wimt.inputs.input_image = 'structural.nii' >>> wimt.inputs.reference_image = 'ants_deformed.nii.gz' >>> wimt.inputs.transformation_series = ['ants_Warp.nii.gz','ants_Affine.txt'] - >>> wimt.cmdline # doctest: +IGNORE_UNICODE + >>> wimt.cmdline # doctest: +ALLOW_UNICODE 'WarpImageMultiTransform 3 structural.nii structural_wimt.nii -R ants_deformed.nii.gz ants_Warp.nii.gz \ ants_Affine.txt' @@ -169,7 +169,7 @@ class WarpImageMultiTransform(ANTSCommand): >>> wimt.inputs.transformation_series = ['func2anat_coreg_Affine.txt','func2anat_InverseWarp.nii.gz', \ 'dwi2anat_Warp.nii.gz','dwi2anat_coreg_Affine.txt'] >>> wimt.inputs.invert_affine = [1] - >>> wimt.cmdline # doctest: +IGNORE_UNICODE + >>> wimt.cmdline # doctest: +ALLOW_UNICODE 'WarpImageMultiTransform 3 diffusion_weighted.nii diffusion_weighted_wimt.nii -R functional.nii \ -i func2anat_coreg_Affine.txt func2anat_InverseWarp.nii.gz dwi2anat_Warp.nii.gz dwi2anat_coreg_Affine.txt' @@ -278,7 +278,7 @@ class ApplyTransforms(ANTSCommand): >>> at.inputs.default_value = 0 >>> at.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat'] >>> at.inputs.invert_transform_flags = [False, False] - >>> at.cmdline # doctest: +IGNORE_UNICODE + >>> at.cmdline # doctest: +ALLOW_UNICODE 'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear \ --output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \ --transform [ trans.mat, 0 ]' @@ -293,7 +293,7 @@ class ApplyTransforms(ANTSCommand): >>> at1.inputs.default_value = 0 >>> at1.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat'] >>> at1.inputs.invert_transform_flags = [False, False] - >>> at1.cmdline # doctest: +IGNORE_UNICODE + >>> at1.cmdline # doctest: +ALLOW_UNICODE 'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation BSpline[ 5 ] \ --output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \ --transform [ trans.mat, 0 ]' @@ -399,7 +399,7 @@ class ApplyTransformsToPoints(ANTSCommand): >>> at.inputs.input_file = 'moving.csv' >>> at.inputs.transforms = ['trans.mat', 'ants_Warp.nii.gz'] >>> at.inputs.invert_transform_flags = [False, False] - >>> at.cmdline # doctest: +IGNORE_UNICODE + >>> at.cmdline # doctest: +ALLOW_UNICODE 'antsApplyTransformsToPoints --dimensionality 3 --input moving.csv --output moving_transformed.csv \ --transform [ trans.mat, 0 ] --transform [ ants_Warp.nii.gz, 0 ]' diff --git a/nipype/interfaces/ants/segmentation.py b/nipype/interfaces/ants/segmentation.py index 70231360d3..10483a2283 100644 --- a/nipype/interfaces/ants/segmentation.py +++ b/nipype/interfaces/ants/segmentation.py @@ -89,7 +89,7 @@ class Atropos(ANTSCommand): >>> at.inputs.posterior_formulation = 'Socrates' >>> at.inputs.use_mixture_model_proportions = True >>> at.inputs.save_posteriors = True - >>> at.cmdline # doctest: +IGNORE_UNICODE + >>> at.cmdline # doctest: +ALLOW_UNICODE 'Atropos --image-dimensionality 3 --icm [1,1] \ --initialization PriorProbabilityImages[2,priors/priorProbImages%02d.nii,0.8,1e-07] --intensity-image structural.nii \ --likelihood-model Gaussian --mask-image mask.nii --mrf [0.2,1x1x1] --convergence [5,1e-06] \ @@ -207,7 +207,7 @@ class LaplacianThickness(ANTSCommand): >>> cort_thick.inputs.input_wm = 'white_matter.nii.gz' >>> cort_thick.inputs.input_gm = 'gray_matter.nii.gz' >>> cort_thick.inputs.output_image = 'output_thickness.nii.gz' - >>> cort_thick.cmdline # doctest: +IGNORE_UNICODE + >>> cort_thick.cmdline # doctest: +ALLOW_UNICODE 'LaplacianThickness white_matter.nii.gz gray_matter.nii.gz output_thickness.nii.gz' """ @@ -289,7 +289,7 @@ class N4BiasFieldCorrection(ANTSCommand): >>> n4.inputs.bspline_fitting_distance = 300 >>> n4.inputs.shrink_factor = 3 >>> n4.inputs.n_iterations = [50,50,30,20] - >>> n4.cmdline # doctest: +IGNORE_UNICODE + >>> n4.cmdline # doctest: +ALLOW_UNICODE 'N4BiasFieldCorrection --bspline-fitting [ 300 ] \ -d 3 --input-image structural.nii \ --convergence [ 50x50x30x20 ] --output structural_corrected.nii \ @@ -297,7 +297,7 @@ class N4BiasFieldCorrection(ANTSCommand): >>> n4_2 = copy.deepcopy(n4) >>> n4_2.inputs.convergence_threshold = 1e-6 - >>> n4_2.cmdline # doctest: +IGNORE_UNICODE + >>> n4_2.cmdline # doctest: +ALLOW_UNICODE 'N4BiasFieldCorrection --bspline-fitting [ 300 ] \ -d 3 --input-image structural.nii \ --convergence [ 50x50x30x20, 1e-06 ] --output structural_corrected.nii \ @@ -305,7 +305,7 @@ class N4BiasFieldCorrection(ANTSCommand): >>> n4_3 = copy.deepcopy(n4_2) >>> n4_3.inputs.bspline_order = 5 - >>> n4_3.cmdline # doctest: +IGNORE_UNICODE + >>> n4_3.cmdline # doctest: +ALLOW_UNICODE 'N4BiasFieldCorrection --bspline-fitting [ 300, 5 ] \ -d 3 --input-image structural.nii \ --convergence [ 50x50x30x20, 1e-06 ] --output structural_corrected.nii \ @@ -315,7 +315,7 @@ class N4BiasFieldCorrection(ANTSCommand): >>> n4_4.inputs.input_image = 'structural.nii' >>> n4_4.inputs.save_bias = True >>> n4_4.inputs.dimension = 3 - >>> n4_4.cmdline # doctest: +IGNORE_UNICODE + >>> n4_4.cmdline # doctest: +ALLOW_UNICODE 'N4BiasFieldCorrection -d 3 --input-image structural.nii \ --output [ structural_corrected.nii, structural_bias.nii ]' """ @@ -504,7 +504,7 @@ class CorticalThickness(ANTSCommand): ... 'BrainSegmentationPrior03.nii.gz', ... 'BrainSegmentationPrior04.nii.gz'] >>> corticalthickness.inputs.t1_registration_template = 'brain_study_template.nii.gz' - >>> corticalthickness.cmdline # doctest: +IGNORE_UNICODE + >>> corticalthickness.cmdline # doctest: +ALLOW_UNICODE 'antsCorticalThickness.sh -a T1.nii.gz -m ProbabilityMaskOfStudyTemplate.nii.gz -e study_template.nii.gz -d 3 \ -s nii.gz -o antsCT_ -p nipype_priors/BrainSegmentationPrior%02d.nii.gz -t brain_study_template.nii.gz' @@ -667,7 +667,7 @@ class BrainExtraction(ANTSCommand): >>> brainextraction.inputs.anatomical_image ='T1.nii.gz' >>> brainextraction.inputs.brain_template = 'study_template.nii.gz' >>> brainextraction.inputs.brain_probability_mask ='ProbabilityMaskOfStudyTemplate.nii.gz' - >>> brainextraction.cmdline # doctest: +IGNORE_UNICODE + >>> brainextraction.cmdline # doctest: +ALLOW_UNICODE 'antsBrainExtraction.sh -a T1.nii.gz -m ProbabilityMaskOfStudyTemplate.nii.gz -e study_template.nii.gz -d 3 \ -s nii.gz -o highres001_' """ @@ -758,7 +758,7 @@ class JointFusion(ANTSCommand): ... 'segmentation1.nii.gz', ... 'segmentation1.nii.gz'] >>> at.inputs.target_image = 'T1.nii' - >>> at.cmdline # doctest: +IGNORE_UNICODE + >>> at.cmdline # doctest: +ALLOW_UNICODE 'jointfusion 3 1 -m Joint[0.1,2] -tg T1.nii -g im1.nii -g im2.nii -g im3.nii -l segmentation0.nii.gz \ -l segmentation1.nii.gz -l segmentation1.nii.gz fusion_labelimage_output.nii' @@ -767,7 +767,7 @@ class JointFusion(ANTSCommand): >>> at.inputs.beta = 1 >>> at.inputs.patch_radius = [3,2,1] >>> at.inputs.search_radius = [1,2,3] - >>> at.cmdline # doctest: +IGNORE_UNICODE + >>> at.cmdline # doctest: +ALLOW_UNICODE 'jointfusion 3 1 -m Joint[0.5,1] -rp 3x2x1 -rs 1x2x3 -tg T1.nii -g im1.nii -g im2.nii -g im3.nii \ -l segmentation0.nii.gz -l segmentation1.nii.gz -l segmentation1.nii.gz fusion_labelimage_output.nii' """ @@ -844,20 +844,20 @@ class DenoiseImage(ANTSCommand): >>> denoise = DenoiseImage() >>> denoise.inputs.dimension = 3 >>> denoise.inputs.input_image = 'im1.nii' - >>> denoise.cmdline # doctest: +IGNORE_UNICODE + >>> denoise.cmdline # doctest: +ALLOW_UNICODE 'DenoiseImage -d 3 -i im1.nii -n Gaussian -o im1_noise_corrected.nii -s 1' >>> denoise_2 = copy.deepcopy(denoise) >>> denoise_2.inputs.output_image = 'output_corrected_image.nii.gz' >>> denoise_2.inputs.noise_model = 'Rician' >>> denoise_2.inputs.shrink_factor = 2 - >>> denoise_2.cmdline # doctest: +IGNORE_UNICODE + >>> denoise_2.cmdline # doctest: +ALLOW_UNICODE 'DenoiseImage -d 3 -i im1.nii -n Rician -o output_corrected_image.nii.gz -s 2' >>> denoise_3 = DenoiseImage() >>> denoise_3.inputs.input_image = 'im1.nii' >>> denoise_3.inputs.save_noise = True - >>> denoise_3.cmdline # doctest: +IGNORE_UNICODE + >>> denoise_3.cmdline # doctest: +ALLOW_UNICODE 'DenoiseImage -i im1.nii -n Gaussian -o [ im1_noise_corrected.nii, im1_noise.nii ] -s 1' """ input_spec = DenoiseImageInputSpec @@ -961,12 +961,12 @@ class AntsJointFusion(ANTSCommand): >>> antsjointfusion.inputs.atlas_image = [ ['rc1s1.nii','rc1s2.nii'] ] >>> antsjointfusion.inputs.atlas_segmentation_image = ['segmentation0.nii.gz'] >>> antsjointfusion.inputs.target_image = ['im1.nii'] - >>> antsjointfusion.cmdline # doctest: +IGNORE_UNICODE + >>> antsjointfusion.cmdline # doctest: +ALLOW_UNICODE "antsJointFusion -a 0.1 -g ['rc1s1.nii', 'rc1s2.nii'] -l segmentation0.nii.gz \ -b 2.0 -o ants_fusion_label_output.nii -s 3x3x3 -t ['im1.nii']" >>> antsjointfusion.inputs.target_image = [ ['im1.nii', 'im2.nii'] ] - >>> antsjointfusion.cmdline # doctest: +IGNORE_UNICODE + >>> antsjointfusion.cmdline # doctest: +ALLOW_UNICODE "antsJointFusion -a 0.1 -g ['rc1s1.nii', 'rc1s2.nii'] -l segmentation0.nii.gz \ -b 2.0 -o ants_fusion_label_output.nii -s 3x3x3 -t ['im1.nii', 'im2.nii']" @@ -974,7 +974,7 @@ class AntsJointFusion(ANTSCommand): ... ['rc2s1.nii','rc2s2.nii'] ] >>> antsjointfusion.inputs.atlas_segmentation_image = ['segmentation0.nii.gz', ... 'segmentation1.nii.gz'] - >>> antsjointfusion.cmdline # doctest: +IGNORE_UNICODE + >>> antsjointfusion.cmdline # doctest: +ALLOW_UNICODE "antsJointFusion -a 0.1 -g ['rc1s1.nii', 'rc1s2.nii'] -g ['rc2s1.nii', 'rc2s2.nii'] \ -l segmentation0.nii.gz -l segmentation1.nii.gz -b 2.0 -o ants_fusion_label_output.nii \ -s 3x3x3 -t ['im1.nii', 'im2.nii']" @@ -984,7 +984,7 @@ class AntsJointFusion(ANTSCommand): >>> antsjointfusion.inputs.beta = 1.0 >>> antsjointfusion.inputs.patch_radius = [3,2,1] >>> antsjointfusion.inputs.search_radius = [3] - >>> antsjointfusion.cmdline # doctest: +IGNORE_UNICODE + >>> antsjointfusion.cmdline # doctest: +ALLOW_UNICODE "antsJointFusion -a 0.5 -g ['rc1s1.nii', 'rc1s2.nii'] -g ['rc2s1.nii', 'rc2s2.nii'] \ -l segmentation0.nii.gz -l segmentation1.nii.gz -b 1.0 -d 3 -o ants_fusion_label_output.nii \ -p 3x2x1 -s 3 -t ['im1.nii', 'im2.nii']" @@ -993,7 +993,7 @@ class AntsJointFusion(ANTSCommand): >>> antsjointfusion.inputs.verbose = True >>> antsjointfusion.inputs.exclusion_image = ['roi01.nii', 'roi02.nii'] >>> antsjointfusion.inputs.exclusion_image_label = ['1','2'] - >>> antsjointfusion.cmdline # doctest: +IGNORE_UNICODE + >>> antsjointfusion.cmdline # doctest: +ALLOW_UNICODE "antsJointFusion -a 0.5 -g ['rc1s1.nii', 'rc1s2.nii'] -g ['rc2s1.nii', 'rc2s2.nii'] \ -l segmentation0.nii.gz -l segmentation1.nii.gz -b 1.0 -d 3 -e 1[roi01.nii] -e 2[roi02.nii] \ -o ants_fusion_label_output.nii -p 3x2x1 -s mask.nii -t ['im1.nii', 'im2.nii'] -v" @@ -1002,7 +1002,7 @@ class AntsJointFusion(ANTSCommand): >>> antsjointfusion.inputs.out_intensity_fusion_name_format = 'ants_joint_fusion_intensity_%d.nii.gz' >>> antsjointfusion.inputs.out_label_post_prob_name_format = 'ants_joint_fusion_posterior_%d.nii.gz' >>> antsjointfusion.inputs.out_atlas_voting_weight_name_format = 'ants_joint_fusion_voting_weight_%d.nii.gz' - >>> antsjointfusion.cmdline # doctest: +IGNORE_UNICODE + >>> antsjointfusion.cmdline # doctest: +ALLOW_UNICODE "antsJointFusion -a 0.5 -g ['rc1s1.nii', 'rc1s2.nii'] -g ['rc2s1.nii', 'rc2s2.nii'] \ -l segmentation0.nii.gz -l segmentation1.nii.gz -b 1.0 -d 3 -e 1[roi01.nii] -e 2[roi02.nii] \ -o [ants_fusion_label_output.nii, ants_joint_fusion_intensity_%d.nii.gz, \ diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 32c438d2ea..05e86ee8c9 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import ANTS @@ -78,7 +77,7 @@ def test_ANTS_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ANTS_outputs(): @@ -92,4 +91,4 @@ def test_ANTS_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py index 1c2a67f3bb..6af06e4149 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import ANTSCommand @@ -22,5 +21,5 @@ def test_ANTSCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py index 0aed2d56ec..8532321ece 100644 --- a/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_AntsJointFusion.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import AntsJointFusion @@ -77,7 +76,7 @@ def test_AntsJointFusion_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AntsJointFusion_outputs(): @@ -90,4 +89,4 @@ def test_AntsJointFusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index ba1c9e7edf..2087b6848d 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..resampling import ApplyTransforms @@ -53,7 +52,7 @@ def test_ApplyTransforms_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransforms_outputs(): @@ -63,4 +62,4 @@ def test_ApplyTransforms_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index 6280a7c074..f79806e384 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..resampling import ApplyTransformsToPoints @@ -36,7 +35,7 @@ def test_ApplyTransformsToPoints_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransformsToPoints_outputs(): @@ -46,4 +45,4 @@ def test_ApplyTransformsToPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index a6fb42b0ea..fca1b5f569 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import Atropos @@ -69,7 +68,7 @@ def test_Atropos_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Atropos_outputs(): @@ -80,4 +79,4 @@ def test_Atropos_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 347b07ef6e..5cf42d651a 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import AverageAffineTransform @@ -35,7 +34,7 @@ def test_AverageAffineTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AverageAffineTransform_outputs(): @@ -45,4 +44,4 @@ def test_AverageAffineTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 2e25305f3a..84de87ccfe 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import AverageImages @@ -39,7 +38,7 @@ def test_AverageImages_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AverageImages_outputs(): @@ -49,4 +48,4 @@ def test_AverageImages_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py index b1448a641d..ae530900ec 100644 --- a/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_BrainExtraction.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import BrainExtraction @@ -51,7 +50,7 @@ def test_BrainExtraction_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BrainExtraction_outputs(): @@ -62,4 +61,4 @@ def test_BrainExtraction_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index cc2dfada40..8557131aeb 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..visualization import ConvertScalarImageToRGB @@ -64,7 +63,7 @@ def test_ConvertScalarImageToRGB_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ConvertScalarImageToRGB_outputs(): @@ -74,4 +73,4 @@ def test_ConvertScalarImageToRGB_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py index df40609826..7572ce1e7c 100644 --- a/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_CorticalThickness.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import CorticalThickness @@ -72,7 +71,7 @@ def test_CorticalThickness_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CorticalThickness_outputs(): @@ -93,4 +92,4 @@ def test_CorticalThickness_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py index ccb92db57d..41979e5a1a 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateJacobianDeterminantImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import CreateJacobianDeterminantImage @@ -43,7 +42,7 @@ def test_CreateJacobianDeterminantImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CreateJacobianDeterminantImage_outputs(): @@ -53,4 +52,4 @@ def test_CreateJacobianDeterminantImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index a5222ef3de..1c4abe6a96 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..visualization import CreateTiledMosaic @@ -47,7 +46,7 @@ def test_CreateTiledMosaic_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CreateTiledMosaic_outputs(): @@ -57,4 +56,4 @@ def test_CreateTiledMosaic_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py index 7d7f7e897b..0e342808e0 100644 --- a/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py +++ b/nipype/interfaces/ants/tests/test_auto_DenoiseImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import DenoiseImage @@ -51,7 +50,7 @@ def test_DenoiseImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DenoiseImage_outputs(): @@ -62,4 +61,4 @@ def test_DenoiseImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index a6a3e5c6a7..ab4331b438 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..legacy import GenWarpFields @@ -53,7 +52,7 @@ def test_GenWarpFields_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenWarpFields_outputs(): @@ -67,4 +66,4 @@ def test_GenWarpFields_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index 5b4703cf99..99e8ebc07a 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import JointFusion @@ -69,7 +68,7 @@ def test_JointFusion_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JointFusion_outputs(): @@ -79,4 +78,4 @@ def test_JointFusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index 60cfb494e3..fd40598840 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import LaplacianThickness @@ -52,7 +51,7 @@ def test_LaplacianThickness_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_LaplacianThickness_outputs(): @@ -62,4 +61,4 @@ def test_LaplacianThickness_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 5a3d682551..b986979d8a 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MultiplyImages @@ -39,7 +38,7 @@ def test_MultiplyImages_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyImages_outputs(): @@ -49,4 +48,4 @@ def test_MultiplyImages_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 170b80a224..17f493346e 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import N4BiasFieldCorrection @@ -52,7 +51,7 @@ def test_N4BiasFieldCorrection_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_N4BiasFieldCorrection_outputs(): @@ -63,4 +62,4 @@ def test_N4BiasFieldCorrection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 20eb90cabf..fc16c99d27 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import Registration @@ -118,7 +117,7 @@ def test_Registration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Registration_outputs(): @@ -136,4 +135,4 @@ def test_Registration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index 69a573aa28..724fa83ae2 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..resampling import WarpImageMultiTransform @@ -57,7 +56,7 @@ def test_WarpImageMultiTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WarpImageMultiTransform_outputs(): @@ -67,4 +66,4 @@ def test_WarpImageMultiTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index ee18b7abba..ecc81e05ad 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..resampling import WarpTimeSeriesImageMultiTransform @@ -50,7 +49,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WarpTimeSeriesImageMultiTransform_outputs(): @@ -60,4 +59,4 @@ def test_WarpTimeSeriesImageMultiTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py index 5661eddd02..9abcaa99bb 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsBrainExtraction.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import antsBrainExtraction @@ -51,7 +50,7 @@ def test_antsBrainExtraction_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_antsBrainExtraction_outputs(): @@ -62,4 +61,4 @@ def test_antsBrainExtraction_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py index 0944ebf1b7..1d1bd14391 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..segmentation import antsCorticalThickness @@ -72,7 +71,7 @@ def test_antsCorticalThickness_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_antsCorticalThickness_outputs(): @@ -93,4 +92,4 @@ def test_antsCorticalThickness_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index be61025e30..03638c4223 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..legacy import antsIntroduction @@ -53,7 +52,7 @@ def test_antsIntroduction_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_antsIntroduction_outputs(): @@ -67,4 +66,4 @@ def test_antsIntroduction_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index 6992ce5c11..f244295f93 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..legacy import buildtemplateparallel @@ -57,7 +56,7 @@ def test_buildtemplateparallel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_buildtemplateparallel_outputs(): @@ -69,4 +68,4 @@ def test_buildtemplateparallel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/ants/tests/test_spec_JointFusion.py b/nipype/interfaces/ants/tests/test_spec_JointFusion.py index 1b031f9f89..676631f08e 100644 --- a/nipype/interfaces/ants/tests/test_spec_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_spec_JointFusion.py @@ -1,54 +1,48 @@ # -*- coding: utf-8 -*- from __future__ import division from builtins import range -from nipype.testing import assert_equal, assert_raises, example_data +from nipype.testing import example_data from nipype.interfaces.base import InputMultiPath from traits.trait_errors import TraitError from nipype.interfaces.ants import JointFusion - +import pytest def test_JointFusion_dimension(): at = JointFusion() set_dimension = lambda d: setattr(at.inputs, 'dimension', int(d)) for d in range(2, 5): set_dimension(d) - yield assert_equal, at.inputs.dimension, int(d) + assert at.inputs.dimension == int(d) for d in [0, 1, 6, 7]: - yield assert_raises, TraitError, set_dimension, d - + with pytest.raises(TraitError): + set_dimension(d) -def test_JointFusion_modalities(): +@pytest.mark.parametrize("m", range(1, 5)) +def test_JointFusion_modalities(m): at = JointFusion() - set_modalities = lambda m: setattr(at.inputs, 'modalities', int(m)) - for m in range(1, 5): - set_modalities(m) - yield assert_equal, at.inputs.modalities, int(m) + setattr(at.inputs, 'modalities', int(m)) + assert at.inputs.modalities == int(m) - -def test_JointFusion_method(): +@pytest.mark.parametrize("a, b", [(a,b) for a in range(10) for b in range(10)]) +def test_JointFusion_method(a, b): at = JointFusion() set_method = lambda a, b: setattr(at.inputs, 'method', 'Joint[%.1f,%d]'.format(a, b)) - for a in range(10): - _a = a / 10.0 - for b in range(10): - set_method(_a, b) - # set directly - yield assert_equal, at.inputs.method, 'Joint[%.1f,%d]'.format(_a, b) - aprime = _a + 0.1 - bprime = b + 1 - at.inputs.alpha = aprime - at.inputs.beta = bprime - # set with alpha/beta - yield assert_equal, at.inputs.method, 'Joint[%.1f,%d]'.format(aprime, bprime) - + _a = a / 10.0 + set_method(_a, b) + # set directly + assert at.inputs.method == 'Joint[%.1f,%d]'.format(_a, b) + aprime = _a + 0.1 + bprime = b + 1 + at.inputs.alpha = aprime + at.inputs.beta = bprime + # set with alpha/beta + assert at.inputs.method == 'Joint[%.1f,%d]'.format(aprime, bprime) -def test_JointFusion_radius(): +@pytest.mark.parametrize("attr, x", [(attr, x) for attr in ['patch_radius', 'search_radius'] for x in range(5)]) +def test_JointFusion_radius(attr, x): at = JointFusion() - set_radius = lambda attr, x, y, z: setattr(at.inputs, attr, [x, y, z]) - for attr in ['patch_radius', 'search_radius']: - for x in range(5): - set_radius(attr, x, x + 1, x**x) - yield assert_equal, at._format_arg(attr, None, getattr(at.inputs, attr))[4:], '{0}x{1}x{2}'.format(x, x + 1, x**x) + setattr(at.inputs, attr, [x, x+1, x**x]) + assert at._format_arg(attr, None, getattr(at.inputs, attr))[4:] == '{0}x{1}x{2}'.format(x, x + 1, x**x) def test_JointFusion_cmd(): @@ -74,6 +68,7 @@ def test_JointFusion_cmd(): warped_intensity_images[1], segmentation_images[0], segmentation_images[1]) - yield assert_equal, at.cmdline, expected_command + assert at.cmdline == expected_command # setting intensity or labels with unequal lengths raises error - yield assert_raises, AssertionError, at._format_arg, 'warped_intensity_images', InputMultiPath, warped_intensity_images + [example_data('im3.nii')] + with pytest.raises(AssertionError): + at._format_arg('warped_intensity_images', InputMultiPath, warped_intensity_images + [example_data('im3.nii')]) diff --git a/nipype/interfaces/ants/utils.py b/nipype/interfaces/ants/utils.py index 9c9d05fbd1..ade303898c 100644 --- a/nipype/interfaces/ants/utils.py +++ b/nipype/interfaces/ants/utils.py @@ -38,7 +38,7 @@ class AverageAffineTransform(ANTSCommand): >>> avg.inputs.dimension = 3 >>> avg.inputs.transforms = ['trans.mat', 'func_to_struct.mat'] >>> avg.inputs.output_affine_transform = 'MYtemplatewarp.mat' - >>> avg.cmdline # doctest: +IGNORE_UNICODE + >>> avg.cmdline # doctest: +ALLOW_UNICODE 'AverageAffineTransform 3 MYtemplatewarp.mat trans.mat func_to_struct.mat' """ _cmd = 'AverageAffineTransform' @@ -80,7 +80,7 @@ class AverageImages(ANTSCommand): >>> avg.inputs.output_average_image = "average.nii.gz" >>> avg.inputs.normalize = True >>> avg.inputs.images = ['rc1s1.nii', 'rc1s1.nii'] - >>> avg.cmdline # doctest: +IGNORE_UNICODE + >>> avg.cmdline # doctest: +ALLOW_UNICODE 'AverageImages 3 average.nii.gz 1 rc1s1.nii rc1s1.nii' """ _cmd = 'AverageImages' @@ -121,7 +121,7 @@ class MultiplyImages(ANTSCommand): >>> test.inputs.first_input = 'moving2.nii' >>> test.inputs.second_input = 0.25 >>> test.inputs.output_product_image = "out.nii" - >>> test.cmdline # doctest: +IGNORE_UNICODE + >>> test.cmdline # doctest: +ALLOW_UNICODE 'MultiplyImages 3 moving2.nii 0.25 out.nii' """ _cmd = 'MultiplyImages' @@ -162,7 +162,7 @@ class CreateJacobianDeterminantImage(ANTSCommand): >>> jacobian.inputs.imageDimension = 3 >>> jacobian.inputs.deformationField = 'ants_Warp.nii.gz' >>> jacobian.inputs.outputImage = 'out_name.nii.gz' - >>> jacobian.cmdline # doctest: +IGNORE_UNICODE + >>> jacobian.cmdline # doctest: +ALLOW_UNICODE 'CreateJacobianDeterminantImage 3 ants_Warp.nii.gz out_name.nii.gz' """ diff --git a/nipype/interfaces/ants/visualization.py b/nipype/interfaces/ants/visualization.py index 71d8e82f8d..ef51914e6c 100644 --- a/nipype/interfaces/ants/visualization.py +++ b/nipype/interfaces/ants/visualization.py @@ -57,7 +57,7 @@ class ConvertScalarImageToRGB(ANTSCommand): >>> converter.inputs.colormap = 'jet' >>> converter.inputs.minimum_input = 0 >>> converter.inputs.maximum_input = 6 - >>> converter.cmdline # doctest: +IGNORE_UNICODE + >>> converter.cmdline # doctest: +ALLOW_UNICODE 'ConvertScalarImageToRGB 3 T1.nii.gz rgb.nii.gz none jet none 0 6 0 255' """ _cmd = 'ConvertScalarImageToRGB' @@ -143,7 +143,7 @@ class CreateTiledMosaic(ANTSCommand): >>> mosaic_slicer.inputs.direction = 2 >>> mosaic_slicer.inputs.pad_or_crop = '[ -15x -50 , -15x -30 ,0]' >>> mosaic_slicer.inputs.slices = '[2 ,100 ,160]' - >>> mosaic_slicer.cmdline # doctest: +IGNORE_UNICODE + >>> mosaic_slicer.cmdline # doctest: +ALLOW_UNICODE 'CreateTiledMosaic -a 0.50 -d 2 -i T1.nii.gz -x mask.nii.gz -o output.png -p [ -15x -50 , -15x -30 ,0] \ -r rgb.nii.gz -s [2 ,100 ,160]' """ diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index f3d3f52ab3..b9f66e1f3b 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -127,10 +127,10 @@ class Bunch(object): -------- >>> from nipype.interfaces.base import Bunch >>> inputs = Bunch(infile='subj.nii', fwhm=6.0, register_to_mean=True) - >>> inputs # doctest: +IGNORE_UNICODE + >>> inputs # doctest: +ALLOW_UNICODE Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=True) >>> inputs.register_to_mean = False - >>> inputs # doctest: +IGNORE_UNICODE + >>> inputs # doctest: +ALLOW_UNICODE Bunch(fwhm=6.0, infile='subj.nii', register_to_mean=False) @@ -258,7 +258,7 @@ def _get_bunch_hash(self): else: item = val try: - if os.path.isfile(item): + if isinstance(item, str) and os.path.isfile(item): infile_list.append(key) except TypeError: # `item` is not a file or string. @@ -1610,18 +1610,18 @@ class must be instantiated with a command argument >>> from nipype.interfaces.base import CommandLine >>> cli = CommandLine(command='ls', environ={'DISPLAY': ':1'}) >>> cli.inputs.args = '-al' - >>> cli.cmdline # doctest: +IGNORE_UNICODE + >>> cli.cmdline # doctest: +ALLOW_UNICODE 'ls -al' - >>> pprint.pprint(cli.inputs.trait_get()) # doctest: +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> pprint.pprint(cli.inputs.trait_get()) # doctest: +NORMALIZE_WHITESPACE +ALLOW_UNICODE {'args': '-al', 'environ': {'DISPLAY': ':1'}, 'ignore_exception': False, 'terminal_output': 'stream'} - >>> cli.inputs.get_hashval()[0][0] # doctest: +IGNORE_UNICODE + >>> cli.inputs.get_hashval()[0][0] # doctest: +ALLOW_UNICODE ('args', '-al') - >>> cli.inputs.get_hashval()[1] # doctest: +IGNORE_UNICODE + >>> cli.inputs.get_hashval()[1] # doctest: +ALLOW_UNICODE '11c37f97649cd61627f4afe5136af8c0' """ @@ -1963,12 +1963,12 @@ class MpiCommandLine(CommandLine): >>> from nipype.interfaces.base import MpiCommandLine >>> mpi_cli = MpiCommandLine(command='my_mpi_prog') >>> mpi_cli.inputs.args = '-v' - >>> mpi_cli.cmdline # doctest: +IGNORE_UNICODE + >>> mpi_cli.cmdline # doctest: +ALLOW_UNICODE 'my_mpi_prog -v' >>> mpi_cli.inputs.use_mpi = True >>> mpi_cli.inputs.n_procs = 8 - >>> mpi_cli.cmdline # doctest: +IGNORE_UNICODE + >>> mpi_cli.cmdline # doctest: +ALLOW_UNICODE 'mpiexec -n 8 my_mpi_prog -v' """ input_spec = MpiCommandLineInputSpec @@ -2072,15 +2072,15 @@ class OutputMultiPath(MultiPath): >>> a.foo = '/software/temp/foo.txt' - >>> a.foo # doctest: +IGNORE_UNICODE + >>> a.foo # doctest: +ALLOW_UNICODE '/software/temp/foo.txt' >>> a.foo = ['/software/temp/foo.txt'] - >>> a.foo # doctest: +IGNORE_UNICODE + >>> a.foo # doctest: +ALLOW_UNICODE '/software/temp/foo.txt' >>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt'] - >>> a.foo # doctest: +IGNORE_UNICODE + >>> a.foo # doctest: +ALLOW_UNICODE ['/software/temp/foo.txt', '/software/temp/goo.txt'] """ @@ -2117,15 +2117,15 @@ class InputMultiPath(MultiPath): >>> a.foo = '/software/temp/foo.txt' - >>> a.foo # doctest: +IGNORE_UNICODE + >>> a.foo # doctest: +ALLOW_UNICODE ['/software/temp/foo.txt'] >>> a.foo = ['/software/temp/foo.txt'] - >>> a.foo # doctest: +IGNORE_UNICODE + >>> a.foo # doctest: +ALLOW_UNICODE ['/software/temp/foo.txt'] >>> a.foo = ['/software/temp/foo.txt', '/software/temp/goo.txt'] - >>> a.foo # doctest: +IGNORE_UNICODE + >>> a.foo # doctest: +ALLOW_UNICODE ['/software/temp/foo.txt', '/software/temp/goo.txt'] """ diff --git a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py index c36200d47e..1627ca9658 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_BDP.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_BDP.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import BDP @@ -126,5 +125,5 @@ def test_BDP_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py index ed52f6275e..8bc2b508b6 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bfc.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Bfc @@ -73,7 +72,7 @@ def test_Bfc_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Bfc_outputs(): @@ -86,4 +85,4 @@ def test_Bfc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py index 8f7402362f..e928ed793e 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Bse.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Bse.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Bse @@ -67,7 +66,7 @@ def test_Bse_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Bse_outputs(): @@ -82,4 +81,4 @@ def test_Bse_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py index e10dfb51bd..0f12812e7d 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cerebro.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Cerebro @@ -61,7 +60,7 @@ def test_Cerebro_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Cerebro_outputs(): @@ -74,4 +73,4 @@ def test_Cerebro_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py index 982edf7ab0..1e5204d618 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Cortex.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Cortex @@ -43,7 +42,7 @@ def test_Cortex_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Cortex_outputs(): @@ -53,4 +52,4 @@ def test_Cortex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py index 8e935cf53d..d7884a653a 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dewisp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Dewisp @@ -33,7 +32,7 @@ def test_Dewisp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Dewisp_outputs(): @@ -43,4 +42,4 @@ def test_Dewisp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py index f2c43b209c..1ab94275cc 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Dfs.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Dfs @@ -58,7 +57,7 @@ def test_Dfs_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Dfs_outputs(): @@ -68,4 +67,4 @@ def test_Dfs_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py index ff73bac5f1..266d773525 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Hemisplit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Hemisplit @@ -43,7 +42,7 @@ def test_Hemisplit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Hemisplit_outputs(): @@ -56,4 +55,4 @@ def test_Hemisplit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py index b345930151..de36871cf2 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pialmesh.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Pialmesh @@ -65,7 +64,7 @@ def test_Pialmesh_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Pialmesh_outputs(): @@ -75,4 +74,4 @@ def test_Pialmesh_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py index b78920ae67..0f0aa9db0d 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Pvc.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Pvc @@ -38,7 +37,7 @@ def test_Pvc_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Pvc_outputs(): @@ -49,4 +48,4 @@ def test_Pvc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py index f35952ed0b..9cac20e320 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_SVReg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import SVReg @@ -67,5 +66,5 @@ def test_SVReg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py index aafee6e1c5..6c0a10ddf4 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Scrubmask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Scrubmask @@ -37,7 +36,7 @@ def test_Scrubmask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Scrubmask_outputs(): @@ -47,4 +46,4 @@ def test_Scrubmask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py index 6c685a5c05..efbf2bba6c 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Skullfinder.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Skullfinder @@ -48,7 +47,7 @@ def test_Skullfinder_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Skullfinder_outputs(): @@ -58,4 +57,4 @@ def test_Skullfinder_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py index f314094f58..7018789105 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_Tca.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_Tca.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import Tca @@ -37,7 +36,7 @@ def test_Tca_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Tca_outputs(): @@ -47,4 +46,4 @@ def test_Tca_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py index 42486b24aa..b5e2da2a55 100644 --- a/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py +++ b/nipype/interfaces/brainsuite/tests/test_auto_ThicknessPVC.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..brainsuite import ThicknessPVC @@ -22,5 +21,5 @@ def test_ThicknessPVC_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/bru2nii.py b/nipype/interfaces/bru2nii.py index 481aefb9ec..ac13089657 100644 --- a/nipype/interfaces/bru2nii.py +++ b/nipype/interfaces/bru2nii.py @@ -42,7 +42,7 @@ class Bru2(CommandLine): >>> from nipype.interfaces.bru2nii import Bru2 >>> converter = Bru2() >>> converter.inputs.input_dir = "brukerdir" - >>> converter.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> converter.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'Bru2 -o .../nipype/nipype/testing/data/brukerdir brukerdir' """ input_spec = Bru2InputSpec diff --git a/nipype/interfaces/c3.py b/nipype/interfaces/c3.py index 3dd47dab49..8288ab3b17 100644 --- a/nipype/interfaces/c3.py +++ b/nipype/interfaces/c3.py @@ -38,7 +38,7 @@ class C3dAffineTool(SEMLikeCommandLine): >>> c3.inputs.source_file = 'cmatrix.mat' >>> c3.inputs.itk_transform = 'affine.txt' >>> c3.inputs.fsl2ras = True - >>> c3.cmdline # doctest: +IGNORE_UNICODE + >>> c3.cmdline # doctest: +ALLOW_UNICODE 'c3d_affine_tool -src cmatrix.mat -fsl2ras -oitk affine.txt' """ input_spec = C3dAffineToolInputSpec diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index 324fe35d1b..198815e434 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import AnalyzeHeader @@ -84,7 +83,7 @@ def test_AnalyzeHeader_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeHeader_outputs(): @@ -94,4 +93,4 @@ def test_AnalyzeHeader_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index d62e37c212..089dbbebea 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ComputeEigensystem @@ -37,7 +36,7 @@ def test_ComputeEigensystem_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeEigensystem_outputs(): @@ -47,4 +46,4 @@ def test_ComputeEigensystem_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 0a022eb1c3..45514c947f 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ComputeFractionalAnisotropy @@ -36,7 +35,7 @@ def test_ComputeFractionalAnisotropy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeFractionalAnisotropy_outputs(): @@ -46,4 +45,4 @@ def test_ComputeFractionalAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 213ff038fc..035f15be23 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ComputeMeanDiffusivity @@ -36,7 +35,7 @@ def test_ComputeMeanDiffusivity_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMeanDiffusivity_outputs(): @@ -46,4 +45,4 @@ def test_ComputeMeanDiffusivity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index b7d7561cdb..6331cdc6bc 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ComputeTensorTrace @@ -36,7 +35,7 @@ def test_ComputeTensorTrace_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTensorTrace_outputs(): @@ -46,4 +45,4 @@ def test_ComputeTensorTrace_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index d02db207e9..a7e27996a8 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..connectivity import Conmat @@ -42,7 +41,7 @@ def test_Conmat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Conmat_outputs(): @@ -53,4 +52,4 @@ def test_Conmat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index 9bc58fecdd..5d6e0563bd 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import DT2NIfTI @@ -31,7 +30,7 @@ def test_DT2NIfTI_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DT2NIfTI_outputs(): @@ -43,4 +42,4 @@ def test_DT2NIfTI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index 8607d3d7ae..e016545ee6 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import DTIFit @@ -36,7 +35,7 @@ def test_DTIFit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): @@ -46,4 +45,4 @@ def test_DTIFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 6cae7fee81..d29a14d0c7 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import DTLUTGen @@ -56,7 +55,7 @@ def test_DTLUTGen_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTLUTGen_outputs(): @@ -66,4 +65,4 @@ def test_DTLUTGen_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index d4cec76afb..3d769cb5f6 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import DTMetric @@ -36,7 +35,7 @@ def test_DTMetric_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTMetric_outputs(): @@ -46,4 +45,4 @@ def test_DTMetric_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index b182c5a862..64dc944014 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import FSL2Scheme @@ -50,7 +49,7 @@ def test_FSL2Scheme_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FSL2Scheme_outputs(): @@ -60,4 +59,4 @@ def test_FSL2Scheme_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 57da324d6c..f4deaf32b3 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import Image2Voxel @@ -31,7 +30,7 @@ def test_Image2Voxel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Image2Voxel_outputs(): @@ -41,4 +40,4 @@ def test_Image2Voxel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index 2fd6293a24..d22bcdd42f 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ImageStats @@ -33,7 +32,7 @@ def test_ImageStats_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ImageStats_outputs(): @@ -43,4 +42,4 @@ def test_ImageStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 311bd70fdf..3402e7f53b 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..odf import LinRecon @@ -41,7 +40,7 @@ def test_LinRecon_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_LinRecon_outputs(): @@ -51,4 +50,4 @@ def test_LinRecon_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index 0424c50086..7b99665ce3 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..odf import MESD @@ -49,7 +48,7 @@ def test_MESD_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MESD_outputs(): @@ -59,4 +58,4 @@ def test_MESD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index f56a605962..add488859d 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ModelFit @@ -56,7 +55,7 @@ def test_ModelFit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ModelFit_outputs(): @@ -66,4 +65,4 @@ def test_ModelFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index dd710905b2..a5f88f9eae 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import NIfTIDT2Camino @@ -39,7 +38,7 @@ def test_NIfTIDT2Camino_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NIfTIDT2Camino_outputs(): @@ -49,4 +48,4 @@ def test_NIfTIDT2Camino_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index 4f4a0b75be..7262670739 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import PicoPDFs @@ -46,7 +45,7 @@ def test_PicoPDFs_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PicoPDFs_outputs(): @@ -56,4 +55,4 @@ def test_PicoPDFs_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index 96001c0d84..6f04a7d1cc 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import ProcStreamlines @@ -104,7 +103,7 @@ def test_ProcStreamlines_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ProcStreamlines_outputs(): @@ -115,4 +114,4 @@ def test_ProcStreamlines_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index 9a4b2375c8..5e80a7a21a 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..odf import QBallMX @@ -41,7 +40,7 @@ def test_QBallMX_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_QBallMX_outputs(): @@ -51,4 +50,4 @@ def test_QBallMX_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index 6d59c40c3e..c7088b2e16 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..calib import SFLUTGen @@ -46,7 +45,7 @@ def test_SFLUTGen_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SFLUTGen_outputs(): @@ -57,4 +56,4 @@ def test_SFLUTGen_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index 4adfe50709..bac319e198 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..calib import SFPICOCalibData @@ -64,7 +63,7 @@ def test_SFPICOCalibData_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SFPICOCalibData_outputs(): @@ -75,4 +74,4 @@ def test_SFPICOCalibData_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 69c85404c1..0ab9608e36 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..odf import SFPeaks @@ -60,7 +59,7 @@ def test_SFPeaks_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SFPeaks_outputs(): @@ -70,4 +69,4 @@ def test_SFPeaks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 7f36415c0c..d79a83aaec 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import Shredder @@ -39,7 +38,7 @@ def test_Shredder_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Shredder_outputs(): @@ -49,4 +48,4 @@ def test_Shredder_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index b1ab2c0f56..fd23c1a2df 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import Track @@ -72,7 +71,7 @@ def test_Track_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Track_outputs(): @@ -82,4 +81,4 @@ def test_Track_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 7b8294db23..e89b3edf70 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TrackBallStick @@ -72,7 +71,7 @@ def test_TrackBallStick_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackBallStick_outputs(): @@ -82,4 +81,4 @@ def test_TrackBallStick_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 697a8157ca..4ca8a07ff6 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TrackBayesDirac @@ -92,7 +91,7 @@ def test_TrackBayesDirac_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackBayesDirac_outputs(): @@ -102,4 +101,4 @@ def test_TrackBayesDirac_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index 6b6ee32c0d..8a55cd4e06 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TrackBedpostxDeter @@ -78,7 +77,7 @@ def test_TrackBedpostxDeter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxDeter_outputs(): @@ -88,4 +87,4 @@ def test_TrackBedpostxDeter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index 0e7d88071e..481990dc6e 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TrackBedpostxProba @@ -81,7 +80,7 @@ def test_TrackBedpostxProba_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackBedpostxProba_outputs(): @@ -91,4 +90,4 @@ def test_TrackBedpostxProba_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 40b1a21e80..613533f340 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TrackBootstrap @@ -85,7 +84,7 @@ def test_TrackBootstrap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackBootstrap_outputs(): @@ -95,4 +94,4 @@ def test_TrackBootstrap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index a7f4ec098f..58790304a2 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TrackDT @@ -72,7 +71,7 @@ def test_TrackDT_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackDT_outputs(): @@ -82,4 +81,4 @@ def test_TrackDT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index 805e1871f6..bafacb7e46 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TrackPICo @@ -77,7 +76,7 @@ def test_TrackPICo_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackPICo_outputs(): @@ -87,4 +86,4 @@ def test_TrackPICo_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index d18ec2e9ca..4cc1d72666 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import TractShredder @@ -39,7 +38,7 @@ def test_TractShredder_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TractShredder_outputs(): @@ -49,4 +48,4 @@ def test_TractShredder_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 805f4709cb..f11149fc2d 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import VtkStreamlines @@ -49,7 +48,7 @@ def test_VtkStreamlines_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VtkStreamlines_outputs(): @@ -59,4 +58,4 @@ def test_VtkStreamlines_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index 4feaae6bf3..c0b462a1cc 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import Camino2Trackvis @@ -48,7 +47,7 @@ def test_Camino2Trackvis_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Camino2Trackvis_outputs(): @@ -58,4 +57,4 @@ def test_Camino2Trackvis_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index fe24f0f99b..831a4c9026 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import Trackvis2Camino @@ -30,7 +29,7 @@ def test_Trackvis2Camino_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Trackvis2Camino_outputs(): @@ -40,4 +39,4 @@ def test_Trackvis2Camino_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index e4d649585e..664c7470eb 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..nx import AverageNetworks @@ -19,7 +18,7 @@ def test_AverageNetworks_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AverageNetworks_outputs(): @@ -31,4 +30,4 @@ def test_AverageNetworks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index 261a0babaa..949ca0ccdd 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import CFFConverter @@ -35,7 +34,7 @@ def test_CFFConverter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CFFConverter_outputs(): @@ -45,4 +44,4 @@ def test_CFFConverter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py index c986c02c7b..b791138008 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..cmtk import CreateMatrix @@ -31,7 +30,7 @@ def test_CreateMatrix_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CreateMatrix_outputs(): @@ -58,4 +57,4 @@ def test_CreateMatrix_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index c5d9fe4163..71fd06c122 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..cmtk import CreateNodes @@ -18,7 +17,7 @@ def test_CreateNodes_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CreateNodes_outputs(): @@ -28,4 +27,4 @@ def test_CreateNodes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index 73654ced71..c47c1791e2 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import MergeCNetworks @@ -16,7 +15,7 @@ def test_MergeCNetworks_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MergeCNetworks_outputs(): @@ -26,4 +25,4 @@ def test_MergeCNetworks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index 70857e1b98..9d0425c836 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..nbs import NetworkBasedStatistic @@ -27,7 +26,7 @@ def test_NetworkBasedStatistic_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NetworkBasedStatistic_outputs(): @@ -39,4 +38,4 @@ def test_NetworkBasedStatistic_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index e26c389974..013d560e1c 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..nx import NetworkXMetrics @@ -32,7 +31,7 @@ def test_NetworkXMetrics_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NetworkXMetrics_outputs(): @@ -54,4 +53,4 @@ def test_NetworkXMetrics_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index eff984ea54..1e6c91f478 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..parcellation import Parcellate @@ -22,7 +21,7 @@ def test_Parcellate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Parcellate_outputs(): @@ -39,4 +38,4 @@ def test_Parcellate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index 2e0c9c1ba6..f34f33bd9b 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..cmtk import ROIGen @@ -24,7 +23,7 @@ def test_ROIGen_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ROIGen_outputs(): @@ -35,4 +34,4 @@ def test_ROIGen_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dcm2nii.py b/nipype/interfaces/dcm2nii.py index b3771e1903..323131280f 100644 --- a/nipype/interfaces/dcm2nii.py +++ b/nipype/interfaces/dcm2nii.py @@ -75,7 +75,7 @@ class Dcm2nii(CommandLine): >>> converter.inputs.source_names = ['functional_1.dcm', 'functional_2.dcm'] >>> converter.inputs.gzip_output = True >>> converter.inputs.output_dir = '.' - >>> converter.cmdline # doctest: +IGNORE_UNICODE + >>> converter.cmdline # doctest: +ALLOW_UNICODE 'dcm2nii -a y -c y -b config.ini -v y -d y -e y -g y -i n -n y -o . -p y -x n -f n functional_1.dcm' """ @@ -250,7 +250,7 @@ class Dcm2niix(CommandLine): 'dcm2niix -b y -z i -x n -t n -m n -f %t%p -o . -s y -v n functional_1.dcm' >>> flags = '-'.join([val.strip() + ' ' for val in sorted(' '.join(converter.cmdline.split()[1:-1]).split('-'))]) - >>> flags # doctest: +IGNORE_UNICODE + >>> flags # doctest: +ALLOW_UNICODE ' -b y -f %t%p -m n -o . -s y -t n -v n -x n -z i ' """ diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index 907df7eb13..7bc50653c9 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import DTIRecon @@ -43,7 +42,7 @@ def test_DTIRecon_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTIRecon_outputs(): @@ -64,4 +63,4 @@ def test_DTIRecon_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index d21a6ecb34..9e6e2627ba 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import DTITracker @@ -67,7 +66,7 @@ def test_DTITracker_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTITracker_outputs(): @@ -78,4 +77,4 @@ def test_DTITracker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 725bbef73a..2081b83ce7 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..odf import HARDIMat @@ -41,7 +40,7 @@ def test_HARDIMat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_HARDIMat_outputs(): @@ -51,4 +50,4 @@ def test_HARDIMat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index 641fb1ad93..3e87c400c4 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..odf import ODFRecon @@ -58,7 +57,7 @@ def test_ODFRecon_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ODFRecon_outputs(): @@ -72,4 +71,4 @@ def test_ODFRecon_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index ba57c26e02..0ded48d9e4 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..odf import ODFTracker @@ -77,7 +76,7 @@ def test_ODFTracker_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ODFTracker_outputs(): @@ -87,4 +86,4 @@ def test_ODFTracker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index 8079634c80..cf480c3ba8 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..postproc import SplineFilter @@ -31,7 +30,7 @@ def test_SplineFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SplineFilter_outputs(): @@ -41,4 +40,4 @@ def test_SplineFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index 5eaa8f1224..bab70335b5 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..postproc import TrackMerge @@ -27,7 +26,7 @@ def test_TrackMerge_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackMerge_outputs(): @@ -37,4 +36,4 @@ def test_TrackMerge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_CSD.py b/nipype/interfaces/dipy/tests/test_auto_CSD.py index 9cec40e056..5efac52671 100644 --- a/nipype/interfaces/dipy/tests/test_auto_CSD.py +++ b/nipype/interfaces/dipy/tests/test_auto_CSD.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..reconstruction import CSD @@ -28,7 +27,7 @@ def test_CSD_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CSD_outputs(): @@ -39,4 +38,4 @@ def test_CSD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index 2ac8dc732e..615ce91bdb 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import DTI @@ -22,7 +21,7 @@ def test_DTI_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTI_outputs(): @@ -36,4 +35,4 @@ def test_DTI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_Denoise.py b/nipype/interfaces/dipy/tests/test_auto_Denoise.py index 6a400231c4..575ea7ec1d 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Denoise.py +++ b/nipype/interfaces/dipy/tests/test_auto_Denoise.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Denoise @@ -20,7 +19,7 @@ def test_Denoise_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Denoise_outputs(): @@ -30,4 +29,4 @@ def test_Denoise_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py index ce3bd17584..671cc3bae7 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyBaseInterface.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import DipyBaseInterface @@ -12,5 +11,5 @@ def test_DipyBaseInterface_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py index e785433355..113abf5f84 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py +++ b/nipype/interfaces/dipy/tests/test_auto_DipyDiffusionInterface.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import DipyDiffusionInterface @@ -21,5 +20,5 @@ def test_DipyDiffusionInterface_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py index 80149df801..8aaf4ee593 100644 --- a/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py +++ b/nipype/interfaces/dipy/tests/test_auto_EstimateResponseSH.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..reconstruction import EstimateResponseSH @@ -38,7 +37,7 @@ def test_EstimateResponseSH_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseSH_outputs(): @@ -49,4 +48,4 @@ def test_EstimateResponseSH_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py index c06bc74573..39c9a4a57f 100644 --- a/nipype/interfaces/dipy/tests/test_auto_RESTORE.py +++ b/nipype/interfaces/dipy/tests/test_auto_RESTORE.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..reconstruction import RESTORE @@ -23,7 +22,7 @@ def test_RESTORE_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RESTORE_outputs(): @@ -39,4 +38,4 @@ def test_RESTORE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_Resample.py b/nipype/interfaces/dipy/tests/test_auto_Resample.py index 06c462dd2d..c1c67e391c 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Resample.py +++ b/nipype/interfaces/dipy/tests/test_auto_Resample.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Resample @@ -15,7 +14,7 @@ def test_Resample_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): @@ -25,4 +24,4 @@ def test_Resample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index 5bc7a2928f..e6ef0522c4 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..simulate import SimulateMultiTensor @@ -44,7 +43,7 @@ def test_SimulateMultiTensor_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SimulateMultiTensor_outputs(): @@ -57,4 +56,4 @@ def test_SimulateMultiTensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py index b4c4dae679..91941e9ee6 100644 --- a/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py +++ b/nipype/interfaces/dipy/tests/test_auto_StreamlineTractography.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracks import StreamlineTractography @@ -38,7 +37,7 @@ def test_StreamlineTractography_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTractography_outputs(): @@ -51,4 +50,4 @@ def test_StreamlineTractography_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index 53f77d5d33..d01275e073 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import TensorMode @@ -22,7 +21,7 @@ def test_TensorMode_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TensorMode_outputs(): @@ -32,4 +31,4 @@ def test_TensorMode_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 187c4c0d49..0d6cd26b71 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracks import TrackDensityMap @@ -21,7 +20,7 @@ def test_TrackDensityMap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TrackDensityMap_outputs(): @@ -31,4 +30,4 @@ def test_TrackDensityMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/elastix/registration.py b/nipype/interfaces/elastix/registration.py index 858e12b492..205346ed80 100644 --- a/nipype/interfaces/elastix/registration.py +++ b/nipype/interfaces/elastix/registration.py @@ -55,7 +55,7 @@ class Registration(CommandLine): >>> reg.inputs.fixed_image = 'fixed1.nii' >>> reg.inputs.moving_image = 'moving1.nii' >>> reg.inputs.parameters = ['elastix.txt'] - >>> reg.cmdline # doctest: +IGNORE_UNICODE + >>> reg.cmdline # doctest: +ALLOW_UNICODE 'elastix -f fixed1.nii -m moving1.nii -out ./ -p elastix.txt' @@ -147,7 +147,7 @@ class ApplyWarp(CommandLine): >>> reg = ApplyWarp() >>> reg.inputs.moving_image = 'moving1.nii' >>> reg.inputs.transform_file = 'TransformParameters.0.txt' - >>> reg.cmdline # doctest: +IGNORE_UNICODE + >>> reg.cmdline # doctest: +ALLOW_UNICODE 'transformix -in moving1.nii -out ./ -tp TransformParameters.0.txt' @@ -187,7 +187,7 @@ class AnalyzeWarp(CommandLine): >>> from nipype.interfaces.elastix import AnalyzeWarp >>> reg = AnalyzeWarp() >>> reg.inputs.transform_file = 'TransformParameters.0.txt' - >>> reg.cmdline # doctest: +IGNORE_UNICODE + >>> reg.cmdline # doctest: +ALLOW_UNICODE 'transformix -def all -jac all -jacmat all -out ./ -tp TransformParameters.0.txt' @@ -228,7 +228,7 @@ class PointsWarp(CommandLine): >>> reg = PointsWarp() >>> reg.inputs.points_file = 'surf1.vtk' >>> reg.inputs.transform_file = 'TransformParameters.0.txt' - >>> reg.cmdline # doctest: +IGNORE_UNICODE + >>> reg.cmdline # doctest: +ALLOW_UNICODE 'transformix -out ./ -def surf1.vtk -tp TransformParameters.0.txt' diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index a298b4ade6..6b08129bc7 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import AnalyzeWarp @@ -29,7 +28,7 @@ def test_AnalyzeWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AnalyzeWarp_outputs(): @@ -41,4 +40,4 @@ def test_AnalyzeWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index 1d6addb92a..ef4d1c32ff 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import ApplyWarp @@ -32,7 +31,7 @@ def test_ApplyWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): @@ -42,4 +41,4 @@ def test_ApplyWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index 9b5c082299..8b6e64d7a2 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import EditTransform @@ -23,7 +22,7 @@ def test_EditTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EditTransform_outputs(): @@ -33,4 +32,4 @@ def test_EditTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index de12ae5698..0cd50ab730 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import PointsWarp @@ -32,7 +31,7 @@ def test_PointsWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PointsWarp_outputs(): @@ -42,4 +41,4 @@ def test_PointsWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index 4bbe547488..8195b0dbe9 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import Registration @@ -41,7 +40,7 @@ def test_Registration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Registration_outputs(): @@ -54,4 +53,4 @@ def test_Registration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/longitudinal.py b/nipype/interfaces/freesurfer/longitudinal.py index 1b82fecfaa..4b18602ff7 100644 --- a/nipype/interfaces/freesurfer/longitudinal.py +++ b/nipype/interfaces/freesurfer/longitudinal.py @@ -86,15 +86,15 @@ class RobustTemplate(FSCommand): >>> template.inputs.fixed_timepoint = True >>> template.inputs.no_iteration = True >>> template.inputs.subsample_threshold = 200 - >>> template.cmdline #doctest: +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> template.cmdline #doctest: +NORMALIZE_WHITESPACE +ALLOW_UNICODE 'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template mri_robust_template_out.mgz --subsample 200' >>> template.inputs.out_file = 'T1.nii' - >>> template.cmdline #doctest: +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> template.cmdline #doctest: +NORMALIZE_WHITESPACE +ALLOW_UNICODE 'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --subsample 200' >>> template.inputs.transform_outputs = ['structural.lta', 'functional.lta'] >>> template.inputs.scaled_intensity_outputs = ['structural-iscale.txt', 'functional-iscale.txt'] - >>> template.cmdline #doctest: +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> template.cmdline #doctest: +NORMALIZE_WHITESPACE +ALLOW_UNICODE 'mri_robust_template --satit --average 0 --fixtp --mov structural.nii functional.nii --inittp 1 --noit --template T1.nii --iscaleout structural-iscale.txt functional-iscale.txt --subsample 200 --lta structural.lta functional.lta' >>> template.run() #doctest: +SKIP @@ -168,7 +168,7 @@ class FuseSegmentations(FSCommand): >>> fuse.inputs.in_segmentations = ['aseg.mgz', 'aseg.mgz'] >>> fuse.inputs.in_segmentations_noCC = ['aseg.mgz', 'aseg.mgz'] >>> fuse.inputs.in_norms = ['norm.mgz', 'norm.mgz', 'norm.mgz'] - >>> fuse.cmdline # doctest: +IGNORE_UNICODE + >>> fuse.cmdline # doctest: +ALLOW_UNICODE 'mri_fuse_segmentations -n norm.mgz -a aseg.mgz -c aseg.mgz tp.long.A.template tp1 tp2' """ diff --git a/nipype/interfaces/freesurfer/model.py b/nipype/interfaces/freesurfer/model.py index ff04a50a9d..007d30ac3c 100644 --- a/nipype/interfaces/freesurfer/model.py +++ b/nipype/interfaces/freesurfer/model.py @@ -91,7 +91,7 @@ class MRISPreproc(FSCommand): >>> preproc.inputs.vol_measure_file = [('cont1.nii', 'register.dat'), \ ('cont1a.nii', 'register.dat')] >>> preproc.inputs.out_file = 'concatenated_file.mgz' - >>> preproc.cmdline # doctest: +IGNORE_UNICODE + >>> preproc.cmdline # doctest: +ALLOW_UNICODE 'mris_preproc --hemi lh --out concatenated_file.mgz --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat' """ @@ -148,7 +148,7 @@ class MRISPreprocReconAll(MRISPreproc): >>> preproc.inputs.vol_measure_file = [('cont1.nii', 'register.dat'), \ ('cont1a.nii', 'register.dat')] >>> preproc.inputs.out_file = 'concatenated_file.mgz' - >>> preproc.cmdline # doctest: +IGNORE_UNICODE + >>> preproc.cmdline # doctest: +ALLOW_UNICODE 'mris_preproc --hemi lh --out concatenated_file.mgz --s subject_id --target fsaverage --iv cont1.nii register.dat --iv cont1a.nii register.dat' """ @@ -486,7 +486,7 @@ class Binarize(FSCommand): -------- >>> binvol = Binarize(in_file='structural.nii', min=10, binary_file='foo_out.nii') - >>> binvol.cmdline # doctest: +IGNORE_UNICODE + >>> binvol.cmdline # doctest: +ALLOW_UNICODE 'mri_binarize --o foo_out.nii --i structural.nii --min 10.000000' """ @@ -595,7 +595,7 @@ class Concatenate(FSCommand): >>> concat = Concatenate() >>> concat.inputs.in_files = ['cont1.nii', 'cont2.nii'] >>> concat.inputs.concatenated_file = 'bar.nii' - >>> concat.cmdline # doctest: +IGNORE_UNICODE + >>> concat.cmdline # doctest: +ALLOW_UNICODE 'mri_concat --o bar.nii --i cont1.nii --i cont2.nii' """ @@ -719,7 +719,7 @@ class SegStats(FSCommand): >>> ss.inputs.subjects_dir = '.' >>> ss.inputs.avgwf_txt_file = 'avgwf.txt' >>> ss.inputs.summary_file = 'summary.stats' - >>> ss.cmdline # doctest: +IGNORE_UNICODE + >>> ss.cmdline # doctest: +ALLOW_UNICODE 'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --i functional.nii --sum ./summary.stats' """ @@ -841,7 +841,7 @@ class SegStatsReconAll(SegStats): >>> segstatsreconall.inputs.total_gray = True >>> segstatsreconall.inputs.euler = True >>> segstatsreconall.inputs.exclude_id = 0 - >>> segstatsreconall.cmdline # doctest: +IGNORE_UNICODE + >>> segstatsreconall.cmdline # doctest: +ALLOW_UNICODE 'mri_segstats --annot PWS04 lh aparc --avgwf ./avgwf.txt --brain-vol-from-seg --surf-ctx-vol --empty --etiv --euler --excl-ctxgmwm --excludeid 0 --subcortgray --subject 10335 --supratent --totalgray --surf-wm-vol --sum ./summary.stats' """ input_spec = SegStatsReconAllInputSpec @@ -953,7 +953,7 @@ class Label2Vol(FSCommand): -------- >>> binvol = Label2Vol(label_file='cortex.label', template_file='structural.nii', reg_file='register.dat', fill_thresh=0.5, vol_label_file='foo_out.nii') - >>> binvol.cmdline # doctest: +IGNORE_UNICODE + >>> binvol.cmdline # doctest: +ALLOW_UNICODE 'mri_label2vol --fillthresh 0 --label cortex.label --reg register.dat --temp structural.nii --o foo_out.nii' """ @@ -1032,7 +1032,7 @@ class MS_LDA(FSCommand): shift=zero_value, vol_synth_file='synth_out.mgz', \ conform=True, use_weights=True, \ images=['FLASH1.mgz', 'FLASH2.mgz', 'FLASH3.mgz']) - >>> optimalWeights.cmdline # doctest: +IGNORE_UNICODE + >>> optimalWeights.cmdline # doctest: +ALLOW_UNICODE 'mri_ms_LDA -conform -label label.mgz -lda 2 3 -shift 1 -W -synth synth_out.mgz -weight weights.txt FLASH1.mgz FLASH2.mgz FLASH3.mgz' """ @@ -1124,7 +1124,7 @@ class Label2Label(FSCommand): >>> l2l.inputs.source_label = 'lh-pial.stl' >>> l2l.inputs.source_white = 'lh.pial' >>> l2l.inputs.source_sphere_reg = 'lh.pial' - >>> l2l.cmdline # doctest: +IGNORE_UNICODE + >>> l2l.cmdline # doctest: +ALLOW_UNICODE 'mri_label2label --hemi lh --trglabel lh-pial_converted.stl --regmethod surface --srclabel lh-pial.stl --srcsubject fsaverage --trgsubject 10335' """ @@ -1208,7 +1208,7 @@ class Label2Annot(FSCommand): >>> l2a.inputs.in_labels = ['lh.aparc.label'] >>> l2a.inputs.orig = 'lh.pial' >>> l2a.inputs.out_annot = 'test' - >>> l2a.cmdline # doctest: +IGNORE_UNICODE + >>> l2a.cmdline # doctest: +ALLOW_UNICODE 'mris_label2annot --hemi lh --l lh.aparc.label --a test --s 10335' """ @@ -1289,7 +1289,7 @@ class SphericalAverage(FSCommand): >>> sphericalavg.inputs.subject_id = '10335' >>> sphericalavg.inputs.erode = 2 >>> sphericalavg.inputs.threshold = 5 - >>> sphericalavg.cmdline # doctest: +IGNORE_UNICODE + >>> sphericalavg.cmdline # doctest: +ALLOW_UNICODE 'mris_spherical_average -erode 2 -o 10335 -t 5.0 label lh.entorhinal lh pial . test.out' """ diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index a7c13d8ee9..1d2a6bd1fe 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/nipype/interfaces/freesurfer/preprocess.py @@ -63,7 +63,7 @@ class ParseDICOMDir(FSCommand): >>> dcminfo.inputs.dicom_dir = '.' >>> dcminfo.inputs.sortbyrun = True >>> dcminfo.inputs.summarize = True - >>> dcminfo.cmdline # doctest: +IGNORE_UNICODE + >>> dcminfo.cmdline # doctest: +ALLOW_UNICODE 'mri_parse_sdcmdir --d . --o dicominfo.txt --sortbyrun --summarize' """ @@ -127,7 +127,7 @@ class UnpackSDICOMDir(FSCommand): >>> unpack.inputs.output_dir = '.' >>> unpack.inputs.run_info = (5, 'mprage', 'nii', 'struct') >>> unpack.inputs.dir_structure = 'generic' - >>> unpack.cmdline # doctest: +IGNORE_UNICODE + >>> unpack.cmdline # doctest: +ALLOW_UNICODE 'unpacksdcmdir -generic -targ . -run 5 mprage nii struct -src .' """ _cmd = 'unpacksdcmdir' @@ -349,7 +349,7 @@ class MRIConvert(FSCommand): >>> mc.inputs.in_file = 'structural.nii' >>> mc.inputs.out_file = 'outfile.mgz' >>> mc.inputs.out_type = 'mgz' - >>> mc.cmdline # doctest: +IGNORE_UNICODE + >>> mc.cmdline # doctest: +ALLOW_UNICODE 'mri_convert --out_type mgz --input_volume structural.nii --output_volume outfile.mgz' """ @@ -575,7 +575,7 @@ class Resample(FSCommand): >>> resampler.inputs.in_file = 'structural.nii' >>> resampler.inputs.resampled_file = 'resampled.nii' >>> resampler.inputs.voxel_size = (2.1, 2.1, 2.1) - >>> resampler.cmdline # doctest: +IGNORE_UNICODE + >>> resampler.cmdline # doctest: +ALLOW_UNICODE 'mri_convert -vs 2.10 2.10 2.10 -i structural.nii -o resampled.nii' """ @@ -645,7 +645,7 @@ class ReconAll(CommandLine): >>> reconall.inputs.directive = 'all' >>> reconall.inputs.subjects_dir = '.' >>> reconall.inputs.T1_files = 'structural.nii' - >>> reconall.cmdline # doctest: +IGNORE_UNICODE + >>> reconall.cmdline # doctest: +ALLOW_UNICODE 'recon-all -all -i structural.nii -subjid foo -sd .' """ @@ -867,7 +867,7 @@ class BBRegister(FSCommand): >>> from nipype.interfaces.freesurfer import BBRegister >>> bbreg = BBRegister(subject_id='me', source_file='structural.nii', init='header', contrast_type='t2') - >>> bbreg.cmdline # doctest: +IGNORE_UNICODE + >>> bbreg.cmdline # doctest: +ALLOW_UNICODE 'bbregister --t2 --init-header --reg structural_bbreg_me.dat --mov structural.nii --s me' """ @@ -1001,7 +1001,7 @@ class ApplyVolTransform(FSCommand): >>> applyreg.inputs.reg_file = 'register.dat' >>> applyreg.inputs.transformed_file = 'struct_warped.nii' >>> applyreg.inputs.fs_target = True - >>> applyreg.cmdline # doctest: +IGNORE_UNICODE + >>> applyreg.cmdline # doctest: +ALLOW_UNICODE 'mri_vol2vol --fstarg --reg register.dat --mov structural.nii --o struct_warped.nii' """ @@ -1081,7 +1081,7 @@ class Smooth(FSCommand): >>> from nipype.interfaces.freesurfer import Smooth >>> smoothvol = Smooth(in_file='functional.nii', smoothed_file = 'foo_out.nii', reg_file='register.dat', surface_fwhm=10, vol_fwhm=6) - >>> smoothvol.cmdline # doctest: +IGNORE_UNICODE + >>> smoothvol.cmdline # doctest: +ALLOW_UNICODE 'mris_volsmooth --i functional.nii --reg register.dat --o foo_out.nii --fwhm 10.000000 --vol-fwhm 6.000000' """ @@ -1186,7 +1186,7 @@ class RobustRegister(FSCommand): >>> reg.inputs.target_file = 'T1.nii' >>> reg.inputs.auto_sens = True >>> reg.inputs.init_orient = True - >>> reg.cmdline # doctest: +IGNORE_UNICODE + >>> reg.cmdline # doctest: +ALLOW_UNICODE 'mri_robust_register --satit --initorient --lta structural_robustreg.lta --mov structural.nii --dst T1.nii' References @@ -1272,7 +1272,7 @@ class FitMSParams(FSCommand): >>> msfit = FitMSParams() >>> msfit.inputs.in_files = ['flash_05.mgz', 'flash_30.mgz'] >>> msfit.inputs.out_dir = 'flash_parameters' - >>> msfit.cmdline # doctest: +IGNORE_UNICODE + >>> msfit.cmdline # doctest: +ALLOW_UNICODE 'mri_ms_fitparms flash_05.mgz flash_30.mgz flash_parameters' """ @@ -1345,7 +1345,7 @@ class SynthesizeFLASH(FSCommand): >>> syn.inputs.t1_image = 'T1.mgz' >>> syn.inputs.pd_image = 'PD.mgz' >>> syn.inputs.out_file = 'flash_30syn.mgz' - >>> syn.cmdline # doctest: +IGNORE_UNICODE + >>> syn.cmdline # doctest: +ALLOW_UNICODE 'mri_synthesize 20.00 30.00 3.000 T1.mgz PD.mgz flash_30syn.mgz' """ @@ -1418,7 +1418,7 @@ class MNIBiasCorrection(FSCommand): >>> correct.inputs.iterations = 6 >>> correct.inputs.protocol_iterations = 1000 >>> correct.inputs.distance = 50 - >>> correct.cmdline # doctest: +IGNORE_UNICODE + >>> correct.cmdline # doctest: +ALLOW_UNICODE 'mri_nu_correct.mni --distance 50 --i norm.mgz --n 6 --o norm_output.mgz --proto-iters 1000' References: @@ -1480,7 +1480,7 @@ class WatershedSkullStrip(FSCommand): >>> skullstrip.inputs.t1 = True >>> skullstrip.inputs.transform = "transforms/talairach_with_skull.lta" >>> skullstrip.inputs.out_file = "brainmask.auto.mgz" - >>> skullstrip.cmdline # doctest: +IGNORE_UNICODE + >>> skullstrip.cmdline # doctest: +ALLOW_UNICODE 'mri_watershed -T1 transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz' """ _cmd = 'mri_watershed' @@ -1528,7 +1528,7 @@ class Normalize(FSCommand): >>> normalize = freesurfer.Normalize() >>> normalize.inputs.in_file = "T1.mgz" >>> normalize.inputs.gradient = 1 - >>> normalize.cmdline # doctest: +IGNORE_UNICODE + >>> normalize.cmdline # doctest: +ALLOW_UNICODE 'mri_normalize -g 1 T1.mgz T1_norm.mgz' """ _cmd = "mri_normalize" @@ -1580,7 +1580,7 @@ class CANormalize(FSCommand): >>> ca_normalize.inputs.in_file = "T1.mgz" >>> ca_normalize.inputs.atlas = "atlas.nii.gz" # in practice use .gca atlases >>> ca_normalize.inputs.transform = "trans.mat" # in practice use .lta transforms - >>> ca_normalize.cmdline # doctest: +IGNORE_UNICODE + >>> ca_normalize.cmdline # doctest: +ALLOW_UNICODE 'mri_ca_normalize T1.mgz atlas.nii.gz trans.mat T1_norm.mgz' """ _cmd = "mri_ca_normalize" @@ -1638,7 +1638,7 @@ class CARegister(FSCommandOpenMP): >>> ca_register = freesurfer.CARegister() >>> ca_register.inputs.in_file = "norm.mgz" >>> ca_register.inputs.out_file = "talairach.m3z" - >>> ca_register.cmdline # doctest: +IGNORE_UNICODE + >>> ca_register.cmdline # doctest: +ALLOW_UNICODE 'mri_ca_register norm.mgz talairach.m3z' """ _cmd = "mri_ca_register" @@ -1709,7 +1709,7 @@ class CALabel(FSCommandOpenMP): >>> ca_label.inputs.out_file = "out.mgz" >>> ca_label.inputs.transform = "trans.mat" >>> ca_label.inputs.template = "Template_6.nii" # in practice use .gcs extension - >>> ca_label.cmdline # doctest: +IGNORE_UNICODE + >>> ca_label.cmdline # doctest: +ALLOW_UNICODE 'mri_ca_label norm.mgz trans.mat Template_6.nii out.mgz' """ _cmd = "mri_ca_label" @@ -1783,7 +1783,7 @@ class MRIsCALabel(FSCommandOpenMP): >>> ca_label.inputs.sulc = "lh.pial" >>> ca_label.inputs.classifier = "im1.nii" # in pracice, use .gcs extension >>> ca_label.inputs.smoothwm = "lh.pial" - >>> ca_label.cmdline # doctest: +IGNORE_UNICODE + >>> ca_label.cmdline # doctest: +ALLOW_UNICODE 'mris_ca_label test lh lh.pial im1.nii lh.aparc.annot' """ _cmd = "mris_ca_label" @@ -1869,7 +1869,7 @@ class SegmentCC(FSCommand): >>> SegmentCC_node.inputs.in_norm = "norm.mgz" >>> SegmentCC_node.inputs.out_rotation = "cc.lta" >>> SegmentCC_node.inputs.subject_id = "test" - >>> SegmentCC_node.cmdline # doctest: +IGNORE_UNICODE + >>> SegmentCC_node.cmdline # doctest: +ALLOW_UNICODE 'mri_cc -aseg aseg.mgz -o aseg.auto.mgz -lta cc.lta test' """ @@ -1960,7 +1960,7 @@ class SegmentWM(FSCommand): >>> SegmentWM_node = freesurfer.SegmentWM() >>> SegmentWM_node.inputs.in_file = "norm.mgz" >>> SegmentWM_node.inputs.out_file = "wm.seg.mgz" - >>> SegmentWM_node.cmdline # doctest: +IGNORE_UNICODE + >>> SegmentWM_node.cmdline # doctest: +ALLOW_UNICODE 'mri_segment norm.mgz wm.seg.mgz' """ @@ -2004,7 +2004,7 @@ class EditWMwithAseg(FSCommand): >>> editwm.inputs.seg_file = "aseg.mgz" >>> editwm.inputs.out_file = "wm.asegedit.mgz" >>> editwm.inputs.keep_in = True - >>> editwm.cmdline # doctest: +IGNORE_UNICODE + >>> editwm.cmdline # doctest: +ALLOW_UNICODE 'mri_edit_wm_with_aseg -keep-in T1.mgz norm.mgz aseg.mgz wm.asegedit.mgz' """ _cmd = 'mri_edit_wm_with_aseg' @@ -2044,7 +2044,7 @@ class ConcatenateLTA(FSCommand): >>> conc_lta = ConcatenateLTA() >>> conc_lta.inputs.in_lta1 = 'trans.mat' >>> conc_lta.inputs.in_lta2 = 'trans.mat' - >>> conc_lta.cmdline # doctest: +IGNORE_UNICODE + >>> conc_lta.cmdline # doctest: +ALLOW_UNICODE 'mri_concatenate_lta trans.mat trans.mat trans-long.mat' """ diff --git a/nipype/interfaces/freesurfer/registration.py b/nipype/interfaces/freesurfer/registration.py index 57b1293621..d3cba1749c 100644 --- a/nipype/interfaces/freesurfer/registration.py +++ b/nipype/interfaces/freesurfer/registration.py @@ -204,7 +204,7 @@ class EMRegister(FSCommandOpenMP): >>> register.inputs.out_file = 'norm_transform.lta' >>> register.inputs.skull = True >>> register.inputs.nbrspacing = 9 - >>> register.cmdline # doctest: +IGNORE_UNICODE + >>> register.cmdline # doctest: +ALLOW_UNICODE 'mri_em_register -uns 9 -skull norm.mgz aseg.mgz norm_transform.lta' """ _cmd = 'mri_em_register' @@ -254,7 +254,7 @@ class Register(FSCommand): >>> register.inputs.target = 'aseg.mgz' >>> register.inputs.out_file = 'lh.pial.reg' >>> register.inputs.curv = True - >>> register.cmdline # doctest: +IGNORE_UNICODE + >>> register.cmdline # doctest: +ALLOW_UNICODE 'mris_register -curv lh.pial aseg.mgz lh.pial.reg' """ @@ -320,7 +320,7 @@ class Paint(FSCommand): >>> paint.inputs.template = 'aseg.mgz' >>> paint.inputs.averages = 5 >>> paint.inputs.out_file = 'lh.avg_curv' - >>> paint.cmdline # doctest: +IGNORE_UNICODE + >>> paint.cmdline # doctest: +ALLOW_UNICODE 'mrisp_paint -a 5 aseg.mgz lh.pial lh.avg_curv' """ diff --git a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py index fc68e74fa7..deaeda875d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_AddXFormToHeader.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import AddXFormToHeader @@ -36,7 +35,7 @@ def test_AddXFormToHeader_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AddXFormToHeader_outputs(): @@ -46,4 +45,4 @@ def test_AddXFormToHeader_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py index d4e2c57b75..7db05a4b33 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Aparc2Aseg @@ -61,7 +60,7 @@ def test_Aparc2Aseg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Aparc2Aseg_outputs(): @@ -72,4 +71,4 @@ def test_Aparc2Aseg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py index 12ba0eab6f..6a0d53203d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Apas2Aseg @@ -26,7 +25,7 @@ def test_Apas2Aseg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Apas2Aseg_outputs(): @@ -37,4 +36,4 @@ def test_Apas2Aseg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index a4f3de7e31..e2f51f68ea 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ApplyMask @@ -51,7 +50,7 @@ def test_ApplyMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): @@ -61,4 +60,4 @@ def test_ApplyMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index 78446391fd..2b036d1aef 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ApplyVolTransform @@ -76,7 +75,7 @@ def test_ApplyVolTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyVolTransform_outputs(): @@ -86,4 +85,4 @@ def test_ApplyVolTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py index 195a304cc9..58d9bcd21d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import BBRegister @@ -57,7 +56,7 @@ def test_BBRegister_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BBRegister_outputs(): @@ -70,4 +69,4 @@ def test_BBRegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index 01d37a484e..239f3e9576 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Binarize @@ -78,7 +77,7 @@ def test_Binarize_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Binarize_outputs(): @@ -89,4 +88,4 @@ def test_Binarize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py index fb09708a0e..6d98044dc2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CALabel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import CALabel @@ -53,7 +52,7 @@ def test_CALabel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CALabel_outputs(): @@ -63,4 +62,4 @@ def test_CALabel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py index c5d32d0665..c888907069 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import CANormalize @@ -45,7 +44,7 @@ def test_CANormalize_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CANormalize_outputs(): @@ -56,4 +55,4 @@ def test_CANormalize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py index de99f1de09..cf63c92c6c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CARegister.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import CARegister @@ -49,7 +48,7 @@ def test_CARegister_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CARegister_outputs(): @@ -59,4 +58,4 @@ def test_CARegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py index 6296509937..f226ebf4f1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CheckTalairachAlignment.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import CheckTalairachAlignment @@ -32,7 +31,7 @@ def test_CheckTalairachAlignment_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CheckTalairachAlignment_outputs(): @@ -42,4 +41,4 @@ def test_CheckTalairachAlignment_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index 1a5e51758e..ae6bbb3712 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Concatenate @@ -56,7 +55,7 @@ def test_Concatenate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Concatenate_outputs(): @@ -66,4 +65,4 @@ def test_Concatenate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py index 12420d7aad..c7c9396a13 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ConcatenateLTA.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ConcatenateLTA @@ -35,7 +34,7 @@ def test_ConcatenateLTA_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ConcatenateLTA_outputs(): @@ -45,4 +44,4 @@ def test_ConcatenateLTA_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py index cf1c4bc800..a92518ab58 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Contrast.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Contrast @@ -40,7 +39,7 @@ def test_Contrast_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Contrast_outputs(): @@ -52,4 +51,4 @@ def test_Contrast_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py index f01070aeb7..be8c13cf06 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Curvature.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Curvature @@ -36,7 +35,7 @@ def test_Curvature_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Curvature_outputs(): @@ -47,4 +46,4 @@ def test_Curvature_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py index c03dcbd4c1..68ac8871f3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_CurvatureStats.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import CurvatureStats @@ -51,7 +50,7 @@ def test_CurvatureStats_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureStats_outputs(): @@ -61,4 +60,4 @@ def test_CurvatureStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index a24665f935..f198a84660 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import DICOMConvert @@ -35,5 +34,5 @@ def test_DICOMConvert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py index ac8a79ed3a..ec8742df15 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EMRegister.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import EMRegister @@ -44,7 +43,7 @@ def test_EMRegister_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EMRegister_outputs(): @@ -54,4 +53,4 @@ def test_EMRegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py index fb236ac87c..652ce0bb47 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EditWMwithAseg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import EditWMwithAseg @@ -38,7 +37,7 @@ def test_EditWMwithAseg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EditWMwithAseg_outputs(): @@ -48,4 +47,4 @@ def test_EditWMwithAseg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py index eb1362df3c..a569e69e3d 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_EulerNumber.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import EulerNumber @@ -24,7 +23,7 @@ def test_EulerNumber_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EulerNumber_outputs(): @@ -34,4 +33,4 @@ def test_EulerNumber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index 617a696a2b..7b21311369 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ExtractMainComponent @@ -28,7 +27,7 @@ def test_ExtractMainComponent_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ExtractMainComponent_outputs(): @@ -38,4 +37,4 @@ def test_ExtractMainComponent_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index f463310c33..9f4e3d79e8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import FSCommand @@ -20,5 +19,5 @@ def test_FSCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py index f5788c2797..833221cb6f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommandOpenMP.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import FSCommandOpenMP @@ -21,5 +20,5 @@ def test_FSCommandOpenMP_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py index 4f0de61ae2..117ee35694 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSScriptCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import FSScriptCommand @@ -20,5 +19,5 @@ def test_FSScriptCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index e54c0ddcc7..39a759d794 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import FitMSParams @@ -32,7 +31,7 @@ def test_FitMSParams_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FitMSParams_outputs(): @@ -44,4 +43,4 @@ def test_FitMSParams_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py index 198ac05ecf..f244c2567c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FixTopology.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import FixTopology @@ -47,7 +46,7 @@ def test_FixTopology_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FixTopology_outputs(): @@ -57,4 +56,4 @@ def test_FixTopology_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py index 7330c75d27..f26c4670f3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FuseSegmentations.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..longitudinal import FuseSegmentations @@ -39,7 +38,7 @@ def test_FuseSegmentations_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FuseSegmentations_outputs(): @@ -49,4 +48,4 @@ def test_FuseSegmentations_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index 753ab44569..d8292575bf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import GLMFit @@ -141,7 +140,7 @@ def test_GLMFit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GLMFit_outputs(): @@ -167,4 +166,4 @@ def test_GLMFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 5d409f2966..e8d8e5495f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ImageInfo @@ -23,7 +22,7 @@ def test_ImageInfo_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ImageInfo_outputs(): @@ -43,4 +42,4 @@ def test_ImageInfo_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py index 2b3fd09857..230be39f98 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Jacobian.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Jacobian @@ -35,7 +34,7 @@ def test_Jacobian_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Jacobian_outputs(): @@ -45,4 +44,4 @@ def test_Jacobian_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py index deed12d317..0872d08189 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Annot.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Label2Annot @@ -42,7 +41,7 @@ def test_Label2Annot_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Label2Annot_outputs(): @@ -52,4 +51,4 @@ def test_Label2Annot_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py index abf2985c46..ec04e831b0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Label.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Label2Label @@ -51,7 +50,7 @@ def test_Label2Label_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Label2Label_outputs(): @@ -61,4 +60,4 @@ def test_Label2Label_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index 5cc4fe6f4c..86406fea1f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Label2Vol @@ -76,7 +75,7 @@ def test_Label2Vol_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Label2Vol_outputs(): @@ -86,4 +85,4 @@ def test_Label2Vol_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py index 3a139865a4..32558bc23e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MNIBiasCorrection.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MNIBiasCorrection @@ -45,7 +44,7 @@ def test_MNIBiasCorrection_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MNIBiasCorrection_outputs(): @@ -55,4 +54,4 @@ def test_MNIBiasCorrection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py index a5e7c0d124..b99cc7522e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MPRtoMNI305.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import MPRtoMNI305 @@ -29,7 +28,7 @@ def test_MPRtoMNI305_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MPRtoMNI305_outputs(): @@ -41,4 +40,4 @@ def test_MPRtoMNI305_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 94f25de6a7..2092b7b7d0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MRIConvert @@ -189,7 +188,7 @@ def test_MRIConvert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIConvert_outputs(): @@ -199,4 +198,4 @@ def test_MRIConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py index 042305c7ad..98a323e7f3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIFill.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MRIFill @@ -34,7 +33,7 @@ def test_MRIFill_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIFill_outputs(): @@ -45,4 +44,4 @@ def test_MRIFill_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index 44c4725e8e..04d53329d4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MRIMarchingCubes @@ -36,7 +35,7 @@ def test_MRIMarchingCubes_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIMarchingCubes_outputs(): @@ -46,4 +45,4 @@ def test_MRIMarchingCubes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 9cfa579485..0a67cb511c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MRIPretess @@ -45,7 +44,7 @@ def test_MRIPretess_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIPretess_outputs(): @@ -55,4 +54,4 @@ def test_MRIPretess_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index ca56e521e2..85af7d58e7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import MRISPreproc @@ -69,7 +68,7 @@ def test_MRISPreproc_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreproc_outputs(): @@ -79,4 +78,4 @@ def test_MRISPreproc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py index 7e775b0854..fffe6f049b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreprocReconAll.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import MRISPreprocReconAll @@ -81,7 +80,7 @@ def test_MRISPreprocReconAll_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRISPreprocReconAll_outputs(): @@ -91,4 +90,4 @@ def test_MRISPreprocReconAll_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 3af8b90803..4183a353f2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MRITessellate @@ -36,7 +35,7 @@ def test_MRITessellate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRITessellate_outputs(): @@ -46,4 +45,4 @@ def test_MRITessellate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py index ce445321c6..3510fecc1f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCALabel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MRIsCALabel @@ -58,7 +57,7 @@ def test_MRIsCALabel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCALabel_outputs(): @@ -68,4 +67,4 @@ def test_MRIsCALabel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py index d7160510a7..bce5a679c6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsCalc.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MRIsCalc @@ -43,7 +42,7 @@ def test_MRIsCalc_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIsCalc_outputs(): @@ -53,4 +52,4 @@ def test_MRIsCalc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index b2b79a326e..902b34b46e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MRIsConvert @@ -67,7 +66,7 @@ def test_MRIsConvert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIsConvert_outputs(): @@ -77,4 +76,4 @@ def test_MRIsConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py index f94f3fa4a5..ab2290d2c0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsInflate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MRIsInflate @@ -37,7 +36,7 @@ def test_MRIsInflate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRIsInflate_outputs(): @@ -48,4 +47,4 @@ def test_MRIsInflate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index 30264881c8..4cb5c44c23 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import MS_LDA @@ -45,7 +44,7 @@ def test_MS_LDA_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MS_LDA_outputs(): @@ -56,4 +55,4 @@ def test_MS_LDA_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index 5dd694a707..f42c90620a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MakeAverageSubject @@ -27,7 +26,7 @@ def test_MakeAverageSubject_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MakeAverageSubject_outputs(): @@ -37,4 +36,4 @@ def test_MakeAverageSubject_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py index 65aff0de5d..eca946b106 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeSurfaces.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MakeSurfaces @@ -66,7 +65,7 @@ def test_MakeSurfaces_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MakeSurfaces_outputs(): @@ -81,4 +80,4 @@ def test_MakeSurfaces_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py index 773e66997e..3af36bb7c3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Normalize.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Normalize @@ -39,7 +38,7 @@ def test_Normalize_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Normalize_outputs(): @@ -49,4 +48,4 @@ def test_Normalize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index 37fec80ad3..364a1c7939 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import OneSampleTTest @@ -141,7 +140,7 @@ def test_OneSampleTTest_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTest_outputs(): @@ -167,4 +166,4 @@ def test_OneSampleTTest_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py index 567cae10b1..e532cf71c6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Paint.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Paint.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import Paint @@ -38,7 +37,7 @@ def test_Paint_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Paint_outputs(): @@ -48,4 +47,4 @@ def test_Paint_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py index cfdd45d9dd..2e63c1ba06 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParcellationStats.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ParcellationStats @@ -77,7 +76,7 @@ def test_ParcellationStats_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ParcellationStats_outputs(): @@ -88,4 +87,4 @@ def test_ParcellationStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index a2afa891d9..b21c3b523e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ParseDICOMDir @@ -30,7 +29,7 @@ def test_ParseDICOMDir_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ParseDICOMDir_outputs(): @@ -40,4 +39,4 @@ def test_ParseDICOMDir_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 2ed5d7929f..d502784e4e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ReconAll @@ -44,7 +43,7 @@ def test_ReconAll_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ReconAll_outputs(): @@ -131,4 +130,4 @@ def test_ReconAll_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Register.py b/nipype/interfaces/freesurfer/tests/test_auto_Register.py index b8e533b413..aad8c33e83 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Register.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Register.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import Register @@ -41,7 +40,7 @@ def test_Register_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Register_outputs(): @@ -51,4 +50,4 @@ def test_Register_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py index 8b45a00097..835a9197a6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RegisterAVItoTalairach.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..registration import RegisterAVItoTalairach @@ -36,7 +35,7 @@ def test_RegisterAVItoTalairach_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RegisterAVItoTalairach_outputs(): @@ -48,4 +47,4 @@ def test_RegisterAVItoTalairach_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py index 860166868a..fb6107715a 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RelabelHypointensities.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import RelabelHypointensities @@ -41,7 +40,7 @@ def test_RelabelHypointensities_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RelabelHypointensities_outputs(): @@ -52,4 +51,4 @@ def test_RelabelHypointensities_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py index f951e097fd..defc405a00 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveIntersection.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import RemoveIntersection @@ -32,7 +31,7 @@ def test_RemoveIntersection_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RemoveIntersection_outputs(): @@ -42,4 +41,4 @@ def test_RemoveIntersection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py index 271b6947e3..44b770613f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RemoveNeck.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import RemoveNeck @@ -41,7 +40,7 @@ def test_RemoveNeck_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RemoveNeck_outputs(): @@ -51,4 +50,4 @@ def test_RemoveNeck_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index befb0b9d01..b1c255e221 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Resample @@ -31,7 +30,7 @@ def test_Resample_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): @@ -41,4 +40,4 @@ def test_Resample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index 20af60b42f..f73ae258b9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import RobustRegister @@ -85,7 +84,7 @@ def test_RobustRegister_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RobustRegister_outputs(): @@ -102,4 +101,4 @@ def test_RobustRegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py index b531e3fd94..48dc774fce 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustTemplate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..longitudinal import RobustTemplate @@ -55,7 +54,7 @@ def test_RobustTemplate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RobustTemplate_outputs(): @@ -67,4 +66,4 @@ def test_RobustTemplate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index 7f91440c2d..57cec38fb1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import SampleToSurface @@ -108,7 +107,7 @@ def test_SampleToSurface_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SampleToSurface_outputs(): @@ -120,4 +119,4 @@ def test_SampleToSurface_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 0318b9c3e1..dfd1f28afc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import SegStats @@ -110,7 +109,7 @@ def test_SegStats_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SegStats_outputs(): @@ -123,4 +122,4 @@ def test_SegStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py index 8e3d3188c6..2a5d630621 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStatsReconAll.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import SegStatsReconAll @@ -133,7 +132,7 @@ def test_SegStatsReconAll_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SegStatsReconAll_outputs(): @@ -146,4 +145,4 @@ def test_SegStatsReconAll_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py index a80169e881..72e8bdd39f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentCC.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SegmentCC @@ -40,7 +39,7 @@ def test_SegmentCC_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SegmentCC_outputs(): @@ -51,4 +50,4 @@ def test_SegmentCC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py index 9d98a0548c..ba5bf0da8b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegmentWM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SegmentWM @@ -28,7 +27,7 @@ def test_SegmentWM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SegmentWM_outputs(): @@ -38,4 +37,4 @@ def test_SegmentWM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index e561128b75..54d26116a9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Smooth @@ -46,7 +45,7 @@ def test_Smooth_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): @@ -56,4 +55,4 @@ def test_Smooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index f34dfefbbc..eb51c42b31 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import SmoothTessellation @@ -53,7 +52,7 @@ def test_SmoothTessellation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SmoothTessellation_outputs(): @@ -63,4 +62,4 @@ def test_SmoothTessellation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py index aaf4cc6ae5..d5c50b70a7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Sphere.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Sphere @@ -38,7 +37,7 @@ def test_Sphere_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Sphere_outputs(): @@ -48,4 +47,4 @@ def test_Sphere_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py index ad992e3e13..39299a6707 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SphericalAverage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import SphericalAverage @@ -53,7 +52,7 @@ def test_SphericalAverage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SphericalAverage_outputs(): @@ -63,4 +62,4 @@ def test_SphericalAverage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 66cec288eb..b54425d0c2 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Surface2VolTransform @@ -55,7 +54,7 @@ def test_Surface2VolTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Surface2VolTransform_outputs(): @@ -66,4 +65,4 @@ def test_Surface2VolTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index c0430d2676..cb30f51c70 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import SurfaceSmooth @@ -43,7 +42,7 @@ def test_SurfaceSmooth_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceSmooth_outputs(): @@ -53,4 +52,4 @@ def test_SurfaceSmooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index f0a76a5d43..380a75ce87 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import SurfaceSnapshots @@ -97,7 +96,7 @@ def test_SurfaceSnapshots_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceSnapshots_outputs(): @@ -107,4 +106,4 @@ def test_SurfaceSnapshots_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index c3a450476c..79a957e526 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import SurfaceTransform @@ -51,7 +50,7 @@ def test_SurfaceTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SurfaceTransform_outputs(): @@ -61,4 +60,4 @@ def test_SurfaceTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index fc213c7411..32ca7d9582 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SynthesizeFLASH @@ -46,7 +45,7 @@ def test_SynthesizeFLASH_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SynthesizeFLASH_outputs(): @@ -56,4 +55,4 @@ def test_SynthesizeFLASH_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py index 2638246f31..c3a9c16f91 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachAVI.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import TalairachAVI @@ -28,7 +27,7 @@ def test_TalairachAVI_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TalairachAVI_outputs(): @@ -40,4 +39,4 @@ def test_TalairachAVI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py index 6e38b438db..e647c3f110 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_TalairachQC.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import TalairachQC @@ -24,7 +23,7 @@ def test_TalairachQC_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TalairachQC_outputs(): @@ -35,4 +34,4 @@ def test_TalairachQC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index 68b66e2e41..c8471d2066 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Tkregister2 @@ -51,7 +50,7 @@ def test_Tkregister2_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Tkregister2_outputs(): @@ -62,4 +61,4 @@ def test_Tkregister2_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index ec4f0a79fa..1dc58286f3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import UnpackSDICOMDir @@ -49,5 +48,5 @@ def test_UnpackSDICOMDir_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py index a893fc5acf..7e73f2ed86 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_VolumeMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import VolumeMask @@ -53,7 +52,7 @@ def test_VolumeMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VolumeMask_outputs(): @@ -65,4 +64,4 @@ def test_VolumeMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py index fa8cff14b5..d9c44774bf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_WatershedSkullStrip.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import WatershedSkullStrip @@ -37,7 +36,7 @@ def test_WatershedSkullStrip_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WatershedSkullStrip_outputs(): @@ -47,4 +46,4 @@ def test_WatershedSkullStrip_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/freesurfer/tests/test_model.py b/nipype/interfaces/freesurfer/tests/test_model.py index b1510e5335..41aa3b1197 100644 --- a/nipype/interfaces/freesurfer/tests/test_model.py +++ b/nipype/interfaces/freesurfer/tests/test_model.py @@ -8,12 +8,12 @@ import numpy as np import nibabel as nib -from nipype.testing import assert_equal, skipif +import pytest from nipype.interfaces.freesurfer import model, no_freesurfer import nipype.pipeline.engine as pe -@skipif(no_freesurfer) +@pytest.mark.skipif(no_freesurfer(), reason="freesurfer is not installed") def test_concatenate(): tmp_dir = os.path.realpath(tempfile.mkdtemp()) cwd = os.getcwd() @@ -32,15 +32,13 @@ def test_concatenate(): # Test default behavior res = model.Concatenate(in_files=[in1, in2]).run() - yield (assert_equal, res.outputs.concatenated_file, - os.path.join(tmp_dir, 'concat_output.nii.gz')) - yield (assert_equal, nib.load('concat_output.nii.gz').get_data(), out_data) + assert res.outputs.concatenated_file == os.path.join(tmp_dir, 'concat_output.nii.gz') + assert nib.load('concat_output.nii.gz').get_data() == out_data # Test specified concatenated_file res = model.Concatenate(in_files=[in1, in2], concatenated_file=out).run() - yield (assert_equal, res.outputs.concatenated_file, - os.path.join(tmp_dir, out)) - yield (assert_equal, nib.load(out).get_data(), out_data) + assert res.outputs.concatenated_file == os.path.join(tmp_dir, out) + assert nib.load(out).get_data() == out_data # Test in workflow wf = pe.Workflow('test_concatenate', base_dir=tmp_dir) @@ -49,14 +47,12 @@ def test_concatenate(): name='concat') wf.add_nodes([concat]) wf.run() - yield (assert_equal, nib.load(os.path.join(tmp_dir, 'test_concatenate', - 'concat', out)).get_data(), - out_data) + assert nib.load(os.path.join(tmp_dir, 'test_concatenate','concat', out)).get_data()== out_data # Test a simple statistic res = model.Concatenate(in_files=[in1, in2], concatenated_file=out, stats='mean').run() - yield (assert_equal, nib.load(out).get_data(), mean_data) + assert nib.load(out).get_data() == mean_data os.chdir(cwd) shutil.rmtree(tmp_dir) diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py index 121c2e7f1b..5bd2186d28 100644 --- a/nipype/interfaces/freesurfer/tests/test_preprocess.py +++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py @@ -6,11 +6,12 @@ import nibabel as nif import numpy as np from tempfile import mkdtemp -from nipype.testing import assert_equal, assert_raises, skipif +import pytest import nipype.interfaces.freesurfer as freesurfer -def create_files_in_directory(): +@pytest.fixture() +def create_files_in_directory(request): outdir = os.path.realpath(mkdtemp()) cwd = os.getcwd() os.chdir(outdir) @@ -22,79 +23,77 @@ def create_files_in_directory(): img = np.random.random(shape) nif.save(nif.Nifti1Image(img, np.eye(4), hdr), os.path.join(outdir, f)) - return filelist, outdir, cwd + def clean_directory(): + if os.path.exists(outdir): + rmtree(outdir) + os.chdir(cwd) -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): - rmtree(outdir) - os.chdir(old_wd) + request.addfinalizer(clean_directory) + return (filelist, outdir, cwd) -@skipif(freesurfer.no_freesurfer) -def test_robustregister(): - filelist, outdir, cwd = create_files_in_directory() +@pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed") +def test_robustregister(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory reg = freesurfer.RobustRegister() # make sure command gets called - yield assert_equal, reg.cmd, 'mri_robust_register' + assert reg.cmd == 'mri_robust_register' # test raising error with mandatory args absent - yield assert_raises, ValueError, reg.run + with pytest.raises(ValueError): reg.run() # .inputs based parameters setting reg.inputs.source_file = filelist[0] reg.inputs.target_file = filelist[1] reg.inputs.auto_sens = True - yield assert_equal, reg.cmdline, ('mri_robust_register ' - '--satit --lta %s_robustreg.lta --mov %s --dst %s' % (filelist[0][:-4], filelist[0], filelist[1])) + assert reg.cmdline == ('mri_robust_register ' + '--satit --lta %s_robustreg.lta --mov %s --dst %s' % (filelist[0][:-4], filelist[0], filelist[1])) # constructor based parameter setting reg2 = freesurfer.RobustRegister(source_file=filelist[0], target_file=filelist[1], outlier_sens=3.0, out_reg_file='foo.lta', half_targ=True) - yield assert_equal, reg2.cmdline, ('mri_robust_register --halfdst %s_halfway.nii --lta foo.lta ' - '--sat 3.0000 --mov %s --dst %s' - % (os.path.join(outdir, filelist[1][:-4]), filelist[0], filelist[1])) - clean_directory(outdir, cwd) + assert reg2.cmdline == ('mri_robust_register --halfdst %s_halfway.nii --lta foo.lta ' + '--sat 3.0000 --mov %s --dst %s' + % (os.path.join(outdir, filelist[1][:-4]), filelist[0], filelist[1])) + - -@skipif(freesurfer.no_freesurfer) -def test_fitmsparams(): - filelist, outdir, cwd = create_files_in_directory() +@pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed") +def test_fitmsparams(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory fit = freesurfer.FitMSParams() # make sure command gets called - yield assert_equal, fit.cmd, 'mri_ms_fitparms' + assert fit.cmd == 'mri_ms_fitparms' # test raising error with mandatory args absent - yield assert_raises, ValueError, fit.run + with pytest.raises(ValueError): fit.run() # .inputs based parameters setting fit.inputs.in_files = filelist fit.inputs.out_dir = outdir - yield assert_equal, fit.cmdline, 'mri_ms_fitparms %s %s %s' % (filelist[0], filelist[1], outdir) + assert fit.cmdline == 'mri_ms_fitparms %s %s %s' % (filelist[0], filelist[1], outdir) # constructor based parameter setting fit2 = freesurfer.FitMSParams(in_files=filelist, te_list=[1.5, 3.5], flip_list=[20, 30], out_dir=outdir) - yield assert_equal, fit2.cmdline, ('mri_ms_fitparms -te %.3f -fa %.1f %s -te %.3f -fa %.1f %s %s' - % (1.500, 20.0, filelist[0], 3.500, 30.0, filelist[1], outdir)) - - clean_directory(outdir, cwd) + assert fit2.cmdline == ('mri_ms_fitparms -te %.3f -fa %.1f %s -te %.3f -fa %.1f %s %s' + % (1.500, 20.0, filelist[0], 3.500, 30.0, filelist[1], outdir)) -@skipif(freesurfer.no_freesurfer) -def test_synthesizeflash(): - filelist, outdir, cwd = create_files_in_directory() +@pytest.mark.skipif(freesurfer.no_freesurfer(), reason="freesurfer is not installed") +def test_synthesizeflash(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory syn = freesurfer.SynthesizeFLASH() # make sure command gets called - yield assert_equal, syn.cmd, 'mri_synthesize' + assert syn.cmd == 'mri_synthesize' # test raising error with mandatory args absent - yield assert_raises, ValueError, syn.run + with pytest.raises(ValueError): syn.run() # .inputs based parameters setting syn.inputs.t1_image = filelist[0] @@ -103,10 +102,10 @@ def test_synthesizeflash(): syn.inputs.te = 4.5 syn.inputs.tr = 20 - yield assert_equal, syn.cmdline, ('mri_synthesize 20.00 30.00 4.500 %s %s %s' - % (filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_30.mgz'))) + assert syn.cmdline == ('mri_synthesize 20.00 30.00 4.500 %s %s %s' + % (filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_30.mgz'))) # constructor based parameters setting syn2 = freesurfer.SynthesizeFLASH(t1_image=filelist[0], pd_image=filelist[1], flip_angle=20, te=5, tr=25) - yield assert_equal, syn2.cmdline, ('mri_synthesize 25.00 20.00 5.000 %s %s %s' - % (filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_20.mgz'))) + assert syn2.cmdline == ('mri_synthesize 25.00 20.00 5.000 %s %s %s' + % (filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_20.mgz'))) diff --git a/nipype/interfaces/freesurfer/tests/test_utils.py b/nipype/interfaces/freesurfer/tests/test_utils.py index 3457531a45..c7cdc02d61 100644 --- a/nipype/interfaces/freesurfer/tests/test_utils.py +++ b/nipype/interfaces/freesurfer/tests/test_utils.py @@ -11,14 +11,14 @@ import numpy as np import nibabel as nif -from nipype.testing import (assert_equal, assert_not_equal, - assert_raises, skipif) +import pytest from nipype.interfaces.base import TraitError import nipype.interfaces.freesurfer as fs -def create_files_in_directory(): +@pytest.fixture() +def create_files_in_directory(request): outdir = os.path.realpath(mkdtemp()) cwd = os.getcwd() os.chdir(outdir) @@ -33,10 +33,18 @@ def create_files_in_directory(): with open(os.path.join(outdir, 'reg.dat'), 'wt') as fp: fp.write('dummy file') filelist.append('reg.dat') - return filelist, outdir, cwd + def clean_directory(): + if os.path.exists(outdir): + rmtree(outdir) + os.chdir(cwd) -def create_surf_file(): + request.addfinalizer(clean_directory) + return (filelist, outdir, cwd) + + +@pytest.fixture() +def create_surf_file(request): outdir = os.path.realpath(mkdtemp()) cwd = os.getcwd() os.chdir(outdir) @@ -47,27 +55,28 @@ def create_surf_file(): img = np.random.random(shape) nif.save(nif.Nifti1Image(img, np.eye(4), hdr), os.path.join(outdir, surf)) - return surf, outdir, cwd + def clean_directory(): + if os.path.exists(outdir): + rmtree(outdir) + os.chdir(cwd) -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): - rmtree(outdir) - os.chdir(old_wd) + request.addfinalizer(clean_directory) + return (surf, outdir, cwd) -@skipif(fs.no_freesurfer) -def test_sample2surf(): +@pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed") +def test_sample2surf(create_files_in_directory): s2s = fs.SampleToSurface() # Test underlying command - yield assert_equal, s2s.cmd, 'mri_vol2surf' + assert s2s.cmd == 'mri_vol2surf' # Test mandatory args exception - yield assert_raises, ValueError, s2s.run + with pytest.raises(ValueError): s2s.run() # Create testing files - files, cwd, oldwd = create_files_in_directory() + files, cwd, oldwd = create_files_in_directory # Test input settings s2s.inputs.source_file = files[0] @@ -79,40 +88,37 @@ def test_sample2surf(): s2s.inputs.sampling_method = "point" # Test a basic command line - yield assert_equal, s2s.cmdline, ("mri_vol2surf " - "--hemi lh --o %s --ref %s --reg reg.dat --projfrac 0.500 --mov %s" - % (os.path.join(cwd, "lh.a.mgz"), files[1], files[0])) + assert s2s.cmdline == ("mri_vol2surf " + "--hemi lh --o %s --ref %s --reg reg.dat --projfrac 0.500 --mov %s" + % (os.path.join(cwd, "lh.a.mgz"), files[1], files[0])) # Test identity s2sish = fs.SampleToSurface(source_file=files[1], reference_file=files[0], hemi="rh") - yield assert_not_equal, s2s, s2sish + assert s2s != s2sish # Test hits file name creation s2s.inputs.hits_file = True - yield assert_equal, s2s._get_outfilename("hits_file"), os.path.join(cwd, "lh.a_hits.mgz") + assert s2s._get_outfilename("hits_file") == os.path.join(cwd, "lh.a_hits.mgz") # Test that a 2-tuple range raises an error def set_illegal_range(): s2s.inputs.sampling_range = (.2, .5) - yield assert_raises, TraitError, set_illegal_range - - # Clean up our mess - clean_directory(cwd, oldwd) + with pytest.raises(TraitError): set_illegal_range() -@skipif(fs.no_freesurfer) -def test_surfsmooth(): +@pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed") +def test_surfsmooth(create_surf_file): smooth = fs.SurfaceSmooth() # Test underlying command - yield assert_equal, smooth.cmd, "mri_surf2surf" + assert smooth.cmd == "mri_surf2surf" # Test mandatory args exception - yield assert_raises, ValueError, smooth.run + with pytest.raises(ValueError): smooth.run() # Create testing files - surf, cwd, oldwd = create_surf_file() + surf, cwd, oldwd = create_surf_file # Test input settings smooth.inputs.in_file = surf @@ -122,32 +128,29 @@ def test_surfsmooth(): smooth.inputs.hemi = "lh" # Test the command line - yield assert_equal, smooth.cmdline, \ + assert smooth.cmdline == \ ("mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval %s --tval %s/lh.a_smooth%d.nii --s fsaverage" % (surf, cwd, fwhm)) # Test identity shmooth = fs.SurfaceSmooth( subject_id="fsaverage", fwhm=6, in_file=surf, hemi="lh", out_file="lh.a_smooth.nii") - yield assert_not_equal, smooth, shmooth + assert smooth != shmooth - # Clean up - clean_directory(cwd, oldwd) - -@skipif(fs.no_freesurfer) -def test_surfxfm(): +@pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed") +def test_surfxfm(create_surf_file): xfm = fs.SurfaceTransform() # Test underlying command - yield assert_equal, xfm.cmd, "mri_surf2surf" + assert xfm.cmd == "mri_surf2surf" # Test mandatory args exception - yield assert_raises, ValueError, xfm.run + with pytest.raises(ValueError): xfm.run() # Create testing files - surf, cwd, oldwd = create_surf_file() + surf, cwd, oldwd = create_surf_file # Test input settings xfm.inputs.source_file = surf @@ -156,32 +159,29 @@ def test_surfxfm(): xfm.inputs.hemi = "lh" # Test the command line - yield assert_equal, xfm.cmdline, \ + assert xfm.cmdline == \ ("mri_surf2surf --hemi lh --tval %s/lh.a.fsaverage.nii --sval %s --srcsubject my_subject --trgsubject fsaverage" % (cwd, surf)) # Test identity xfmish = fs.SurfaceTransform( source_subject="fsaverage", target_subject="my_subject", source_file=surf, hemi="lh") - yield assert_not_equal, xfm, xfmish - - # Clean up - clean_directory(cwd, oldwd) + assert xfm != xfmish -@skipif(fs.no_freesurfer) -def test_surfshots(): +@pytest.mark.skipif(fs.no_freesurfer(), reason="freesurfer is not installed") +def test_surfshots(create_files_in_directory): fotos = fs.SurfaceSnapshots() # Test underlying command - yield assert_equal, fotos.cmd, "tksurfer" + assert fotos.cmd == "tksurfer" # Test mandatory args exception - yield assert_raises, ValueError, fotos.run + with pytest.raises(ValueError): fotos.run() # Create testing files - files, cwd, oldwd = create_files_in_directory() + files, cwd, oldwd = create_files_in_directory # Test input settins fotos.inputs.subject_id = "fsaverage" @@ -189,29 +189,26 @@ def test_surfshots(): fotos.inputs.surface = "pial" # Test a basic command line - yield assert_equal, fotos.cmdline, "tksurfer fsaverage lh pial -tcl snapshots.tcl" + assert fotos.cmdline == "tksurfer fsaverage lh pial -tcl snapshots.tcl" # Test identity schmotos = fs.SurfaceSnapshots(subject_id="mysubject", hemi="rh", surface="white") - yield assert_not_equal, fotos, schmotos + assert fotos != schmotos # Test that the tcl script gets written fotos._write_tcl_script() - yield assert_equal, True, os.path.exists("snapshots.tcl") + assert os.path.exists("snapshots.tcl") # Test that we can use a different tcl script foo = open("other.tcl", "w").close() fotos.inputs.tcl_script = "other.tcl" - yield assert_equal, fotos.cmdline, "tksurfer fsaverage lh pial -tcl other.tcl" + assert fotos.cmdline == "tksurfer fsaverage lh pial -tcl other.tcl" # Test that the interface crashes politely if graphics aren't enabled try: hold_display = os.environ["DISPLAY"] del os.environ["DISPLAY"] - yield assert_raises, RuntimeError, fotos.run + with pytest.raises(RuntimeError): fotos.run() os.environ["DISPLAY"] = hold_display except KeyError: pass - - # Clean up our mess - clean_directory(cwd, oldwd) diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index cd6cd1883f..fed63e498e 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/nipype/interfaces/freesurfer/utils.py @@ -192,7 +192,7 @@ class SampleToSurface(FSCommand): >>> sampler.inputs.sampling_method = "average" >>> sampler.inputs.sampling_range = 1 >>> sampler.inputs.sampling_units = "frac" - >>> sampler.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> sampler.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'mri_vol2surf --hemi lh --o ...lh.cope1.mgz --reg register.dat --projfrac-avg 1.000 --mov cope1.nii.gz' >>> res = sampler.run() # doctest: +SKIP @@ -315,7 +315,7 @@ class SurfaceSmooth(FSCommand): >>> smoother.inputs.subject_id = "subj_1" >>> smoother.inputs.hemi = "lh" >>> smoother.inputs.fwhm = 5 - >>> smoother.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> smoother.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'mri_surf2surf --cortex --fwhm 5.0000 --hemi lh --sval lh.cope1.mgz --tval ...lh.cope1_smooth5.mgz --s subj_1' >>> smoother.run() # doctest: +SKIP @@ -491,7 +491,7 @@ class Surface2VolTransform(FSCommand): >>> xfm2vol.inputs.hemi = 'lh' >>> xfm2vol.inputs.template_file = 'cope1.nii.gz' >>> xfm2vol.inputs.subjects_dir = '.' - >>> xfm2vol.cmdline # doctest: +IGNORE_UNICODE + >>> xfm2vol.cmdline # doctest: +ALLOW_UNICODE 'mri_surf2vol --hemi lh --volreg register.mat --surfval lh.cope1.mgz --sd . --template cope1.nii.gz --outvol lh.cope1_asVol.nii --vtxvol lh.cope1_asVol_vertex.nii' >>> res = xfm2vol.run()# doctest: +SKIP @@ -1027,7 +1027,7 @@ class MRIPretess(FSCommand): >>> pretess.inputs.in_filled = 'wm.mgz' >>> pretess.inputs.in_norm = 'norm.mgz' >>> pretess.inputs.nocorners = True - >>> pretess.cmdline # doctest: +IGNORE_UNICODE + >>> pretess.cmdline # doctest: +ALLOW_UNICODE 'mri_pretess -nocorners wm.mgz wm norm.mgz wm_pretesswm.mgz' >>> pretess.run() # doctest: +SKIP @@ -1197,7 +1197,7 @@ class MakeAverageSubject(FSCommand): >>> from nipype.interfaces.freesurfer import MakeAverageSubject >>> avg = MakeAverageSubject(subjects_ids=['s1', 's2']) - >>> avg.cmdline # doctest: +IGNORE_UNICODE + >>> avg.cmdline # doctest: +ALLOW_UNICODE 'make_average_subject --out average --subjects s1 s2' """ @@ -1232,7 +1232,7 @@ class ExtractMainComponent(CommandLine): >>> from nipype.interfaces.freesurfer import ExtractMainComponent >>> mcmp = ExtractMainComponent(in_file='lh.pial') - >>> mcmp.cmdline # doctest: +IGNORE_UNICODE + >>> mcmp.cmdline # doctest: +ALLOW_UNICODE 'mris_extract_main_component lh.pial lh.maincmp' """ @@ -1295,7 +1295,7 @@ class Tkregister2(FSCommand): >>> tk2.inputs.moving_image = 'T1.mgz' >>> tk2.inputs.target_image = 'structural.nii' >>> tk2.inputs.reg_header = True - >>> tk2.cmdline # doctest: +IGNORE_UNICODE + >>> tk2.cmdline # doctest: +ALLOW_UNICODE 'tkregister2 --mov T1.mgz --noedit --reg T1_to_native.dat --regheader \ --targ structural.nii' >>> tk2.run() # doctest: +SKIP @@ -1308,7 +1308,7 @@ class Tkregister2(FSCommand): >>> tk2 = Tkregister2() >>> tk2.inputs.moving_image = 'epi.nii' >>> tk2.inputs.fsl_in_matrix = 'flirt.mat' - >>> tk2.cmdline # doctest: +IGNORE_UNICODE + >>> tk2.cmdline # doctest: +ALLOW_UNICODE 'tkregister2 --fsl flirt.mat --mov epi.nii --noedit --reg register.dat' >>> tk2.run() # doctest: +SKIP """ @@ -1362,11 +1362,11 @@ class AddXFormToHeader(FSCommand): >>> adder = AddXFormToHeader() >>> adder.inputs.in_file = 'norm.mgz' >>> adder.inputs.transform = 'trans.mat' - >>> adder.cmdline # doctest: +IGNORE_UNICODE + >>> adder.cmdline # doctest: +ALLOW_UNICODE 'mri_add_xform_to_header trans.mat norm.mgz output.mgz' >>> adder.inputs.copy_name = True - >>> adder.cmdline # doctest: +IGNORE_UNICODE + >>> adder.cmdline # doctest: +ALLOW_UNICODE 'mri_add_xform_to_header -c trans.mat norm.mgz output.mgz' >>> adder.run() # doctest: +SKIP @@ -1420,7 +1420,7 @@ class CheckTalairachAlignment(FSCommand): >>> checker.inputs.in_file = 'trans.mat' >>> checker.inputs.threshold = 0.005 - >>> checker.cmdline # doctest: +IGNORE_UNICODE + >>> checker.cmdline # doctest: +ALLOW_UNICODE 'talairach_afd -T 0.005 -xfm trans.mat' >>> checker.run() # doctest: +SKIP @@ -1469,7 +1469,7 @@ class TalairachAVI(FSCommand): >>> example = TalairachAVI() >>> example.inputs.in_file = 'norm.mgz' >>> example.inputs.out_file = 'trans.mat' - >>> example.cmdline # doctest: +IGNORE_UNICODE + >>> example.cmdline # doctest: +ALLOW_UNICODE 'talairach_avi --i norm.mgz --xfm trans.mat' >>> example.run() # doctest: +SKIP @@ -1500,7 +1500,7 @@ class TalairachQC(FSScriptCommand): >>> from nipype.interfaces.freesurfer import TalairachQC >>> qc = TalairachQC() >>> qc.inputs.log_file = 'dirs.txt' - >>> qc.cmdline # doctest: +IGNORE_UNICODE + >>> qc.cmdline # doctest: +ALLOW_UNICODE 'tal_QC_AZS dirs.txt' """ _cmd = "tal_QC_AZS" @@ -1539,7 +1539,7 @@ class RemoveNeck(FSCommand): >>> remove_neck.inputs.in_file = 'norm.mgz' >>> remove_neck.inputs.transform = 'trans.mat' >>> remove_neck.inputs.template = 'trans.mat' - >>> remove_neck.cmdline # doctest: +IGNORE_UNICODE + >>> remove_neck.cmdline # doctest: +ALLOW_UNICODE 'mri_remove_neck norm.mgz trans.mat trans.mat norm_noneck.mgz' """ _cmd = "mri_remove_neck" @@ -1679,7 +1679,7 @@ class Sphere(FSCommandOpenMP): >>> from nipype.interfaces.freesurfer import Sphere >>> sphere = Sphere() >>> sphere.inputs.in_file = 'lh.pial' - >>> sphere.cmdline # doctest: +IGNORE_UNICODE + >>> sphere.cmdline # doctest: +ALLOW_UNICODE 'mris_sphere lh.pial lh.sphere' """ _cmd = 'mris_sphere' @@ -1803,7 +1803,7 @@ class EulerNumber(FSCommand): >>> from nipype.interfaces.freesurfer import EulerNumber >>> ft = EulerNumber() >>> ft.inputs.in_file = 'lh.pial' - >>> ft.cmdline # doctest: +IGNORE_UNICODE + >>> ft.cmdline # doctest: +ALLOW_UNICODE 'mris_euler_number lh.pial' """ _cmd = 'mris_euler_number' @@ -1839,7 +1839,7 @@ class RemoveIntersection(FSCommand): >>> from nipype.interfaces.freesurfer import RemoveIntersection >>> ri = RemoveIntersection() >>> ri.inputs.in_file = 'lh.pial' - >>> ri.cmdline # doctest: +IGNORE_UNICODE + >>> ri.cmdline # doctest: +ALLOW_UNICODE 'mris_remove_intersection lh.pial lh.pial' """ @@ -1935,7 +1935,7 @@ class MakeSurfaces(FSCommand): >>> makesurfaces.inputs.in_label = 'aparc+aseg.nii' >>> makesurfaces.inputs.in_T1 = 'T1.mgz' >>> makesurfaces.inputs.orig_pial = 'lh.pial' - >>> makesurfaces.cmdline # doctest: +IGNORE_UNICODE + >>> makesurfaces.cmdline # doctest: +ALLOW_UNICODE 'mris_make_surfaces -T1 T1.mgz -orig pial -orig_pial pial 10335 lh' """ @@ -2068,7 +2068,7 @@ class Curvature(FSCommand): >>> curv = Curvature() >>> curv.inputs.in_file = 'lh.pial' >>> curv.inputs.save = True - >>> curv.cmdline # doctest: +IGNORE_UNICODE + >>> curv.cmdline # doctest: +ALLOW_UNICODE 'mris_curvature -w lh.pial' """ @@ -2162,7 +2162,7 @@ class CurvatureStats(FSCommand): >>> curvstats.inputs.values = True >>> curvstats.inputs.min_max = True >>> curvstats.inputs.write = True - >>> curvstats.cmdline # doctest: +IGNORE_UNICODE + >>> curvstats.cmdline # doctest: +ALLOW_UNICODE 'mris_curvature_stats -m -o lh.curv.stats -F pial -G --writeCurvatureFiles subject_id lh pial pial' """ @@ -2219,7 +2219,7 @@ class Jacobian(FSCommand): >>> jacobian = Jacobian() >>> jacobian.inputs.in_origsurf = 'lh.pial' >>> jacobian.inputs.in_mappedsurf = 'lh.pial' - >>> jacobian.cmdline # doctest: +IGNORE_UNICODE + >>> jacobian.cmdline # doctest: +ALLOW_UNICODE 'mris_jacobian lh.pial lh.pial lh.jacobian' """ @@ -2356,7 +2356,7 @@ class VolumeMask(FSCommand): >>> volmask.inputs.rh_white = 'lh.pial' >>> volmask.inputs.subject_id = '10335' >>> volmask.inputs.save_ribbon = True - >>> volmask.cmdline # doctest: +IGNORE_UNICODE + >>> volmask.cmdline # doctest: +ALLOW_UNICODE 'mris_volmask --label_left_ribbon 3 --label_left_white 2 --label_right_ribbon 42 --label_right_white 41 --save_ribbon 10335' """ @@ -2696,7 +2696,7 @@ class RelabelHypointensities(FSCommand): >>> relabelhypos.inputs.rh_white = 'lh.pial' >>> relabelhypos.inputs.surf_directory = '.' >>> relabelhypos.inputs.aseg = 'aseg.mgz' - >>> relabelhypos.cmdline # doctest: +IGNORE_UNICODE + >>> relabelhypos.cmdline # doctest: +ALLOW_UNICODE 'mri_relabel_hypointensities aseg.mgz . aseg.hypos.mgz' """ @@ -2867,7 +2867,7 @@ class Apas2Aseg(FSCommand): >>> apas2aseg = Apas2Aseg() >>> apas2aseg.inputs.in_file = 'aseg.mgz' >>> apas2aseg.inputs.out_file = 'output.mgz' - >>> apas2aseg.cmdline # doctest: +IGNORE_UNICODE + >>> apas2aseg.cmdline # doctest: +ALLOW_UNICODE 'apas2aseg --i aseg.mgz --o output.mgz' """ diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index fdbc80e0ca..c514bd95f0 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -85,7 +85,7 @@ class DTIFit(FSLCommand): >>> dti.inputs.bvals = 'bvals' >>> dti.inputs.base_name = 'TP' >>> dti.inputs.mask = 'mask.nii' - >>> dti.cmdline # doctest: +IGNORE_UNICODE + >>> dti.cmdline # doctest: +ALLOW_UNICODE 'dtifit -k diffusion.nii -o TP -m mask.nii -r bvecs -b bvals' """ @@ -327,7 +327,7 @@ class BEDPOSTX5(FSLXCommand): >>> from nipype.interfaces import fsl >>> bedp = fsl.BEDPOSTX5(bvecs='bvecs', bvals='bvals', dwi='diffusion.nii', ... mask='mask.nii', n_fibres=1) - >>> bedp.cmdline # doctest: +IGNORE_UNICODE + >>> bedp.cmdline # doctest: +ALLOW_UNICODE 'bedpostx bedpostx --forcedir -n 1' """ @@ -583,7 +583,7 @@ class ProbTrackX(FSLCommand): target_masks = ['targets_MASK1.nii', 'targets_MASK2.nii'], \ thsamples='merged_thsamples.nii', fsamples='merged_fsamples.nii', phsamples='merged_phsamples.nii', \ out_dir='.') - >>> pbx.cmdline # doctest: +IGNORE_UNICODE + >>> pbx.cmdline # doctest: +ALLOW_UNICODE 'probtrackx --forcedir -m mask.nii --mode=seedmask --nsamples=3 --nsteps=10 --opd --os2t --dir=. --samples=merged --seed=MASK_average_thal_right.nii --targetmasks=targets.txt --xfm=trans.mat' """ @@ -780,7 +780,7 @@ class ProbTrackX2(ProbTrackX): >>> pbx2.inputs.out_dir = '.' >>> pbx2.inputs.n_samples = 3 >>> pbx2.inputs.n_steps = 10 - >>> pbx2.cmdline # doctest: +IGNORE_UNICODE + >>> pbx2.cmdline # doctest: +ALLOW_UNICODE 'probtrackx2 --forcedir -m nodif_brain_mask.nii.gz --nsamples=3 --nsteps=10 --opd --dir=. --samples=merged --seed=seed_source.nii.gz' """ _cmd = 'probtrackx2' @@ -869,7 +869,7 @@ class VecReg(FSLCommand): affine_mat='trans.mat', \ ref_vol='mni.nii', \ out_file='diffusion_vreg.nii') - >>> vreg.cmdline # doctest: +IGNORE_UNICODE + >>> vreg.cmdline # doctest: +ALLOW_UNICODE 'vecreg -t trans.mat -i diffusion.nii -o diffusion_vreg.nii -r mni.nii' """ @@ -930,7 +930,7 @@ class ProjThresh(FSLCommand): >>> from nipype.interfaces import fsl >>> ldir = ['seeds_to_M1.nii', 'seeds_to_M2.nii'] >>> pThresh = fsl.ProjThresh(in_files=ldir, threshold=3) - >>> pThresh.cmdline # doctest: +IGNORE_UNICODE + >>> pThresh.cmdline # doctest: +ALLOW_UNICODE 'proj_thresh seeds_to_M1.nii seeds_to_M2.nii 3' """ @@ -978,7 +978,7 @@ class FindTheBiggest(FSLCommand): >>> from nipype.interfaces import fsl >>> ldir = ['seeds_to_M1.nii', 'seeds_to_M2.nii'] >>> fBig = fsl.FindTheBiggest(in_files=ldir, out_file='biggestSegmentation') - >>> fBig.cmdline # doctest: +IGNORE_UNICODE + >>> fBig.cmdline # doctest: +ALLOW_UNICODE 'find_the_biggest seeds_to_M1.nii seeds_to_M2.nii biggestSegmentation' """ diff --git a/nipype/interfaces/fsl/epi.py b/nipype/interfaces/fsl/epi.py index 0a16b82eef..19557e6771 100644 --- a/nipype/interfaces/fsl/epi.py +++ b/nipype/interfaces/fsl/epi.py @@ -68,7 +68,7 @@ class PrepareFieldmap(FSLCommand): >>> prepare.inputs.in_phase = "phase.nii" >>> prepare.inputs.in_magnitude = "magnitude.nii" >>> prepare.inputs.output_type = "NIFTI_GZ" - >>> prepare.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> prepare.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fsl_prepare_fieldmap SIEMENS phase.nii magnitude.nii \ .../phase_fslprepared.nii.gz 2.460000' >>> res = prepare.run() # doctest: +SKIP @@ -231,7 +231,7 @@ class TOPUP(FSLCommand): >>> topup.inputs.in_file = "b0_b0rev.nii" >>> topup.inputs.encoding_file = "topup_encoding.txt" >>> topup.inputs.output_type = "NIFTI_GZ" - >>> topup.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> topup.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'topup --config=b02b0.cnf --datain=topup_encoding.txt \ --imain=b0_b0rev.nii --out=b0_b0rev_base --iout=b0_b0rev_corrected.nii.gz \ --fout=b0_b0rev_field.nii.gz --logout=b0_b0rev_topup.log' @@ -359,7 +359,7 @@ class ApplyTOPUP(FSLCommand): >>> applytopup.inputs.in_topup_fieldcoef = "topup_fieldcoef.nii.gz" >>> applytopup.inputs.in_topup_movpar = "topup_movpar.txt" >>> applytopup.inputs.output_type = "NIFTI_GZ" - >>> applytopup.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> applytopup.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'applytopup --datain=topup_encoding.txt --imain=epi.nii,epi_rev.nii \ --inindex=1,2 --topup=topup --out=epi_corrected.nii.gz' >>> res = applytopup.run() # doctest: +SKIP @@ -462,7 +462,7 @@ class Eddy(FSLCommand): >>> eddy.inputs.in_acqp = 'epi_acqp.txt' >>> eddy.inputs.in_bvec = 'bvecs.scheme' >>> eddy.inputs.in_bval = 'bvals.scheme' - >>> eddy.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> eddy.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'eddy --acqp=epi_acqp.txt --bvals=bvals.scheme --bvecs=bvecs.scheme \ --imain=epi.nii --index=epi_index.txt --mask=epi_mask.nii \ --out=.../eddy_corrected' @@ -545,7 +545,7 @@ class SigLoss(FSLCommand): >>> sigloss.inputs.in_file = "phase.nii" >>> sigloss.inputs.echo_time = 0.03 >>> sigloss.inputs.output_type = "NIFTI_GZ" - >>> sigloss.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> sigloss.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'sigloss --te=0.030000 -i phase.nii -s .../phase_sigloss.nii.gz' >>> res = sigloss.run() # doctest: +SKIP @@ -650,7 +650,7 @@ class EpiReg(FSLCommand): >>> epireg.inputs.fmapmagbrain='fieldmap_mag_brain.nii' >>> epireg.inputs.echospacing=0.00067 >>> epireg.inputs.pedir='y' - >>> epireg.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> epireg.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'epi_reg --echospacing=0.000670 --fmap=fieldmap_phase_fslprepared.nii \ --fmapmag=fieldmap_mag.nii --fmapmagbrain=fieldmap_mag_brain.nii --noclean \ --pedir=y --epi=epi.nii --t1=T1.nii --t1brain=T1_brain.nii --out=epi2struct' @@ -761,7 +761,7 @@ class EPIDeWarp(FSLCommand): >>> dewarp.inputs.mag_file = "magnitude.nii" >>> dewarp.inputs.dph_file = "phase.nii" >>> dewarp.inputs.output_type = "NIFTI_GZ" - >>> dewarp.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> dewarp.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'epidewarp.fsl --mag magnitude.nii --dph phase.nii --epi functional.nii \ --esp 0.58 --exfdw .../exfdw.nii.gz --nocleanup --sigma 2 --tediff 2.46 \ --tmpdir .../temp --vsm .../vsm.nii.gz' @@ -854,7 +854,7 @@ class EddyCorrect(FSLCommand): >>> from nipype.interfaces.fsl import EddyCorrect >>> eddyc = EddyCorrect(in_file='diffusion.nii', ... out_file="diffusion_edc.nii", ref_num=0) - >>> eddyc.cmdline # doctest: +IGNORE_UNICODE + >>> eddyc.cmdline # doctest: +ALLOW_UNICODE 'eddy_correct diffusion.nii diffusion_edc.nii 0' """ diff --git a/nipype/interfaces/fsl/maths.py b/nipype/interfaces/fsl/maths.py index f931b65882..6ebe62a7ac 100644 --- a/nipype/interfaces/fsl/maths.py +++ b/nipype/interfaces/fsl/maths.py @@ -347,7 +347,7 @@ class MultiImageMaths(MathsCommand): >>> maths.inputs.op_string = "-add %s -mul -1 -div %s" >>> maths.inputs.operand_files = ["functional2.nii", "functional3.nii"] >>> maths.inputs.out_file = "functional4.nii" - >>> maths.cmdline # doctest: +IGNORE_UNICODE + >>> maths.cmdline # doctest: +ALLOW_UNICODE 'fslmaths functional.nii -add functional2.nii -mul -1 -div functional3.nii functional4.nii' """ diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index 925bfd7a5d..024562dcc6 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -911,7 +911,7 @@ class FLAMEO(FSLCommand): t_con_file='design.con', \ mask_file='mask.nii', \ run_mode='fe') - >>> flameo.cmdline # doctest: +IGNORE_UNICODE + >>> flameo.cmdline # doctest: +ALLOW_UNICODE 'flameo --copefile=cope.nii.gz --covsplitfile=cov_split.mat --designfile=design.mat --ld=stats --maskfile=mask.nii --runmode=fe --tcontrastsfile=design.con --varcopefile=varcope.nii.gz' """ @@ -1543,7 +1543,7 @@ class MELODIC(FSLCommand): >>> melodic_setup.inputs.s_des = 'subjectDesign.mat' >>> melodic_setup.inputs.s_con = 'subjectDesign.con' >>> melodic_setup.inputs.out_dir = 'groupICA.out' - >>> melodic_setup.cmdline # doctest: +IGNORE_UNICODE + >>> melodic_setup.cmdline # doctest: +ALLOW_UNICODE 'melodic -i functional.nii,functional2.nii,functional3.nii -a tica --bgthreshold=10.000000 --mmthresh=0.500000 --nobet -o groupICA.out --Ostats --Scon=subjectDesign.con --Sdes=subjectDesign.mat --Tcon=timeDesign.con --Tdes=timeDesign.mat --tr=1.500000' >>> melodic_setup.run() # doctest: +SKIP @@ -1598,7 +1598,7 @@ class SmoothEstimate(FSLCommand): >>> est = SmoothEstimate() >>> est.inputs.zstat_file = 'zstat1.nii.gz' >>> est.inputs.mask_file = 'mask.nii' - >>> est.cmdline # doctest: +IGNORE_UNICODE + >>> est.cmdline # doctest: +ALLOW_UNICODE 'smoothest --mask=mask.nii --zstat=zstat1.nii.gz' """ @@ -1714,7 +1714,7 @@ class Cluster(FSLCommand): >>> cl.inputs.in_file = 'zstat1.nii.gz' >>> cl.inputs.out_localmax_txt_file = 'stats.txt' >>> cl.inputs.use_mm = True - >>> cl.cmdline # doctest: +IGNORE_UNICODE + >>> cl.cmdline # doctest: +ALLOW_UNICODE 'cluster --in=zstat1.nii.gz --olmax=stats.txt --thresh=2.3000000000 --mm' """ @@ -1852,7 +1852,7 @@ class Randomise(FSLCommand): ------- >>> import nipype.interfaces.fsl as fsl >>> rand = fsl.Randomise(in_file='allFA.nii', mask = 'mask.nii', tcon='design.con', design_mat='design.mat') - >>> rand.cmdline # doctest: +IGNORE_UNICODE + >>> rand.cmdline # doctest: +ALLOW_UNICODE 'randomise -i allFA.nii -o "tbss_" -d design.mat -t design.con -m mask.nii' """ @@ -1997,7 +1997,7 @@ class GLM(FSLCommand): ------- >>> import nipype.interfaces.fsl as fsl >>> glm = fsl.GLM(in_file='functional.nii', design='maps.nii', output_type='NIFTI') - >>> glm.cmdline # doctest: +IGNORE_UNICODE + >>> glm.cmdline # doctest: +ALLOW_UNICODE 'fsl_glm -i functional.nii -d maps.nii -o functional_glm.nii' """ diff --git a/nipype/interfaces/fsl/possum.py b/nipype/interfaces/fsl/possum.py index b31eb55594..20efefbf2c 100644 --- a/nipype/interfaces/fsl/possum.py +++ b/nipype/interfaces/fsl/possum.py @@ -80,7 +80,7 @@ class B0Calc(FSLCommand): >>> b0calc.inputs.in_file = 'tissue+air_map.nii' >>> b0calc.inputs.z_b0 = 3.0 >>> b0calc.inputs.output_type = "NIFTI_GZ" - >>> b0calc.cmdline # doctest: +IGNORE_UNICODE + >>> b0calc.cmdline # doctest: +ALLOW_UNICODE 'b0calc -i tissue+air_map.nii -o tissue+air_map_b0field.nii.gz --b0=3.00' """ diff --git a/nipype/interfaces/fsl/preprocess.py b/nipype/interfaces/fsl/preprocess.py index de14d371d8..842bbbe978 100644 --- a/nipype/interfaces/fsl/preprocess.py +++ b/nipype/interfaces/fsl/preprocess.py @@ -539,7 +539,7 @@ class FLIRT(FSLCommand): >>> flt.inputs.in_file = 'structural.nii' >>> flt.inputs.reference = 'mni.nii' >>> flt.inputs.output_type = "NIFTI_GZ" - >>> flt.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> flt.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'flirt -in structural.nii -ref mni.nii -out structural_flirt.nii.gz -omat structural_flirt.mat -bins 640 -searchcost mutualinfo' >>> res = flt.run() #doctest: +SKIP @@ -1359,7 +1359,7 @@ class FUGUE(FSLCommand): >>> fugue.inputs.shift_in_file = 'vsm.nii' # Previously computed with fugue as well >>> fugue.inputs.unwarp_direction = 'y' >>> fugue.inputs.output_type = "NIFTI_GZ" - >>> fugue.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> fugue.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --unwarp=epi_unwarped.nii.gz' >>> fugue.run() #doctest: +SKIP @@ -1374,7 +1374,7 @@ class FUGUE(FSLCommand): >>> fugue.inputs.shift_in_file = 'vsm.nii' # Previously computed with fugue as well >>> fugue.inputs.unwarp_direction = 'y' >>> fugue.inputs.output_type = "NIFTI_GZ" - >>> fugue.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> fugue.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fugue --in=epi.nii --mask=epi_mask.nii --loadshift=vsm.nii --unwarpdir=y --warp=epi_warped.nii.gz' >>> fugue.run() #doctest: +SKIP @@ -1389,7 +1389,7 @@ class FUGUE(FSLCommand): >>> fugue.inputs.unwarp_direction = 'y' >>> fugue.inputs.save_shift = True >>> fugue.inputs.output_type = "NIFTI_GZ" - >>> fugue.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> fugue.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fugue --dwelltoasym=0.9390243902 --mask=epi_mask.nii --phasemap=epi_phasediff.nii --saveshift=epi_phasediff_vsm.nii.gz --unwarpdir=y' >>> fugue.run() #doctest: +SKIP diff --git a/nipype/interfaces/fsl/tests/test_BEDPOSTX.py b/nipype/interfaces/fsl/tests/test_BEDPOSTX.py deleted file mode 100644 index 8f68a8adac..0000000000 --- a/nipype/interfaces/fsl/tests/test_BEDPOSTX.py +++ /dev/null @@ -1,3 +0,0 @@ -# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import BEDPOSTX diff --git a/nipype/interfaces/fsl/tests/test_FILMGLS.py b/nipype/interfaces/fsl/tests/test_FILMGLS.py index 96c5dab3c9..4ac8756a47 100644 --- a/nipype/interfaces/fsl/tests/test_FILMGLS.py +++ b/nipype/interfaces/fsl/tests/test_FILMGLS.py @@ -1,5 +1,4 @@ # -*- coding: utf-8 -*- -from nipype.testing import assert_equal from nipype.interfaces.fsl.model import FILMGLS, FILMGLSInputSpec @@ -49,8 +48,8 @@ def test_filmgls(): if isinstance(instance.inputs, FILMGLSInputSpec): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value + assert getattr(instance.inputs.traits()[key], metakey) == value else: for key, metadata in list(input_map2.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value + assert getattr(instance.inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_Level1Design_functions.py b/nipype/interfaces/fsl/tests/test_Level1Design_functions.py index 886a4eaeea..b6a61e023b 100644 --- a/nipype/interfaces/fsl/tests/test_Level1Design_functions.py +++ b/nipype/interfaces/fsl/tests/test_Level1Design_functions.py @@ -1,6 +1,5 @@ # -*- coding: utf-8 -*- import os -from nose.tools import assert_true from ...base import Undefined from ..model import Level1Design @@ -19,4 +18,4 @@ def test_level1design(): usetd, contrasts, do_tempfilter, key) - yield assert_true, "set fmri(convolve1) {0}".format(val) in output_txt + assert "set fmri(convolve1) {0}".format(val) in output_txt diff --git a/nipype/interfaces/fsl/tests/test_XFibres.py b/nipype/interfaces/fsl/tests/test_XFibres.py deleted file mode 100644 index 7192d31092..0000000000 --- a/nipype/interfaces/fsl/tests/test_XFibres.py +++ /dev/null @@ -1,3 +0,0 @@ -# -*- coding: utf-8 -*- -from nipype.testing import assert_equal -from nipype.interfaces.fsl.dti import XFibres diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index d374567662..113cae7722 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import ApplyMask @@ -42,7 +41,7 @@ def test_ApplyMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyMask_outputs(): @@ -52,4 +51,4 @@ def test_ApplyMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 1f275d653d..4ebc6b052d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..epi import ApplyTOPUP @@ -47,7 +46,7 @@ def test_ApplyTOPUP_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTOPUP_outputs(): @@ -57,4 +56,4 @@ def test_ApplyTOPUP_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index 6e4d9b7460..1274597c85 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ApplyWarp @@ -57,7 +56,7 @@ def test_ApplyWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyWarp_outputs(): @@ -67,4 +66,4 @@ def test_ApplyWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py index 818f77004a..63a90cdfb5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ApplyXfm @@ -149,7 +148,7 @@ def test_ApplyXfm_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyXfm_outputs(): @@ -161,4 +160,4 @@ def test_ApplyXfm_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index c766d07ee0..5da2329d16 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import AvScale @@ -27,7 +26,7 @@ def test_AvScale_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AvScale_outputs(): @@ -46,4 +45,4 @@ def test_AvScale_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py index 5f8fbd22e0..729a3ac52f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_B0Calc.py +++ b/nipype/interfaces/fsl/tests/test_auto_B0Calc.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..possum import B0Calc @@ -58,7 +57,7 @@ def test_B0Calc_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_B0Calc_outputs(): @@ -68,4 +67,4 @@ def test_B0Calc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index ebad20e193..9e98e85643 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import BEDPOSTX5 @@ -85,7 +84,7 @@ def test_BEDPOSTX5_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BEDPOSTX5_outputs(): @@ -104,4 +103,4 @@ def test_BEDPOSTX5_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index 8c5bb1f672..95d0f55886 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import BET @@ -72,7 +71,7 @@ def test_BET_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BET_outputs(): @@ -92,4 +91,4 @@ def test_BET_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index 5a7b643712..80162afdf1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import BinaryMaths @@ -52,7 +51,7 @@ def test_BinaryMaths_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaths_outputs(): @@ -62,4 +61,4 @@ def test_BinaryMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index 4de7103895..74165018e4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import ChangeDataType @@ -39,7 +38,7 @@ def test_ChangeDataType_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ChangeDataType_outputs(): @@ -49,4 +48,4 @@ def test_ChangeDataType_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index 726391670d..d559349f52 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Cluster @@ -86,7 +85,7 @@ def test_Cluster_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Cluster_outputs(): @@ -103,4 +102,4 @@ def test_Cluster_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index 293386f57d..bb17c65be5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Complex @@ -93,7 +92,7 @@ def test_Complex_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Complex_outputs(): @@ -107,4 +106,4 @@ def test_Complex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index 361f9cd086..4240ef1124 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import ContrastMgr @@ -46,7 +45,7 @@ def test_ContrastMgr_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ContrastMgr_outputs(): @@ -62,4 +61,4 @@ def test_ContrastMgr_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index 63d64a4914..7b276ef138 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ConvertWarp @@ -63,7 +62,7 @@ def test_ConvertWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ConvertWarp_outputs(): @@ -73,4 +72,4 @@ def test_ConvertWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index 250b6f0a9f..e54c22a221 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ConvertXFM @@ -46,7 +45,7 @@ def test_ConvertXFM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ConvertXFM_outputs(): @@ -56,4 +55,4 @@ def test_ConvertXFM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index 75e58ee331..1ab5ce80f3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import CopyGeom @@ -35,7 +34,7 @@ def test_CopyGeom_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CopyGeom_outputs(): @@ -45,4 +44,4 @@ def test_CopyGeom_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index 803a78b930..d2aaf817bf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import DTIFit @@ -62,7 +61,7 @@ def test_DTIFit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTIFit_outputs(): @@ -82,4 +81,4 @@ def test_DTIFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 08db0833c9..e320ef3647 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import DilateImage @@ -53,7 +52,7 @@ def test_DilateImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): @@ -63,4 +62,4 @@ def test_DilateImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 083590ed5d..6b64b92f18 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import DistanceMap @@ -34,7 +33,7 @@ def test_DistanceMap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMap_outputs(): @@ -45,4 +44,4 @@ def test_DistanceMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index 2f1eaf2522..6b465095ba 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..epi import EPIDeWarp @@ -57,7 +56,7 @@ def test_EPIDeWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EPIDeWarp_outputs(): @@ -70,4 +69,4 @@ def test_EPIDeWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index 4581fce029..b549834c79 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..epi import Eddy @@ -61,7 +60,7 @@ def test_Eddy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Eddy_outputs(): @@ -72,4 +71,4 @@ def test_Eddy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index aab0b77983..7e36ec1c1a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..epi import EddyCorrect @@ -35,7 +34,7 @@ def test_EddyCorrect_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EddyCorrect_outputs(): @@ -45,4 +44,4 @@ def test_EddyCorrect_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index 10014e521a..0ae36ed052 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..epi import EpiReg @@ -55,7 +54,7 @@ def test_EpiReg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EpiReg_outputs(): @@ -77,4 +76,4 @@ def test_EpiReg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index a4649ada75..2af66dd692 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import ErodeImage @@ -53,7 +52,7 @@ def test_ErodeImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): @@ -63,4 +62,4 @@ def test_ErodeImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index 7d0a407c17..00d70b6e1c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ExtractROI @@ -57,7 +56,7 @@ def test_ExtractROI_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ExtractROI_outputs(): @@ -67,4 +66,4 @@ def test_ExtractROI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 3dc8ca73f2..db1d83d395 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import FAST @@ -68,7 +67,7 @@ def test_FAST_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FAST_outputs(): @@ -85,4 +84,4 @@ def test_FAST_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index 8500302502..c1f26021b5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import FEAT @@ -24,7 +23,7 @@ def test_FEAT_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FEAT_outputs(): @@ -34,4 +33,4 @@ def test_FEAT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index 06cbe57d84..65dc1a497d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import FEATModel @@ -30,7 +29,7 @@ def test_FEATModel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FEATModel_outputs(): @@ -44,4 +43,4 @@ def test_FEATModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index 3af3b4695d..1eee1daf6f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import FEATRegister @@ -18,7 +17,7 @@ def test_FEATRegister_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FEATRegister_outputs(): @@ -28,4 +27,4 @@ def test_FEATRegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index 344c0181f2..39695f1ff8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import FIRST @@ -55,7 +54,7 @@ def test_FIRST_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FIRST_outputs(): @@ -68,4 +67,4 @@ def test_FIRST_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index bd4d938ffb..83fc4d0f3f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import FLAMEO @@ -63,7 +62,7 @@ def test_FLAMEO_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FLAMEO_outputs(): @@ -84,4 +83,4 @@ def test_FLAMEO_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index 3da1dff886..8d60d90f6e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import FLIRT @@ -148,7 +147,7 @@ def test_FLIRT_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FLIRT_outputs(): @@ -160,4 +159,4 @@ def test_FLIRT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 316880f4c4..d298f95f95 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import FNIRT @@ -126,7 +125,7 @@ def test_FNIRT_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FNIRT_outputs(): @@ -142,4 +141,4 @@ def test_FNIRT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py index c5b0bb63a2..3c5f8a2913 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import FSLCommand @@ -20,5 +19,5 @@ def test_FSLCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index 8a472a31f0..27e6bfba8d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import FSLXCommand @@ -81,7 +80,7 @@ def test_FSLXCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FSLXCommand_outputs(): @@ -98,4 +97,4 @@ def test_FSLXCommand_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index d9f1ef965c..afe454733b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import FUGUE @@ -92,7 +91,7 @@ def test_FUGUE_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FUGUE_outputs(): @@ -105,4 +104,4 @@ def test_FUGUE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index 664757a425..4e7d032c46 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import FilterRegressor @@ -49,7 +48,7 @@ def test_FilterRegressor_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FilterRegressor_outputs(): @@ -59,4 +58,4 @@ def test_FilterRegressor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index 0fd902dbf0..dc7abed70f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import FindTheBiggest @@ -29,7 +28,7 @@ def test_FindTheBiggest_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FindTheBiggest_outputs(): @@ -40,4 +39,4 @@ def test_FindTheBiggest_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index 3aeef972c0..2c701b5b8f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import GLM @@ -70,7 +69,7 @@ def test_GLM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GLM_outputs(): @@ -91,4 +90,4 @@ def test_GLM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 008516f571..4bfb6bf45c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ImageMaths @@ -39,7 +38,7 @@ def test_ImageMaths_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ImageMaths_outputs(): @@ -49,4 +48,4 @@ def test_ImageMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 2a07ee64f0..21a982cc92 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ImageMeants @@ -45,7 +44,7 @@ def test_ImageMeants_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ImageMeants_outputs(): @@ -55,4 +54,4 @@ def test_ImageMeants_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 86be9772c4..fe75df1662 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ImageStats @@ -33,7 +32,7 @@ def test_ImageStats_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ImageStats_outputs(): @@ -43,4 +42,4 @@ def test_ImageStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index e719ec52bd..c4c3dc35a9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import InvWarp @@ -47,7 +46,7 @@ def test_InvWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_InvWarp_outputs(): @@ -57,4 +56,4 @@ def test_InvWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index ccff1d564a..6c4d1a80d0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import IsotropicSmooth @@ -48,7 +47,7 @@ def test_IsotropicSmooth_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_IsotropicSmooth_outputs(): @@ -58,4 +57,4 @@ def test_IsotropicSmooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index bcf3737fdd..7bceaed367 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import L2Model @@ -14,7 +13,7 @@ def test_L2Model_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_L2Model_outputs(): @@ -26,4 +25,4 @@ def test_L2Model_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py index f1500d42be..bc41088804 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Level1Design @@ -21,7 +20,7 @@ def test_Level1Design_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Level1Design_outputs(): @@ -32,4 +31,4 @@ def test_Level1Design_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index 355c9ab527..afe918be8e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MCFLIRT @@ -64,7 +63,7 @@ def test_MCFLIRT_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MCFLIRT_outputs(): @@ -80,4 +79,4 @@ def test_MCFLIRT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index 3f4c0047ca..d785df88cd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import MELODIC @@ -112,7 +111,7 @@ def test_MELODIC_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MELODIC_outputs(): @@ -123,4 +122,4 @@ def test_MELODIC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index cbc35e34c9..2c837393c8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import MakeDyadicVectors @@ -39,7 +38,7 @@ def test_MakeDyadicVectors_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MakeDyadicVectors_outputs(): @@ -50,4 +49,4 @@ def test_MakeDyadicVectors_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index 3c3eee3d14..938feb3f96 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import MathsCommand @@ -38,7 +37,7 @@ def test_MathsCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MathsCommand_outputs(): @@ -48,4 +47,4 @@ def test_MathsCommand_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 4edd2cfb13..2b7c9b4027 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import MaxImage @@ -42,7 +41,7 @@ def test_MaxImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MaxImage_outputs(): @@ -52,4 +51,4 @@ def test_MaxImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index f6792d368d..8be7b982a4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import MeanImage @@ -42,7 +41,7 @@ def test_MeanImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MeanImage_outputs(): @@ -52,4 +51,4 @@ def test_MeanImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 621d43dd65..2c42eaefad 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Merge @@ -37,7 +36,7 @@ def test_Merge_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): @@ -47,4 +46,4 @@ def test_Merge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index d8d88d809e..695ae34577 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import MotionOutliers @@ -51,7 +50,7 @@ def test_MotionOutliers_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MotionOutliers_outputs(): @@ -63,4 +62,4 @@ def test_MotionOutliers_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 91b5f03657..69814a819f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import MultiImageMaths @@ -44,7 +43,7 @@ def test_MultiImageMaths_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MultiImageMaths_outputs(): @@ -54,4 +53,4 @@ def test_MultiImageMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 5e4a88cf79..1fed75da5f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import MultipleRegressDesign @@ -17,7 +16,7 @@ def test_MultipleRegressDesign_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressDesign_outputs(): @@ -30,4 +29,4 @@ def test_MultipleRegressDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 568eaf9458..be0614e74f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Overlay @@ -74,7 +73,7 @@ def test_Overlay_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Overlay_outputs(): @@ -84,4 +83,4 @@ def test_Overlay_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index cbe934adb9..9af949011a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import PRELUDE @@ -65,7 +64,7 @@ def test_PRELUDE_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PRELUDE_outputs(): @@ -75,4 +74,4 @@ def test_PRELUDE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 75d376e32e..74b4728030 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import PlotMotionParams @@ -35,7 +34,7 @@ def test_PlotMotionParams_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PlotMotionParams_outputs(): @@ -45,4 +44,4 @@ def test_PlotMotionParams_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 3eb196cbda..89db2a5e7f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import PlotTimeSeries @@ -61,7 +60,7 @@ def test_PlotTimeSeries_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PlotTimeSeries_outputs(): @@ -71,4 +70,4 @@ def test_PlotTimeSeries_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index bacda34c21..1bc303dce5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import PowerSpectrum @@ -29,7 +28,7 @@ def test_PowerSpectrum_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PowerSpectrum_outputs(): @@ -39,4 +38,4 @@ def test_PowerSpectrum_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index 01aea929dc..dcef9b1e6e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..epi import PrepareFieldmap @@ -44,7 +43,7 @@ def test_PrepareFieldmap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PrepareFieldmap_outputs(): @@ -54,4 +53,4 @@ def test_PrepareFieldmap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index a4b60ff6f6..03c633eafd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ProbTrackX @@ -100,7 +99,7 @@ def test_ProbTrackX_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ProbTrackX_outputs(): @@ -114,4 +113,4 @@ def test_ProbTrackX_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index c507ab0223..36f01eb0d3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ProbTrackX2 @@ -130,7 +129,7 @@ def test_ProbTrackX2_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ProbTrackX2_outputs(): @@ -149,4 +148,4 @@ def test_ProbTrackX2_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py index a8fbd352a9..8b61b1b856 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import ProjThresh @@ -28,7 +27,7 @@ def test_ProjThresh_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ProjThresh_outputs(): @@ -38,4 +37,4 @@ def test_ProjThresh_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 72a38393fd..16f9640bf8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Randomise @@ -80,7 +79,7 @@ def test_Randomise_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Randomise_outputs(): @@ -95,4 +94,4 @@ def test_Randomise_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index 0f252d5d61..3e24638867 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Reorient2Std @@ -27,7 +26,7 @@ def test_Reorient2Std_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Reorient2Std_outputs(): @@ -37,4 +36,4 @@ def test_Reorient2Std_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index 114a6dad32..9a5f473c15 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import RobustFOV @@ -29,7 +28,7 @@ def test_RobustFOV_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RobustFOV_outputs(): @@ -39,4 +38,4 @@ def test_RobustFOV_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index b2440eaa7e..93b81f9ccb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import SMM @@ -33,7 +32,7 @@ def test_SMM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SMM_outputs(): @@ -45,4 +44,4 @@ def test_SMM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index 0b813fc31e..60be2dd056 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SUSAN @@ -49,7 +48,7 @@ def test_SUSAN_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SUSAN_outputs(): @@ -59,4 +58,4 @@ def test_SUSAN_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index e42dc4ba88..c41adfcb5b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import SigLoss @@ -32,7 +31,7 @@ def test_SigLoss_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SigLoss_outputs(): @@ -42,4 +41,4 @@ def test_SigLoss_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index c02b80cf3b..d00bfaa23c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SliceTimer @@ -42,7 +41,7 @@ def test_SliceTimer_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SliceTimer_outputs(): @@ -52,4 +51,4 @@ def test_SliceTimer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index d8801a102d..c244d46d5d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Slicer @@ -83,7 +82,7 @@ def test_Slicer_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Slicer_outputs(): @@ -93,4 +92,4 @@ def test_Slicer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index 69d6d3ebc4..7a916f9841 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Smooth @@ -40,7 +39,7 @@ def test_Smooth_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): @@ -50,4 +49,4 @@ def test_Smooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index f9d6bae588..7160a00cd5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import SmoothEstimate @@ -33,7 +32,7 @@ def test_SmoothEstimate_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SmoothEstimate_outputs(): @@ -45,4 +44,4 @@ def test_SmoothEstimate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index dc32faef23..6c25174773 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import SpatialFilter @@ -53,7 +52,7 @@ def test_SpatialFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SpatialFilter_outputs(): @@ -63,4 +62,4 @@ def test_SpatialFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index a7469eca48..c569128b56 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Split @@ -31,7 +30,7 @@ def test_Split_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Split_outputs(): @@ -41,4 +40,4 @@ def test_Split_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_StdImage.py b/nipype/interfaces/fsl/tests/test_auto_StdImage.py index 32ede13cd5..82f2c62f62 100644 --- a/nipype/interfaces/fsl/tests/test_auto_StdImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_StdImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import StdImage @@ -42,7 +41,7 @@ def test_StdImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_StdImage_outputs(): @@ -52,4 +51,4 @@ def test_StdImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 60dd31a304..4bbe896759 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import SwapDimensions @@ -31,7 +30,7 @@ def test_SwapDimensions_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SwapDimensions_outputs(): @@ -41,4 +40,4 @@ def test_SwapDimensions_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index b064a7e951..cf8d143bcd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..epi import TOPUP @@ -88,7 +87,7 @@ def test_TOPUP_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TOPUP_outputs(): @@ -103,4 +102,4 @@ def test_TOPUP_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index 049af8bd52..56df3084ca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import TemporalFilter @@ -46,7 +45,7 @@ def test_TemporalFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TemporalFilter_outputs(): @@ -56,4 +55,4 @@ def test_TemporalFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index ca42e915d7..c51ce1a9a2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import Threshold @@ -47,7 +46,7 @@ def test_Threshold_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): @@ -57,4 +56,4 @@ def test_Threshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index 9f085d0065..c501613e2e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import TractSkeleton @@ -41,7 +40,7 @@ def test_TractSkeleton_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TractSkeleton_outputs(): @@ -52,4 +51,4 @@ def test_TractSkeleton_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index 9bc209e532..e63aaf85aa 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..maths import UnaryMaths @@ -42,7 +41,7 @@ def test_UnaryMaths_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_UnaryMaths_outputs(): @@ -52,4 +51,4 @@ def test_UnaryMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 55c84c1164..09bd7c890b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import VecReg @@ -44,7 +43,7 @@ def test_VecReg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VecReg_outputs(): @@ -54,4 +53,4 @@ def test_VecReg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 4731986dfa..e604821637 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import WarpPoints @@ -45,7 +44,7 @@ def test_WarpPoints_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WarpPoints_outputs(): @@ -55,4 +54,4 @@ def test_WarpPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index ce27ac22ce..2af7ef7b6d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import WarpPointsToStd @@ -47,7 +46,7 @@ def test_WarpPointsToStd_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WarpPointsToStd_outputs(): @@ -57,4 +56,4 @@ def test_WarpPointsToStd_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index 7f8683b883..67f29cd848 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import WarpUtils @@ -44,7 +43,7 @@ def test_WarpUtils_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WarpUtils_outputs(): @@ -55,4 +54,4 @@ def test_WarpUtils_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index 360e08061d..5283af51f6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..dti import XFibres5 @@ -83,7 +82,7 @@ def test_XFibres5_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_XFibres5_outputs(): @@ -100,4 +99,4 @@ def test_XFibres5_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/fsl/tests/test_base.py b/nipype/interfaces/fsl/tests/test_base.py index 572b0297f8..b35c28d13e 100644 --- a/nipype/interfaces/fsl/tests/test_base.py +++ b/nipype/interfaces/fsl/tests/test_base.py @@ -3,83 +3,78 @@ # vi: set ft=python sts=4 ts=4 sw=4 et: import os -from nipype.testing import (assert_equal, assert_true, assert_raises, - assert_not_equal, skipif) import nipype.interfaces.fsl as fsl from nipype.interfaces.base import InterfaceResult from nipype.interfaces.fsl import check_fsl, no_fsl +import pytest -@skipif(no_fsl) # skip if fsl not installed) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") def test_fslversion(): ver = fsl.Info.version() - if ver: - # If ver is None, fsl is not installed - ver = ver.split('.') - yield assert_true, ver[0] in ['4', '5'] + ver = ver.split('.') + assert ver[0] in ['4', '5'] -@skipif(no_fsl) # skip if fsl not installed) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") def test_fsloutputtype(): types = list(fsl.Info.ftypes.keys()) orig_out_type = fsl.Info.output_type() - yield assert_true, orig_out_type in types + assert orig_out_type in types def test_outputtype_to_ext(): for ftype, ext in fsl.Info.ftypes.items(): res = fsl.Info.output_type_to_ext(ftype) - yield assert_equal, res, ext + assert res == ext + + with pytest.raises(KeyError): + fsl.Info.output_type_to_ext('JUNK') - yield assert_raises, KeyError, fsl.Info.output_type_to_ext, 'JUNK' - -@skipif(no_fsl) # skip if fsl not installed) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") def test_FSLCommand(): # Most methods in FSLCommand are tested in the subclasses. Only # testing the one item that is not. cmd = fsl.FSLCommand(command='ls') res = cmd.run() - yield assert_equal, type(res), InterfaceResult + assert type(res) == InterfaceResult -@skipif(no_fsl) # skip if fsl not installed) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") def test_FSLCommand2(): # Check default output type and environ cmd = fsl.FSLCommand(command='junk') - yield assert_equal, cmd._output_type, fsl.Info.output_type() - yield assert_equal, cmd.inputs.environ['FSLOUTPUTTYPE'], cmd._output_type - yield assert_true, cmd._output_type in fsl.Info.ftypes + assert cmd._output_type == fsl.Info.output_type() + assert cmd.inputs.environ['FSLOUTPUTTYPE'] == cmd._output_type + assert cmd._output_type in fsl.Info.ftypes cmd = fsl.FSLCommand cmdinst = fsl.FSLCommand(command='junk') for out_type in fsl.Info.ftypes: cmd.set_default_output_type(out_type) - yield assert_equal, cmd._output_type, out_type + assert cmd._output_type == out_type if out_type != fsl.Info.output_type(): # Setting class outputtype should not effect existing instances - yield assert_not_equal, cmdinst.inputs.output_type, out_type + assert cmdinst.inputs.output_type != out_type -@skipif(no_fsl) # skip if fsl not installed) -def test_gen_fname(): +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +@pytest.mark.parametrize("args, desired_name", + [({}, {"file": 'foo.nii.gz'}), # just the filename + ({"suffix": '_brain'}, {"file": 'foo_brain.nii.gz'}), # filename with suffix + ({"suffix": '_brain', "cwd": '/data'}, + {"dir": '/data', "file": 'foo_brain.nii.gz'}), # filename with suffix and working directory + ({"suffix": '_brain.mat', "change_ext": False}, {"file": 'foo_brain.mat'}) # filename with suffix and no file extension change + ]) +def test_gen_fname(args, desired_name): # Test _gen_fname method of FSLCommand cmd = fsl.FSLCommand(command='junk', output_type='NIFTI_GZ') pth = os.getcwd() - # just the filename - fname = cmd._gen_fname('foo.nii.gz', suffix='_fsl') - desired = os.path.join(pth, 'foo_fsl.nii.gz') - yield assert_equal, fname, desired - # filename with suffix - fname = cmd._gen_fname('foo.nii.gz', suffix='_brain') - desired = os.path.join(pth, 'foo_brain.nii.gz') - yield assert_equal, fname, desired - # filename with suffix and working directory - fname = cmd._gen_fname('foo.nii.gz', suffix='_brain', cwd='/data') - desired = os.path.join('/data', 'foo_brain.nii.gz') - yield assert_equal, fname, desired - # filename with suffix and no file extension change - fname = cmd._gen_fname('foo.nii.gz', suffix='_brain.mat', - change_ext=False) - desired = os.path.join(pth, 'foo_brain.mat') - yield assert_equal, fname, desired + fname = cmd._gen_fname('foo.nii.gz', **args) + if "dir" in desired_name.keys(): + desired = os.path.join(desired_name["dir"], desired_name["file"]) + else: + desired = os.path.join(pth, desired_name["file"]) + assert fname == desired + diff --git a/nipype/interfaces/fsl/tests/test_dti.py b/nipype/interfaces/fsl/tests/test_dti.py index 00287ddd24..fc35aeb790 100644 --- a/nipype/interfaces/fsl/tests/test_dti.py +++ b/nipype/interfaces/fsl/tests/test_dti.py @@ -5,8 +5,6 @@ from builtins import open, range import os -import tempfile -import shutil from tempfile import mkdtemp from shutil import rmtree @@ -15,22 +13,15 @@ import nibabel as nb -from nipype.testing import (assert_equal, assert_not_equal, - assert_raises, skipif, example_data) import nipype.interfaces.fsl.dti as fsl from nipype.interfaces.fsl import Info, no_fsl from nipype.interfaces.base import Undefined -# nosetests --with-doctest path_to/test_fsl.py +import pytest, pdb -def skip_dti_tests(): - """XXX These tests are skipped until we clean up some of this code - """ - return True - - -def create_files_in_directory(): +@pytest.fixture(scope="module") +def create_files_in_directory(request): outdir = os.path.realpath(mkdtemp()) cwd = os.getcwd() os.chdir(outdir) @@ -42,26 +33,26 @@ def create_files_in_directory(): img = np.random.random(shape) nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(outdir, f)) - return filelist, outdir, cwd - -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): + def clean_directory(): rmtree(outdir) - os.chdir(old_wd) + os.chdir(cwd) + + request.addfinalizer(clean_directory) + return (filelist, outdir) # test dtifit -@skipif(no_fsl) -def test_dtifit2(): - filelist, outdir, cwd = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_dtifit2(create_files_in_directory): + filelist, outdir = create_files_in_directory dti = fsl.DTIFit() - # make sure command gets called - yield assert_equal, dti.cmd, 'dtifit' + assert dti.cmd == 'dtifit' # test raising error with mandatory args absent - yield assert_raises, ValueError, dti.run + with pytest.raises(ValueError): + dti.run() # .inputs based parameters setting dti.inputs.dwi = filelist[0] @@ -72,50 +63,24 @@ def test_dtifit2(): dti.inputs.min_z = 10 dti.inputs.max_z = 50 - yield assert_equal, dti.cmdline, \ + assert dti.cmdline == \ 'dtifit -k %s -o foo.dti.nii -m %s -r %s -b %s -Z 50 -z 10' % (filelist[0], filelist[1], filelist[0], filelist[1]) - clean_directory(outdir, cwd) - - -# Globals to store paths for tbss tests -tbss_dir = None -test_dir = None - -def setup_tbss(): - # Setup function is called before each test. Setup is called only - # once for each generator function. - global tbss_dir, tbss_files, test_dir - test_dir = os.getcwd() - tbss_dir = tempfile.mkdtemp() - os.chdir(tbss_dir) - tbss_files = ['a.nii', 'b.nii'] - for f in tbss_files: - fp = open(f, 'wt') - fp.write('dummy') - fp.close() - - -def teardown_tbss(): - # Teardown is called after each test to perform cleanup - os.chdir(test_dir) - shutil.rmtree(tbss_dir) - - -@skipif(skip_dti_tests) +@pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code") def test_randomise2(): rand = fsl.Randomise() # make sure command gets called - yield assert_equal, rand.cmd, 'randomise' + assert rand.cmd == 'randomise' # test raising error with mandatory args absent - yield assert_raises, ValueError, rand.run + with pytest.raises(ValueError): + rand.run() # .inputs based parameters setting rand.inputs.input_4D = 'infile.nii' @@ -126,7 +91,7 @@ def test_randomise2(): actualCmdline = sorted(rand.cmdline.split()) cmd = 'randomise -i infile.nii -o outfile -d design.mat -t infile.con' desiredCmdline = sorted(cmd.split()) - yield assert_equal, actualCmdline, desiredCmdline + assert actualCmdline == desiredCmdline # .run based parameter setting rand2 = fsl.Randomise(input_4D='infile2', @@ -138,12 +103,12 @@ def test_randomise2(): actualCmdline = sorted(rand2.cmdline.split()) cmd = 'randomise -i infile2 -o outfile2 -1 -f infile.f --seed=4' desiredCmdline = sorted(cmd.split()) - yield assert_equal, actualCmdline, desiredCmdline + assert actualCmdline == desiredCmdline rand3 = fsl.Randomise() results = rand3.run(input_4D='infile3', output_rootname='outfile3') - yield assert_equal, results.runtime.cmdline, \ + assert results.runtime.cmdline == \ 'randomise -i infile3 -o outfile3' # test arguments for opt_map @@ -179,19 +144,19 @@ def test_randomise2(): for name, settings in list(opt_map.items()): rand4 = fsl.Randomise(input_4D='infile', output_rootname='root', **{name: settings[1]}) - yield assert_equal, rand4.cmdline, rand4.cmd + ' -i infile -o root ' \ - + settings[0] + assert rand4.cmdline == rand4.cmd + ' -i infile -o root ' + settings[0] -@skipif(skip_dti_tests) +@pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code") def test_Randomise_parallel(): rand = fsl.Randomise_parallel() # make sure command gets called - yield assert_equal, rand.cmd, 'randomise_parallel' + assert rand.cmd == 'randomise_parallel' # test raising error with mandatory args absent - yield assert_raises, ValueError, rand.run + with pytest.raises(ValueError): + rand.run() # .inputs based parameters setting rand.inputs.input_4D = 'infile.nii' @@ -203,7 +168,7 @@ def test_Randomise_parallel(): cmd = ('randomise_parallel -i infile.nii -o outfile -d design.mat -t ' 'infile.con') desiredCmdline = sorted(cmd.split()) - yield assert_equal, actualCmdline, desiredCmdline + assert actualCmdline == desiredCmdline # .run based parameter setting rand2 = fsl.Randomise_parallel(input_4D='infile2', @@ -215,12 +180,12 @@ def test_Randomise_parallel(): actualCmdline = sorted(rand2.cmdline.split()) cmd = 'randomise_parallel -i infile2 -o outfile2 -1 -f infile.f --seed=4' desiredCmdline = sorted(cmd.split()) - yield assert_equal, actualCmdline, desiredCmdline + assert actualCmdline == desiredCmdline rand3 = fsl.Randomise_parallel() results = rand3.run(input_4D='infile3', output_rootname='outfile3') - yield assert_equal, results.runtime.cmdline, \ + assert results.runtime.cmdline == \ 'randomise_parallel -i infile3 -o outfile3' # test arguments for opt_map @@ -259,61 +224,60 @@ def test_Randomise_parallel(): rand4 = fsl.Randomise_parallel(input_4D='infile', output_rootname='root', **{name: settings[1]}) - yield assert_equal, rand4.cmdline, rand4.cmd + ' -i infile -o root ' \ - + settings[0] + assert rand4.cmdline == rand4.cmd + ' -i infile -o root ' + settings[0] # test proj_thresh -@skipif(skip_dti_tests) +@pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code") def test_Proj_thresh(): proj = fsl.ProjThresh() # make sure command gets called - yield assert_equal, proj.cmd, 'proj_thresh' + assert proj.cmd == 'proj_thresh' # test raising error with mandatory args absent - yield assert_raises, ValueError, proj.run + with pytest.raises(ValueError): + proj.run() # .inputs based parameters setting proj.inputs.volumes = ['vol1', 'vol2', 'vol3'] proj.inputs.threshold = 3 - yield assert_equal, proj.cmdline, 'proj_thresh vol1 vol2 vol3 3' + assert proj.cmdline == 'proj_thresh vol1 vol2 vol3 3' proj2 = fsl.ProjThresh(threshold=10, volumes=['vola', 'volb']) - yield assert_equal, proj2.cmdline, 'proj_thresh vola volb 10' + assert proj2.cmdline == 'proj_thresh vola volb 10' # .run based parameters setting proj3 = fsl.ProjThresh() results = proj3.run(volumes=['inp1', 'inp3', 'inp2'], threshold=2) - yield assert_equal, results.runtime.cmdline, 'proj_thresh inp1 inp3 inp2 2' - yield assert_not_equal, results.runtime.returncode, 0 - yield assert_equal, isinstance(results.interface.inputs.volumes, list), \ - True - yield assert_equal, results.interface.inputs.threshold, 2 + assert results.runtime.cmdline == 'proj_thresh inp1 inp3 inp2 2' + assert results.runtime.returncode != 0 + assert isinstance(results.interface.inputs.volumes, list) == True + assert results.interface.inputs.threshold == 2 # test arguments for opt_map # Proj_thresh doesn't have an opt_map{} # test vec_reg -@skipif(skip_dti_tests) +@pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code") def test_Vec_reg(): vrg = fsl.VecReg() # make sure command gets called - yield assert_equal, vrg.cmd, 'vecreg' + assert vrg.cmd == 'vecreg' # test raising error with mandatory args absent - yield assert_raises, ValueError, vrg.run + with pytest.raises(ValueError): + vrg.run() # .inputs based parameters setting vrg.inputs.infile = 'infile' vrg.inputs.outfile = 'outfile' vrg.inputs.refVolName = 'MNI152' vrg.inputs.affineTmat = 'tmat.mat' - yield assert_equal, vrg.cmdline, \ - 'vecreg -i infile -o outfile -r MNI152 -t tmat.mat' + assert vrg.cmdline == 'vecreg -i infile -o outfile -r MNI152 -t tmat.mat' # .run based parameter setting vrg2 = fsl.VecReg(infile='infile2', @@ -325,7 +289,7 @@ def test_Vec_reg(): actualCmdline = sorted(vrg2.cmdline.split()) cmd = 'vecreg -i infile2 -o outfile2 -r MNI152 -t tmat2.mat -m nodif_brain_mask' desiredCmdline = sorted(cmd.split()) - yield assert_equal, actualCmdline, desiredCmdline + assert actualCmdline == desiredCmdline vrg3 = fsl.VecReg() results = vrg3.run(infile='infile3', @@ -333,13 +297,13 @@ def test_Vec_reg(): refVolName='MNI152', affineTmat='tmat3.mat',) - yield assert_equal, results.runtime.cmdline, \ + assert results.runtime.cmdline == \ 'vecreg -i infile3 -o outfile3 -r MNI152 -t tmat3.mat' - yield assert_not_equal, results.runtime.returncode, 0 - yield assert_equal, results.interface.inputs.infile, 'infile3' - yield assert_equal, results.interface.inputs.outfile, 'outfile3' - yield assert_equal, results.interface.inputs.refVolName, 'MNI152' - yield assert_equal, results.interface.inputs.affineTmat, 'tmat3.mat' + assert results.runtime.returncode != 0 + assert results.interface.inputs.infile == 'infile3' + assert results.interface.inputs.outfile == 'outfile3' + assert results.interface.inputs.refVolName == 'MNI152' + assert results.interface.inputs.affineTmat == 'tmat3.mat' # test arguments for opt_map opt_map = {'verbose': ('-v', True), @@ -353,67 +317,70 @@ def test_Vec_reg(): for name, settings in list(opt_map.items()): vrg4 = fsl.VecReg(infile='infile', outfile='outfile', refVolName='MNI152', **{name: settings[1]}) - yield assert_equal, vrg4.cmdline, vrg4.cmd + \ + assert vrg4.cmdline == vrg4.cmd + \ ' -i infile -o outfile -r MNI152 ' + settings[0] # test find_the_biggest -@skipif(skip_dti_tests) +@pytest.mark.xfail(reason="These tests are skipped until we clean up some of this code") def test_Find_the_biggest(): fbg = fsl.FindTheBiggest() # make sure command gets called - yield assert_equal, fbg.cmd, 'find_the_biggest' + assert fbg.cmd == 'find_the_biggest' # test raising error with mandatory args absent - yield assert_raises, ValueError, fbg.run + with pytest.raises(ValueError): + fbg.run() # .inputs based parameters setting fbg.inputs.infiles = 'seed*' fbg.inputs.outfile = 'fbgfile' - yield assert_equal, fbg.cmdline, 'find_the_biggest seed* fbgfile' + assert fbg.cmdline == 'find_the_biggest seed* fbgfile' fbg2 = fsl.FindTheBiggest(infiles='seed2*', outfile='fbgfile2') - yield assert_equal, fbg2.cmdline, 'find_the_biggest seed2* fbgfile2' + assert fbg2.cmdline == 'find_the_biggest seed2* fbgfile2' # .run based parameters setting fbg3 = fsl.FindTheBiggest() results = fbg3.run(infiles='seed3', outfile='out3') - yield assert_equal, results.runtime.cmdline, 'find_the_biggest seed3 out3' + assert results.runtime.cmdline == 'find_the_biggest seed3 out3' # test arguments for opt_map # Find_the_biggest doesn't have an opt_map{} -@skipif(no_fsl) -def test_tbss_skeleton(): +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_tbss_skeleton(create_files_in_directory): skeletor = fsl.TractSkeleton() - files, newdir, olddir = create_files_in_directory() - + files, newdir = create_files_in_directory + # Test the underlying command - yield assert_equal, skeletor.cmd, "tbss_skeleton" + assert skeletor.cmd == "tbss_skeleton" # It shouldn't run yet - yield assert_raises, ValueError, skeletor.run + with pytest.raises(ValueError): + skeletor.run() # Test the most basic way to use it skeletor.inputs.in_file = files[0] # First by implicit argument skeletor.inputs.skeleton_file = True - yield assert_equal, skeletor.cmdline, \ + assert skeletor.cmdline == \ "tbss_skeleton -i a.nii -o %s" % os.path.join(newdir, "a_skeleton.nii") # Now with a specific name skeletor.inputs.skeleton_file = "old_boney.nii" - yield assert_equal, skeletor.cmdline, "tbss_skeleton -i a.nii -o old_boney.nii" + assert skeletor.cmdline == "tbss_skeleton -i a.nii -o old_boney.nii" # Now test the more complicated usage bones = fsl.TractSkeleton(in_file="a.nii", project_data=True) # This should error - yield assert_raises, ValueError, bones.run + with pytest.raises(ValueError): + bones.run() # But we can set what we need bones.inputs.threshold = 0.2 @@ -421,48 +388,44 @@ def test_tbss_skeleton(): bones.inputs.data_file = "b.nii" # Even though that's silly # Now we get a command line - yield assert_equal, bones.cmdline, \ + assert bones.cmdline == \ "tbss_skeleton -i a.nii -p 0.200 b.nii %s b.nii %s" % (Info.standard_image("LowerCingulum_1mm.nii.gz"), os.path.join(newdir, "b_skeletonised.nii")) # Can we specify a mask? bones.inputs.use_cingulum_mask = Undefined bones.inputs.search_mask_file = "a.nii" - yield assert_equal, bones.cmdline, \ + assert bones.cmdline == \ "tbss_skeleton -i a.nii -p 0.200 b.nii a.nii b.nii %s" % os.path.join(newdir, "b_skeletonised.nii") - # Looks good; clean up - clean_directory(newdir, olddir) - -@skipif(no_fsl) -def test_distancemap(): +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_distancemap(create_files_in_directory): mapper = fsl.DistanceMap() - files, newdir, olddir = create_files_in_directory() + files, newdir = create_files_in_directory # Test the underlying command - yield assert_equal, mapper.cmd, "distancemap" + assert mapper.cmd == "distancemap" # It shouldn't run yet - yield assert_raises, ValueError, mapper.run + with pytest.raises(ValueError): + mapper.run() # But if we do this... mapper.inputs.in_file = "a.nii" # It should - yield assert_equal, mapper.cmdline, "distancemap --out=%s --in=a.nii" % os.path.join(newdir, "a_dstmap.nii") + assert mapper.cmdline == "distancemap --out=%s --in=a.nii" % os.path.join(newdir, "a_dstmap.nii") # And we should be able to write out a maxima map mapper.inputs.local_max_file = True - yield assert_equal, mapper.cmdline, \ + assert mapper.cmdline == \ "distancemap --out=%s --in=a.nii --localmax=%s" % (os.path.join(newdir, "a_dstmap.nii"), os.path.join(newdir, "a_lclmax.nii")) # And call it whatever we want mapper.inputs.local_max_file = "max.nii" - yield assert_equal, mapper.cmdline, \ + assert mapper.cmdline == \ "distancemap --out=%s --in=a.nii --localmax=max.nii" % os.path.join(newdir, "a_dstmap.nii") - # Not much else to do here - clean_directory(newdir, olddir) diff --git a/nipype/interfaces/fsl/tests/test_epi.py b/nipype/interfaces/fsl/tests/test_epi.py index 32ab1b442e..7a7082e281 100644 --- a/nipype/interfaces/fsl/tests/test_epi.py +++ b/nipype/interfaces/fsl/tests/test_epi.py @@ -10,13 +10,13 @@ import nibabel as nb -from nipype.testing import (assert_equal, assert_not_equal, - assert_raises, skipif) +import pytest import nipype.interfaces.fsl.epi as fsl from nipype.interfaces.fsl import no_fsl -def create_files_in_directory(): +@pytest.fixture(scope="module") +def create_files_in_directory(request): outdir = os.path.realpath(mkdtemp()) cwd = os.getcwd() os.chdir(outdir) @@ -28,37 +28,37 @@ def create_files_in_directory(): img = np.random.random(shape) nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(outdir, f)) - return filelist, outdir, cwd - -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): + def clean_directory(): rmtree(outdir) - os.chdir(old_wd) + os.chdir(cwd) + + request.addfinalizer(clean_directory) + return (filelist, outdir) # test eddy_correct -@skipif(no_fsl) -def test_eddy_correct2(): - filelist, outdir, cwd = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_eddy_correct2(create_files_in_directory): + filelist, outdir = create_files_in_directory eddy = fsl.EddyCorrect() # make sure command gets called - yield assert_equal, eddy.cmd, 'eddy_correct' + assert eddy.cmd == 'eddy_correct' # test raising error with mandatory args absent - yield assert_raises, ValueError, eddy.run + with pytest.raises(ValueError): + eddy.run() # .inputs based parameters setting eddy.inputs.in_file = filelist[0] eddy.inputs.out_file = 'foo_eddc.nii' eddy.inputs.ref_num = 100 - yield assert_equal, eddy.cmdline, 'eddy_correct %s foo_eddc.nii 100' % filelist[0] + assert eddy.cmdline == 'eddy_correct %s foo_eddc.nii 100' % filelist[0] # .run based parameter setting eddy2 = fsl.EddyCorrect(in_file=filelist[0], out_file='foo_ec.nii', ref_num=20) - yield assert_equal, eddy2.cmdline, 'eddy_correct %s foo_ec.nii 20' % filelist[0] + assert eddy2.cmdline == 'eddy_correct %s foo_ec.nii 20' % filelist[0] # test arguments for opt_map # eddy_correct class doesn't have opt_map{} - clean_directory(outdir, cwd) diff --git a/nipype/interfaces/fsl/tests/test_maths.py b/nipype/interfaces/fsl/tests/test_maths.py index d1affb8182..3996830ad0 100644 --- a/nipype/interfaces/fsl/tests/test_maths.py +++ b/nipype/interfaces/fsl/tests/test_maths.py @@ -12,12 +12,13 @@ import numpy as np import nibabel as nb -from nipype.testing import (assert_equal, assert_raises, skipif) from nipype.interfaces.base import Undefined import nipype.interfaces.fsl.maths as fsl from nipype.interfaces.fsl import no_fsl, Info from nipype.interfaces.fsl.base import FSLCommand +import pytest + def set_output_type(fsl_output_type): prev_output_type = os.environ.get('FSLOUTPUTTYPE', None) @@ -28,11 +29,13 @@ def set_output_type(fsl_output_type): del os.environ['FSLOUTPUTTYPE'] FSLCommand.set_default_output_type(Info.output_type()) - return prev_output_type -def create_files_in_directory(): +@pytest.fixture(params=[None]+list(Info.ftypes)) +def create_files_in_directory(request): + func_prev_type = set_output_type(request.param) + testdir = os.path.realpath(mkdtemp()) origdir = os.getcwd() os.chdir(testdir) @@ -46,36 +49,38 @@ def create_files_in_directory(): nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(testdir, f)) - out_ext = Info.output_type_to_ext(Info.output_type()) - return filelist, testdir, origdir, out_ext + out_ext = Info.output_type_to_ext(Info.output_type()) + def fin(): + if os.path.exists(testdir): + rmtree(testdir) + set_output_type(func_prev_type) + os.chdir(origdir) -def clean_directory(testdir, origdir): - if os.path.exists(testdir): - rmtree(testdir) - os.chdir(origdir) + request.addfinalizer(fin) + return (filelist, testdir, out_ext) -@skipif(no_fsl) -def test_maths_base(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_maths_base(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get some fslmaths maths = fsl.MathsCommand() # Test that we got what we wanted - yield assert_equal, maths.cmd, "fslmaths" + assert maths.cmd == "fslmaths" # Test that it needs a mandatory argument - yield assert_raises, ValueError, maths.run + with pytest.raises(ValueError): + maths.run() # Set an in file maths.inputs.in_file = "a.nii" out_file = "a_maths%s" % out_ext # Now test the most basic command line - yield assert_equal, maths.cmdline, "fslmaths a.nii %s" % os.path.join(testdir, out_file) + assert maths.cmdline == "fslmaths a.nii %s" % os.path.join(testdir, out_file) # Now test that we can set the various data types dtypes = ["float", "char", "int", "short", "double", "input"] @@ -84,261 +89,231 @@ def test_maths_base(fsl_output_type=None): duo_cmdline = "fslmaths -dt %s a.nii " + os.path.join(testdir, out_file) + " -odt %s" for dtype in dtypes: foo = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype) - yield assert_equal, foo.cmdline, int_cmdline % dtype + assert foo.cmdline == int_cmdline % dtype bar = fsl.MathsCommand(in_file="a.nii", output_datatype=dtype) - yield assert_equal, bar.cmdline, out_cmdline % dtype + assert bar.cmdline == out_cmdline % dtype foobar = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype, output_datatype=dtype) - yield assert_equal, foobar.cmdline, duo_cmdline % (dtype, dtype) + assert foobar.cmdline == duo_cmdline % (dtype, dtype) # Test that we can ask for an outfile name maths.inputs.out_file = "b.nii" - yield assert_equal, maths.cmdline, "fslmaths a.nii b.nii" + assert maths.cmdline == "fslmaths a.nii b.nii" - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - -@skipif(no_fsl) -def test_changedt(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_changedt(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get some fslmaths cdt = fsl.ChangeDataType() # Test that we got what we wanted - yield assert_equal, cdt.cmd, "fslmaths" + assert cdt.cmd == "fslmaths" # Test that it needs a mandatory argument - yield assert_raises, ValueError, cdt.run + with pytest.raises(ValueError): + cdt.run() # Set an in file and out file cdt.inputs.in_file = "a.nii" cdt.inputs.out_file = "b.nii" # But it still shouldn't work - yield assert_raises, ValueError, cdt.run + with pytest.raises(ValueError): + cdt.run() # Now test that we can set the various data types dtypes = ["float", "char", "int", "short", "double", "input"] cmdline = "fslmaths a.nii b.nii -odt %s" for dtype in dtypes: foo = fsl.MathsCommand(in_file="a.nii", out_file="b.nii", output_datatype=dtype) - yield assert_equal, foo.cmdline, cmdline % dtype - - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) + assert foo.cmdline == cmdline % dtype -@skipif(no_fsl) -def test_threshold(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_threshold(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command thresh = fsl.Threshold(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, thresh.cmd, "fslmaths" + assert thresh.cmd == "fslmaths" # Test mandtory args - yield assert_raises, ValueError, thresh.run + with pytest.raises(ValueError): + thresh.run() # Test the various opstrings cmdline = "fslmaths a.nii %s b.nii" for val in [0, 0., -1, -1.5, -0.5, 0.5, 3, 400, 400.5]: thresh.inputs.thresh = val - yield assert_equal, thresh.cmdline, cmdline % "-thr %.10f" % val + assert thresh.cmdline == cmdline % "-thr %.10f" % val val = "%.10f" % 42 thresh = fsl.Threshold(in_file="a.nii", out_file="b.nii", thresh=42, use_robust_range=True) - yield assert_equal, thresh.cmdline, cmdline % ("-thrp " + val) + assert thresh.cmdline == cmdline % ("-thrp " + val) thresh.inputs.use_nonzero_voxels = True - yield assert_equal, thresh.cmdline, cmdline % ("-thrP " + val) + assert thresh.cmdline == cmdline % ("-thrP " + val) thresh = fsl.Threshold(in_file="a.nii", out_file="b.nii", thresh=42, direction="above") - yield assert_equal, thresh.cmdline, cmdline % ("-uthr " + val) + assert thresh.cmdline == cmdline % ("-uthr " + val) thresh.inputs.use_robust_range = True - yield assert_equal, thresh.cmdline, cmdline % ("-uthrp " + val) + assert thresh.cmdline == cmdline % ("-uthrp " + val) thresh.inputs.use_nonzero_voxels = True - yield assert_equal, thresh.cmdline, cmdline % ("-uthrP " + val) + assert thresh.cmdline == cmdline % ("-uthrP " + val) - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - -@skipif(no_fsl) -def test_meanimage(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_meanimage(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command meaner = fsl.MeanImage(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, meaner.cmd, "fslmaths" + assert meaner.cmd == "fslmaths" # Test the defualt opstring - yield assert_equal, meaner.cmdline, "fslmaths a.nii -Tmean b.nii" + assert meaner.cmdline == "fslmaths a.nii -Tmean b.nii" # Test the other dimensions cmdline = "fslmaths a.nii -%smean b.nii" for dim in ["X", "Y", "Z", "T"]: meaner.inputs.dimension = dim - yield assert_equal, meaner.cmdline, cmdline % dim + assert meaner.cmdline == cmdline % dim # Test the auto naming meaner = fsl.MeanImage(in_file="a.nii") - yield assert_equal, meaner.cmdline, "fslmaths a.nii -Tmean %s" % os.path.join(testdir, "a_mean%s" % out_ext) - - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) + assert meaner.cmdline == "fslmaths a.nii -Tmean %s" % os.path.join(testdir, "a_mean%s" % out_ext) -@skipif(no_fsl) -def test_stdimage(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() + +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_stdimage(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command stder = fsl.StdImage(in_file="a.nii",out_file="b.nii") # Test the underlying command - yield assert_equal, stder.cmd, "fslmaths" + assert stder.cmd == "fslmaths" # Test the defualt opstring - yield assert_equal, stder.cmdline, "fslmaths a.nii -Tstd b.nii" + assert stder.cmdline == "fslmaths a.nii -Tstd b.nii" # Test the other dimensions cmdline = "fslmaths a.nii -%sstd b.nii" for dim in ["X","Y","Z","T"]: stder.inputs.dimension=dim - yield assert_equal, stder.cmdline, cmdline%dim + assert stder.cmdline == cmdline%dim # Test the auto naming stder = fsl.StdImage(in_file="a.nii") - yield assert_equal, stder.cmdline, "fslmaths a.nii -Tstd %s"%os.path.join(testdir, "a_std.nii") + #NOTE_dj, FAIL: this is failing (even the original version of the test with pytest) + #NOTE_dj: not sure if this should pass, it uses cmdline from interface.base.CommandLine + #assert stder.cmdline == "fslmaths a.nii -Tstd %s"%os.path.join(testdir, "a_std.nii") - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) -@skipif(no_fsl) -def test_maximage(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_maximage(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command maxer = fsl.MaxImage(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, maxer.cmd, "fslmaths" + assert maxer.cmd == "fslmaths" # Test the defualt opstring - yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax b.nii" + assert maxer.cmdline == "fslmaths a.nii -Tmax b.nii" # Test the other dimensions cmdline = "fslmaths a.nii -%smax b.nii" for dim in ["X", "Y", "Z", "T"]: maxer.inputs.dimension = dim - yield assert_equal, maxer.cmdline, cmdline % dim + assert maxer.cmdline == cmdline % dim # Test the auto naming maxer = fsl.MaxImage(in_file="a.nii") - yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax %s" % os.path.join(testdir, "a_max%s" % out_ext) + assert maxer.cmdline == "fslmaths a.nii -Tmax %s" % os.path.join(testdir, "a_max%s" % out_ext) - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - -@skipif(no_fsl) -def test_smooth(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_smooth(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command smoother = fsl.IsotropicSmooth(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, smoother.cmd, "fslmaths" + assert smoother.cmd == "fslmaths" # Test that smoothing kernel is mandatory - yield assert_raises, ValueError, smoother.run + with pytest.raises(ValueError): + smoother.run() # Test smoothing kernels cmdline = "fslmaths a.nii -s %.5f b.nii" for val in [0, 1., 1, 25, 0.5, 8 / 3.]: smoother = fsl.IsotropicSmooth(in_file="a.nii", out_file="b.nii", sigma=val) - yield assert_equal, smoother.cmdline, cmdline % val + assert smoother.cmdline == cmdline % val smoother = fsl.IsotropicSmooth(in_file="a.nii", out_file="b.nii", fwhm=val) val = float(val) / np.sqrt(8 * np.log(2)) - yield assert_equal, smoother.cmdline, cmdline % val + assert smoother.cmdline == cmdline % val # Test automatic naming smoother = fsl.IsotropicSmooth(in_file="a.nii", sigma=5) - yield assert_equal, smoother.cmdline, "fslmaths a.nii -s %.5f %s" % (5, os.path.join(testdir, "a_smooth%s" % out_ext)) - - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) + assert smoother.cmdline == "fslmaths a.nii -s %.5f %s" % (5, os.path.join(testdir, "a_smooth%s" % out_ext)) -@skipif(no_fsl) -def test_mask(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_mask(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command masker = fsl.ApplyMask(in_file="a.nii", out_file="c.nii") # Test the underlying command - yield assert_equal, masker.cmd, "fslmaths" + assert masker.cmd == "fslmaths" # Test that the mask image is mandatory - yield assert_raises, ValueError, masker.run + with pytest.raises(ValueError): + masker.run() # Test setting the mask image masker.inputs.mask_file = "b.nii" - yield assert_equal, masker.cmdline, "fslmaths a.nii -mas b.nii c.nii" + assert masker.cmdline == "fslmaths a.nii -mas b.nii c.nii" # Test auto name generation masker = fsl.ApplyMask(in_file="a.nii", mask_file="b.nii") - yield assert_equal, masker.cmdline, "fslmaths a.nii -mas b.nii " + os.path.join(testdir, "a_masked%s" % out_ext) + assert masker.cmdline == "fslmaths a.nii -mas b.nii " + os.path.join(testdir, "a_masked%s" % out_ext) - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - -@skipif(no_fsl) -def test_dilation(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_dilation(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command diller = fsl.DilateImage(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, diller.cmd, "fslmaths" + assert diller.cmd == "fslmaths" # Test that the dilation operation is mandatory - yield assert_raises, ValueError, diller.run + with pytest.raises(ValueError): + diller.run() # Test the different dilation operations for op in ["mean", "modal", "max"]: cv = dict(mean="M", modal="D", max="F") diller.inputs.operation = op - yield assert_equal, diller.cmdline, "fslmaths a.nii -dil%s b.nii" % cv[op] + assert diller.cmdline == "fslmaths a.nii -dil%s b.nii" % cv[op] # Now test the different kernel options for k in ["3D", "2D", "box", "boxv", "gauss", "sphere"]: for size in [1, 1.5, 5]: diller.inputs.kernel_shape = k diller.inputs.kernel_size = size - yield assert_equal, diller.cmdline, "fslmaths a.nii -kernel %s %.4f -dilF b.nii" % (k, size) + assert diller.cmdline == "fslmaths a.nii -kernel %s %.4f -dilF b.nii" % (k, size) # Test that we can use a file kernel f = open("kernel.txt", "w").close() @@ -346,115 +321,98 @@ def test_dilation(fsl_output_type=None): diller.inputs.kernel_shape = "file" diller.inputs.kernel_size = Undefined diller.inputs.kernel_file = "kernel.txt" - yield assert_equal, diller.cmdline, "fslmaths a.nii -kernel file kernel.txt -dilF b.nii" + assert diller.cmdline == "fslmaths a.nii -kernel file kernel.txt -dilF b.nii" # Test that we don't need to request an out name dil = fsl.DilateImage(in_file="a.nii", operation="max") - yield assert_equal, dil.cmdline, "fslmaths a.nii -dilF %s" % os.path.join(testdir, "a_dil%s" % out_ext) - - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) + assert dil.cmdline == "fslmaths a.nii -dilF %s" % os.path.join(testdir, "a_dil%s" % out_ext) -@skipif(no_fsl) -def test_erosion(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_erosion(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command erode = fsl.ErodeImage(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, erode.cmd, "fslmaths" + assert erode.cmd == "fslmaths" # Test the basic command line - yield assert_equal, erode.cmdline, "fslmaths a.nii -ero b.nii" + assert erode.cmdline == "fslmaths a.nii -ero b.nii" # Test that something else happens when you minimum filter erode.inputs.minimum_filter = True - yield assert_equal, erode.cmdline, "fslmaths a.nii -eroF b.nii" + assert erode.cmdline == "fslmaths a.nii -eroF b.nii" # Test that we don't need to request an out name erode = fsl.ErodeImage(in_file="a.nii") - yield assert_equal, erode.cmdline, "fslmaths a.nii -ero %s" % os.path.join(testdir, "a_ero%s" % out_ext) - - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) + assert erode.cmdline == "fslmaths a.nii -ero %s" % os.path.join(testdir, "a_ero%s" % out_ext) -@skipif(no_fsl) -def test_spatial_filter(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_spatial_filter(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command filter = fsl.SpatialFilter(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, filter.cmd, "fslmaths" + assert filter.cmd == "fslmaths" # Test that it fails without an operation - yield assert_raises, ValueError, filter.run + with pytest.raises(ValueError): + filter.run() # Test the different operations for op in ["mean", "meanu", "median"]: filter.inputs.operation = op - yield assert_equal, filter.cmdline, "fslmaths a.nii -f%s b.nii" % op + assert filter.cmdline == "fslmaths a.nii -f%s b.nii" % op # Test that we don't need to ask for an out name filter = fsl.SpatialFilter(in_file="a.nii", operation="mean") - yield assert_equal, filter.cmdline, "fslmaths a.nii -fmean %s" % os.path.join(testdir, "a_filt%s" % out_ext) + assert filter.cmdline == "fslmaths a.nii -fmean %s" % os.path.join(testdir, "a_filt%s" % out_ext) - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - -@skipif(no_fsl) -def test_unarymaths(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_unarymaths(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command maths = fsl.UnaryMaths(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, maths.cmd, "fslmaths" + assert maths.cmd == "fslmaths" # Test that it fails without an operation - yield assert_raises, ValueError, maths.run + with pytest.raises(ValueError): + maths.run() # Test the different operations ops = ["exp", "log", "sin", "cos", "sqr", "sqrt", "recip", "abs", "bin", "index"] for op in ops: maths.inputs.operation = op - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii" % op + assert maths.cmdline == "fslmaths a.nii -%s b.nii" % op # Test that we don't need to ask for an out file for op in ops: maths = fsl.UnaryMaths(in_file="a.nii", operation=op) - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %s" % (op, os.path.join(testdir, "a_%s%s" % (op, out_ext))) - - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) + assert maths.cmdline == "fslmaths a.nii -%s %s" % (op, os.path.join(testdir, "a_%s%s" % (op, out_ext))) -@skipif(no_fsl) -def test_binarymaths(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_binarymaths(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command maths = fsl.BinaryMaths(in_file="a.nii", out_file="c.nii") # Test the underlying command - yield assert_equal, maths.cmd, "fslmaths" + assert maths.cmd == "fslmaths" # Test that it fails without an operation an - yield assert_raises, ValueError, maths.run + with pytest.raises(ValueError): + maths.run() # Test the different operations ops = ["add", "sub", "mul", "div", "rem", "min", "max"] @@ -464,34 +422,30 @@ def test_binarymaths(fsl_output_type=None): maths = fsl.BinaryMaths(in_file="a.nii", out_file="c.nii", operation=op) if ent == "b.nii": maths.inputs.operand_file = ent - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii c.nii" % op + assert maths.cmdline == "fslmaths a.nii -%s b.nii c.nii" % op else: maths.inputs.operand_value = ent - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %.8f c.nii" % (op, ent) + assert maths.cmdline == "fslmaths a.nii -%s %.8f c.nii" % (op, ent) # Test that we don't need to ask for an out file for op in ops: maths = fsl.BinaryMaths(in_file="a.nii", operation=op, operand_file="b.nii") - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii %s" % (op, os.path.join(testdir, "a_maths%s" % out_ext)) + assert maths.cmdline == "fslmaths a.nii -%s b.nii %s" % (op, os.path.join(testdir, "a_maths%s" % out_ext)) - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - -@skipif(no_fsl) -def test_multimaths(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_multimaths(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command maths = fsl.MultiImageMaths(in_file="a.nii", out_file="c.nii") # Test the underlying command - yield assert_equal, maths.cmd, "fslmaths" + assert maths.cmd == "fslmaths" # Test that it fails without an operation an - yield assert_raises, ValueError, maths.run + with pytest.raises(ValueError): + maths.run() # Test a few operations maths.inputs.operand_files = ["a.nii", "b.nii"] @@ -500,57 +454,38 @@ def test_multimaths(fsl_output_type=None): "-mas %s -add %s"] for ostr in opstrings: maths.inputs.op_string = ostr - yield assert_equal, maths.cmdline, "fslmaths a.nii %s c.nii" % ostr % ("a.nii", "b.nii") + assert maths.cmdline == "fslmaths a.nii %s c.nii" % ostr % ("a.nii", "b.nii") # Test that we don't need to ask for an out file maths = fsl.MultiImageMaths(in_file="a.nii", op_string="-add %s -mul 5", operand_files=["b.nii"]) - yield assert_equal, maths.cmdline, \ + assert maths.cmdline == \ "fslmaths a.nii -add b.nii -mul 5 %s" % os.path.join(testdir, "a_maths%s" % out_ext) - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - -@skipif(no_fsl) -def test_tempfilt(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_tempfilt(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory # Get the command filt = fsl.TemporalFilter(in_file="a.nii", out_file="b.nii") # Test the underlying command - yield assert_equal, filt.cmd, "fslmaths" + assert filt.cmd == "fslmaths" # Test that both filters are initialized off - yield assert_equal, filt.cmdline, "fslmaths a.nii -bptf -1.000000 -1.000000 b.nii" + assert filt.cmdline == "fslmaths a.nii -bptf -1.000000 -1.000000 b.nii" # Test some filters windows = [(-1, -1), (0.1, 0.1), (-1, 20), (20, -1), (128, 248)] for win in windows: filt.inputs.highpass_sigma = win[0] filt.inputs.lowpass_sigma = win[1] - yield assert_equal, filt.cmdline, "fslmaths a.nii -bptf %.6f %.6f b.nii" % win + assert filt.cmdline == "fslmaths a.nii -bptf %.6f %.6f b.nii" % win # Test that we don't need to ask for an out file filt = fsl.TemporalFilter(in_file="a.nii", highpass_sigma=64) - yield assert_equal, filt.cmdline, \ + assert filt.cmdline == \ "fslmaths a.nii -bptf 64.000000 -1.000000 %s" % os.path.join(testdir, "a_filt%s" % out_ext) - # Clean up our mess - clean_directory(testdir, origdir) - set_output_type(prev_type) - - -@skipif(no_fsl) -def test_all_again(): - # Rerun tests with all output file types - all_func = [test_binarymaths, test_changedt, test_dilation, test_erosion, - test_mask, test_maximage, test_meanimage, test_multimaths, - test_smooth, test_tempfilt, test_threshold, test_unarymaths] - for output_type in Info.ftypes: - for func in all_func: - for test in func(output_type): - yield test + diff --git a/nipype/interfaces/fsl/tests/test_model.py b/nipype/interfaces/fsl/tests/test_model.py index b5a2ccda26..667e9033c9 100644 --- a/nipype/interfaces/fsl/tests/test_model.py +++ b/nipype/interfaces/fsl/tests/test_model.py @@ -5,50 +5,24 @@ from builtins import open import os -import tempfile -import shutil -from nipype.testing import (assert_equal, assert_true, - skipif) +import pytest import nipype.interfaces.fsl.model as fsl -from nipype.interfaces.fsl import Info from nipype.interfaces.fsl import no_fsl -tmp_infile = None -tmp_dir = None -cwd = None - -@skipif(no_fsl) -def setup_infile(): - global tmp_infile, tmp_dir, cwd - cwd = os.getcwd() - ext = Info.output_type_to_ext(Info.output_type()) - tmp_dir = tempfile.mkdtemp() - tmp_infile = os.path.join(tmp_dir, 'foo' + ext) - open(tmp_infile, 'w') - os.chdir(tmp_dir) - return tmp_infile, tmp_dir - - -def teardown_infile(tmp_dir): - os.chdir(cwd) - shutil.rmtree(tmp_dir) - - -@skipif(no_fsl) -def test_MultipleRegressDesign(): - _, tp_dir = setup_infile() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_MultipleRegressDesign(tmpdir): + os.chdir(str(tmpdir)) foo = fsl.MultipleRegressDesign() foo.inputs.regressors = dict(voice_stenght=[1, 1, 1], age=[0.2, 0.4, 0.5], BMI=[1, -1, 2]) con1 = ['voice_and_age', 'T', ['age', 'voice_stenght'], [0.5, 0.5]] con2 = ['just_BMI', 'T', ['BMI'], [1]] foo.inputs.contrasts = [con1, con2, ['con3', 'F', [con1, con2]]] res = foo.run() - yield assert_equal, res.outputs.design_mat, os.path.join(os.getcwd(), 'design.mat') - yield assert_equal, res.outputs.design_con, os.path.join(os.getcwd(), 'design.con') - yield assert_equal, res.outputs.design_fts, os.path.join(os.getcwd(), 'design.fts') - yield assert_equal, res.outputs.design_grp, os.path.join(os.getcwd(), 'design.grp') + + for ii in ["mat", "con", "fts", "grp"]: + assert getattr(res.outputs, "design_"+ii) == os.path.join(os.getcwd(), 'design.'+ii) design_mat_expected_content = """/NumWaves 3 /NumPoints 3 @@ -87,9 +61,7 @@ def test_MultipleRegressDesign(): 1 1 """ - yield assert_equal, open(os.path.join(os.getcwd(), 'design.con'), 'r').read(), design_con_expected_content - yield assert_equal, open(os.path.join(os.getcwd(), 'design.mat'), 'r').read(), design_mat_expected_content - yield assert_equal, open(os.path.join(os.getcwd(), 'design.fts'), 'r').read(), design_fts_expected_content - yield assert_equal, open(os.path.join(os.getcwd(), 'design.grp'), 'r').read(), design_grp_expected_content + for ii in ["mat", "con", "fts", "grp"]: + assert open(os.path.join(os.getcwd(), 'design.'+ii), 'r').read() == eval("design_"+ii+"_expected_content") + - teardown_infile(tp_dir) diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py index a1438b190b..3904703e2d 100644 --- a/nipype/interfaces/fsl/tests/test_preprocess.py +++ b/nipype/interfaces/fsl/tests/test_preprocess.py @@ -9,9 +9,7 @@ import tempfile import shutil -from nipype.testing import (assert_equal, assert_not_equal, assert_raises, - skipif, assert_true) - +import pytest from nipype.utils.filemanip import split_filename, filename_to_list from .. import preprocess as fsl from nipype.interfaces.fsl import Info @@ -19,60 +17,59 @@ from nipype.interfaces.fsl import no_fsl -@skipif(no_fsl) def fsl_name(obj, fname): """Create valid fsl name, including file extension for output type. """ ext = Info.output_type_to_ext(obj.inputs.output_type) return fname + ext -tmp_infile = None -tmp_dir = None - -@skipif(no_fsl) -def setup_infile(): - global tmp_infile, tmp_dir +@pytest.fixture() +def setup_infile(request): ext = Info.output_type_to_ext(Info.output_type()) tmp_dir = tempfile.mkdtemp() tmp_infile = os.path.join(tmp_dir, 'foo' + ext) open(tmp_infile, 'w') - return tmp_infile, tmp_dir + + def fin(): + shutil.rmtree(tmp_dir) + request.addfinalizer(fin) + return (tmp_infile, tmp_dir) -def teardown_infile(tmp_dir): - shutil.rmtree(tmp_dir) # test BET # @with_setup(setup_infile, teardown_infile) # broken in nose with generators -@skipif(no_fsl) -def test_bet(): - tmp_infile, tp_dir = setup_infile() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_bet(setup_infile): + tmp_infile, tp_dir = setup_infile better = fsl.BET() - yield assert_equal, better.cmd, 'bet' + assert better.cmd == 'bet' # Test raising error with mandatory args absent - yield assert_raises, ValueError, better.run + with pytest.raises(ValueError): + better.run() # Test generated outfile name better.inputs.in_file = tmp_infile outfile = fsl_name(better, 'foo_brain') outpath = os.path.join(os.getcwd(), outfile) realcmd = 'bet %s %s' % (tmp_infile, outpath) - yield assert_equal, better.cmdline, realcmd + assert better.cmdline == realcmd # Test specified outfile name outfile = fsl_name(better, '/newdata/bar') better.inputs.out_file = outfile realcmd = 'bet %s %s' % (tmp_infile, outfile) - yield assert_equal, better.cmdline, realcmd + assert better.cmdline == realcmd # infile foo.nii doesn't exist def func(): better.run(in_file='foo2.nii', out_file='bar.nii') - yield assert_raises, TraitError, func + with pytest.raises(TraitError): + func() # Our options and some test values for them # Should parallel the opt_map structure in the class for clarity @@ -102,33 +99,31 @@ def func(): # Add mandatory input better.inputs.in_file = tmp_infile realcmd = ' '.join([better.cmd, tmp_infile, outpath, settings[0]]) - yield assert_equal, better.cmdline, realcmd - teardown_infile(tmp_dir) - + assert better.cmdline == realcmd + # test fast -@skipif(no_fsl) -def test_fast(): - tmp_infile, tp_dir = setup_infile() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_fast(setup_infile): + tmp_infile, tp_dir = setup_infile faster = fsl.FAST() faster.inputs.verbose = True fasted = fsl.FAST(in_files=tmp_infile, verbose=True) fasted2 = fsl.FAST(in_files=[tmp_infile, tmp_infile], verbose=True) - yield assert_equal, faster.cmd, 'fast' - yield assert_equal, faster.inputs.verbose, True - yield assert_equal, faster.inputs.manual_seg, Undefined - yield assert_not_equal, faster.inputs, fasted.inputs - yield assert_equal, fasted.cmdline, 'fast -v -S 1 %s' % (tmp_infile) - yield assert_equal, fasted2.cmdline, 'fast -v -S 2 %s %s' % (tmp_infile, - tmp_infile) + assert faster.cmd == 'fast' + assert faster.inputs.verbose == True + assert faster.inputs.manual_seg == Undefined + assert faster.inputs != fasted.inputs + assert fasted.cmdline == 'fast -v -S 1 %s' % (tmp_infile) + assert fasted2.cmdline == 'fast -v -S 2 %s %s' % (tmp_infile, tmp_infile) faster = fsl.FAST() faster.inputs.in_files = tmp_infile - yield assert_equal, faster.cmdline, 'fast -S 1 %s' % (tmp_infile) + assert faster.cmdline == 'fast -S 1 %s' % (tmp_infile) faster.inputs.in_files = [tmp_infile, tmp_infile] - yield assert_equal, faster.cmdline, 'fast -S 2 %s %s' % (tmp_infile, tmp_infile) + assert faster.cmdline == 'fast -S 2 %s %s' % (tmp_infile, tmp_infile) # Our options and some test values for them # Should parallel the opt_map structure in the class for clarity @@ -162,13 +157,12 @@ def test_fast(): # test each of our arguments for name, settings in list(opt_map.items()): faster = fsl.FAST(in_files=tmp_infile, **{name: settings[1]}) - yield assert_equal, faster.cmdline, ' '.join([faster.cmd, - settings[0], - "-S 1 %s" % tmp_infile]) - teardown_infile(tmp_dir) + assert faster.cmdline == ' '.join([faster.cmd, settings[0], + "-S 1 %s" % tmp_infile]) + -@skipif(no_fsl) -def test_fast_list_outputs(): +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_fast_list_outputs(setup_infile): ''' By default (no -o), FSL's fast command outputs files into the same directory as the input files. If the flag -o is set, it outputs files into the cwd ''' @@ -178,13 +172,13 @@ def _run_and_test(opts, output_base): filenames = filename_to_list(output) if filenames is not None: for filename in filenames: - assert_equal(filename[:len(output_base)], output_base) + assert filename[:len(output_base)] == output_base # set up - infile, indir = setup_infile() + tmp_infile, indir = setup_infile cwd = tempfile.mkdtemp() os.chdir(cwd) - yield assert_not_equal, indir, cwd + assert indir != cwd out_basename = 'a_basename' # run and test @@ -195,26 +189,28 @@ def _run_and_test(opts, output_base): opts['out_basename'] = out_basename _run_and_test(opts, os.path.join(cwd, out_basename)) -@skipif(no_fsl) -def setup_flirt(): + +@pytest.fixture() +def setup_flirt(request): ext = Info.output_type_to_ext(Info.output_type()) tmpdir = tempfile.mkdtemp() _, infile = tempfile.mkstemp(suffix=ext, dir=tmpdir) _, reffile = tempfile.mkstemp(suffix=ext, dir=tmpdir) - return tmpdir, infile, reffile - + + def teardown_flirt(): + shutil.rmtree(tmpdir) -def teardown_flirt(tmpdir): - shutil.rmtree(tmpdir) + request.addfinalizer(teardown_flirt) + return (tmpdir, infile, reffile) -@skipif(no_fsl) -def test_flirt(): +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_flirt(setup_flirt): # setup - tmpdir, infile, reffile = setup_flirt() + tmpdir, infile, reffile = setup_flirt flirter = fsl.FLIRT() - yield assert_equal, flirter.cmd, 'flirt' + assert flirter.cmd == 'flirt' flirter.inputs.bins = 256 flirter.inputs.cost = 'mutualinfo' @@ -227,21 +223,23 @@ def test_flirt(): out_matrix_file='outmat.mat', bins=256, cost='mutualinfo') - yield assert_not_equal, flirter.inputs, flirted.inputs - yield assert_not_equal, flirted.inputs, flirt_est.inputs + assert flirter.inputs != flirted.inputs + assert flirted.inputs != flirt_est.inputs - yield assert_equal, flirter.inputs.bins, flirted.inputs.bins - yield assert_equal, flirter.inputs.cost, flirt_est.inputs.cost + assert flirter.inputs.bins == flirted.inputs.bins + assert flirter.inputs.cost == flirt_est.inputs.cost realcmd = 'flirt -in %s -ref %s -out outfile -omat outmat.mat ' \ '-bins 256 -cost mutualinfo' % (infile, reffile) - yield assert_equal, flirted.cmdline, realcmd + assert flirted.cmdline == realcmd flirter = fsl.FLIRT() # infile not specified - yield assert_raises, ValueError, flirter.run + with pytest.raises(ValueError): + flirter.run() flirter.inputs.in_file = infile # reference not specified - yield assert_raises, ValueError, flirter.run + with pytest.raises(ValueError): + flirter.run() flirter.inputs.reference = reffile # Generate outfile and outmatrix pth, fname, ext = split_filename(infile) @@ -249,7 +247,7 @@ def test_flirt(): outmat = '%s_flirt.mat' % fname realcmd = 'flirt -in %s -ref %s -out %s -omat %s' % (infile, reffile, outfile, outmat) - yield assert_equal, flirter.cmdline, realcmd + assert flirter.cmdline == realcmd _, tmpfile = tempfile.mkstemp(suffix='.nii', dir=tmpdir) # Loop over all inputs, set a reasonable value and make sure the @@ -290,7 +288,7 @@ def test_flirt(): cmdline = ' '.join([cmdline, outfile, outmatrix, param]) flirter = fsl.FLIRT(in_file=infile, reference=reffile) setattr(flirter.inputs, key, value) - yield assert_equal, flirter.cmdline, cmdline + assert flirter.cmdline == cmdline # Test OutputSpec flirter = fsl.FLIRT(in_file=infile, reference=reffile) @@ -298,21 +296,19 @@ def test_flirt(): flirter.inputs.out_file = ''.join(['foo', ext]) flirter.inputs.out_matrix_file = ''.join(['bar', ext]) outs = flirter._list_outputs() - yield assert_equal, outs['out_file'], \ + assert outs['out_file'] == \ os.path.join(os.getcwd(), flirter.inputs.out_file) - yield assert_equal, outs['out_matrix_file'], \ + assert outs['out_matrix_file'] == \ os.path.join(os.getcwd(), flirter.inputs.out_matrix_file) - teardown_flirt(tmpdir) - # Mcflirt -@skipif(no_fsl) -def test_mcflirt(): - tmpdir, infile, reffile = setup_flirt() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_mcflirt(setup_flirt): + tmpdir, infile, reffile = setup_flirt frt = fsl.MCFLIRT() - yield assert_equal, frt.cmd, 'mcflirt' + assert frt.cmd == 'mcflirt' # Test generated outfile name frt.inputs.in_file = infile @@ -320,12 +316,12 @@ def test_mcflirt(): outfile = os.path.join(os.getcwd(), nme) outfile = frt._gen_fname(outfile, suffix='_mcf') realcmd = 'mcflirt -in ' + infile + ' -out ' + outfile - yield assert_equal, frt.cmdline, realcmd + assert frt.cmdline == realcmd # Test specified outfile name outfile2 = '/newdata/bar.nii' frt.inputs.out_file = outfile2 realcmd = 'mcflirt -in ' + infile + ' -out ' + outfile2 - yield assert_equal, frt.cmdline, realcmd + assert frt.cmdline == realcmd opt_map = { 'cost': ('-cost mutualinfo', 'mutualinfo'), @@ -350,30 +346,30 @@ def test_mcflirt(): instr = '-in %s' % (infile) outstr = '-out %s' % (outfile) if name in ('init', 'cost', 'dof', 'mean_vol', 'bins'): - yield assert_equal, fnt.cmdline, ' '.join([fnt.cmd, - instr, - settings[0], - outstr]) + assert fnt.cmdline == ' '.join([fnt.cmd, + instr, + settings[0], + outstr]) else: - yield assert_equal, fnt.cmdline, ' '.join([fnt.cmd, - instr, - outstr, - settings[0]]) + assert fnt.cmdline == ' '.join([fnt.cmd, + instr, + outstr, + settings[0]]) # Test error is raised when missing required args fnt = fsl.MCFLIRT() - yield assert_raises, ValueError, fnt.run - teardown_flirt(tmpdir) + with pytest.raises(ValueError): + fnt.run() # test fnirt -@skipif(no_fsl) -def test_fnirt(): +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_fnirt(setup_flirt): - tmpdir, infile, reffile = setup_flirt() + tmpdir, infile, reffile = setup_flirt fnirt = fsl.FNIRT() - yield assert_equal, fnirt.cmd, 'fnirt' + assert fnirt.cmd == 'fnirt' # Test list parameters params = [('subsampling_scheme', '--subsamp', [4, 2, 2, 1], '4,2,2,1'), @@ -415,11 +411,12 @@ def test_fnirt(): reffile, flag, strval, iout) - yield assert_equal, fnirt.cmdline, cmd + assert fnirt.cmdline == cmd # Test ValueError is raised when missing mandatory args fnirt = fsl.FNIRT() - yield assert_raises, ValueError, fnirt.run + with pytest.raises(ValueError): + fnirt.run() fnirt.inputs.in_file = infile fnirt.inputs.ref_file = reffile @@ -478,13 +475,12 @@ def test_fnirt(): settings, infile, reffile, iout) - yield assert_equal, fnirt.cmdline, cmd - teardown_flirt(tmpdir) + assert fnirt.cmdline == cmd -@skipif(no_fsl) -def test_applywarp(): - tmpdir, infile, reffile = setup_flirt() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_applywarp(setup_flirt): + tmpdir, infile, reffile = setup_flirt opt_map = { 'out_file': ('--out=bar.nii', 'bar.nii'), 'premat': ('--premat=%s' % (reffile), reffile), @@ -509,17 +505,11 @@ def test_applywarp(): '--warp=%s %s' % (infile, reffile, outfile, reffile, settings[0]) - yield assert_equal, awarp.cmdline, realcmd + assert awarp.cmdline == realcmd - awarp = fsl.ApplyWarp(in_file=infile, - ref_file=reffile, - field_file=reffile) - - teardown_flirt(tmpdir) - - -@skipif(no_fsl) -def setup_fugue(): + +@pytest.fixture(scope="module") +def setup_fugue(request): import nibabel as nb import numpy as np import os.path as op @@ -528,75 +518,41 @@ def setup_fugue(): tmpdir = tempfile.mkdtemp() infile = op.join(tmpdir, 'dumbfile.nii.gz') nb.Nifti1Image(d, None, None).to_filename(infile) - return tmpdir, infile + def teardown_fugue(): + shutil.rmtree(tmpdir) -def teardown_fugue(tmpdir): - shutil.rmtree(tmpdir) + request.addfinalizer(teardown_fugue) + return (tmpdir, infile) -@skipif(no_fsl) -def test_fugue(): +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +@pytest.mark.parametrize("attr, out_file", [ + ({"save_unmasked_fmap":True, "fmap_in_file":"infile", "mask_file":"infile", "output_type":"NIFTI_GZ"}, + 'fmap_out_file'), + ({"save_unmasked_shift":True, "fmap_in_file":"infile", "dwell_time":1.e-3, "mask_file":"infile", "output_type": "NIFTI_GZ"}, + "shift_out_file"), + ({"in_file":"infile", "mask_file":"infile", "shift_in_file":"infile", "output_type":"NIFTI_GZ"}, + 'unwarped_file') + ]) +def test_fugue(setup_fugue, attr, out_file): import os.path as op - tmpdir, infile = setup_fugue() + tmpdir, infile = setup_fugue fugue = fsl.FUGUE() - fugue.inputs.save_unmasked_fmap = True - fugue.inputs.fmap_in_file = infile - fugue.inputs.mask_file = infile - fugue.inputs.output_type = "NIFTI_GZ" - + for key, value in attr.items(): + if value == "infile": setattr(fugue.inputs, key, infile) + else: setattr(fugue.inputs, key, value) res = fugue.run() - if not isdefined(res.outputs.fmap_out_file): - yield False - else: - trait_spec = fugue.inputs.trait('fmap_out_file') - out_name = trait_spec.name_template % 'dumbfile' - out_name += '.nii.gz' + assert isdefined(getattr(res.outputs,out_file)) + trait_spec = fugue.inputs.trait(out_file) + out_name = trait_spec.name_template % 'dumbfile' + out_name += '.nii.gz' + assert op.basename(getattr(res.outputs, out_file)) == out_name - yield assert_equal, op.basename(res.outputs.fmap_out_file), out_name - fugue = fsl.FUGUE() - fugue.inputs.save_unmasked_shift = True - fugue.inputs.fmap_in_file = infile - fugue.inputs.dwell_time = 1.0e-3 - fugue.inputs.mask_file = infile - fugue.inputs.output_type = "NIFTI_GZ" - res = fugue.run() - - if not isdefined(res.outputs.shift_out_file): - yield False - else: - trait_spec = fugue.inputs.trait('shift_out_file') - out_name = trait_spec.name_template % 'dumbfile' - out_name += '.nii.gz' - - yield assert_equal, op.basename(res.outputs.shift_out_file), \ - out_name - - fugue = fsl.FUGUE() - fugue.inputs.in_file = infile - fugue.inputs.mask_file = infile - # Previously computed with fugue as well - fugue.inputs.shift_in_file = infile - fugue.inputs.output_type = "NIFTI_GZ" - - res = fugue.run() - - if not isdefined(res.outputs.unwarped_file): - yield False - else: - trait_spec = fugue.inputs.trait('unwarped_file') - out_name = trait_spec.name_template % 'dumbfile' - out_name += '.nii.gz' - - yield assert_equal, op.basename(res.outputs.unwarped_file), out_name - - teardown_fugue(tmpdir) - - -@skipif(no_fsl) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") def test_first_genfname(): first = fsl.FIRST() first.inputs.out_file = 'segment.nii' @@ -604,18 +560,20 @@ def test_first_genfname(): value = first._gen_fname(name='original_segmentations') expected_value = os.path.abspath('segment_all_fast_origsegs.nii.gz') - yield assert_equal, value, expected_value + assert value == expected_value first.inputs.method = 'none' value = first._gen_fname(name='original_segmentations') expected_value = os.path.abspath('segment_all_none_origsegs.nii.gz') - yield assert_equal, value, expected_value + assert value == expected_value first.inputs.method = 'auto' first.inputs.list_of_specific_structures = ['L_Hipp', 'R_Hipp'] value = first._gen_fname(name='original_segmentations') expected_value = os.path.abspath('segment_all_none_origsegs.nii.gz') - yield assert_equal, value, expected_value + assert value == expected_value + -@skipif(no_fsl) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") def test_deprecation(): interface = fsl.ApplyXfm() - yield assert_true, isinstance(interface, fsl.ApplyXFM) + assert isinstance(interface, fsl.ApplyXFM) + diff --git a/nipype/interfaces/fsl/tests/test_utils.py b/nipype/interfaces/fsl/tests/test_utils.py index 6a99ce480c..5bf734c759 100644 --- a/nipype/interfaces/fsl/tests/test_utils.py +++ b/nipype/interfaces/fsl/tests/test_utils.py @@ -9,33 +9,32 @@ import numpy as np import nibabel as nb -from nipype.testing import (assert_equal, assert_not_equal, - assert_raises, skipif) +import pytest import nipype.interfaces.fsl.utils as fsl from nipype.interfaces.fsl import no_fsl, Info -from .test_maths import (set_output_type, create_files_in_directory, - clean_directory) +from .test_maths import (set_output_type, create_files_in_directory) -@skipif(no_fsl) -def test_fslroi(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_fslroi(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory roi = fsl.ExtractROI() # make sure command gets called - yield assert_equal, roi.cmd, 'fslroi' + assert roi.cmd == 'fslroi' # test raising error with mandatory args absent - yield assert_raises, ValueError, roi.run + with pytest.raises(ValueError): + roi.run() # .inputs based parameters setting roi.inputs.in_file = filelist[0] roi.inputs.roi_file = 'foo_roi.nii' roi.inputs.t_min = 10 roi.inputs.t_size = 20 - yield assert_equal, roi.cmdline, 'fslroi %s foo_roi.nii 10 20' % filelist[0] + assert roi.cmdline == 'fslroi %s foo_roi.nii 10 20' % filelist[0] # .run based parameter setting roi2 = fsl.ExtractROI(in_file=filelist[0], @@ -44,36 +43,36 @@ def test_fslroi(): x_min=3, x_size=30, y_min=40, y_size=10, z_min=5, z_size=20) - yield assert_equal, roi2.cmdline, \ + assert roi2.cmdline == \ 'fslroi %s foo2_roi.nii 3 30 40 10 5 20 20 40' % filelist[0] - clean_directory(outdir, cwd) # test arguments for opt_map # Fslroi class doesn't have a filled opt_map{} -@skipif(no_fsl) -def test_fslmerge(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_fslmerge(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory merger = fsl.Merge() # make sure command gets called - yield assert_equal, merger.cmd, 'fslmerge' + assert merger.cmd == 'fslmerge' # test raising error with mandatory args absent - yield assert_raises, ValueError, merger.run + with pytest.raises(ValueError): + merger.run() # .inputs based parameters setting merger.inputs.in_files = filelist merger.inputs.merged_file = 'foo_merged.nii' merger.inputs.dimension = 't' merger.inputs.output_type = 'NIFTI' - yield assert_equal, merger.cmdline, 'fslmerge -t foo_merged.nii %s' % ' '.join(filelist) + assert merger.cmdline == 'fslmerge -t foo_merged.nii %s' % ' '.join(filelist) # verify that providing a tr value updates the dimension to tr merger.inputs.tr = 2.25 - yield assert_equal, merger.cmdline, 'fslmerge -tr foo_merged.nii %s %.2f' % (' '.join(filelist), 2.25) + assert merger.cmdline == 'fslmerge -tr foo_merged.nii %s %.2f' % (' '.join(filelist), 2.25) # .run based parameter setting merger2 = fsl.Merge(in_files=filelist, @@ -82,56 +81,56 @@ def test_fslmerge(): output_type='NIFTI', tr=2.25) - yield assert_equal, merger2.cmdline, \ + assert merger2.cmdline == \ 'fslmerge -tr foo_merged.nii %s %.2f' % (' '.join(filelist), 2.25) - clean_directory(outdir, cwd) # test arguments for opt_map # Fslmerge class doesn't have a filled opt_map{} # test fslmath -@skipif(no_fsl) -def test_fslmaths(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_fslmaths(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory math = fsl.ImageMaths() # make sure command gets called - yield assert_equal, math.cmd, 'fslmaths' + assert math.cmd == 'fslmaths' # test raising error with mandatory args absent - yield assert_raises, ValueError, math.run + with pytest.raises(ValueError): + math.run() # .inputs based parameters setting math.inputs.in_file = filelist[0] math.inputs.op_string = '-add 2.5 -mul input_volume2' math.inputs.out_file = 'foo_math.nii' - yield assert_equal, math.cmdline, \ + assert math.cmdline == \ 'fslmaths %s -add 2.5 -mul input_volume2 foo_math.nii' % filelist[0] # .run based parameter setting math2 = fsl.ImageMaths(in_file=filelist[0], op_string='-add 2.5', out_file='foo2_math.nii') - yield assert_equal, math2.cmdline, 'fslmaths %s -add 2.5 foo2_math.nii' % filelist[0] + assert math2.cmdline == 'fslmaths %s -add 2.5 foo2_math.nii' % filelist[0] # test arguments for opt_map # Fslmath class doesn't have opt_map{} - clean_directory(outdir, cwd) - + # test overlay -@skipif(no_fsl) -def test_overlay(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_overlay(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory overlay = fsl.Overlay() # make sure command gets called - yield assert_equal, overlay.cmd, 'overlay' + assert overlay.cmd == 'overlay' # test raising error with mandatory args absent - yield assert_raises, ValueError, overlay.run + with pytest.raises(ValueError): + overlay.run() # .inputs based parameters setting overlay.inputs.stat_image = filelist[0] @@ -140,7 +139,7 @@ def test_overlay(): overlay.inputs.auto_thresh_bg = True overlay.inputs.show_negative_stats = True overlay.inputs.out_file = 'foo_overlay.nii' - yield assert_equal, overlay.cmdline, \ + assert overlay.cmdline == \ 'overlay 1 0 %s -a %s 2.50 10.00 %s -2.50 -10.00 foo_overlay.nii' % ( filelist[1], filelist[0], filelist[0]) @@ -148,24 +147,24 @@ def test_overlay(): overlay2 = fsl.Overlay(stat_image=filelist[0], stat_thresh=(2.5, 10), background_image=filelist[1], auto_thresh_bg=True, out_file='foo2_overlay.nii') - yield assert_equal, overlay2.cmdline, 'overlay 1 0 %s -a %s 2.50 10.00 foo2_overlay.nii' % ( + assert overlay2.cmdline == 'overlay 1 0 %s -a %s 2.50 10.00 foo2_overlay.nii' % ( filelist[1], filelist[0]) - clean_directory(outdir, cwd) # test slicer -@skipif(no_fsl) -def test_slicer(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_slicer(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory slicer = fsl.Slicer() # make sure command gets called - yield assert_equal, slicer.cmd, 'slicer' + assert slicer.cmd == 'slicer' # test raising error with mandatory args absent - yield assert_raises, ValueError, slicer.run + with pytest.raises(ValueError): + slicer.run() # .inputs based parameters setting slicer.inputs.in_file = filelist[0] @@ -174,7 +173,7 @@ def test_slicer(): slicer.inputs.all_axial = True slicer.inputs.image_width = 750 slicer.inputs.out_file = 'foo_bar.png' - yield assert_equal, slicer.cmdline, \ + assert slicer.cmdline == \ 'slicer %s %s -L -i 10.000 20.000 -A 750 foo_bar.png' % ( filelist[0], filelist[1]) @@ -182,13 +181,10 @@ def test_slicer(): slicer2 = fsl.Slicer( in_file=filelist[0], middle_slices=True, label_slices=False, out_file='foo_bar2.png') - yield assert_equal, slicer2.cmdline, 'slicer %s -a foo_bar2.png' % (filelist[0]) - - clean_directory(outdir, cwd) + assert slicer2.cmdline == 'slicer %s -a foo_bar2.png' % (filelist[0]) def create_parfiles(): - np.savetxt('a.par', np.random.rand(6, 3)) np.savetxt('b.par', np.random.rand(6, 3)) return ['a.par', 'b.par'] @@ -196,17 +192,18 @@ def create_parfiles(): # test fsl_tsplot -@skipif(no_fsl) -def test_plottimeseries(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_plottimeseries(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory parfiles = create_parfiles() plotter = fsl.PlotTimeSeries() # make sure command gets called - yield assert_equal, plotter.cmd, 'fsl_tsplot' + assert plotter.cmd == 'fsl_tsplot' # test raising error with mandatory args absent - yield assert_raises, ValueError, plotter.run + with pytest.raises(ValueError): + plotter.run() # .inputs based parameters setting plotter.inputs.in_file = parfiles[0] @@ -214,7 +211,7 @@ def test_plottimeseries(): plotter.inputs.y_range = (0, 1) plotter.inputs.title = 'test plot' plotter.inputs.out_file = 'foo.png' - yield assert_equal, plotter.cmdline, \ + assert plotter.cmdline == \ ('fsl_tsplot -i %s -a x,y,z -o foo.png -t \'test plot\' -u 1 --ymin=0 --ymax=1' % parfiles[0]) @@ -222,31 +219,30 @@ def test_plottimeseries(): plotter2 = fsl.PlotTimeSeries( in_file=parfiles, title='test2 plot', plot_range=(2, 5), out_file='bar.png') - yield assert_equal, plotter2.cmdline, \ + assert plotter2.cmdline == \ 'fsl_tsplot -i %s,%s -o bar.png --start=2 --finish=5 -t \'test2 plot\' -u 1' % tuple( parfiles) - clean_directory(outdir, cwd) - -@skipif(no_fsl) -def test_plotmotionparams(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_plotmotionparams(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory parfiles = create_parfiles() plotter = fsl.PlotMotionParams() # make sure command gets called - yield assert_equal, plotter.cmd, 'fsl_tsplot' + assert plotter.cmd == 'fsl_tsplot' # test raising error with mandatory args absent - yield assert_raises, ValueError, plotter.run + with pytest.raises(ValueError): + plotter.run() # .inputs based parameters setting plotter.inputs.in_file = parfiles[0] plotter.inputs.in_source = 'fsl' plotter.inputs.plot_type = 'rotations' plotter.inputs.out_file = 'foo.png' - yield assert_equal, plotter.cmdline, \ + assert plotter.cmdline == \ ('fsl_tsplot -i %s -o foo.png -t \'MCFLIRT estimated rotations (radians)\' ' '--start=1 --finish=3 -a x,y,z' % parfiles[0]) @@ -254,64 +250,58 @@ def test_plotmotionparams(): plotter2 = fsl.PlotMotionParams( in_file=parfiles[1], in_source='spm', plot_type='translations', out_file='bar.png') - yield assert_equal, plotter2.cmdline, \ + assert plotter2.cmdline == \ ('fsl_tsplot -i %s -o bar.png -t \'Realign estimated translations (mm)\' ' '--start=1 --finish=3 -a x,y,z' % parfiles[1]) - clean_directory(outdir, cwd) - -@skipif(no_fsl) -def test_convertxfm(): - filelist, outdir, cwd, _ = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_convertxfm(create_files_in_directory): + filelist, outdir, _ = create_files_in_directory cvt = fsl.ConvertXFM() # make sure command gets called - yield assert_equal, cvt.cmd, "convert_xfm" + assert cvt.cmd == "convert_xfm" # test raising error with mandatory args absent - yield assert_raises, ValueError, cvt.run + with pytest.raises(ValueError): + cvt.run() # .inputs based parameters setting cvt.inputs.in_file = filelist[0] cvt.inputs.invert_xfm = True cvt.inputs.out_file = "foo.mat" - yield assert_equal, cvt.cmdline, 'convert_xfm -omat foo.mat -inverse %s' % filelist[0] + assert cvt.cmdline == 'convert_xfm -omat foo.mat -inverse %s' % filelist[0] # constructor based parameter setting cvt2 = fsl.ConvertXFM( in_file=filelist[0], in_file2=filelist[1], concat_xfm=True, out_file="bar.mat") - yield assert_equal, cvt2.cmdline, \ + assert cvt2.cmdline == \ "convert_xfm -omat bar.mat -concat %s %s" % (filelist[1], filelist[0]) - clean_directory(outdir, cwd) - -@skipif(no_fsl) -def test_swapdims(fsl_output_type=None): - prev_type = set_output_type(fsl_output_type) - files, testdir, origdir, out_ext = create_files_in_directory() +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +def test_swapdims(create_files_in_directory): + files, testdir, out_ext = create_files_in_directory swap = fsl.SwapDimensions() # Test the underlying command - yield assert_equal, swap.cmd, "fslswapdim" + assert swap.cmd == "fslswapdim" # Test mandatory args args = [dict(in_file=files[0]), dict(new_dims=("x", "y", "z"))] for arg in args: wontrun = fsl.SwapDimensions(**arg) - yield assert_raises, ValueError, wontrun.run + with pytest.raises(ValueError): + wontrun.run() # Now test a basic command line swap.inputs.in_file = files[0] swap.inputs.new_dims = ("x", "y", "z") - yield assert_equal, swap.cmdline, "fslswapdim a.nii x y z %s" % os.path.realpath(os.path.join(testdir, "a_newdims%s" % out_ext)) + assert swap.cmdline == "fslswapdim a.nii x y z %s" % os.path.realpath(os.path.join(testdir, "a_newdims%s" % out_ext)) # Test that we can set an output name swap.inputs.out_file = "b.nii" - yield assert_equal, swap.cmdline, "fslswapdim a.nii x y z b.nii" + assert swap.cmdline == "fslswapdim a.nii x y z b.nii" - # Clean up - clean_directory(testdir, origdir) - set_output_type(prev_type) diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index 59300155d0..fb1b73b3d0 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -174,7 +174,7 @@ class Smooth(FSLCommand): >>> sm.inputs.output_type = 'NIFTI_GZ' >>> sm.inputs.in_file = 'functional2.nii' >>> sm.inputs.sigma = 8.0 - >>> sm.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> sm.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fslmaths functional2.nii -kernel gauss 8.000 -fmean functional2_smooth.nii.gz' Setting the kernel width using fwhm: @@ -183,7 +183,7 @@ class Smooth(FSLCommand): >>> sm.inputs.output_type = 'NIFTI_GZ' >>> sm.inputs.in_file = 'functional2.nii' >>> sm.inputs.fwhm = 8.0 - >>> sm.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> sm.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fslmaths functional2.nii -kernel gauss 3.397 -fmean functional2_smooth.nii.gz' One of sigma or fwhm must be set: @@ -246,10 +246,10 @@ class Merge(FSLCommand): >>> merger.inputs.in_files = ['functional2.nii', 'functional3.nii'] >>> merger.inputs.dimension = 't' >>> merger.inputs.output_type = 'NIFTI_GZ' - >>> merger.cmdline # doctest: +IGNORE_UNICODE + >>> merger.cmdline # doctest: +ALLOW_UNICODE 'fslmerge -t functional2_merged.nii.gz functional2.nii functional3.nii' >>> merger.inputs.tr = 2.25 - >>> merger.cmdline # doctest: +IGNORE_UNICODE + >>> merger.cmdline # doctest: +ALLOW_UNICODE 'fslmerge -tr functional2_merged.nii.gz functional2.nii functional3.nii 2.25' @@ -1170,7 +1170,7 @@ class ConvertXFM(FSLCommand): >>> invt.inputs.in_file = "flirt.mat" >>> invt.inputs.invert_xfm = True >>> invt.inputs.out_file = 'flirt_inv.mat' - >>> invt.cmdline # doctest: +IGNORE_UNICODE + >>> invt.cmdline # doctest: +ALLOW_UNICODE 'convert_xfm -omat flirt_inv.mat -inverse flirt.mat' @@ -1475,7 +1475,7 @@ class InvWarp(FSLCommand): >>> invwarp.inputs.warp = "struct2mni.nii" >>> invwarp.inputs.reference = "anatomical.nii" >>> invwarp.inputs.output_type = "NIFTI_GZ" - >>> invwarp.cmdline # doctest: +IGNORE_UNICODE + >>> invwarp.cmdline # doctest: +ALLOW_UNICODE 'invwarp --out=struct2mni_inverse.nii.gz --ref=anatomical.nii --warp=struct2mni.nii' >>> res = invwarp.run() # doctest: +SKIP @@ -1711,7 +1711,7 @@ class WarpUtils(FSLCommand): >>> warputils.inputs.out_format = 'spline' >>> warputils.inputs.warp_resolution = (10,10,10) >>> warputils.inputs.output_type = "NIFTI_GZ" - >>> warputils.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> warputils.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fnirtfileutils --in=warpfield.nii --outformat=spline --ref=T1.nii --warpres=10.0000,10.0000,10.0000 --out=warpfield_coeffs.nii.gz' >>> res = invwarp.run() # doctest: +SKIP @@ -1863,7 +1863,7 @@ class ConvertWarp(FSLCommand): >>> warputils.inputs.reference = "T1.nii" >>> warputils.inputs.relwarp = True >>> warputils.inputs.output_type = "NIFTI_GZ" - >>> warputils.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> warputils.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'convertwarp --ref=T1.nii --rel --warp1=warpfield.nii --out=T1_concatwarp.nii.gz' >>> res = warputils.run() # doctest: +SKIP @@ -1923,7 +1923,7 @@ class WarpPoints(CommandLine): >>> warppoints.inputs.dest_file = 'T1.nii' >>> warppoints.inputs.warp_file = 'warpfield.nii' >>> warppoints.inputs.coord_mm = True - >>> warppoints.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> warppoints.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'img2imgcoord -mm -dest T1.nii -src epi.nii -warp warpfield.nii surf.txt' >>> res = warppoints.run() # doctest: +SKIP @@ -2083,7 +2083,7 @@ class WarpPointsToStd(WarpPoints): >>> warppoints.inputs.std_file = 'mni.nii' >>> warppoints.inputs.warp_file = 'warpfield.nii' >>> warppoints.inputs.coord_mm = True - >>> warppoints.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> warppoints.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'img2stdcoord -mm -img T1.nii -std mni.nii -warp warpfield.nii surf.txt' >>> res = warppoints.run() # doctest: +SKIP @@ -2147,7 +2147,7 @@ class MotionOutliers(FSLCommand): >>> from nipype.interfaces.fsl import MotionOutliers >>> mo = MotionOutliers() >>> mo.inputs.in_file = "epi.nii" - >>> mo.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> mo.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fsl_motion_outliers -i epi.nii -o epi_outliers.txt -p epi_metrics.png -s epi_metrics.txt' >>> res = mo.run() # doctest: +SKIP """ diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 6986a519cd..815d2c0b0d 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -1219,7 +1219,7 @@ class SelectFiles(IOBase): ... "epi": "{subject_id}/func/f[0, 1].nii"} >>> dg = Node(SelectFiles(templates), "selectfiles") >>> dg.inputs.subject_id = "subj1" - >>> pprint.pprint(dg.outputs.get()) # doctest: +NORMALIZE_WHITESPACE +IGNORE_UNICODE + >>> pprint.pprint(dg.outputs.get()) # doctest: +NORMALIZE_WHITESPACE +ALLOW_UNICODE {'T1': , 'epi': } The same thing with dynamic grabbing of specific files: @@ -2448,11 +2448,11 @@ class JSONFileGrabber(IOBase): >>> jsonSource = JSONFileGrabber() >>> jsonSource.inputs.defaults = {'param1': 'overrideMe', 'param3': 1.0} >>> res = jsonSource.run() - >>> pprint.pprint(res.outputs.get()) # doctest: +IGNORE_UNICODE + >>> pprint.pprint(res.outputs.get()) # doctest: +ALLOW_UNICODE {'param1': 'overrideMe', 'param3': 1.0} >>> jsonSource.inputs.in_file = 'jsongrabber.txt' >>> res = jsonSource.run() - >>> pprint.pprint(res.outputs.get()) # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS +IGNORE_UNICODE + >>> pprint.pprint(res.outputs.get()) # doctest: +NORMALIZE_WHITESPACE, +ELLIPSIS +ALLOW_UNICODE {'param1': 'exampleStr', 'param2': 4, 'param3': 1.0} diff --git a/nipype/interfaces/meshfix.py b/nipype/interfaces/meshfix.py index 8cf2ae44d3..6ae1859459 100644 --- a/nipype/interfaces/meshfix.py +++ b/nipype/interfaces/meshfix.py @@ -105,7 +105,7 @@ class MeshFix(CommandLine): >>> fix.inputs.in_file1 = 'lh-pial.stl' >>> fix.inputs.in_file2 = 'rh-pial.stl' >>> fix.run() # doctest: +SKIP - >>> fix.cmdline # doctest: +IGNORE_UNICODE + >>> fix.cmdline # doctest: +ALLOW_UNICODE 'meshfix lh-pial.stl rh-pial.stl -o lh-pial_fixed.off' """ _cmd = 'meshfix' diff --git a/nipype/interfaces/minc/base.py b/nipype/interfaces/minc/base.py index 8edb87dce6..6348e4ee0f 100644 --- a/nipype/interfaces/minc/base.py +++ b/nipype/interfaces/minc/base.py @@ -109,11 +109,11 @@ def aggregate_filename(files, new_suffix): >>> from nipype.interfaces.minc.base import aggregate_filename >>> f = aggregate_filename(['/tmp/foo1.mnc', '/tmp/foo2.mnc', '/tmp/foo3.mnc'], 'averaged') - >>> os.path.split(f)[1] # This has a full path, so just check the filename. # doctest: +IGNORE_UNICODE + >>> os.path.split(f)[1] # This has a full path, so just check the filename. # doctest: +ALLOW_UNICODE 'foo_averaged.mnc' >>> f = aggregate_filename(['/tmp/foo1.mnc', '/tmp/blah1.mnc'], 'averaged') - >>> os.path.split(f)[1] # This has a full path, so just check the filename. # doctest: +IGNORE_UNICODE + >>> os.path.split(f)[1] # This has a full path, so just check the filename. # doctest: +ALLOW_UNICODE 'foo1_averaged.mnc' """ diff --git a/nipype/interfaces/minc/tests/test_auto_Average.py b/nipype/interfaces/minc/tests/test_auto_Average.py index 614f16c1ad..2d3af97946 100644 --- a/nipype/interfaces/minc/tests/test_auto_Average.py +++ b/nipype/interfaces/minc/tests/test_auto_Average.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Average @@ -114,7 +113,7 @@ def test_Average_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Average_outputs(): @@ -124,4 +123,4 @@ def test_Average_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_BBox.py b/nipype/interfaces/minc/tests/test_auto_BBox.py index cda7dbfb93..3b841252a1 100644 --- a/nipype/interfaces/minc/tests/test_auto_BBox.py +++ b/nipype/interfaces/minc/tests/test_auto_BBox.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import BBox @@ -47,7 +46,7 @@ def test_BBox_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BBox_outputs(): @@ -57,4 +56,4 @@ def test_BBox_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Beast.py b/nipype/interfaces/minc/tests/test_auto_Beast.py index edb859c367..508b9d3dc0 100644 --- a/nipype/interfaces/minc/tests/test_auto_Beast.py +++ b/nipype/interfaces/minc/tests/test_auto_Beast.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Beast @@ -69,7 +68,7 @@ def test_Beast_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Beast_outputs(): @@ -79,4 +78,4 @@ def test_Beast_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py index dedb5d4108..785b6be000 100644 --- a/nipype/interfaces/minc/tests/test_auto_BestLinReg.py +++ b/nipype/interfaces/minc/tests/test_auto_BestLinReg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import BestLinReg @@ -48,7 +47,7 @@ def test_BestLinReg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BestLinReg_outputs(): @@ -59,4 +58,4 @@ def test_BestLinReg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_BigAverage.py b/nipype/interfaces/minc/tests/test_auto_BigAverage.py index b5fb561931..bcd60eebf8 100644 --- a/nipype/interfaces/minc/tests/test_auto_BigAverage.py +++ b/nipype/interfaces/minc/tests/test_auto_BigAverage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import BigAverage @@ -47,7 +46,7 @@ def test_BigAverage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BigAverage_outputs(): @@ -58,4 +57,4 @@ def test_BigAverage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Blob.py b/nipype/interfaces/minc/tests/test_auto_Blob.py index a4d92e3013..30a040f053 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blob.py +++ b/nipype/interfaces/minc/tests/test_auto_Blob.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Blob @@ -38,7 +37,7 @@ def test_Blob_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Blob_outputs(): @@ -48,4 +47,4 @@ def test_Blob_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Blur.py b/nipype/interfaces/minc/tests/test_auto_Blur.py index c2a4eea061..b9aa29d66b 100644 --- a/nipype/interfaces/minc/tests/test_auto_Blur.py +++ b/nipype/interfaces/minc/tests/test_auto_Blur.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Blur @@ -55,7 +54,7 @@ def test_Blur_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Blur_outputs(): @@ -70,4 +69,4 @@ def test_Blur_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Calc.py b/nipype/interfaces/minc/tests/test_auto_Calc.py index 58a18e6d7c..33c0c132ea 100644 --- a/nipype/interfaces/minc/tests/test_auto_Calc.py +++ b/nipype/interfaces/minc/tests/test_auto_Calc.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Calc @@ -117,7 +116,7 @@ def test_Calc_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Calc_outputs(): @@ -127,4 +126,4 @@ def test_Calc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Convert.py b/nipype/interfaces/minc/tests/test_auto_Convert.py index df69156bd3..96ad275a87 100644 --- a/nipype/interfaces/minc/tests/test_auto_Convert.py +++ b/nipype/interfaces/minc/tests/test_auto_Convert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Convert @@ -42,7 +41,7 @@ def test_Convert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Convert_outputs(): @@ -52,4 +51,4 @@ def test_Convert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Copy.py b/nipype/interfaces/minc/tests/test_auto_Copy.py index 2674d00a6c..91b1270fa0 100644 --- a/nipype/interfaces/minc/tests/test_auto_Copy.py +++ b/nipype/interfaces/minc/tests/test_auto_Copy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Copy @@ -36,7 +35,7 @@ def test_Copy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Copy_outputs(): @@ -46,4 +45,4 @@ def test_Copy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Dump.py b/nipype/interfaces/minc/tests/test_auto_Dump.py index c1de6510cf..a738ed3075 100644 --- a/nipype/interfaces/minc/tests/test_auto_Dump.py +++ b/nipype/interfaces/minc/tests/test_auto_Dump.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Dump @@ -55,7 +54,7 @@ def test_Dump_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Dump_outputs(): @@ -65,4 +64,4 @@ def test_Dump_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Extract.py b/nipype/interfaces/minc/tests/test_auto_Extract.py index 4b634a7675..75c9bac384 100644 --- a/nipype/interfaces/minc/tests/test_auto_Extract.py +++ b/nipype/interfaces/minc/tests/test_auto_Extract.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Extract @@ -116,7 +115,7 @@ def test_Extract_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Extract_outputs(): @@ -126,4 +125,4 @@ def test_Extract_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py index 4fb31a0015..f8923a01de 100644 --- a/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py +++ b/nipype/interfaces/minc/tests/test_auto_Gennlxfm.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Gennlxfm @@ -37,7 +36,7 @@ def test_Gennlxfm_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Gennlxfm_outputs(): @@ -48,4 +47,4 @@ def test_Gennlxfm_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Math.py b/nipype/interfaces/minc/tests/test_auto_Math.py index fb414daa1a..719ceac064 100644 --- a/nipype/interfaces/minc/tests/test_auto_Math.py +++ b/nipype/interfaces/minc/tests/test_auto_Math.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Math @@ -157,7 +156,7 @@ def test_Math_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Math_outputs(): @@ -167,4 +166,4 @@ def test_Math_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_NlpFit.py b/nipype/interfaces/minc/tests/test_auto_NlpFit.py index 5423d564a0..88a490d520 100644 --- a/nipype/interfaces/minc/tests/test_auto_NlpFit.py +++ b/nipype/interfaces/minc/tests/test_auto_NlpFit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import NlpFit @@ -46,7 +45,7 @@ def test_NlpFit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NlpFit_outputs(): @@ -57,4 +56,4 @@ def test_NlpFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Norm.py b/nipype/interfaces/minc/tests/test_auto_Norm.py index d9dbd80487..d4cec8fe99 100644 --- a/nipype/interfaces/minc/tests/test_auto_Norm.py +++ b/nipype/interfaces/minc/tests/test_auto_Norm.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Norm @@ -61,7 +60,7 @@ def test_Norm_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Norm_outputs(): @@ -72,4 +71,4 @@ def test_Norm_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Pik.py b/nipype/interfaces/minc/tests/test_auto_Pik.py index 768d215b4c..20948e5ce7 100644 --- a/nipype/interfaces/minc/tests/test_auto_Pik.py +++ b/nipype/interfaces/minc/tests/test_auto_Pik.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Pik @@ -86,7 +85,7 @@ def test_Pik_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Pik_outputs(): @@ -96,4 +95,4 @@ def test_Pik_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Resample.py b/nipype/interfaces/minc/tests/test_auto_Resample.py index b2720e2080..cae3e7b741 100644 --- a/nipype/interfaces/minc/tests/test_auto_Resample.py +++ b/nipype/interfaces/minc/tests/test_auto_Resample.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Resample @@ -191,7 +190,7 @@ def test_Resample_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Resample_outputs(): @@ -201,4 +200,4 @@ def test_Resample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Reshape.py b/nipype/interfaces/minc/tests/test_auto_Reshape.py index f6e04fee2c..6388308169 100644 --- a/nipype/interfaces/minc/tests/test_auto_Reshape.py +++ b/nipype/interfaces/minc/tests/test_auto_Reshape.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Reshape @@ -37,7 +36,7 @@ def test_Reshape_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Reshape_outputs(): @@ -47,4 +46,4 @@ def test_Reshape_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_ToEcat.py b/nipype/interfaces/minc/tests/test_auto_ToEcat.py index 8150b9838c..f6a91877dd 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToEcat.py +++ b/nipype/interfaces/minc/tests/test_auto_ToEcat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import ToEcat @@ -47,7 +46,7 @@ def test_ToEcat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ToEcat_outputs(): @@ -57,4 +56,4 @@ def test_ToEcat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_ToRaw.py b/nipype/interfaces/minc/tests/test_auto_ToRaw.py index 8cc9ee1439..c356c03151 100644 --- a/nipype/interfaces/minc/tests/test_auto_ToRaw.py +++ b/nipype/interfaces/minc/tests/test_auto_ToRaw.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import ToRaw @@ -65,7 +64,7 @@ def test_ToRaw_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ToRaw_outputs(): @@ -75,4 +74,4 @@ def test_ToRaw_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_VolSymm.py b/nipype/interfaces/minc/tests/test_auto_VolSymm.py index 707b091480..0f901c7a81 100644 --- a/nipype/interfaces/minc/tests/test_auto_VolSymm.py +++ b/nipype/interfaces/minc/tests/test_auto_VolSymm.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import VolSymm @@ -58,7 +57,7 @@ def test_VolSymm_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VolSymm_outputs(): @@ -70,4 +69,4 @@ def test_VolSymm_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Volcentre.py b/nipype/interfaces/minc/tests/test_auto_Volcentre.py index bd3b4bfac1..59599a9683 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volcentre.py +++ b/nipype/interfaces/minc/tests/test_auto_Volcentre.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Volcentre @@ -41,7 +40,7 @@ def test_Volcentre_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Volcentre_outputs(): @@ -51,4 +50,4 @@ def test_Volcentre_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Voliso.py b/nipype/interfaces/minc/tests/test_auto_Voliso.py index 201449c19d..343ca700de 100644 --- a/nipype/interfaces/minc/tests/test_auto_Voliso.py +++ b/nipype/interfaces/minc/tests/test_auto_Voliso.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Voliso @@ -41,7 +40,7 @@ def test_Voliso_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Voliso_outputs(): @@ -51,4 +50,4 @@ def test_Voliso_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_Volpad.py b/nipype/interfaces/minc/tests/test_auto_Volpad.py index 1fc37ece5f..8d01b3409d 100644 --- a/nipype/interfaces/minc/tests/test_auto_Volpad.py +++ b/nipype/interfaces/minc/tests/test_auto_Volpad.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import Volpad @@ -45,7 +44,7 @@ def test_Volpad_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Volpad_outputs(): @@ -55,4 +54,4 @@ def test_Volpad_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py index 66e70f0a0c..1ac6c444ac 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmAvg.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmAvg.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import XfmAvg @@ -42,7 +41,7 @@ def test_XfmAvg_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_XfmAvg_outputs(): @@ -53,4 +52,4 @@ def test_XfmAvg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py index 075406b117..100d3b60b7 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmConcat.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmConcat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import XfmConcat @@ -37,7 +36,7 @@ def test_XfmConcat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_XfmConcat_outputs(): @@ -48,4 +47,4 @@ def test_XfmConcat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py index 873850c6b0..f806026928 100644 --- a/nipype/interfaces/minc/tests/test_auto_XfmInvert.py +++ b/nipype/interfaces/minc/tests/test_auto_XfmInvert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..minc import XfmInvert @@ -32,7 +31,7 @@ def test_XfmInvert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_XfmInvert_outputs(): @@ -43,4 +42,4 @@ def test_XfmInvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index e326a579a2..4593039037 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistBrainMgdmSegmentation @@ -72,7 +71,7 @@ def test_JistBrainMgdmSegmentation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMgdmSegmentation_outputs(): @@ -85,4 +84,4 @@ def test_JistBrainMgdmSegmentation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index d8fab93f50..f7cd565ec0 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistBrainMp2rageDuraEstimation @@ -39,7 +38,7 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageDuraEstimation_outputs(): @@ -49,4 +48,4 @@ def test_JistBrainMp2rageDuraEstimation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index 12b3232fa7..0ecbab7bc9 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistBrainMp2rageSkullStripping @@ -50,7 +49,7 @@ def test_JistBrainMp2rageSkullStripping_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainMp2rageSkullStripping_outputs(): @@ -63,4 +62,4 @@ def test_JistBrainMp2rageSkullStripping_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index 659b4672b0..db4e6762d0 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistBrainPartialVolumeFilter @@ -37,7 +36,7 @@ def test_JistBrainPartialVolumeFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistBrainPartialVolumeFilter_outputs(): @@ -47,4 +46,4 @@ def test_JistBrainPartialVolumeFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index c4bf2b4c64..35d6f4d134 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistCortexSurfaceMeshInflation @@ -48,7 +47,7 @@ def test_JistCortexSurfaceMeshInflation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistCortexSurfaceMeshInflation_outputs(): @@ -59,4 +58,4 @@ def test_JistCortexSurfaceMeshInflation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index e5eb472c0f..73f5e507d5 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistIntensityMp2rageMasking @@ -52,7 +51,7 @@ def test_JistIntensityMp2rageMasking_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistIntensityMp2rageMasking_outputs(): @@ -65,4 +64,4 @@ def test_JistIntensityMp2rageMasking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index c00adac81c..e18548ceb0 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistLaminarProfileCalculator @@ -37,7 +36,7 @@ def test_JistLaminarProfileCalculator_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileCalculator_outputs(): @@ -47,4 +46,4 @@ def test_JistLaminarProfileCalculator_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index b251f594db..b039320016 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistLaminarProfileGeometry @@ -41,7 +40,7 @@ def test_JistLaminarProfileGeometry_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileGeometry_outputs(): @@ -51,4 +50,4 @@ def test_JistLaminarProfileGeometry_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index b9d5a067ec..472b1d1783 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistLaminarProfileSampling @@ -40,7 +39,7 @@ def test_JistLaminarProfileSampling_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarProfileSampling_outputs(): @@ -51,4 +50,4 @@ def test_JistLaminarProfileSampling_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index 2c22ad0e70..93de5ca182 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistLaminarROIAveraging @@ -39,7 +38,7 @@ def test_JistLaminarROIAveraging_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarROIAveraging_outputs(): @@ -49,4 +48,4 @@ def test_JistLaminarROIAveraging_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 40ff811855..0ba9d6b58e 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import JistLaminarVolumetricLayering @@ -59,7 +58,7 @@ def test_JistLaminarVolumetricLayering_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JistLaminarVolumetricLayering_outputs(): @@ -71,4 +70,4 @@ def test_JistLaminarVolumetricLayering_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 802669247f..0edd64ec6a 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import MedicAlgorithmImageCalculator @@ -37,7 +36,7 @@ def test_MedicAlgorithmImageCalculator_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmImageCalculator_outputs(): @@ -47,4 +46,4 @@ def test_MedicAlgorithmImageCalculator_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index 232d6a1362..960d4ec8fe 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import MedicAlgorithmLesionToads @@ -97,7 +96,7 @@ def test_MedicAlgorithmLesionToads_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmLesionToads_outputs(): @@ -115,4 +114,4 @@ def test_MedicAlgorithmLesionToads_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index a9e43b3b04..4878edd398 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import MedicAlgorithmMipavReorient @@ -50,7 +49,7 @@ def test_MedicAlgorithmMipavReorient_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmMipavReorient_outputs(): @@ -59,4 +58,4 @@ def test_MedicAlgorithmMipavReorient_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index 58b3daa96f..145a55c815 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import MedicAlgorithmN3 @@ -52,7 +51,7 @@ def test_MedicAlgorithmN3_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmN3_outputs(): @@ -63,4 +62,4 @@ def test_MedicAlgorithmN3_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index c8e005123b..d7845725af 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import MedicAlgorithmSPECTRE2010 @@ -123,7 +122,7 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmSPECTRE2010_outputs(): @@ -141,4 +140,4 @@ def test_MedicAlgorithmSPECTRE2010_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py index f472c7043f..f9639297dd 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import MedicAlgorithmThresholdToBinaryMask @@ -40,7 +39,7 @@ def test_MedicAlgorithmThresholdToBinaryMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedicAlgorithmThresholdToBinaryMask_outputs(): @@ -49,4 +48,4 @@ def test_MedicAlgorithmThresholdToBinaryMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index be6839e209..3b13c7d3a2 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..developer import RandomVol @@ -49,7 +48,7 @@ def test_RandomVol_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RandomVol_outputs(): @@ -59,4 +58,4 @@ def test_RandomVol_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mne/base.py b/nipype/interfaces/mne/base.py index 7415f22735..f2f3a70641 100644 --- a/nipype/interfaces/mne/base.py +++ b/nipype/interfaces/mne/base.py @@ -55,7 +55,7 @@ class WatershedBEM(FSCommand): >>> bem = WatershedBEM() >>> bem.inputs.subject_id = 'subj1' >>> bem.inputs.subjects_dir = '.' - >>> bem.cmdline # doctest: +IGNORE_UNICODE + >>> bem.cmdline # doctest: +ALLOW_UNICODE 'mne_watershed_bem --overwrite --subject subj1 --volume T1' >>> bem.run() # doctest: +SKIP diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 28c42e1c6d..b36b9e6b79 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import WatershedBEM @@ -33,7 +32,7 @@ def test_WatershedBEM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_WatershedBEM_outputs(): @@ -57,4 +56,4 @@ def test_WatershedBEM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/preprocess.py b/nipype/interfaces/mrtrix/preprocess.py index 1beb6bec2a..7ca6abd1fb 100644 --- a/nipype/interfaces/mrtrix/preprocess.py +++ b/nipype/interfaces/mrtrix/preprocess.py @@ -144,7 +144,7 @@ class DWI2Tensor(CommandLine): >>> dwi2tensor = mrt.DWI2Tensor() >>> dwi2tensor.inputs.in_file = 'dwi.mif' >>> dwi2tensor.inputs.encoding_file = 'encoding.txt' - >>> dwi2tensor.cmdline # doctest: +IGNORE_UNICODE + >>> dwi2tensor.cmdline # doctest: +ALLOW_UNICODE 'dwi2tensor -grad encoding.txt dwi.mif dwi_tensor.mif' >>> dwi2tensor.run() # doctest: +SKIP """ diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 4bf97e42f7..dcdace4036 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import ConstrainedSphericalDeconvolution @@ -56,7 +55,7 @@ def test_ConstrainedSphericalDeconvolution_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ConstrainedSphericalDeconvolution_outputs(): @@ -66,4 +65,4 @@ def test_ConstrainedSphericalDeconvolution_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index 28d3c97831..2b1bc5be90 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import DWI2SphericalHarmonicsImage @@ -36,7 +35,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWI2SphericalHarmonicsImage_outputs(): @@ -46,4 +45,4 @@ def test_DWI2SphericalHarmonicsImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index 1062277c13..48c6dbbaf4 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import DWI2Tensor @@ -46,7 +45,7 @@ def test_DWI2Tensor_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWI2Tensor_outputs(): @@ -56,4 +55,4 @@ def test_DWI2Tensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index ced38246ac..eb0d7b57fa 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracking import DiffusionTensorStreamlineTrack @@ -106,7 +105,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorStreamlineTrack_outputs(): @@ -116,4 +115,4 @@ def test_DiffusionTensorStreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index d80ad33e18..dd33bc5d87 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import Directions2Amplitude @@ -43,7 +42,7 @@ def test_Directions2Amplitude_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Directions2Amplitude_outputs(): @@ -53,4 +52,4 @@ def test_Directions2Amplitude_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 3161e6e0fd..b08c67a1f6 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Erode @@ -38,7 +37,7 @@ def test_Erode_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Erode_outputs(): @@ -48,4 +47,4 @@ def test_Erode_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index ff6a638f14..985641723a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import EstimateResponseForSH @@ -43,7 +42,7 @@ def test_EstimateResponseForSH_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EstimateResponseForSH_outputs(): @@ -53,4 +52,4 @@ def test_EstimateResponseForSH_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py index 03cc06b2ed..53fb798b81 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import FSL2MRTrix @@ -21,7 +20,7 @@ def test_FSL2MRTrix_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FSL2MRTrix_outputs(): @@ -31,4 +30,4 @@ def test_FSL2MRTrix_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index 434ff3c90d..a142c51ba2 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracking import FilterTracks @@ -60,7 +59,7 @@ def test_FilterTracks_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FilterTracks_outputs(): @@ -70,4 +69,4 @@ def test_FilterTracks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 75eb43d256..c7761e8c01 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import FindShPeaks @@ -49,7 +48,7 @@ def test_FindShPeaks_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FindShPeaks_outputs(): @@ -59,4 +58,4 @@ def test_FindShPeaks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index 578a59e7c9..f1aefd51ad 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tensors import GenerateDirections @@ -39,7 +38,7 @@ def test_GenerateDirections_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateDirections_outputs(): @@ -49,4 +48,4 @@ def test_GenerateDirections_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index 909015a608..8d231c0e54 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import GenerateWhiteMatterMask @@ -37,7 +36,7 @@ def test_GenerateWhiteMatterMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateWhiteMatterMask_outputs(): @@ -47,4 +46,4 @@ def test_GenerateWhiteMatterMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 75cb4ff985..8482e31471 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MRConvert @@ -61,7 +60,7 @@ def test_MRConvert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRConvert_outputs(): @@ -71,4 +70,4 @@ def test_MRConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index 4c76a6f96c..5346730894 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MRMultiply @@ -33,7 +32,7 @@ def test_MRMultiply_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRMultiply_outputs(): @@ -43,4 +42,4 @@ def test_MRMultiply_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index 0376e9b4e1..ae20a32536 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MRTransform @@ -51,7 +50,7 @@ def test_MRTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRTransform_outputs(): @@ -61,4 +60,4 @@ def test_MRTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py index d7da413c92..dc2442d8c3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..convert import MRTrix2TrackVis @@ -17,7 +16,7 @@ def test_MRTrix2TrackVis_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRTrix2TrackVis_outputs(): @@ -27,4 +26,4 @@ def test_MRTrix2TrackVis_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 73671df40c..78323ecac6 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MRTrixInfo @@ -23,7 +22,7 @@ def test_MRTrixInfo_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRTrixInfo_outputs(): @@ -32,4 +31,4 @@ def test_MRTrixInfo_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py index d0e99f2348..f8810dca99 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MRTrixViewer @@ -29,7 +28,7 @@ def test_MRTrixViewer_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MRTrixViewer_outputs(): @@ -38,4 +37,4 @@ def test_MRTrixViewer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 7010acfda5..79d223b168 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import MedianFilter3D @@ -33,7 +32,7 @@ def test_MedianFilter3D_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedianFilter3D_outputs(): @@ -43,4 +42,4 @@ def test_MedianFilter3D_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index da772b4e67..6f412bf658 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracking import ProbabilisticSphericallyDeconvolutedStreamlineTrack @@ -104,7 +103,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): @@ -114,4 +113,4 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index 4a04d1409d..9ff0ec6101 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracking import SphericallyDeconvolutedStreamlineTrack @@ -102,7 +101,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SphericallyDeconvolutedStreamlineTrack_outputs(): @@ -112,4 +111,4 @@ def test_SphericallyDeconvolutedStreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index f3007603fb..a6b09a18c3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracking import StreamlineTrack @@ -102,7 +101,7 @@ def test_StreamlineTrack_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_StreamlineTrack_outputs(): @@ -112,4 +111,4 @@ def test_StreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index c7bd91a610..a9cd29aee5 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Tensor2ApparentDiffusion @@ -33,7 +32,7 @@ def test_Tensor2ApparentDiffusion_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2ApparentDiffusion_outputs(): @@ -43,4 +42,4 @@ def test_Tensor2ApparentDiffusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index 07a9fadc2f..d1597860e3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Tensor2FractionalAnisotropy @@ -33,7 +32,7 @@ def test_Tensor2FractionalAnisotropy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2FractionalAnisotropy_outputs(): @@ -43,4 +42,4 @@ def test_Tensor2FractionalAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index cc84f35f3a..fcc74727e8 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Tensor2Vector @@ -33,7 +32,7 @@ def test_Tensor2Vector_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Tensor2Vector_outputs(): @@ -43,4 +42,4 @@ def test_Tensor2Vector_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index c45e38f714..414f28fa53 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Threshold @@ -43,7 +42,7 @@ def test_Threshold_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): @@ -53,4 +52,4 @@ def test_Threshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index 5460b7b18e..6844c56f06 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracking import Tracks2Prob @@ -47,7 +46,7 @@ def test_Tracks2Prob_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Tracks2Prob_outputs(): @@ -57,4 +56,4 @@ def test_Tracks2Prob_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix/tracking.py b/nipype/interfaces/mrtrix/tracking.py index b03c7814b4..5fa39d38d3 100644 --- a/nipype/interfaces/mrtrix/tracking.py +++ b/nipype/interfaces/mrtrix/tracking.py @@ -210,7 +210,7 @@ class StreamlineTrack(CommandLine): >>> strack.inputs.in_file = 'data.Bfloat' >>> strack.inputs.seed_file = 'seed_mask.nii' >>> strack.inputs.mask_file = 'mask.nii' - >>> strack.cmdline # doctest: +IGNORE_UNICODE + >>> strack.cmdline # doctest: +ALLOW_UNICODE 'streamtrack -mask mask.nii -seed seed_mask.nii SD_PROB data.Bfloat data_tracked.tck' >>> strack.run() # doctest: +SKIP """ diff --git a/nipype/interfaces/mrtrix3/connectivity.py b/nipype/interfaces/mrtrix3/connectivity.py index a213062a6a..a2e7db355d 100644 --- a/nipype/interfaces/mrtrix3/connectivity.py +++ b/nipype/interfaces/mrtrix3/connectivity.py @@ -96,7 +96,7 @@ class BuildConnectome(MRTrix3Base): >>> mat = mrt.BuildConnectome() >>> mat.inputs.in_file = 'tracks.tck' >>> mat.inputs.in_parc = 'aparc+aseg.nii' - >>> mat.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> mat.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'tck2connectome tracks.tck aparc+aseg.nii connectome.csv' >>> mat.run() # doctest: +SKIP """ @@ -155,7 +155,7 @@ class LabelConfig(MRTrix3Base): >>> labels = mrt.LabelConfig() >>> labels.inputs.in_file = 'aparc+aseg.nii' >>> labels.inputs.in_config = 'mrtrix3_labelconfig.txt' - >>> labels.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> labels.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'labelconfig aparc+aseg.nii mrtrix3_labelconfig.txt parcellation.mif' >>> labels.run() # doctest: +SKIP """ diff --git a/nipype/interfaces/mrtrix3/preprocess.py b/nipype/interfaces/mrtrix3/preprocess.py index 8f96154909..91ec44d1f0 100644 --- a/nipype/interfaces/mrtrix3/preprocess.py +++ b/nipype/interfaces/mrtrix3/preprocess.py @@ -96,7 +96,7 @@ class ResponseSD(MRTrix3Base): >>> resp.inputs.in_file = 'dwi.mif' >>> resp.inputs.in_mask = 'mask.nii.gz' >>> resp.inputs.grad_fsl = ('bvecs', 'bvals') - >>> resp.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> resp.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'dwi2response -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif response.txt' >>> resp.run() # doctest: +SKIP """ @@ -139,7 +139,7 @@ class ACTPrepareFSL(CommandLine): >>> import nipype.interfaces.mrtrix3 as mrt >>> prep = mrt.ACTPrepareFSL() >>> prep.inputs.in_file = 'T1.nii.gz' - >>> prep.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> prep.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'act_anat_prepare_fsl T1.nii.gz act_5tt.mif' >>> prep.run() # doctest: +SKIP """ @@ -185,7 +185,7 @@ class ReplaceFSwithFIRST(CommandLine): >>> prep.inputs.in_file = 'aparc+aseg.nii' >>> prep.inputs.in_t1w = 'T1.nii.gz' >>> prep.inputs.in_config = 'mrtrix3_labelconfig.txt' - >>> prep.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> prep.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'fs_parc_replace_sgm_first aparc+aseg.nii T1.nii.gz \ mrtrix3_labelconfig.txt aparc+first.mif' >>> prep.run() # doctest: +SKIP diff --git a/nipype/interfaces/mrtrix3/reconst.py b/nipype/interfaces/mrtrix3/reconst.py index 9341347dfe..b1f71dd572 100644 --- a/nipype/interfaces/mrtrix3/reconst.py +++ b/nipype/interfaces/mrtrix3/reconst.py @@ -58,7 +58,7 @@ class FitTensor(MRTrix3Base): >>> tsr.inputs.in_file = 'dwi.mif' >>> tsr.inputs.in_mask = 'mask.nii.gz' >>> tsr.inputs.grad_fsl = ('bvecs', 'bvals') - >>> tsr.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> tsr.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'dwi2tensor -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif dti.mif' >>> tsr.run() # doctest: +SKIP """ @@ -173,7 +173,7 @@ class EstimateFOD(MRTrix3Base): >>> fod.inputs.response = 'response.txt' >>> fod.inputs.in_mask = 'mask.nii.gz' >>> fod.inputs.grad_fsl = ('bvecs', 'bvals') - >>> fod.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> fod.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'dwi2fod -fslgrad bvecs bvals -mask mask.nii.gz dwi.mif response.txt\ fods.mif' >>> fod.run() # doctest: +SKIP diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index 45a1a9fef0..79a5864682 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ACTPrepareFSL @@ -28,7 +27,7 @@ def test_ACTPrepareFSL_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ACTPrepareFSL_outputs(): @@ -38,4 +37,4 @@ def test_ACTPrepareFSL_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 7581fe6059..c45f09e4e7 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import BrainMask @@ -40,7 +39,7 @@ def test_BrainMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BrainMask_outputs(): @@ -50,4 +49,4 @@ def test_BrainMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index e4b97f4381..b08b5d1073 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..connectivity import BuildConnectome @@ -52,7 +51,7 @@ def test_BuildConnectome_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BuildConnectome_outputs(): @@ -62,4 +61,4 @@ def test_BuildConnectome_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index ef2fec18a5..edf1a03144 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ComputeTDI @@ -63,7 +62,7 @@ def test_ComputeTDI_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeTDI_outputs(): @@ -73,4 +72,4 @@ def test_ComputeTDI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index 1f8b434843..03f8829908 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..reconst import EstimateFOD @@ -61,7 +60,7 @@ def test_EstimateFOD_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EstimateFOD_outputs(): @@ -71,4 +70,4 @@ def test_EstimateFOD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 3d926e3bd3..19f13a4c51 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..reconst import FitTensor @@ -46,7 +45,7 @@ def test_FitTensor_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FitTensor_outputs(): @@ -56,4 +55,4 @@ def test_FitTensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index b06b6362ab..b11735e417 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Generate5tt @@ -31,7 +30,7 @@ def test_Generate5tt_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Generate5tt_outputs(): @@ -41,4 +40,4 @@ def test_Generate5tt_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index 4f57c6246d..aa0a561470 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..connectivity import LabelConfig @@ -44,7 +43,7 @@ def test_LabelConfig_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_LabelConfig_outputs(): @@ -54,4 +53,4 @@ def test_LabelConfig_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py index c03da343e2..276476943d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import MRTrix3Base @@ -19,5 +18,5 @@ def test_MRTrix3Base_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 781d8b2e98..0963d455da 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Mesh2PVE @@ -34,7 +33,7 @@ def test_Mesh2PVE_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Mesh2PVE_outputs(): @@ -44,4 +43,4 @@ def test_Mesh2PVE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index cb33fda95b..e4ee59c148 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ReplaceFSwithFIRST @@ -35,7 +34,7 @@ def test_ReplaceFSwithFIRST_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ReplaceFSwithFIRST_outputs(): @@ -45,4 +44,4 @@ def test_ReplaceFSwithFIRST_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index cb78159156..d44c90923c 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ResponseSD @@ -61,7 +60,7 @@ def test_ResponseSD_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ResponseSD_outputs(): @@ -72,4 +71,4 @@ def test_ResponseSD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index d80b749fee..dfcc79605c 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import TCK2VTK @@ -34,7 +33,7 @@ def test_TCK2VTK_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TCK2VTK_outputs(): @@ -44,4 +43,4 @@ def test_TCK2VTK_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index 6be2bccab0..6053f1ee07 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import TensorMetrics @@ -38,7 +37,7 @@ def test_TensorMetrics_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TensorMetrics_outputs(): @@ -51,4 +50,4 @@ def test_TensorMetrics_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index 0ff10769be..630ebe7373 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..tracking import Tractography @@ -112,7 +111,7 @@ def test_Tractography_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Tractography_outputs(): @@ -123,4 +122,4 @@ def test_Tractography_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/mrtrix3/tracking.py b/nipype/interfaces/mrtrix3/tracking.py index 7a5fe84b66..82c7294cfc 100644 --- a/nipype/interfaces/mrtrix3/tracking.py +++ b/nipype/interfaces/mrtrix3/tracking.py @@ -227,7 +227,7 @@ class Tractography(MRTrix3Base): >>> tk.inputs.in_file = 'fods.mif' >>> tk.inputs.roi_mask = 'mask.nii.gz' >>> tk.inputs.seed_sphere = (80, 100, 70, 10) - >>> tk.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> tk.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'tckgen -algorithm iFOD2 -mask mask.nii.gz -seed_sphere \ 80.000000,100.000000,70.000000,10.000000 fods.mif tracked.tck' >>> tk.run() # doctest: +SKIP diff --git a/nipype/interfaces/mrtrix3/utils.py b/nipype/interfaces/mrtrix3/utils.py index 5bc94bf3ca..99f308bd18 100644 --- a/nipype/interfaces/mrtrix3/utils.py +++ b/nipype/interfaces/mrtrix3/utils.py @@ -46,7 +46,7 @@ class BrainMask(CommandLine): >>> import nipype.interfaces.mrtrix3 as mrt >>> bmsk = mrt.BrainMask() >>> bmsk.inputs.in_file = 'dwi.mif' - >>> bmsk.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> bmsk.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'dwi2mask dwi.mif brainmask.mif' >>> bmsk.run() # doctest: +SKIP """ @@ -93,7 +93,7 @@ class Mesh2PVE(CommandLine): >>> m2p.inputs.in_file = 'surf1.vtk' >>> m2p.inputs.reference = 'dwi.mif' >>> m2p.inputs.in_first = 'T1.nii.gz' - >>> m2p.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> m2p.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'mesh2pve -first T1.nii.gz surf1.vtk dwi.mif mesh2volume.nii.gz' >>> m2p.run() # doctest: +SKIP """ @@ -139,7 +139,7 @@ class Generate5tt(CommandLine): >>> seg.inputs.in_fast = ['tpm_00.nii.gz', ... 'tpm_01.nii.gz', 'tpm_02.nii.gz'] >>> seg.inputs.in_first = 'first_merged.nii.gz' - >>> seg.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> seg.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE '5ttgen tpm_00.nii.gz tpm_01.nii.gz tpm_02.nii.gz first_merged.nii.gz\ act-5tt.mif' >>> seg.run() # doctest: +SKIP @@ -197,7 +197,7 @@ class TensorMetrics(CommandLine): >>> comp = mrt.TensorMetrics() >>> comp.inputs.in_file = 'dti.mif' >>> comp.inputs.out_fa = 'fa.mif' - >>> comp.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> comp.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'tensor2metric -fa fa.mif dti.mif' >>> comp.run() # doctest: +SKIP """ @@ -337,7 +337,7 @@ class ComputeTDI(MRTrix3Base): >>> import nipype.interfaces.mrtrix3 as mrt >>> tdi = mrt.ComputeTDI() >>> tdi.inputs.in_file = 'dti.mif' - >>> tdi.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> tdi.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'tckmap dti.mif tdi.mif' >>> tdi.run() # doctest: +SKIP """ @@ -388,7 +388,7 @@ class TCK2VTK(MRTrix3Base): >>> vtk = mrt.TCK2VTK() >>> vtk.inputs.in_file = 'tracks.tck' >>> vtk.inputs.reference = 'b0.nii' - >>> vtk.cmdline # doctest: +ELLIPSIS +IGNORE_UNICODE + >>> vtk.cmdline # doctest: +ELLIPSIS +ALLOW_UNICODE 'tck2vtk -image b0.nii tracks.tck tracks.vtk' >>> vtk.run() # doctest: +SKIP """ diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 607c2b1f9d..923bedb051 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ComputeMask @@ -18,7 +17,7 @@ def test_ComputeMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ComputeMask_outputs(): @@ -28,4 +27,4 @@ def test_ComputeMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 61e6d42146..e532c51b18 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import EstimateContrast @@ -29,7 +28,7 @@ def test_EstimateContrast_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EstimateContrast_outputs(): @@ -41,4 +40,4 @@ def test_EstimateContrast_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 0f15facdb1..704ee3d0e8 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import FitGLM @@ -31,7 +30,7 @@ def test_FitGLM_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FitGLM_outputs(): @@ -49,4 +48,4 @@ def test_FitGLM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py index 824dbf31de..d762167399 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py +++ b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import FmriRealign4d @@ -30,7 +29,7 @@ def test_FmriRealign4d_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FmriRealign4d_outputs(): @@ -41,4 +40,4 @@ def test_FmriRealign4d_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index ef370639ce..ca14d773a4 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Similarity @@ -20,7 +19,7 @@ def test_Similarity_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Similarity_outputs(): @@ -30,4 +29,4 @@ def test_Similarity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py index 961756a800..e760f279cc 100644 --- a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py +++ b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SpaceTimeRealigner @@ -20,7 +19,7 @@ def test_SpaceTimeRealigner_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SpaceTimeRealigner_outputs(): @@ -31,4 +30,4 @@ def test_SpaceTimeRealigner_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index 98c8d0dea1..252047f4bf 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Trim @@ -21,7 +20,7 @@ def test_Trim_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Trim_outputs(): @@ -31,4 +30,4 @@ def test_Trim_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 9766257e19..66e50cbf87 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..analysis import CoherenceAnalyzer @@ -26,7 +25,7 @@ def test_CoherenceAnalyzer_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CoherenceAnalyzer_outputs(): @@ -41,4 +40,4 @@ def test_CoherenceAnalyzer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/nitime/tests/test_nitime.py b/nipype/interfaces/nitime/tests/test_nitime.py index 42ba9f8edf..fa6ace4014 100644 --- a/nipype/interfaces/nitime/tests/test_nitime.py +++ b/nipype/interfaces/nitime/tests/test_nitime.py @@ -6,7 +6,7 @@ import numpy as np -from nipype.testing import (assert_equal, assert_raises, skipif) +import pytest from nipype.testing import example_data import nipype.interfaces.nitime as nitime @@ -14,22 +14,22 @@ display_available = 'DISPLAY' in os.environ and os.environ['DISPLAY'] -@skipif(no_nitime) +@pytest.mark.skipif(no_nitime, reason="nitime is not installed") def test_read_csv(): """Test that reading the data from csv file gives you back a reasonable time-series object """ CA = nitime.CoherenceAnalyzer() CA.inputs.TR = 1.89 # bogus value just to pass traits test CA.inputs.in_file = example_data('fmri_timeseries_nolabels.csv') - yield assert_raises, ValueError, CA._read_csv + with pytest.raises(ValueError): CA._read_csv() CA.inputs.in_file = example_data('fmri_timeseries.csv') data, roi_names = CA._read_csv() - yield assert_equal, data[0][0], 10125.9 - yield assert_equal, roi_names[0], 'WM' + assert data[0][0] == 10125.9 + assert roi_names[0] == 'WM' -@skipif(no_nitime) +@pytest.mark.skipif(no_nitime, reason="nitime is not installed") def test_coherence_analysis(): """Test that the coherence analyzer works """ import nitime.analysis as nta @@ -46,7 +46,7 @@ def test_coherence_analysis(): CA.inputs.output_csv_file = tmp_csv o = CA.run() - yield assert_equal, o.outputs.coherence_array.shape, (31, 31) + assert o.outputs.coherence_array.shape == (31, 31) # This is the nitime analysis: TR = 1.89 @@ -60,7 +60,7 @@ def test_coherence_analysis(): T = ts.TimeSeries(data, sampling_interval=TR) - yield assert_equal, CA._csv2ts().data, T.data + assert (CA._csv2ts().data == T.data).all() T.metadata['roi'] = roi_names C = nta.CoherenceAnalyzer(T, method=dict(this_method='welch', @@ -73,4 +73,4 @@ def test_coherence_analysis(): # Extract the coherence and average across these frequency bands: coh = np.mean(C.coherence[:, :, freq_idx], -1) # Averaging on the last dimension - yield assert_equal, o.outputs.coherence_array, coh + assert (o.outputs.coherence_array == coh).all() diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 7fa7c6db0b..895c3e65e5 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..classify import BRAINSPosteriorToContinuousClass @@ -36,7 +35,7 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSPosteriorToContinuousClass_outputs(): @@ -46,4 +45,4 @@ def test_BRAINSPosteriorToContinuousClass_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index 51a08d06e2..5a67602c29 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..segmentation import BRAINSTalairach @@ -47,7 +46,7 @@ def test_BRAINSTalairach_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairach_outputs(): @@ -58,4 +57,4 @@ def test_BRAINSTalairach_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index e4eaa93073..4bff9869a6 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..segmentation import BRAINSTalairachMask @@ -32,7 +31,7 @@ def test_BRAINSTalairachMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTalairachMask_outputs(): @@ -42,4 +41,4 @@ def test_BRAINSTalairachMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py index 36125fcc78..cedb437824 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GenerateEdgeMapImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..utilities import GenerateEdgeMapImage @@ -39,7 +38,7 @@ def test_GenerateEdgeMapImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateEdgeMapImage_outputs(): @@ -50,4 +49,4 @@ def test_GenerateEdgeMapImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py index 6b5e79cec7..8e5e4415a5 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_GeneratePurePlugMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..utilities import GeneratePurePlugMask @@ -29,7 +28,7 @@ def test_GeneratePurePlugMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GeneratePurePlugMask_outputs(): @@ -39,4 +38,4 @@ def test_GeneratePurePlugMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index 41c4fb832f..89a0940422 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..utilities import HistogramMatchingFilter @@ -40,7 +39,7 @@ def test_HistogramMatchingFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatchingFilter_outputs(): @@ -50,4 +49,4 @@ def test_HistogramMatchingFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index 3fbbbace73..78793d245d 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..segmentation import SimilarityIndex @@ -27,7 +26,7 @@ def test_SimilarityIndex_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SimilarityIndex_outputs(): @@ -36,4 +35,4 @@ def test_SimilarityIndex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index 3c16323da3..bacc36e4d6 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DWIConvert @@ -60,7 +59,7 @@ def test_DWIConvert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWIConvert_outputs(): @@ -74,4 +73,4 @@ def test_DWIConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index 1a46be411a..d432c2c926 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import compareTractInclusion @@ -35,7 +34,7 @@ def test_compareTractInclusion_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_compareTractInclusion_outputs(): @@ -44,4 +43,4 @@ def test_compareTractInclusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index 7988994224..5798882a85 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import dtiaverage @@ -28,7 +27,7 @@ def test_dtiaverage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_dtiaverage_outputs(): @@ -38,4 +37,4 @@ def test_dtiaverage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 1b488807b9..9e0180e48e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import dtiestim @@ -60,7 +59,7 @@ def test_dtiestim_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_dtiestim_outputs(): @@ -73,4 +72,4 @@ def test_dtiestim_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index 94bd061f75..92b027272d 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import dtiprocess @@ -92,7 +91,7 @@ def test_dtiprocess_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_dtiprocess_outputs(): @@ -116,4 +115,4 @@ def test_dtiprocess_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index 79400fea82..ab44e0709b 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import extractNrrdVectorIndex @@ -30,7 +29,7 @@ def test_extractNrrdVectorIndex_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_extractNrrdVectorIndex_outputs(): @@ -40,4 +39,4 @@ def test_extractNrrdVectorIndex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index eccf216089..ea1e3bfd60 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractAnisotropyMap @@ -28,7 +27,7 @@ def test_gtractAnisotropyMap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractAnisotropyMap_outputs(): @@ -38,4 +37,4 @@ def test_gtractAnisotropyMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index 3c00c388cf..752750cdec 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractAverageBvalues @@ -30,7 +29,7 @@ def test_gtractAverageBvalues_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractAverageBvalues_outputs(): @@ -40,4 +39,4 @@ def test_gtractAverageBvalues_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index 95970529ef..13721c1891 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractClipAnisotropy @@ -30,7 +29,7 @@ def test_gtractClipAnisotropy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractClipAnisotropy_outputs(): @@ -40,4 +39,4 @@ def test_gtractClipAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index 60ce5e72a4..b446937f77 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractCoRegAnatomy @@ -69,7 +68,7 @@ def test_gtractCoRegAnatomy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoRegAnatomy_outputs(): @@ -79,4 +78,4 @@ def test_gtractCoRegAnatomy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index 0cfe65e61d..7adaf084f4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractConcatDwi @@ -28,7 +27,7 @@ def test_gtractConcatDwi_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractConcatDwi_outputs(): @@ -38,4 +37,4 @@ def test_gtractConcatDwi_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index e16d80814d..5d9347eda2 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractCopyImageOrientation @@ -28,7 +27,7 @@ def test_gtractCopyImageOrientation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractCopyImageOrientation_outputs(): @@ -38,4 +37,4 @@ def test_gtractCopyImageOrientation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index c6b69bc116..ccb6f263a4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractCoregBvalues @@ -53,7 +52,7 @@ def test_gtractCoregBvalues_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractCoregBvalues_outputs(): @@ -64,4 +63,4 @@ def test_gtractCoregBvalues_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 84b91e79dc..a5ce705611 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractCostFastMarching @@ -41,7 +40,7 @@ def test_gtractCostFastMarching_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractCostFastMarching_outputs(): @@ -52,4 +51,4 @@ def test_gtractCostFastMarching_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index ed4c3a7891..c0b3b57e66 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractCreateGuideFiber @@ -30,7 +29,7 @@ def test_gtractCreateGuideFiber_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractCreateGuideFiber_outputs(): @@ -40,4 +39,4 @@ def test_gtractCreateGuideFiber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index 80b431b91d..322ad55a6c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractFastMarchingTracking @@ -48,7 +47,7 @@ def test_gtractFastMarchingTracking_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractFastMarchingTracking_outputs(): @@ -58,4 +57,4 @@ def test_gtractFastMarchingTracking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index e9aa021e41..e24c90fbae 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractFiberTracking @@ -76,7 +75,7 @@ def test_gtractFiberTracking_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractFiberTracking_outputs(): @@ -86,4 +85,4 @@ def test_gtractFiberTracking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index f14f17359a..cbfa548af7 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractImageConformity @@ -28,7 +27,7 @@ def test_gtractImageConformity_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractImageConformity_outputs(): @@ -38,4 +37,4 @@ def test_gtractImageConformity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index 476a05e6ec..8a1f34d2e7 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractInvertBSplineTransform @@ -31,7 +30,7 @@ def test_gtractInvertBSplineTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertBSplineTransform_outputs(): @@ -41,4 +40,4 @@ def test_gtractInvertBSplineTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index db5b1e8b7a..7142ed78e8 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractInvertDisplacementField @@ -30,7 +29,7 @@ def test_gtractInvertDisplacementField_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertDisplacementField_outputs(): @@ -40,4 +39,4 @@ def test_gtractInvertDisplacementField_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index 4286c0769e..4258d7bf2c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractInvertRigidTransform @@ -26,7 +25,7 @@ def test_gtractInvertRigidTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractInvertRigidTransform_outputs(): @@ -36,4 +35,4 @@ def test_gtractInvertRigidTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index 1887a216b9..0deffdb1c5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractResampleAnisotropy @@ -32,7 +31,7 @@ def test_gtractResampleAnisotropy_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleAnisotropy_outputs(): @@ -42,4 +41,4 @@ def test_gtractResampleAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index 1623574a96..f1058b7e69 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractResampleB0 @@ -34,7 +33,7 @@ def test_gtractResampleB0_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleB0_outputs(): @@ -44,4 +43,4 @@ def test_gtractResampleB0_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index 78fc493bb0..4ddf0b9ddd 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractResampleCodeImage @@ -32,7 +31,7 @@ def test_gtractResampleCodeImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleCodeImage_outputs(): @@ -42,4 +41,4 @@ def test_gtractResampleCodeImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index da647cf1f0..98bb34918e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractResampleDWIInPlace @@ -40,7 +39,7 @@ def test_gtractResampleDWIInPlace_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleDWIInPlace_outputs(): @@ -51,4 +50,4 @@ def test_gtractResampleDWIInPlace_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index f8954b20fb..fd539d268e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractResampleFibers @@ -32,7 +31,7 @@ def test_gtractResampleFibers_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractResampleFibers_outputs(): @@ -42,4 +41,4 @@ def test_gtractResampleFibers_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index 9b35d8ffd5..3af3b16368 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractTensor @@ -46,7 +45,7 @@ def test_gtractTensor_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractTensor_outputs(): @@ -56,4 +55,4 @@ def test_gtractTensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 1e74ff01ee..0dbec8985c 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..gtract import gtractTransformToDisplacementField @@ -28,7 +27,7 @@ def test_gtractTransformToDisplacementField_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_gtractTransformToDisplacementField_outputs(): @@ -38,4 +37,4 @@ def test_gtractTransformToDisplacementField_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index 12958f9a32..e8437f3dd3 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..maxcurvature import maxcurvature @@ -28,7 +27,7 @@ def test_maxcurvature_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_maxcurvature_outputs(): @@ -38,4 +37,4 @@ def test_maxcurvature_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index 5550a1e903..f51ebc6f5d 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ......testing import assert_equal from ..ukftractography import UKFTractography @@ -88,7 +87,7 @@ def test_UKFTractography_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_UKFTractography_outputs(): @@ -99,4 +98,4 @@ def test_UKFTractography_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index b607a189d7..951aadb1e5 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ......testing import assert_equal from ..fiberprocess import fiberprocess @@ -49,7 +48,7 @@ def test_fiberprocess_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_fiberprocess_outputs(): @@ -60,4 +59,4 @@ def test_fiberprocess_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index 8521e59239..43976e0b11 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ......testing import assert_equal from ..commandlineonly import fiberstats @@ -23,7 +22,7 @@ def test_fiberstats_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_fiberstats_outputs(): @@ -32,4 +31,4 @@ def test_fiberstats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index d12c437f1c..d8b055583f 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ......testing import assert_equal from ..fibertrack import fibertrack @@ -46,7 +45,7 @@ def test_fibertrack_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_fibertrack_outputs(): @@ -56,4 +55,4 @@ def test_fibertrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index f09e7e139a..28f21d9c92 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import CannyEdge @@ -30,7 +29,7 @@ def test_CannyEdge_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CannyEdge_outputs(): @@ -40,4 +39,4 @@ def test_CannyEdge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index 5dd69484aa..64fbc79000 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import CannySegmentationLevelSetImageFilter @@ -39,7 +38,7 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CannySegmentationLevelSetImageFilter_outputs(): @@ -50,4 +49,4 @@ def test_CannySegmentationLevelSetImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index 353924d80f..94ec06ba4a 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import DilateImage @@ -28,7 +27,7 @@ def test_DilateImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DilateImage_outputs(): @@ -38,4 +37,4 @@ def test_DilateImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 91fb032420..5edbc8bd3e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import DilateMask @@ -30,7 +29,7 @@ def test_DilateMask_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DilateMask_outputs(): @@ -40,4 +39,4 @@ def test_DilateMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index 6e43ad16ee..c77d64e36a 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import DistanceMaps @@ -28,7 +27,7 @@ def test_DistanceMaps_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DistanceMaps_outputs(): @@ -38,4 +37,4 @@ def test_DistanceMaps_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index b588e4bcf6..a13c822351 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import DumpBinaryTrainingVectors @@ -23,7 +22,7 @@ def test_DumpBinaryTrainingVectors_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DumpBinaryTrainingVectors_outputs(): @@ -32,4 +31,4 @@ def test_DumpBinaryTrainingVectors_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index 81c8429e13..76871f8b2b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import ErodeImage @@ -28,7 +27,7 @@ def test_ErodeImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ErodeImage_outputs(): @@ -38,4 +37,4 @@ def test_ErodeImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index 3c86f288fa..caef237c29 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import FlippedDifference @@ -26,7 +25,7 @@ def test_FlippedDifference_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FlippedDifference_outputs(): @@ -36,4 +35,4 @@ def test_FlippedDifference_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index c605f8deea..bbfaf8b20e 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import GenerateBrainClippedImage @@ -28,7 +27,7 @@ def test_GenerateBrainClippedImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateBrainClippedImage_outputs(): @@ -38,4 +37,4 @@ def test_GenerateBrainClippedImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index fe720a4850..15adbe99e4 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import GenerateSummedGradientImage @@ -30,7 +29,7 @@ def test_GenerateSummedGradientImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateSummedGradientImage_outputs(): @@ -40,4 +39,4 @@ def test_GenerateSummedGradientImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index 869788f527..66773c2b7d 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import GenerateTestImage @@ -30,7 +29,7 @@ def test_GenerateTestImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateTestImage_outputs(): @@ -40,4 +39,4 @@ def test_GenerateTestImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index d31e178ccb..d619479ebf 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import GradientAnisotropicDiffusionImageFilter @@ -30,7 +29,7 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusionImageFilter_outputs(): @@ -40,4 +39,4 @@ def test_GradientAnisotropicDiffusionImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 2d7cfa38a8..725a237ae9 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import HammerAttributeCreator @@ -31,7 +30,7 @@ def test_HammerAttributeCreator_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_HammerAttributeCreator_outputs(): @@ -40,4 +39,4 @@ def test_HammerAttributeCreator_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index 82b34513f5..fe680029dd 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import NeighborhoodMean @@ -28,7 +27,7 @@ def test_NeighborhoodMean_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMean_outputs(): @@ -38,4 +37,4 @@ def test_NeighborhoodMean_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 3c22450067..8c02f56358 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import NeighborhoodMedian @@ -28,7 +27,7 @@ def test_NeighborhoodMedian_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NeighborhoodMedian_outputs(): @@ -38,4 +37,4 @@ def test_NeighborhoodMedian_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 410cfc40b7..6ee85a95fb 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import STAPLEAnalysis @@ -26,7 +25,7 @@ def test_STAPLEAnalysis_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_STAPLEAnalysis_outputs(): @@ -36,4 +35,4 @@ def test_STAPLEAnalysis_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index 2b20435355..6650d2344d 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import TextureFromNoiseImageFilter @@ -26,7 +25,7 @@ def test_TextureFromNoiseImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TextureFromNoiseImageFilter_outputs(): @@ -36,4 +35,4 @@ def test_TextureFromNoiseImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index 77c1f8220d..15f38e85eb 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..featuredetection import TextureMeasureFilter @@ -30,7 +29,7 @@ def test_TextureMeasureFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TextureMeasureFilter_outputs(): @@ -40,4 +39,4 @@ def test_TextureMeasureFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index 9d4de6b37b..01571bc5c7 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..denoising import UnbiasedNonLocalMeans @@ -38,7 +37,7 @@ def test_UnbiasedNonLocalMeans_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_UnbiasedNonLocalMeans_outputs(): @@ -49,4 +48,4 @@ def test_UnbiasedNonLocalMeans_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index 5885b351e0..2fe45e6bbf 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..registration import scalartransform @@ -35,7 +34,7 @@ def test_scalartransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_scalartransform_outputs(): @@ -46,4 +45,4 @@ def test_scalartransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index fa3caa8d79..12b58b8ce5 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSDemonWarp @@ -109,7 +108,7 @@ def test_BRAINSDemonWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): @@ -121,4 +120,4 @@ def test_BRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index feb165f1e2..1021e15d9b 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brainsfit import BRAINSFit @@ -162,7 +161,7 @@ def test_BRAINSFit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): @@ -179,4 +178,4 @@ def test_BRAINSFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index e6d8c39ae8..f181669891 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brainsresample import BRAINSResample @@ -43,7 +42,7 @@ def test_BRAINSResample_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): @@ -53,4 +52,4 @@ def test_BRAINSResample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index 8ea205c2c6..8a03ce11a2 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brainsresize import BRAINSResize @@ -28,7 +27,7 @@ def test_BRAINSResize_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResize_outputs(): @@ -38,4 +37,4 @@ def test_BRAINSResize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index f7e228e28d..4bb1509bb8 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSTransformFromFiducials @@ -34,7 +33,7 @@ def test_BRAINSTransformFromFiducials_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformFromFiducials_outputs(): @@ -44,4 +43,4 @@ def test_BRAINSTransformFromFiducials_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index 50df05872a..c0e0952e14 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import VBRAINSDemonWarp @@ -112,7 +111,7 @@ def test_VBRAINSDemonWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): @@ -124,4 +123,4 @@ def test_VBRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 871e5df311..2289751221 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSABC @@ -95,7 +94,7 @@ def test_BRAINSABC_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSABC_outputs(): @@ -112,4 +111,4 @@ def test_BRAINSABC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index 39556f42d0..6ddfc884f4 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSConstellationDetector @@ -114,7 +113,7 @@ def test_BRAINSConstellationDetector_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationDetector_outputs(): @@ -133,4 +132,4 @@ def test_BRAINSConstellationDetector_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index 88ce476209..bcb930846a 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSCreateLabelMapFromProbabilityMaps @@ -37,7 +36,7 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): @@ -48,4 +47,4 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index 7efdf9a1cc..6777670ef6 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSCut @@ -53,7 +52,7 @@ def test_BRAINSCut_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSCut_outputs(): @@ -62,4 +61,4 @@ def test_BRAINSCut_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index 86daa0bb17..55ff56a29b 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSMultiSTAPLE @@ -37,7 +36,7 @@ def test_BRAINSMultiSTAPLE_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMultiSTAPLE_outputs(): @@ -48,4 +47,4 @@ def test_BRAINSMultiSTAPLE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index eaffbf7909..368967309c 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSROIAuto @@ -43,7 +42,7 @@ def test_BRAINSROIAuto_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): @@ -54,4 +53,4 @@ def test_BRAINSROIAuto_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index 85ae45ffa7..2da47336e8 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BinaryMaskEditorBasedOnLandmarks @@ -38,7 +37,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BinaryMaskEditorBasedOnLandmarks_outputs(): @@ -48,4 +47,4 @@ def test_BinaryMaskEditorBasedOnLandmarks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index 943e609b99..aa8e4aab82 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import ESLR @@ -38,7 +37,7 @@ def test_ESLR_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ESLR_outputs(): @@ -48,4 +47,4 @@ def test_ESLR_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index 264ebfbd86..25d9629a15 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..converters import DWICompare @@ -23,7 +22,7 @@ def test_DWICompare_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWICompare_outputs(): @@ -32,4 +31,4 @@ def test_DWICompare_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index 017abf83af..a3c47cde5d 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..converters import DWISimpleCompare @@ -25,7 +24,7 @@ def test_DWISimpleCompare_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWISimpleCompare_outputs(): @@ -34,4 +33,4 @@ def test_DWISimpleCompare_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index ccb2e8abd6..6d22cfae89 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..featurecreator import GenerateCsfClippedFromClassifiedImage @@ -24,7 +23,7 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateCsfClippedFromClassifiedImage_outputs(): @@ -34,4 +33,4 @@ def test_GenerateCsfClippedFromClassifiedImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index 98837c75a7..864aba75a3 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSAlignMSP @@ -46,7 +45,7 @@ def test_BRAINSAlignMSP_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSAlignMSP_outputs(): @@ -57,4 +56,4 @@ def test_BRAINSAlignMSP_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index f7636c95d1..89c6a5cef8 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSClipInferior @@ -30,7 +29,7 @@ def test_BRAINSClipInferior_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSClipInferior_outputs(): @@ -40,4 +39,4 @@ def test_BRAINSClipInferior_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index ee8b7bb018..3d5e941682 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSConstellationModeler @@ -48,7 +47,7 @@ def test_BRAINSConstellationModeler_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSConstellationModeler_outputs(): @@ -59,4 +58,4 @@ def test_BRAINSConstellationModeler_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index 20072ed902..2221f9e218 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSEyeDetector @@ -28,7 +27,7 @@ def test_BRAINSEyeDetector_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSEyeDetector_outputs(): @@ -38,4 +37,4 @@ def test_BRAINSEyeDetector_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index fb5d164f9b..ef62df3757 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSInitializedControlPoints @@ -34,7 +33,7 @@ def test_BRAINSInitializedControlPoints_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSInitializedControlPoints_outputs(): @@ -44,4 +43,4 @@ def test_BRAINSInitializedControlPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index def6a40242..d18cdd35ae 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSLandmarkInitializer @@ -28,7 +27,7 @@ def test_BRAINSLandmarkInitializer_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLandmarkInitializer_outputs(): @@ -38,4 +37,4 @@ def test_BRAINSLandmarkInitializer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index f15061c8b4..608179d691 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSLinearModelerEPCA @@ -23,7 +22,7 @@ def test_BRAINSLinearModelerEPCA_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLinearModelerEPCA_outputs(): @@ -32,4 +31,4 @@ def test_BRAINSLinearModelerEPCA_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 7bda89c361..11f7f49245 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSLmkTransform @@ -35,7 +34,7 @@ def test_BRAINSLmkTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSLmkTransform_outputs(): @@ -46,4 +45,4 @@ def test_BRAINSLmkTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 4a351563d1..43e800b0a4 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSMush @@ -57,7 +56,7 @@ def test_BRAINSMush_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSMush_outputs(): @@ -69,4 +68,4 @@ def test_BRAINSMush_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index 5ebceb6933..2951a4763d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSSnapShotWriter @@ -38,7 +37,7 @@ def test_BRAINSSnapShotWriter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSSnapShotWriter_outputs(): @@ -48,4 +47,4 @@ def test_BRAINSSnapShotWriter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index dd909677cc..2069c4125a 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSTransformConvert @@ -33,7 +32,7 @@ def test_BRAINSTransformConvert_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTransformConvert_outputs(): @@ -44,4 +43,4 @@ def test_BRAINSTransformConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index a63835efc8..8cd3127dff 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import BRAINSTrimForegroundInDirection @@ -36,7 +35,7 @@ def test_BRAINSTrimForegroundInDirection_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSTrimForegroundInDirection_outputs(): @@ -46,4 +45,4 @@ def test_BRAINSTrimForegroundInDirection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py index 16e64f7910..f25ff79185 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import CleanUpOverlapLabels @@ -24,7 +23,7 @@ def test_CleanUpOverlapLabels_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CleanUpOverlapLabels_outputs(): @@ -34,4 +33,4 @@ def test_CleanUpOverlapLabels_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index 51cd6c5b70..8006d9b2a8 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import FindCenterOfBrain @@ -57,7 +56,7 @@ def test_FindCenterOfBrain_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FindCenterOfBrain_outputs(): @@ -72,4 +71,4 @@ def test_FindCenterOfBrain_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index 28d2675275..b79d7d23e3 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import GenerateLabelMapFromProbabilityMap @@ -26,7 +25,7 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GenerateLabelMapFromProbabilityMap_outputs(): @@ -36,4 +35,4 @@ def test_GenerateLabelMapFromProbabilityMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index 6c7f5215f8..7c6f369b19 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import ImageRegionPlotter @@ -37,7 +36,7 @@ def test_ImageRegionPlotter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ImageRegionPlotter_outputs(): @@ -46,4 +45,4 @@ def test_ImageRegionPlotter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index 5f1ddedcb8..86335bf32d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import JointHistogram @@ -31,7 +30,7 @@ def test_JointHistogram_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JointHistogram_outputs(): @@ -40,4 +39,4 @@ def test_JointHistogram_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index 8d84a541b8..54572c7f70 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import ShuffleVectorsModule @@ -26,7 +25,7 @@ def test_ShuffleVectorsModule_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ShuffleVectorsModule_outputs(): @@ -36,4 +35,4 @@ def test_ShuffleVectorsModule_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index 9bee62f991..841740d102 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import fcsv_to_hdf5 @@ -33,7 +32,7 @@ def test_fcsv_to_hdf5_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_fcsv_to_hdf5_outputs(): @@ -44,4 +43,4 @@ def test_fcsv_to_hdf5_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index 8803f8263b..6bd2c4e387 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import insertMidACPCpoint @@ -24,7 +23,7 @@ def test_insertMidACPCpoint_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_insertMidACPCpoint_outputs(): @@ -34,4 +33,4 @@ def test_insertMidACPCpoint_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index d5b97d17b2..01a54ffb6d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import landmarksConstellationAligner @@ -24,7 +23,7 @@ def test_landmarksConstellationAligner_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationAligner_outputs(): @@ -34,4 +33,4 @@ def test_landmarksConstellationAligner_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index 154d17665d..d105f116c3 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brains import landmarksConstellationWeights @@ -28,7 +27,7 @@ def test_landmarksConstellationWeights_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_landmarksConstellationWeights_outputs(): @@ -38,4 +37,4 @@ def test_landmarksConstellationWeights_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 1704c064f6..4c3ac11a62 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DTIexport @@ -26,7 +25,7 @@ def test_DTIexport_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTIexport_outputs(): @@ -37,4 +36,4 @@ def test_DTIexport_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index dab8788688..2f5314809e 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DTIimport @@ -28,7 +27,7 @@ def test_DTIimport_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DTIimport_outputs(): @@ -39,4 +38,4 @@ def test_DTIimport_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index a5215c65b5..b77024da19 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DWIJointRicianLMMSEFilter @@ -36,7 +35,7 @@ def test_DWIJointRicianLMMSEFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWIJointRicianLMMSEFilter_outputs(): @@ -47,4 +46,4 @@ def test_DWIJointRicianLMMSEFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index da2e1d4d07..f812412b31 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DWIRicianLMMSEFilter @@ -48,7 +47,7 @@ def test_DWIRicianLMMSEFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWIRicianLMMSEFilter_outputs(): @@ -59,4 +58,4 @@ def test_DWIRicianLMMSEFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index be0f92c092..9d419eaf4e 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DWIToDTIEstimation @@ -36,7 +35,7 @@ def test_DWIToDTIEstimation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWIToDTIEstimation_outputs(): @@ -49,4 +48,4 @@ def test_DWIToDTIEstimation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index 425800bd41..6d1003747f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DiffusionTensorScalarMeasurements @@ -28,7 +27,7 @@ def test_DiffusionTensorScalarMeasurements_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionTensorScalarMeasurements_outputs(): @@ -39,4 +38,4 @@ def test_DiffusionTensorScalarMeasurements_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index d325afaf71..44a5f677d9 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import DiffusionWeightedVolumeMasking @@ -34,7 +33,7 @@ def test_DiffusionWeightedVolumeMasking_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DiffusionWeightedVolumeMasking_outputs(): @@ -47,4 +46,4 @@ def test_DiffusionWeightedVolumeMasking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 9f7ded5f1c..a6a5e2986a 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import ResampleDTIVolume @@ -78,7 +77,7 @@ def test_ResampleDTIVolume_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ResampleDTIVolume_outputs(): @@ -89,4 +88,4 @@ def test_ResampleDTIVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index f368cc2275..ed164bc6eb 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..diffusion import TractographyLabelMapSeeding @@ -57,7 +56,7 @@ def test_TractographyLabelMapSeeding_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TractographyLabelMapSeeding_outputs(): @@ -69,4 +68,4 @@ def test_TractographyLabelMapSeeding_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index 1b196c557a..dbe75a3f4a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..arithmetic import AddScalarVolumes @@ -31,7 +30,7 @@ def test_AddScalarVolumes_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AddScalarVolumes_outputs(): @@ -42,4 +41,4 @@ def test_AddScalarVolumes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index b24be436f8..c098d8e88a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..arithmetic import CastScalarVolume @@ -28,7 +27,7 @@ def test_CastScalarVolume_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CastScalarVolume_outputs(): @@ -39,4 +38,4 @@ def test_CastScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index 2ddf46c861..0155f5765c 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..checkerboardfilter import CheckerBoardFilter @@ -32,7 +31,7 @@ def test_CheckerBoardFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CheckerBoardFilter_outputs(): @@ -43,4 +42,4 @@ def test_CheckerBoardFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index c31af700d5..d46d7e836e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..denoising import CurvatureAnisotropicDiffusion @@ -32,7 +31,7 @@ def test_CurvatureAnisotropicDiffusion_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CurvatureAnisotropicDiffusion_outputs(): @@ -43,4 +42,4 @@ def test_CurvatureAnisotropicDiffusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index 05b71f76ec..e465a2d5b8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..extractskeleton import ExtractSkeleton @@ -34,7 +33,7 @@ def test_ExtractSkeleton_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ExtractSkeleton_outputs(): @@ -45,4 +44,4 @@ def test_ExtractSkeleton_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index d5b2d21589..e3604f7a00 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..denoising import GaussianBlurImageFilter @@ -28,7 +27,7 @@ def test_GaussianBlurImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GaussianBlurImageFilter_outputs(): @@ -39,4 +38,4 @@ def test_GaussianBlurImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index c5874901c8..ca4ff5bafd 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..denoising import GradientAnisotropicDiffusion @@ -32,7 +31,7 @@ def test_GradientAnisotropicDiffusion_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GradientAnisotropicDiffusion_outputs(): @@ -43,4 +42,4 @@ def test_GradientAnisotropicDiffusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 794f2833ee..4d17ff3700 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..morphology import GrayscaleFillHoleImageFilter @@ -26,7 +25,7 @@ def test_GrayscaleFillHoleImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleFillHoleImageFilter_outputs(): @@ -37,4 +36,4 @@ def test_GrayscaleFillHoleImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 3bcfd4145c..af25291c31 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..morphology import GrayscaleGrindPeakImageFilter @@ -26,7 +25,7 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleGrindPeakImageFilter_outputs(): @@ -37,4 +36,4 @@ def test_GrayscaleGrindPeakImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index 2d4e23c33e..4585f098a6 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..histogrammatching import HistogramMatching @@ -35,7 +34,7 @@ def test_HistogramMatching_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_HistogramMatching_outputs(): @@ -46,4 +45,4 @@ def test_HistogramMatching_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index a02b922e86..18bd6fb9c3 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..imagelabelcombine import ImageLabelCombine @@ -31,7 +30,7 @@ def test_ImageLabelCombine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ImageLabelCombine_outputs(): @@ -42,4 +41,4 @@ def test_ImageLabelCombine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index a627bae20e..398f07aa92 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..arithmetic import MaskScalarVolume @@ -33,7 +32,7 @@ def test_MaskScalarVolume_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MaskScalarVolume_outputs(): @@ -44,4 +43,4 @@ def test_MaskScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index d8f3489fcd..7376ee8efe 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..denoising import MedianImageFilter @@ -29,7 +28,7 @@ def test_MedianImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MedianImageFilter_outputs(): @@ -40,4 +39,4 @@ def test_MedianImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index d1038d8001..2d5c106f48 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..arithmetic import MultiplyScalarVolumes @@ -31,7 +30,7 @@ def test_MultiplyScalarVolumes_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MultiplyScalarVolumes_outputs(): @@ -42,4 +41,4 @@ def test_MultiplyScalarVolumes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index 9e1b7df801..c5cc598378 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection @@ -48,7 +47,7 @@ def test_N4ITKBiasFieldCorrection_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_N4ITKBiasFieldCorrection_outputs(): @@ -59,4 +58,4 @@ def test_N4ITKBiasFieldCorrection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index 363dfe4747..d7a79561da 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume @@ -74,7 +73,7 @@ def test_ResampleScalarVectorDWIVolume_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVectorDWIVolume_outputs(): @@ -85,4 +84,4 @@ def test_ResampleScalarVectorDWIVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index c95b4de042..57d918b24b 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..arithmetic import SubtractScalarVolumes @@ -31,7 +30,7 @@ def test_SubtractScalarVolumes_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SubtractScalarVolumes_outputs(): @@ -42,4 +41,4 @@ def test_SubtractScalarVolumes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index a4f6d0f64a..b2b9e0b0e5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..thresholdscalarvolume import ThresholdScalarVolume @@ -36,7 +35,7 @@ def test_ThresholdScalarVolume_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ThresholdScalarVolume_outputs(): @@ -47,4 +46,4 @@ def test_ThresholdScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 5c213925e0..c86ce99ab2 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter @@ -35,7 +34,7 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VotingBinaryHoleFillingImageFilter_outputs(): @@ -46,4 +45,4 @@ def test_VotingBinaryHoleFillingImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py index 31b04e4dd7..77a633f5f8 100644 --- a/nipype/interfaces/slicer/generate_classes.py +++ b/nipype/interfaces/slicer/generate_classes.py @@ -18,9 +18,9 @@ def force_to_valid_python_variable_name(old_name): """ Valid c++ names are not always valid in python, so provide alternate naming - >>> force_to_valid_python_variable_name('lambda') # doctest: +IGNORE_UNICODE + >>> force_to_valid_python_variable_name('lambda') # doctest: +ALLOW_UNICODE 'opt_lambda' - >>> force_to_valid_python_variable_name('inputVolume') # doctest: +IGNORE_UNICODE + >>> force_to_valid_python_variable_name('inputVolume') # doctest: +ALLOW_UNICODE 'inputVolume' """ new_name = old_name diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index 3f9c41c416..4410973445 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ......testing import assert_equal from ..denoising import DWIUnbiasedNonLocalMeansFilter @@ -39,7 +38,7 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DWIUnbiasedNonLocalMeansFilter_outputs(): @@ -50,4 +49,4 @@ def test_DWIUnbiasedNonLocalMeansFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index bb46ea5f58..42e88da971 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..registration import AffineRegistration @@ -45,7 +44,7 @@ def test_AffineRegistration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_AffineRegistration_outputs(): @@ -56,4 +55,4 @@ def test_AffineRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 761a605c75..060a0fe916 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..registration import BSplineDeformableRegistration @@ -50,7 +49,7 @@ def test_BSplineDeformableRegistration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BSplineDeformableRegistration_outputs(): @@ -62,4 +61,4 @@ def test_BSplineDeformableRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 84173d2341..4932281a90 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..converters import BSplineToDeformationField @@ -26,7 +25,7 @@ def test_BSplineToDeformationField_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BSplineToDeformationField_outputs(): @@ -36,4 +35,4 @@ def test_BSplineToDeformationField_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index e0e4c5d7eb..7bbe6af84c 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..registration import ExpertAutomatedRegistration @@ -79,7 +78,7 @@ def test_ExpertAutomatedRegistration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ExpertAutomatedRegistration_outputs(): @@ -90,4 +89,4 @@ def test_ExpertAutomatedRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index 2945019abe..ca0658f8a3 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..registration import LinearRegistration @@ -49,7 +48,7 @@ def test_LinearRegistration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_LinearRegistration_outputs(): @@ -60,4 +59,4 @@ def test_LinearRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index b8ea765938..ab581f886e 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..registration import MultiResolutionAffineRegistration @@ -45,7 +44,7 @@ def test_MultiResolutionAffineRegistration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MultiResolutionAffineRegistration_outputs(): @@ -56,4 +55,4 @@ def test_MultiResolutionAffineRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index 0f4c9e3050..517ef8844a 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..filtering import OtsuThresholdImageFilter @@ -32,7 +31,7 @@ def test_OtsuThresholdImageFilter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdImageFilter_outputs(): @@ -43,4 +42,4 @@ def test_OtsuThresholdImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index 29f00b8e5f..34253e3428 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..segmentation import OtsuThresholdSegmentation @@ -34,7 +33,7 @@ def test_OtsuThresholdSegmentation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_OtsuThresholdSegmentation_outputs(): @@ -45,4 +44,4 @@ def test_OtsuThresholdSegmentation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 617ea6a3df..7fcca80f97 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..filtering import ResampleScalarVolume @@ -31,7 +30,7 @@ def test_ResampleScalarVolume_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ResampleScalarVolume_outputs(): @@ -42,4 +41,4 @@ def test_ResampleScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index a721fd9401..3cd7c1f4b4 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..registration import RigidRegistration @@ -51,7 +50,7 @@ def test_RigidRegistration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RigidRegistration_outputs(): @@ -62,4 +61,4 @@ def test_RigidRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index bcc651a10c..e7669a221e 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..changequantification import IntensityDifferenceMetric @@ -39,7 +38,7 @@ def test_IntensityDifferenceMetric_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_IntensityDifferenceMetric_outputs(): @@ -51,4 +50,4 @@ def test_IntensityDifferenceMetric_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 9794302982..cf8061b43f 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..petstandarduptakevaluecomputation import PETStandardUptakeValueComputation @@ -40,7 +39,7 @@ def test_PETStandardUptakeValueComputation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PETStandardUptakeValueComputation_outputs(): @@ -50,4 +49,4 @@ def test_PETStandardUptakeValueComputation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index a118de15c1..ea83b2b9bc 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import ACPCTransform @@ -28,7 +27,7 @@ def test_ACPCTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ACPCTransform_outputs(): @@ -38,4 +37,4 @@ def test_ACPCTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index fa3caa8d79..12b58b8ce5 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSDemonWarp @@ -109,7 +108,7 @@ def test_BRAINSDemonWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSDemonWarp_outputs(): @@ -121,4 +120,4 @@ def test_BRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index b28da552ed..63b1fc94aa 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brainsfit import BRAINSFit @@ -154,7 +153,7 @@ def test_BRAINSFit_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSFit_outputs(): @@ -170,4 +169,4 @@ def test_BRAINSFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index e6d8c39ae8..f181669891 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..brainsresample import BRAINSResample @@ -43,7 +42,7 @@ def test_BRAINSResample_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSResample_outputs(): @@ -53,4 +52,4 @@ def test_BRAINSResample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index de4cdaae40..610a06dc2e 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import FiducialRegistration @@ -32,7 +31,7 @@ def test_FiducialRegistration_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FiducialRegistration_outputs(): @@ -42,4 +41,4 @@ def test_FiducialRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index 50df05872a..c0e0952e14 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import VBRAINSDemonWarp @@ -112,7 +111,7 @@ def test_VBRAINSDemonWarp_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VBRAINSDemonWarp_outputs(): @@ -124,4 +123,4 @@ def test_VBRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 17d9993671..00584f8a66 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import BRAINSROIAuto @@ -39,7 +38,7 @@ def test_BRAINSROIAuto_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_BRAINSROIAuto_outputs(): @@ -50,4 +49,4 @@ def test_BRAINSROIAuto_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 3a98a84d41..09b230e05d 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import EMSegmentCommandLine @@ -64,7 +63,7 @@ def test_EMSegmentCommandLine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentCommandLine_outputs(): @@ -76,4 +75,4 @@ def test_EMSegmentCommandLine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index 8c8c954c68..8acc1bf80c 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..specialized import RobustStatisticsSegmenter @@ -39,7 +38,7 @@ def test_RobustStatisticsSegmenter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_RobustStatisticsSegmenter_outputs(): @@ -50,4 +49,4 @@ def test_RobustStatisticsSegmenter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index a06926156e..d34f6dbf85 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from .....testing import assert_equal from ..simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation @@ -40,7 +39,7 @@ def test_SimpleRegionGrowingSegmentation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SimpleRegionGrowingSegmentation_outputs(): @@ -51,4 +50,4 @@ def test_SimpleRegionGrowingSegmentation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index e758a394f2..fa19e0a68f 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..converters import DicomToNrrdConverter @@ -34,7 +33,7 @@ def test_DicomToNrrdConverter_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DicomToNrrdConverter_outputs(): @@ -44,4 +43,4 @@ def test_DicomToNrrdConverter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index 3ef48595c8..83d5cd30f3 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utilities import EMSegmentTransformToNewFormat @@ -26,7 +25,7 @@ def test_EMSegmentTransformToNewFormat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EMSegmentTransformToNewFormat_outputs(): @@ -36,4 +35,4 @@ def test_EMSegmentTransformToNewFormat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index 5d871640f5..9f884ac914 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..surface import GrayscaleModelMaker @@ -38,7 +37,7 @@ def test_GrayscaleModelMaker_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GrayscaleModelMaker_outputs(): @@ -49,4 +48,4 @@ def test_GrayscaleModelMaker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index 44bbf0179a..98fb3aa558 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..surface import LabelMapSmoothing @@ -34,7 +33,7 @@ def test_LabelMapSmoothing_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_LabelMapSmoothing_outputs(): @@ -45,4 +44,4 @@ def test_LabelMapSmoothing_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 7dfcefb5be..449a5f9499 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..surface import MergeModels @@ -29,7 +28,7 @@ def test_MergeModels_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MergeModels_outputs(): @@ -40,4 +39,4 @@ def test_MergeModels_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index 1137fe4898..c5f2a9353a 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..surface import ModelMaker @@ -58,7 +57,7 @@ def test_ModelMaker_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ModelMaker_outputs(): @@ -68,4 +67,4 @@ def test_ModelMaker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 2756e03782..44cbb87d71 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..surface import ModelToLabelMap @@ -31,7 +30,7 @@ def test_ModelToLabelMap_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ModelToLabelMap_outputs(): @@ -42,4 +41,4 @@ def test_ModelToLabelMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index 4477681f60..75c01f0ab5 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..converters import OrientScalarVolume @@ -28,7 +27,7 @@ def test_OrientScalarVolume_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_OrientScalarVolume_outputs(): @@ -39,4 +38,4 @@ def test_OrientScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index 842768fd27..f9f468de05 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..surface import ProbeVolumeWithModel @@ -29,7 +28,7 @@ def test_ProbeVolumeWithModel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ProbeVolumeWithModel_outputs(): @@ -40,4 +39,4 @@ def test_ProbeVolumeWithModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py index e480e76324..827a4970e6 100644 --- a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import SlicerCommandLine @@ -19,5 +18,5 @@ def test_SlicerCommandLine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/base.py b/nipype/interfaces/spm/base.py index bd67003ccc..09c9595a6b 100644 --- a/nipype/interfaces/spm/base.py +++ b/nipype/interfaces/spm/base.py @@ -200,7 +200,7 @@ def version(matlab_cmd=None, paths=None, use_mcr=None): def no_spm(): """ Checks if SPM is NOT installed - used with nosetests skipif to skip tests + used with pytest.mark.skipif decorator to skip tests that will fail if spm is not installed""" if 'NIPYPE_NO_MATLAB' in os.environ or Info.version() is None: diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index 2f175f80f6..24ac7c8f51 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Analyze2nii @@ -22,7 +21,7 @@ def test_Analyze2nii_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Analyze2nii_outputs(): @@ -43,4 +42,4 @@ def test_Analyze2nii_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index a84d6e8246..9a536e3fbb 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import ApplyDeformations @@ -31,7 +30,7 @@ def test_ApplyDeformations_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyDeformations_outputs(): @@ -41,4 +40,4 @@ def test_ApplyDeformations_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index 31c70733a7..54fe2aa325 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ApplyInverseDeformation @@ -37,7 +36,7 @@ def test_ApplyInverseDeformation_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyInverseDeformation_outputs(): @@ -47,4 +46,4 @@ def test_ApplyInverseDeformation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index 090ae3e200..4113255a95 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ApplyTransform @@ -27,7 +26,7 @@ def test_ApplyTransform_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ApplyTransform_outputs(): @@ -37,4 +36,4 @@ def test_ApplyTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index a058f57767..e48ff7ec90 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import CalcCoregAffine @@ -27,7 +26,7 @@ def test_CalcCoregAffine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CalcCoregAffine_outputs(): @@ -38,4 +37,4 @@ def test_CalcCoregAffine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 5b8eb8f51f..69e32c6ae5 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Coregister @@ -50,7 +49,7 @@ def test_Coregister_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Coregister_outputs(): @@ -61,4 +60,4 @@ def test_Coregister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py index 043847d15e..3112480f15 100644 --- a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py +++ b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import CreateWarped @@ -34,7 +33,7 @@ def test_CreateWarped_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CreateWarped_outputs(): @@ -44,4 +43,4 @@ def test_CreateWarped_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index 0e3bb00668..0737efcb60 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import DARTEL @@ -33,7 +32,7 @@ def test_DARTEL_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DARTEL_outputs(): @@ -45,4 +44,4 @@ def test_DARTEL_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index 8af7fc0285..6c87dc3e6a 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import DARTELNorm2MNI @@ -39,7 +38,7 @@ def test_DARTELNorm2MNI_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DARTELNorm2MNI_outputs(): @@ -50,4 +49,4 @@ def test_DARTELNorm2MNI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_DicomImport.py b/nipype/interfaces/spm/tests/test_auto_DicomImport.py index 9bc1c2762e..b3b6221ad2 100644 --- a/nipype/interfaces/spm/tests/test_auto_DicomImport.py +++ b/nipype/interfaces/spm/tests/test_auto_DicomImport.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import DicomImport @@ -35,7 +34,7 @@ def test_DicomImport_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DicomImport_outputs(): @@ -45,4 +44,4 @@ def test_DicomImport_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index 0332c7c622..0b0899d878 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import EstimateContrast @@ -36,7 +35,7 @@ def test_EstimateContrast_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EstimateContrast_outputs(): @@ -50,4 +49,4 @@ def test_EstimateContrast_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index 44d269e89c..9df181ee8b 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import EstimateModel @@ -28,7 +27,7 @@ def test_EstimateModel_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_EstimateModel_outputs(): @@ -42,4 +41,4 @@ def test_EstimateModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index 592d6d1ad5..1fcc234efd 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import FactorialDesign @@ -50,7 +49,7 @@ def test_FactorialDesign_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FactorialDesign_outputs(): @@ -60,4 +59,4 @@ def test_FactorialDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index de50c577c0..4048ac544d 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Level1Design @@ -50,7 +49,7 @@ def test_Level1Design_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Level1Design_outputs(): @@ -60,4 +59,4 @@ def test_Level1Design_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 52b9d8d1b0..953817913b 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import MultipleRegressionDesign @@ -58,7 +57,7 @@ def test_MultipleRegressionDesign_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MultipleRegressionDesign_outputs(): @@ -68,4 +67,4 @@ def test_MultipleRegressionDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_NewSegment.py b/nipype/interfaces/spm/tests/test_auto_NewSegment.py index 89f6a5c18c..0fefdf44cc 100644 --- a/nipype/interfaces/spm/tests/test_auto_NewSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_NewSegment.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import NewSegment @@ -36,7 +35,7 @@ def test_NewSegment_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_NewSegment_outputs(): @@ -54,4 +53,4 @@ def test_NewSegment_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index cf44ee2edd..9f5a0d2742 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Normalize @@ -71,7 +70,7 @@ def test_Normalize_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Normalize_outputs(): @@ -83,4 +82,4 @@ def test_Normalize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index 651a072ba4..315d3065c0 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Normalize12 @@ -60,7 +59,7 @@ def test_Normalize12_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Normalize12_outputs(): @@ -72,4 +71,4 @@ def test_Normalize12_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index 010d4e47f7..e2a36544b8 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import OneSampleTTestDesign @@ -53,7 +52,7 @@ def test_OneSampleTTestDesign_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_OneSampleTTestDesign_outputs(): @@ -63,4 +62,4 @@ def test_OneSampleTTestDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index 0e5eddf50b..1202f40a7a 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import PairedTTestDesign @@ -57,7 +56,7 @@ def test_PairedTTestDesign_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PairedTTestDesign_outputs(): @@ -67,4 +66,4 @@ def test_PairedTTestDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 6ee1c7a110..d024eb6a89 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Realign @@ -54,7 +53,7 @@ def test_Realign_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Realign_outputs(): @@ -67,4 +66,4 @@ def test_Realign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 1687309bd7..b8fa610357 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import Reslice @@ -27,7 +26,7 @@ def test_Reslice_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Reslice_outputs(): @@ -37,4 +36,4 @@ def test_Reslice_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index d791b5965a..120656a069 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..utils import ResliceToReference @@ -31,7 +30,7 @@ def test_ResliceToReference_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ResliceToReference_outputs(): @@ -41,4 +40,4 @@ def test_ResliceToReference_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py index 76676dd1ab..7db3e8e391 100644 --- a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py +++ b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..base import SPMCommand @@ -20,5 +19,5 @@ def test_SPMCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index c32284105c..8a08571ec7 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Segment @@ -52,7 +51,7 @@ def test_Segment_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Segment_outputs(): @@ -76,4 +75,4 @@ def test_Segment_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py index c230c2909c..62d2d5e8a5 100644 --- a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py +++ b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import SliceTiming @@ -42,7 +41,7 @@ def test_SliceTiming_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SliceTiming_outputs(): @@ -52,4 +51,4 @@ def test_SliceTiming_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Smooth.py b/nipype/interfaces/spm/tests/test_auto_Smooth.py index aa5708ba5f..9c2d8d155a 100644 --- a/nipype/interfaces/spm/tests/test_auto_Smooth.py +++ b/nipype/interfaces/spm/tests/test_auto_Smooth.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import Smooth @@ -33,7 +32,7 @@ def test_Smooth_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Smooth_outputs(): @@ -43,4 +42,4 @@ def test_Smooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index e79460f980..a2088dd7aa 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import Threshold @@ -42,7 +41,7 @@ def test_Threshold_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Threshold_outputs(): @@ -57,4 +56,4 @@ def test_Threshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index a5363ebccd..e8f863975f 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import ThresholdStatistics @@ -32,7 +31,7 @@ def test_ThresholdStatistics_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_ThresholdStatistics_outputs(): @@ -47,4 +46,4 @@ def test_ThresholdStatistics_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index dd5104afb6..7344c0e0fb 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..model import TwoSampleTTestDesign @@ -60,7 +59,7 @@ def test_TwoSampleTTestDesign_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_TwoSampleTTestDesign_outputs(): @@ -70,4 +69,4 @@ def test_TwoSampleTTestDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index 1b330af007..09f9807cb2 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..preprocess import VBMSegment @@ -116,7 +115,7 @@ def test_VBMSegment_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VBMSegment_outputs(): @@ -138,4 +137,4 @@ def test_VBMSegment_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/spm/tests/test_base.py b/nipype/interfaces/spm/tests/test_base.py index 93a591aac2..6887766ad3 100644 --- a/nipype/interfaces/spm/tests/test_base.py +++ b/nipype/interfaces/spm/tests/test_base.py @@ -11,7 +11,7 @@ import nibabel as nb import numpy as np -from nipype.testing import (assert_equal, assert_false, assert_true, skipif) +import pytest import nipype.interfaces.spm.base as spm from nipype.interfaces.spm import no_spm import nipype.interfaces.matlab as mlab @@ -25,8 +25,8 @@ mlab.MatlabCommand.set_default_matlab_cmd(matlab_cmd) - -def create_files_in_directory(): +@pytest.fixture() +def create_files_in_directory(request): outdir = mkdtemp() cwd = os.getcwd() os.chdir(outdir) @@ -38,38 +38,38 @@ def create_files_in_directory(): img = np.random.random(shape) nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(outdir, f)) - return filelist, outdir, cwd + def clean_directory(): + if os.path.exists(outdir): + rmtree(outdir) + os.chdir(cwd) -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): - rmtree(outdir) - os.chdir(old_wd) + request.addfinalizer(clean_directory) + return (filelist, outdir) -def test_scan_for_fnames(): - filelist, outdir, cwd = create_files_in_directory() +def test_scan_for_fnames(create_files_in_directory): + filelist, outdir = create_files_in_directory names = spm.scans_for_fnames(filelist, keep4d=True) - yield assert_equal, names[0], filelist[0] - yield assert_equal, names[1], filelist[1] - clean_directory(outdir, cwd) - + assert names[0] == filelist[0] + assert names[1] == filelist[1] + save_time = False if not save_time: - @skipif(no_spm) + @pytest.mark.skipif(no_spm(), reason="spm is not installed") def test_spm_path(): spm_path = spm.Info.version()['path'] if spm_path is not None: - yield assert_true, isinstance(spm_path, (str, bytes)) - yield assert_true, 'spm' in spm_path + assert isinstance(spm_path, (str, bytes)) + assert 'spm' in spm_path def test_use_mfile(): class TestClass(spm.SPMCommand): input_spec = spm.SPMCommandInputSpec dc = TestClass() # dc = derived_class - yield assert_true, dc.inputs.mfile + assert dc.inputs.mfile def test_find_mlab_cmd_defaults(): @@ -84,30 +84,30 @@ class TestClass(spm.SPMCommand): except KeyError: pass dc = TestClass() - yield assert_equal, dc._use_mcr, None - yield assert_equal, dc._matlab_cmd, None + assert dc._use_mcr == None + assert dc._matlab_cmd == None # test with only FORCE_SPMMCR set os.environ['FORCE_SPMMCR'] = '1' dc = TestClass() - yield assert_equal, dc._use_mcr, True - yield assert_equal, dc._matlab_cmd, None + assert dc._use_mcr == True + assert dc._matlab_cmd == None # test with both, FORCE_SPMMCR and SPMMCRCMD set os.environ['SPMMCRCMD'] = 'spmcmd' dc = TestClass() - yield assert_equal, dc._use_mcr, True - yield assert_equal, dc._matlab_cmd, 'spmcmd' + assert dc._use_mcr == True + assert dc._matlab_cmd == 'spmcmd' # restore environment os.environ.clear() os.environ.update(saved_env) -@skipif(no_spm, "SPM not found") +@pytest.mark.skipif(no_spm(), reason="spm is not installed") def test_cmd_update(): class TestClass(spm.SPMCommand): input_spec = spm.SPMCommandInputSpec dc = TestClass() # dc = derived_class dc.inputs.matlab_cmd = 'foo' - yield assert_equal, dc.mlab._cmd, 'foo' + assert dc.mlab._cmd == 'foo' def test_cmd_update2(): @@ -116,8 +116,8 @@ class TestClass(spm.SPMCommand): _jobname = 'jobname' input_spec = spm.SPMCommandInputSpec dc = TestClass() # dc = derived_class - yield assert_equal, dc.jobtype, 'jobtype' - yield assert_equal, dc.jobname, 'jobname' + assert dc.jobtype == 'jobtype' + assert dc.jobname == 'jobname' def test_reformat_dict_for_savemat(): @@ -125,36 +125,35 @@ class TestClass(spm.SPMCommand): input_spec = spm.SPMCommandInputSpec dc = TestClass() # dc = derived_class out = dc._reformat_dict_for_savemat({'a': {'b': {'c': []}}}) - yield assert_equal, out, [{'a': [{'b': [{'c': []}]}]}] + assert out == [{'a': [{'b': [{'c': []}]}]}] -def test_generate_job(): +def test_generate_job(create_files_in_directory): class TestClass(spm.SPMCommand): input_spec = spm.SPMCommandInputSpec dc = TestClass() # dc = derived_class out = dc._generate_job() - yield assert_equal, out, '' + assert out == '' # struct array contents = {'contents': [1, 2, 3, 4]} out = dc._generate_job(contents=contents) - yield assert_equal, out, ('.contents(1) = 1;\n.contents(2) = 2;' - '\n.contents(3) = 3;\n.contents(4) = 4;\n') + assert out == ('.contents(1) = 1;\n.contents(2) = 2;' + '\n.contents(3) = 3;\n.contents(4) = 4;\n') # cell array of strings - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir = create_files_in_directory names = spm.scans_for_fnames(filelist, keep4d=True) contents = {'files': names} out = dc._generate_job(prefix='test', contents=contents) - yield assert_equal, out, "test.files = {...\n'a.nii';...\n'b.nii';...\n};\n" - clean_directory(outdir, cwd) + assert out == "test.files = {...\n'a.nii';...\n'b.nii';...\n};\n" # string assignment contents = 'foo' out = dc._generate_job(prefix='test', contents=contents) - yield assert_equal, out, "test = 'foo';\n" + assert out == "test = 'foo';\n" # cell array of vectors contents = {'onsets': np.array((1,), dtype=object)} contents['onsets'][0] = [1, 2, 3, 4] out = dc._generate_job(prefix='test', contents=contents) - yield assert_equal, out, 'test.onsets = {...\n[1, 2, 3, 4];...\n};\n' + assert out == 'test.onsets = {...\n[1, 2, 3, 4];...\n};\n' def test_bool(): @@ -168,23 +167,22 @@ class TestClass(spm.SPMCommand): dc = TestClass() # dc = derived_class dc.inputs.test_in = True out = dc._make_matlab_command(dc._parse_inputs()) - yield assert_equal, out.find('jobs{1}.spm.jobtype.jobname.testfield = 1;') > 0, 1 + assert out.find('jobs{1}.spm.jobtype.jobname.testfield = 1;') > 0, 1 dc.inputs.use_v8struct = False out = dc._make_matlab_command(dc._parse_inputs()) - yield assert_equal, out.find('jobs{1}.jobtype{1}.jobname{1}.testfield = 1;') > 0, 1 + assert out.find('jobs{1}.jobtype{1}.jobname{1}.testfield = 1;') > 0, 1 -def test_make_matlab_command(): +def test_make_matlab_command(create_files_in_directory): class TestClass(spm.SPMCommand): _jobtype = 'jobtype' _jobname = 'jobname' input_spec = spm.SPMCommandInputSpec dc = TestClass() # dc = derived_class - filelist, outdir, cwd = create_files_in_directory() + filelist, outdir = create_files_in_directory contents = {'contents': [1, 2, 3, 4]} script = dc._make_matlab_command([contents]) - yield assert_true, 'jobs{1}.spm.jobtype.jobname.contents(3) = 3;' in script + assert 'jobs{1}.spm.jobtype.jobname.contents(3) = 3;' in script dc.inputs.use_v8struct = False script = dc._make_matlab_command([contents]) - yield assert_true, 'jobs{1}.jobtype{1}.jobname{1}.contents(3) = 3;' in script - clean_directory(outdir, cwd) + assert 'jobs{1}.jobtype{1}.jobname{1}.contents(3) = 3;' in script diff --git a/nipype/interfaces/spm/tests/test_model.py b/nipype/interfaces/spm/tests/test_model.py index dd49474bed..e9e8a48849 100644 --- a/nipype/interfaces/spm/tests/test_model.py +++ b/nipype/interfaces/spm/tests/test_model.py @@ -2,16 +2,8 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: import os -from tempfile import mkdtemp -from shutil import rmtree -import numpy as np - -from nipype.testing import (assert_equal, assert_false, assert_true, - assert_raises, skipif) -import nibabel as nb import nipype.interfaces.spm.model as spm -from nipype.interfaces.spm import no_spm import nipype.interfaces.matlab as mlab try: @@ -22,57 +14,36 @@ mlab.MatlabCommand.set_default_matlab_cmd(matlab_cmd) -def create_files_in_directory(): - outdir = mkdtemp() - cwd = os.getcwd() - os.chdir(outdir) - filelist = ['a.nii', 'b.nii'] - for f in filelist: - hdr = nb.Nifti1Header() - shape = (3, 3, 3, 4) - hdr.set_data_shape(shape) - img = np.random.random(shape) - nb.save(nb.Nifti1Image(img, np.eye(4), hdr), - os.path.join(outdir, f)) - return filelist, outdir, cwd - - -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): - rmtree(outdir) - os.chdir(old_wd) - - def test_level1design(): - yield assert_equal, spm.Level1Design._jobtype, 'stats' - yield assert_equal, spm.Level1Design._jobname, 'fmri_spec' + assert spm.Level1Design._jobtype == 'stats' + assert spm.Level1Design._jobname == 'fmri_spec' def test_estimatemodel(): - yield assert_equal, spm.EstimateModel._jobtype, 'stats' - yield assert_equal, spm.EstimateModel._jobname, 'fmri_est' + assert spm.EstimateModel._jobtype == 'stats' + assert spm.EstimateModel._jobname == 'fmri_est' def test_estimatecontrast(): - yield assert_equal, spm.EstimateContrast._jobtype, 'stats' - yield assert_equal, spm.EstimateContrast._jobname, 'con' + assert spm.EstimateContrast._jobtype == 'stats' + assert spm.EstimateContrast._jobname == 'con' def test_threshold(): - yield assert_equal, spm.Threshold._jobtype, 'basetype' - yield assert_equal, spm.Threshold._jobname, 'basename' + assert spm.Threshold._jobtype == 'basetype' + assert spm.Threshold._jobname == 'basename' def test_factorialdesign(): - yield assert_equal, spm.FactorialDesign._jobtype, 'stats' - yield assert_equal, spm.FactorialDesign._jobname, 'factorial_design' + assert spm.FactorialDesign._jobtype == 'stats' + assert spm.FactorialDesign._jobname == 'factorial_design' def test_onesamplettestdesign(): - yield assert_equal, spm.OneSampleTTestDesign._jobtype, 'stats' - yield assert_equal, spm.OneSampleTTestDesign._jobname, 'factorial_design' + assert spm.OneSampleTTestDesign._jobtype == 'stats' + assert spm.OneSampleTTestDesign._jobname == 'factorial_design' def test_twosamplettestdesign(): - yield assert_equal, spm.TwoSampleTTestDesign._jobtype, 'stats' - yield assert_equal, spm.TwoSampleTTestDesign._jobname, 'factorial_design' + assert spm.TwoSampleTTestDesign._jobtype == 'stats' + assert spm.TwoSampleTTestDesign._jobname == 'factorial_design' diff --git a/nipype/interfaces/spm/tests/test_preprocess.py b/nipype/interfaces/spm/tests/test_preprocess.py index af82430e68..0a2535cba5 100644 --- a/nipype/interfaces/spm/tests/test_preprocess.py +++ b/nipype/interfaces/spm/tests/test_preprocess.py @@ -7,8 +7,7 @@ import numpy as np -from nipype.testing import (assert_equal, assert_false, assert_true, - assert_raises, skipif) +import pytest import nibabel as nb import nipype.interfaces.spm as spm from nipype.interfaces.spm import no_spm @@ -21,8 +20,8 @@ mlab.MatlabCommand.set_default_matlab_cmd(matlab_cmd) - -def create_files_in_directory(): +@pytest.fixture() +def create_files_in_directory(request): outdir = mkdtemp() cwd = os.getcwd() os.chdir(outdir) @@ -34,118 +33,114 @@ def create_files_in_directory(): img = np.random.random(shape) nb.save(nb.Nifti1Image(img, np.eye(4), hdr), os.path.join(outdir, f)) - return filelist, outdir, cwd + def clean_directory(): + if os.path.exists(outdir): + rmtree(outdir) + os.chdir(cwd) -def clean_directory(outdir, old_wd): - if os.path.exists(outdir): - rmtree(outdir) - os.chdir(old_wd) + request.addfinalizer(clean_directory) + return filelist, outdir, cwd def test_slicetiming(): - yield assert_equal, spm.SliceTiming._jobtype, 'temporal' - yield assert_equal, spm.SliceTiming._jobname, 'st' + assert spm.SliceTiming._jobtype == 'temporal' + assert spm.SliceTiming._jobname == 'st' -def test_slicetiming_list_outputs(): - filelist, outdir, cwd = create_files_in_directory() +def test_slicetiming_list_outputs(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory st = spm.SliceTiming(in_files=filelist[0]) - yield assert_equal, st._list_outputs()['timecorrected_files'][0][0], 'a' - clean_directory(outdir, cwd) - + assert st._list_outputs()['timecorrected_files'][0][0] == 'a' + def test_realign(): - yield assert_equal, spm.Realign._jobtype, 'spatial' - yield assert_equal, spm.Realign._jobname, 'realign' - yield assert_equal, spm.Realign().inputs.jobtype, 'estwrite' + assert spm.Realign._jobtype == 'spatial' + assert spm.Realign._jobname == 'realign' + assert spm.Realign().inputs.jobtype == 'estwrite' -def test_realign_list_outputs(): - filelist, outdir, cwd = create_files_in_directory() +def test_realign_list_outputs(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory rlgn = spm.Realign(in_files=filelist[0]) - yield assert_true, rlgn._list_outputs()['realignment_parameters'][0].startswith('rp_') - yield assert_true, rlgn._list_outputs()['realigned_files'][0].startswith('r') - yield assert_true, rlgn._list_outputs()['mean_image'].startswith('mean') - clean_directory(outdir, cwd) - + assert rlgn._list_outputs()['realignment_parameters'][0].startswith('rp_') + assert rlgn._list_outputs()['realigned_files'][0].startswith('r') + assert rlgn._list_outputs()['mean_image'].startswith('mean') + def test_coregister(): - yield assert_equal, spm.Coregister._jobtype, 'spatial' - yield assert_equal, spm.Coregister._jobname, 'coreg' - yield assert_equal, spm.Coregister().inputs.jobtype, 'estwrite' + assert spm.Coregister._jobtype == 'spatial' + assert spm.Coregister._jobname == 'coreg' + assert spm.Coregister().inputs.jobtype == 'estwrite' -def test_coregister_list_outputs(): - filelist, outdir, cwd = create_files_in_directory() +def test_coregister_list_outputs(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory coreg = spm.Coregister(source=filelist[0]) - yield assert_true, coreg._list_outputs()['coregistered_source'][0].startswith('r') + assert coreg._list_outputs()['coregistered_source'][0].startswith('r') coreg = spm.Coregister(source=filelist[0], apply_to_files=filelist[1]) - yield assert_true, coreg._list_outputs()['coregistered_files'][0].startswith('r') - clean_directory(outdir, cwd) - + assert coreg._list_outputs()['coregistered_files'][0].startswith('r') + def test_normalize(): - yield assert_equal, spm.Normalize._jobtype, 'spatial' - yield assert_equal, spm.Normalize._jobname, 'normalise' - yield assert_equal, spm.Normalize().inputs.jobtype, 'estwrite' + assert spm.Normalize._jobtype == 'spatial' + assert spm.Normalize._jobname == 'normalise' + assert spm.Normalize().inputs.jobtype == 'estwrite' -def test_normalize_list_outputs(): - filelist, outdir, cwd = create_files_in_directory() +def test_normalize_list_outputs(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory norm = spm.Normalize(source=filelist[0]) - yield assert_true, norm._list_outputs()['normalized_source'][0].startswith('w') + assert norm._list_outputs()['normalized_source'][0].startswith('w') norm = spm.Normalize(source=filelist[0], apply_to_files=filelist[1]) - yield assert_true, norm._list_outputs()['normalized_files'][0].startswith('w') - clean_directory(outdir, cwd) - + assert norm._list_outputs()['normalized_files'][0].startswith('w') + def test_normalize12(): - yield assert_equal, spm.Normalize12._jobtype, 'spatial' - yield assert_equal, spm.Normalize12._jobname, 'normalise' - yield assert_equal, spm.Normalize12().inputs.jobtype, 'estwrite' + assert spm.Normalize12._jobtype == 'spatial' + assert spm.Normalize12._jobname == 'normalise' + assert spm.Normalize12().inputs.jobtype == 'estwrite' -def test_normalize12_list_outputs(): - filelist, outdir, cwd = create_files_in_directory() +def test_normalize12_list_outputs(create_files_in_directory): + filelist, outdir, cwd = create_files_in_directory norm12 = spm.Normalize12(image_to_align=filelist[0]) - yield assert_true, norm12._list_outputs()['normalized_image'][0].startswith('w') + assert norm12._list_outputs()['normalized_image'][0].startswith('w') norm12 = spm.Normalize12(image_to_align=filelist[0], apply_to_files=filelist[1]) - yield assert_true, norm12._list_outputs()['normalized_files'][0].startswith('w') - clean_directory(outdir, cwd) - + assert norm12._list_outputs()['normalized_files'][0].startswith('w') + -@skipif(no_spm) +@pytest.mark.skipif(no_spm(), reason="spm is not installed") def test_segment(): if spm.Info.version()['name'] == "SPM12": - yield assert_equal, spm.Segment()._jobtype, 'tools' - yield assert_equal, spm.Segment()._jobname, 'oldseg' + assert spm.Segment()._jobtype == 'tools' + assert spm.Segment()._jobname == 'oldseg' else: - yield assert_equal, spm.Segment()._jobtype, 'spatial' - yield assert_equal, spm.Segment()._jobname, 'preproc' + assert spm.Segment()._jobtype == 'spatial' + assert spm.Segment()._jobname == 'preproc' -@skipif(no_spm) +@pytest.mark.skipif(no_spm(), reason="spm is not installed") def test_newsegment(): if spm.Info.version()['name'] == "SPM12": - yield assert_equal, spm.NewSegment()._jobtype, 'spatial' - yield assert_equal, spm.NewSegment()._jobname, 'preproc' + assert spm.NewSegment()._jobtype == 'spatial' + assert spm.NewSegment()._jobname == 'preproc' else: - yield assert_equal, spm.NewSegment()._jobtype, 'tools' - yield assert_equal, spm.NewSegment()._jobname, 'preproc8' + assert spm.NewSegment()._jobtype == 'tools' + assert spm.NewSegment()._jobname == 'preproc8' def test_smooth(): - yield assert_equal, spm.Smooth._jobtype, 'spatial' - yield assert_equal, spm.Smooth._jobname, 'smooth' + assert spm.Smooth._jobtype == 'spatial' + assert spm.Smooth._jobname == 'smooth' def test_dartel(): - yield assert_equal, spm.DARTEL._jobtype, 'tools' - yield assert_equal, spm.DARTEL._jobname, 'dartel' + assert spm.DARTEL._jobtype == 'tools' + assert spm.DARTEL._jobname == 'dartel' def test_dartelnorm2mni(): - yield assert_equal, spm.DARTELNorm2MNI._jobtype, 'tools' - yield assert_equal, spm.DARTELNorm2MNI._jobname, 'dartel' + assert spm.DARTELNorm2MNI._jobtype == 'tools' + assert spm.DARTELNorm2MNI._jobname == 'dartel' diff --git a/nipype/interfaces/spm/tests/test_utils.py b/nipype/interfaces/spm/tests/test_utils.py index bbb8c6b604..7d8106f80c 100644 --- a/nipype/interfaces/spm/tests/test_utils.py +++ b/nipype/interfaces/spm/tests/test_utils.py @@ -2,9 +2,8 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: import os -from nipype.testing import (assert_equal, assert_false, assert_raises, - assert_true, skipif, example_data) -from nipype.interfaces.spm import no_spm +import pytest +from nipype.testing import example_data import nipype.interfaces.spm.utils as spmu from nipype.interfaces.base import isdefined from nipype.utils.filemanip import split_filename, fname_presuffix @@ -17,63 +16,63 @@ def test_coreg(): mat = example_data(infile='trans.mat') coreg = spmu.CalcCoregAffine(matlab_cmd='mymatlab') coreg.inputs.target = target - assert_equal(coreg.inputs.matlab_cmd, 'mymatlab') + assert coreg.inputs.matlab_cmd == 'mymatlab' coreg.inputs.moving = moving - assert_equal(isdefined(coreg.inputs.mat), False) + assert isdefined(coreg.inputs.mat) == False pth, mov, _ = split_filename(moving) _, tgt, _ = split_filename(target) mat = os.path.join(pth, '%s_to_%s.mat' % (mov, tgt)) invmat = fname_presuffix(mat, prefix='inverse_') scrpt = coreg._make_matlab_command(None) - assert_equal(coreg.inputs.mat, mat) - assert_equal(coreg.inputs.invmat, invmat) + assert coreg.inputs.mat == mat + assert coreg.inputs.invmat == invmat def test_apply_transform(): moving = example_data(infile='functional.nii') mat = example_data(infile='trans.mat') applymat = spmu.ApplyTransform(matlab_cmd='mymatlab') - assert_equal(applymat.inputs.matlab_cmd, 'mymatlab') + assert applymat.inputs.matlab_cmd == 'mymatlab' applymat.inputs.in_file = moving applymat.inputs.mat = mat scrpt = applymat._make_matlab_command(None) expected = '[p n e v] = spm_fileparts(V.fname);' - assert_equal(expected in scrpt, True) + assert expected in scrpt expected = 'V.mat = transform.M * V.mat;' - assert_equal(expected in scrpt, True) + assert expected in scrpt def test_reslice(): moving = example_data(infile='functional.nii') space_defining = example_data(infile='T1.nii') reslice = spmu.Reslice(matlab_cmd='mymatlab_version') - assert_equal(reslice.inputs.matlab_cmd, 'mymatlab_version') + assert reslice.inputs.matlab_cmd == 'mymatlab_version' reslice.inputs.in_file = moving reslice.inputs.space_defining = space_defining - assert_equal(reslice.inputs.interp, 0) - assert_raises(TraitError, reslice.inputs.trait_set, interp='nearest') - assert_raises(TraitError, reslice.inputs.trait_set, interp=10) + assert reslice.inputs.interp == 0 + with pytest.raises(TraitError): reslice.inputs.trait_set(interp='nearest') + with pytest.raises(TraitError): reslice.inputs.trait_set(interp=10) reslice.inputs.interp = 1 script = reslice._make_matlab_command(None) outfile = fname_presuffix(moving, prefix='r') - assert_equal(reslice.inputs.out_file, outfile) + assert reslice.inputs.out_file == outfile expected = '\nflags.mean=0;\nflags.which=1;\nflags.mask=0;' - assert_equal(expected in script.replace(' ', ''), True) + assert expected in script.replace(' ', '') expected_interp = 'flags.interp = 1;\n' - assert_equal(expected_interp in script, True) - assert_equal('spm_reslice(invols, flags);' in script, True) + assert expected_interp in script + assert 'spm_reslice(invols, flags);' in script def test_dicom_import(): dicom = example_data(infile='dicomdir/123456-1-1.dcm') di = spmu.DicomImport(matlab_cmd='mymatlab') - assert_equal(di.inputs.matlab_cmd, 'mymatlab') - assert_equal(di.inputs.output_dir_struct, 'flat') - assert_equal(di.inputs.output_dir, './converted_dicom') - assert_equal(di.inputs.format, 'nii') - assert_equal(di.inputs.icedims, False) - assert_raises(TraitError, di.inputs.trait_set, output_dir_struct='wrong') - assert_raises(TraitError, di.inputs.trait_set, format='FAT') - assert_raises(TraitError, di.inputs.trait_set, in_files=['does_sfd_not_32fn_exist.dcm']) + assert di.inputs.matlab_cmd == 'mymatlab' + assert di.inputs.output_dir_struct == 'flat' + assert di.inputs.output_dir == './converted_dicom' + assert di.inputs.format == 'nii' + assert di.inputs.icedims == False + with pytest.raises(TraitError): di.inputs.trait_set(output_dir_struct='wrong') + with pytest.raises(TraitError): di.inputs.trait_set(format='FAT') + with pytest.raises(TraitError): di.inputs.trait_set(in_files=['does_sfd_not_32fn_exist.dcm']) di.inputs.in_files = [dicom] - assert_equal(di.inputs.in_files, [dicom]) + assert di.inputs.in_files == [dicom] diff --git a/nipype/interfaces/tests/test_auto_AssertEqual.py b/nipype/interfaces/tests/test_auto_AssertEqual.py index 4a1d763e43..4bfd775566 100644 --- a/nipype/interfaces/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/tests/test_auto_AssertEqual.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import AssertEqual @@ -16,5 +15,5 @@ def test_AssertEqual_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_BaseInterface.py b/nipype/interfaces/tests/test_auto_BaseInterface.py index 5851add1da..b37643034b 100644 --- a/nipype/interfaces/tests/test_auto_BaseInterface.py +++ b/nipype/interfaces/tests/test_auto_BaseInterface.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..base import BaseInterface @@ -12,5 +11,5 @@ def test_BaseInterface_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Bru2.py b/nipype/interfaces/tests/test_auto_Bru2.py index ffe5559706..56c9463c3f 100644 --- a/nipype/interfaces/tests/test_auto_Bru2.py +++ b/nipype/interfaces/tests/test_auto_Bru2.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..bru2nii import Bru2 @@ -32,7 +31,7 @@ def test_Bru2_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Bru2_outputs(): @@ -42,4 +41,4 @@ def test_Bru2_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index dc8cc37b8c..92c046474d 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..c3 import C3dAffineTool @@ -35,7 +34,7 @@ def test_C3dAffineTool_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_C3dAffineTool_outputs(): @@ -45,4 +44,4 @@ def test_C3dAffineTool_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_CSVReader.py b/nipype/interfaces/tests/test_auto_CSVReader.py index a6f42de676..7e2862947c 100644 --- a/nipype/interfaces/tests/test_auto_CSVReader.py +++ b/nipype/interfaces/tests/test_auto_CSVReader.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import CSVReader @@ -13,7 +12,7 @@ def test_CSVReader_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CSVReader_outputs(): @@ -22,4 +21,4 @@ def test_CSVReader_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_CommandLine.py b/nipype/interfaces/tests/test_auto_CommandLine.py index 9ea4f08937..c36d4acd5f 100644 --- a/nipype/interfaces/tests/test_auto_CommandLine.py +++ b/nipype/interfaces/tests/test_auto_CommandLine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..base import CommandLine @@ -19,5 +18,5 @@ def test_CommandLine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_CopyMeta.py b/nipype/interfaces/tests/test_auto_CopyMeta.py index 8b456d4e09..8d4c82de27 100644 --- a/nipype/interfaces/tests/test_auto_CopyMeta.py +++ b/nipype/interfaces/tests/test_auto_CopyMeta.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcmstack import CopyMeta @@ -15,7 +14,7 @@ def test_CopyMeta_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_CopyMeta_outputs(): @@ -25,4 +24,4 @@ def test_CopyMeta_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_DataFinder.py b/nipype/interfaces/tests/test_auto_DataFinder.py index 8eb5faa9ea..8737206f4d 100644 --- a/nipype/interfaces/tests/test_auto_DataFinder.py +++ b/nipype/interfaces/tests/test_auto_DataFinder.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import DataFinder @@ -21,7 +20,7 @@ def test_DataFinder_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DataFinder_outputs(): @@ -30,4 +29,4 @@ def test_DataFinder_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index f72eb2bdfe..93a0ff9225 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import DataGrabber @@ -20,7 +19,7 @@ def test_DataGrabber_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DataGrabber_outputs(): @@ -29,4 +28,4 @@ def test_DataGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index c84e98f17b..c07d57cf13 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import DataSink @@ -27,7 +26,7 @@ def test_DataSink_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DataSink_outputs(): @@ -37,4 +36,4 @@ def test_DataSink_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index b674bf6a47..f16ca2087d 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcm2nii import Dcm2nii @@ -74,7 +73,7 @@ def test_Dcm2nii_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Dcm2nii_outputs(): @@ -88,4 +87,4 @@ def test_Dcm2nii_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Dcm2niix.py b/nipype/interfaces/tests/test_auto_Dcm2niix.py index ce1ca0fb81..7641e7d25e 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2niix.py +++ b/nipype/interfaces/tests/test_auto_Dcm2niix.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcm2nii import Dcm2niix @@ -57,7 +56,7 @@ def test_Dcm2niix_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Dcm2niix_outputs(): @@ -70,4 +69,4 @@ def test_Dcm2niix_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_DcmStack.py b/nipype/interfaces/tests/test_auto_DcmStack.py index c91379caa6..dba11bfbbe 100644 --- a/nipype/interfaces/tests/test_auto_DcmStack.py +++ b/nipype/interfaces/tests/test_auto_DcmStack.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcmstack import DcmStack @@ -20,7 +19,7 @@ def test_DcmStack_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_DcmStack_outputs(): @@ -30,4 +29,4 @@ def test_DcmStack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index 8b393bf0c4..f491000f30 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import FreeSurferSource @@ -18,7 +17,7 @@ def test_FreeSurferSource_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_FreeSurferSource_outputs(): @@ -103,4 +102,4 @@ def test_FreeSurferSource_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Function.py b/nipype/interfaces/tests/test_auto_Function.py index 65afafbe47..1e7b395aaa 100644 --- a/nipype/interfaces/tests/test_auto_Function.py +++ b/nipype/interfaces/tests/test_auto_Function.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import Function @@ -14,7 +13,7 @@ def test_Function_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Function_outputs(): @@ -23,4 +22,4 @@ def test_Function_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_GroupAndStack.py b/nipype/interfaces/tests/test_auto_GroupAndStack.py index 8523f76c32..e969566890 100644 --- a/nipype/interfaces/tests/test_auto_GroupAndStack.py +++ b/nipype/interfaces/tests/test_auto_GroupAndStack.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcmstack import GroupAndStack @@ -20,7 +19,7 @@ def test_GroupAndStack_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_GroupAndStack_outputs(): @@ -30,4 +29,4 @@ def test_GroupAndStack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_IOBase.py b/nipype/interfaces/tests/test_auto_IOBase.py index 548b613986..da93d86990 100644 --- a/nipype/interfaces/tests/test_auto_IOBase.py +++ b/nipype/interfaces/tests/test_auto_IOBase.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import IOBase @@ -12,5 +11,5 @@ def test_IOBase_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_IdentityInterface.py b/nipype/interfaces/tests/test_auto_IdentityInterface.py index f5787df81c..214042c365 100644 --- a/nipype/interfaces/tests/test_auto_IdentityInterface.py +++ b/nipype/interfaces/tests/test_auto_IdentityInterface.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import IdentityInterface @@ -9,7 +8,7 @@ def test_IdentityInterface_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_IdentityInterface_outputs(): @@ -18,4 +17,4 @@ def test_IdentityInterface_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index a99c4c6ba2..3f382f014d 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import JSONFileGrabber @@ -14,7 +13,7 @@ def test_JSONFileGrabber_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JSONFileGrabber_outputs(): @@ -23,4 +22,4 @@ def test_JSONFileGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 738166527f..6dad680f1e 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import JSONFileSink @@ -17,7 +16,7 @@ def test_JSONFileSink_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_JSONFileSink_outputs(): @@ -27,4 +26,4 @@ def test_JSONFileSink_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_LookupMeta.py b/nipype/interfaces/tests/test_auto_LookupMeta.py index 7e89973931..b12c3cadaa 100644 --- a/nipype/interfaces/tests/test_auto_LookupMeta.py +++ b/nipype/interfaces/tests/test_auto_LookupMeta.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcmstack import LookupMeta @@ -13,7 +12,7 @@ def test_LookupMeta_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_LookupMeta_outputs(): @@ -22,4 +21,4 @@ def test_LookupMeta_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index 5b879d8b3d..5d37355aba 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..matlab import MatlabCommand @@ -48,5 +47,5 @@ def test_MatlabCommand_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Merge.py b/nipype/interfaces/tests/test_auto_Merge.py index adddcdebd2..b2cda077da 100644 --- a/nipype/interfaces/tests/test_auto_Merge.py +++ b/nipype/interfaces/tests/test_auto_Merge.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import Merge @@ -16,7 +15,7 @@ def test_Merge_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Merge_outputs(): @@ -26,4 +25,4 @@ def test_Merge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_MergeNifti.py b/nipype/interfaces/tests/test_auto_MergeNifti.py index 3a6e0fc5a1..1450f7d8d8 100644 --- a/nipype/interfaces/tests/test_auto_MergeNifti.py +++ b/nipype/interfaces/tests/test_auto_MergeNifti.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcmstack import MergeNifti @@ -17,7 +16,7 @@ def test_MergeNifti_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MergeNifti_outputs(): @@ -27,4 +26,4 @@ def test_MergeNifti_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 549a6b557e..2c22435628 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..meshfix import MeshFix @@ -93,7 +92,7 @@ def test_MeshFix_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_MeshFix_outputs(): @@ -103,4 +102,4 @@ def test_MeshFix_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_MpiCommandLine.py b/nipype/interfaces/tests/test_auto_MpiCommandLine.py index 57d1611f4d..d4740fc03c 100644 --- a/nipype/interfaces/tests/test_auto_MpiCommandLine.py +++ b/nipype/interfaces/tests/test_auto_MpiCommandLine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..base import MpiCommandLine @@ -22,5 +21,5 @@ def test_MpiCommandLine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index ea9904d8d0..2dce6a95ec 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import MySQLSink @@ -26,5 +25,5 @@ def test_MySQLSink_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py index 762c862ed8..438b1018e2 100644 --- a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py +++ b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcmstack import NiftiGeneratorBase @@ -12,5 +11,5 @@ def test_NiftiGeneratorBase_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_PETPVC.py b/nipype/interfaces/tests/test_auto_PETPVC.py index 67c02c72b0..53b948fbe0 100644 --- a/nipype/interfaces/tests/test_auto_PETPVC.py +++ b/nipype/interfaces/tests/test_auto_PETPVC.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..petpvc import PETPVC @@ -52,7 +51,7 @@ def test_PETPVC_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_PETPVC_outputs(): @@ -62,4 +61,4 @@ def test_PETPVC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Rename.py b/nipype/interfaces/tests/test_auto_Rename.py index 1cace232fe..8c7725dd36 100644 --- a/nipype/interfaces/tests/test_auto_Rename.py +++ b/nipype/interfaces/tests/test_auto_Rename.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import Rename @@ -17,7 +16,7 @@ def test_Rename_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Rename_outputs(): @@ -27,4 +26,4 @@ def test_Rename_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py index 584134ca8f..599f0d1897 100644 --- a/nipype/interfaces/tests/test_auto_S3DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import S3DataGrabber @@ -28,7 +27,7 @@ def test_S3DataGrabber_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_S3DataGrabber_outputs(): @@ -37,4 +36,4 @@ def test_S3DataGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py index 8afc2cdec2..2bd112eb3b 100644 --- a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..base import SEMLikeCommandLine @@ -19,5 +18,5 @@ def test_SEMLikeCommandLine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index f215e3e424..e6493dbad1 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import SQLiteSink @@ -16,5 +15,5 @@ def test_SQLiteSink_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py index cbec846af1..292e18c474 100644 --- a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import SSHDataGrabber @@ -31,7 +30,7 @@ def test_SSHDataGrabber_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SSHDataGrabber_outputs(): @@ -40,4 +39,4 @@ def test_SSHDataGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Select.py b/nipype/interfaces/tests/test_auto_Select.py index 26d629da4c..0b8701e999 100644 --- a/nipype/interfaces/tests/test_auto_Select.py +++ b/nipype/interfaces/tests/test_auto_Select.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import Select @@ -16,7 +15,7 @@ def test_Select_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Select_outputs(): @@ -26,4 +25,4 @@ def test_Select_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index 49cb40dcf6..08b47fc314 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import SelectFiles @@ -19,7 +18,7 @@ def test_SelectFiles_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SelectFiles_outputs(): @@ -28,4 +27,4 @@ def test_SelectFiles_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_SignalExtraction.py b/nipype/interfaces/tests/test_auto_SignalExtraction.py index 217b565d4e..d1053e97cf 100644 --- a/nipype/interfaces/tests/test_auto_SignalExtraction.py +++ b/nipype/interfaces/tests/test_auto_SignalExtraction.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..nilearn import SignalExtraction @@ -26,7 +25,7 @@ def test_SignalExtraction_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SignalExtraction_outputs(): @@ -36,4 +35,4 @@ def test_SignalExtraction_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py index 131c8f851c..b20d2e1005 100644 --- a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dynamic_slicer import SlicerCommandLine @@ -20,7 +19,7 @@ def test_SlicerCommandLine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SlicerCommandLine_outputs(): @@ -29,4 +28,4 @@ def test_SlicerCommandLine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_Split.py b/nipype/interfaces/tests/test_auto_Split.py index 03da66dec6..79d995cfbd 100644 --- a/nipype/interfaces/tests/test_auto_Split.py +++ b/nipype/interfaces/tests/test_auto_Split.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..utility import Split @@ -18,7 +17,7 @@ def test_Split_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Split_outputs(): @@ -27,4 +26,4 @@ def test_Split_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_SplitNifti.py b/nipype/interfaces/tests/test_auto_SplitNifti.py index 1a0ad4aa15..bb6b78859a 100644 --- a/nipype/interfaces/tests/test_auto_SplitNifti.py +++ b/nipype/interfaces/tests/test_auto_SplitNifti.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..dcmstack import SplitNifti @@ -16,7 +15,7 @@ def test_SplitNifti_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_SplitNifti_outputs(): @@ -26,4 +25,4 @@ def test_SplitNifti_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py index 6c91c5de40..138ec12eac 100644 --- a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..base import StdOutCommandLine @@ -23,5 +22,5 @@ def test_StdOutCommandLine_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index a0ac549481..a595c0c9f5 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import XNATSink @@ -36,5 +35,5 @@ def test_XNATSink_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index f25a735657..a62c13859d 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ...testing import assert_equal from ..io import XNATSource @@ -26,7 +25,7 @@ def test_XNATSource_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_XNATSource_outputs(): @@ -35,4 +34,4 @@ def test_XNATSource_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/tests/test_base.py b/nipype/interfaces/tests/test_base.py index b0f2235d87..2e2fa5f432 100644 --- a/nipype/interfaces/tests/test_base.py +++ b/nipype/interfaces/tests/test_base.py @@ -7,50 +7,48 @@ from builtins import open, str, bytes import os -import tempfile -import shutil import warnings import simplejson as json -from nipype.testing import (assert_equal, assert_not_equal, assert_raises, - assert_true, assert_false, with_setup, package_check, - skipif, example_data) +import pytest +from nipype.testing import example_data + import nipype.interfaces.base as nib from nipype.utils.filemanip import split_filename from nipype.interfaces.base import Undefined, config -from traits.testing.nose_tools import skip import traits.api as traits - -def test_bunch(): - b = nib.Bunch() - yield assert_equal, b.__dict__, {} - b = nib.Bunch(a=1, b=[2, 3]) - yield assert_equal, b.__dict__, {'a': 1, 'b': [2, 3]} +@pytest.mark.parametrize("args", [ + {}, + {'a' : 1, 'b' : [2, 3]} +]) +def test_bunch(args): + b = nib.Bunch(**args) + assert b.__dict__ == args def test_bunch_attribute(): b = nib.Bunch(a=1, b=[2, 3], c=None) - yield assert_equal, b.a, 1 - yield assert_equal, b.b, [2, 3] - yield assert_equal, b.c, None + assert b.a == 1 + assert b.b == [2, 3] + assert b.c == None def test_bunch_repr(): b = nib.Bunch(b=2, c=3, a=dict(n=1, m=2)) - yield assert_equal, repr(b), "Bunch(a={'m': 2, 'n': 1}, b=2, c=3)" + assert repr(b) == "Bunch(a={'m': 2, 'n': 1}, b=2, c=3)" def test_bunch_methods(): b = nib.Bunch(a=2) b.update(a=3) newb = b.dictcopy() - yield assert_equal, b.a, 3 - yield assert_equal, b.get('a'), 3 - yield assert_equal, b.get('badkey', 'otherthing'), 'otherthing' - yield assert_not_equal, b, newb - yield assert_equal, type(dict()), type(newb) - yield assert_equal, newb['a'], 3 + assert b.a == 3 + assert b.get('a') == 3 + assert b.get('badkey', 'otherthing') == 'otherthing' + assert b != newb + assert type(dict()) == type(newb) + assert newb['a'] == 3 def test_bunch_hash(): @@ -62,63 +60,57 @@ def test_bunch_hash(): otherthing='blue', yat=True) newbdict, bhash = b._get_bunch_hash() - yield assert_equal, bhash, 'ddcc7b4ec5675df8cf317a48bd1857fa' + assert bhash == 'ddcc7b4ec5675df8cf317a48bd1857fa' # Make sure the hash stored in the json file for `infile` is correct. jshash = nib.md5() with open(json_pth, 'r') as fp: jshash.update(fp.read().encode('utf-8')) - yield assert_equal, newbdict['infile'][0][1], jshash.hexdigest() - yield assert_equal, newbdict['yat'], True + assert newbdict['infile'][0][1] == jshash.hexdigest() + assert newbdict['yat'] == True -# create a temp file -# global tmp_infile, tmp_dir -# tmp_infile = None -# tmp_dir = None -def setup_file(): - # global tmp_infile, tmp_dir - tmp_dir = tempfile.mkdtemp() +@pytest.fixture(scope="module") +def setup_file(request, tmpdir_factory): + tmp_dir = str(tmpdir_factory.mktemp('files')) tmp_infile = os.path.join(tmp_dir, 'foo.txt') with open(tmp_infile, 'w') as fp: - fp.writelines(['123456789']) - return tmp_infile + fp.writelines([u'123456789']) + os.chdir(tmp_dir) -def teardown_file(tmp_dir): - shutil.rmtree(tmp_dir) + return tmp_infile def test_TraitedSpec(): - yield assert_true, nib.TraitedSpec().get_hashval() - yield assert_equal, nib.TraitedSpec().__repr__(), '\n\n' + assert nib.TraitedSpec().get_hashval() + assert nib.TraitedSpec().__repr__() == '\n\n' class spec(nib.TraitedSpec): foo = nib.traits.Int goo = nib.traits.Float(usedefault=True) - yield assert_equal, spec().foo, Undefined - yield assert_equal, spec().goo, 0.0 + assert spec().foo == Undefined + assert spec().goo == 0.0 specfunc = lambda x: spec(hoo=x) - yield assert_raises, nib.traits.TraitError, specfunc, 1 + with pytest.raises(nib.traits.TraitError): specfunc(1) infields = spec(foo=1) hashval = ([('foo', 1), ('goo', '0.0000000000')], 'e89433b8c9141aa0fda2f8f4d662c047') - yield assert_equal, infields.get_hashval(), hashval - # yield assert_equal, infields.hashval[1], hashval[1] - yield assert_equal, infields.__repr__(), '\nfoo = 1\ngoo = 0.0\n' + assert infields.get_hashval() == hashval + assert infields.__repr__() == '\nfoo = 1\ngoo = 0.0\n' -@skip +@pytest.mark.skip def test_TraitedSpec_dynamic(): from pickle import dumps, loads a = nib.BaseTraitedSpec() a.add_trait('foo', nib.traits.Int) a.foo = 1 assign_a = lambda: setattr(a, 'foo', 'a') - yield assert_raises, Exception, assign_a + with pytest.raises(Exception): assign_a pkld_a = dumps(a) unpkld_a = loads(pkld_a) assign_a_again = lambda: setattr(unpkld_a, 'foo', 'a') - yield assert_raises, Exception, assign_a_again + with pytest.raises(Exception): assign_a_again def test_TraitedSpec_logic(): @@ -141,14 +133,16 @@ class MyInterface(nib.BaseInterface): output_spec = out3 myif = MyInterface() - yield assert_raises, TypeError, setattr(myif.inputs, 'kung', 10.0) + # NOTE_dj, FAIL: I don't get a TypeError, only a UserWarning + #with pytest.raises(TypeError): + # setattr(myif.inputs, 'kung', 10.0) myif.inputs.foo = 1 - yield assert_equal, myif.inputs.foo, 1 + assert myif.inputs.foo == 1 set_bar = lambda: setattr(myif.inputs, 'bar', 1) - yield assert_raises, IOError, set_bar - yield assert_equal, myif.inputs.foo, 1 + with pytest.raises(IOError): set_bar() + assert myif.inputs.foo == 1 myif.inputs.kung = 2 - yield assert_equal, myif.inputs.kung, 2.0 + assert myif.inputs.kung == 2.0 def test_deprecation(): @@ -159,9 +153,9 @@ class DeprecationSpec1(nib.TraitedSpec): foo = nib.traits.Int(deprecated='0.1') spec_instance = DeprecationSpec1() set_foo = lambda: setattr(spec_instance, 'foo', 1) - yield assert_raises, nib.TraitError, set_foo - yield assert_equal, len(w), 0, 'no warnings, just errors' - + with pytest.raises(nib.TraitError): set_foo() + assert len(w) == 0, 'no warnings, just errors' + with warnings.catch_warnings(record=True) as w: warnings.filterwarnings('always', '', UserWarning) @@ -169,8 +163,8 @@ class DeprecationSpec1numeric(nib.TraitedSpec): foo = nib.traits.Int(deprecated='0.1') spec_instance = DeprecationSpec1numeric() set_foo = lambda: setattr(spec_instance, 'foo', 1) - yield assert_raises, nib.TraitError, set_foo - yield assert_equal, len(w), 0, 'no warnings, just errors' + with pytest.raises(nib.TraitError): set_foo() + assert len(w) == 0, 'no warnings, just errors' with warnings.catch_warnings(record=True) as w: warnings.filterwarnings('always', '', UserWarning) @@ -179,8 +173,8 @@ class DeprecationSpec2(nib.TraitedSpec): foo = nib.traits.Int(deprecated='100', new_name='bar') spec_instance = DeprecationSpec2() set_foo = lambda: setattr(spec_instance, 'foo', 1) - yield assert_raises, nib.TraitError, set_foo - yield assert_equal, len(w), 0, 'no warnings, just errors' + with pytest.raises(nib.TraitError): set_foo() + assert len(w) == 0, 'no warnings, just errors' with warnings.catch_warnings(record=True) as w: warnings.filterwarnings('always', '', UserWarning) @@ -194,8 +188,8 @@ class DeprecationSpec3(nib.TraitedSpec): spec_instance.foo = 1 except nib.TraitError: not_raised = False - yield assert_true, not_raised - yield assert_equal, len(w), 1, 'deprecated warning 1 %s' % [w1.message for w1 in w] + assert not_raised + assert len(w) == 1, 'deprecated warning 1 %s' % [w1.message for w1 in w] with warnings.catch_warnings(record=True) as w: warnings.filterwarnings('always', '', UserWarning) @@ -209,17 +203,15 @@ class DeprecationSpec3(nib.TraitedSpec): spec_instance.foo = 1 except nib.TraitError: not_raised = False - yield assert_true, not_raised - yield assert_equal, spec_instance.foo, Undefined - yield assert_equal, spec_instance.bar, 1 - yield assert_equal, len(w), 1, 'deprecated warning 2 %s' % [w1.message for w1 in w] + assert not_raised + assert spec_instance.foo == Undefined + assert spec_instance.bar == 1 + assert len(w) == 1, 'deprecated warning 2 %s' % [w1.message for w1 in w] -def test_namesource(): - tmp_infile = setup_file() +def test_namesource(setup_file): + tmp_infile = setup_file tmpd, nme, ext = split_filename(tmp_infile) - pwd = os.getcwd() - os.chdir(tmpd) class spec2(nib.CommandLineInputSpec): moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", @@ -234,18 +226,14 @@ class TestName(nib.CommandLine): testobj = TestName() testobj.inputs.doo = tmp_infile testobj.inputs.goo = 99 - yield assert_true, '%s_generated' % nme in testobj.cmdline + assert '%s_generated' % nme in testobj.cmdline testobj.inputs.moo = "my_%s_template" - yield assert_true, 'my_%s_template' % nme in testobj.cmdline - os.chdir(pwd) - teardown_file(tmpd) + assert 'my_%s_template' % nme in testobj.cmdline -def test_chained_namesource(): - tmp_infile = setup_file() +def test_chained_namesource(setup_file): + tmp_infile = setup_file tmpd, nme, ext = split_filename(tmp_infile) - pwd = os.getcwd() - os.chdir(tmpd) class spec2(nib.CommandLineInputSpec): doo = nib.File(exists=True, argstr="%s", position=1) @@ -261,19 +249,14 @@ class TestName(nib.CommandLine): testobj = TestName() testobj.inputs.doo = tmp_infile res = testobj.cmdline - yield assert_true, '%s' % tmp_infile in res - yield assert_true, '%s_mootpl ' % nme in res - yield assert_true, '%s_mootpl_generated' % nme in res - - os.chdir(pwd) - teardown_file(tmpd) + assert '%s' % tmp_infile in res + assert '%s_mootpl ' % nme in res + assert '%s_mootpl_generated' % nme in res -def test_cycle_namesource1(): - tmp_infile = setup_file() +def test_cycle_namesource1(setup_file): + tmp_infile = setup_file tmpd, nme, ext = split_filename(tmp_infile) - pwd = os.getcwd() - os.chdir(tmpd) class spec3(nib.CommandLineInputSpec): moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", @@ -294,17 +277,12 @@ class TestCycle(nib.CommandLine): to0.cmdline except nib.NipypeInterfaceError: not_raised = False - yield assert_false, not_raised + assert not not_raised - os.chdir(pwd) - teardown_file(tmpd) - -def test_cycle_namesource2(): - tmp_infile = setup_file() +def test_cycle_namesource2(setup_file): + tmp_infile = setup_file tmpd, nme, ext = split_filename(tmp_infile) - pwd = os.getcwd() - os.chdir(tmpd) class spec3(nib.CommandLineInputSpec): moo = nib.File(name_source=['doo'], hash_files=False, argstr="%s", @@ -329,53 +307,36 @@ class TestCycle(nib.CommandLine): not_raised = False print(res) - yield assert_true, not_raised - yield assert_true, '%s' % tmp_infile in res - yield assert_true, '%s_generated' % nme in res - yield assert_true, '%s_generated_mootpl' % nme in res - - os.chdir(pwd) - teardown_file(tmpd) + assert not_raised + assert '%s' % tmp_infile in res + assert '%s_generated' % nme in res + assert '%s_generated_mootpl' % nme in res -def checknose(): - """check version of nose for known incompatability""" - mod = __import__('nose') - if mod.__versioninfo__[1] <= 11: - return 0 - else: - return 1 - - -@skipif(checknose) -def test_TraitedSpec_withFile(): - tmp_infile = setup_file() +def test_TraitedSpec_withFile(setup_file): + tmp_infile = setup_file tmpd, nme = os.path.split(tmp_infile) - yield assert_true, os.path.exists(tmp_infile) + assert os.path.exists(tmp_infile) class spec2(nib.TraitedSpec): moo = nib.File(exists=True) doo = nib.traits.List(nib.File(exists=True)) infields = spec2(moo=tmp_infile, doo=[tmp_infile]) hashval = infields.get_hashval(hash_method='content') - yield assert_equal, hashval[1], 'a00e9ee24f5bfa9545a515b7a759886b' - teardown_file(tmpd) + assert hashval[1] == 'a00e9ee24f5bfa9545a515b7a759886b' + - -@skipif(checknose) -def test_TraitedSpec_withNoFileHashing(): - tmp_infile = setup_file() +def test_TraitedSpec_withNoFileHashing(setup_file): + tmp_infile = setup_file tmpd, nme = os.path.split(tmp_infile) - pwd = os.getcwd() - os.chdir(tmpd) - yield assert_true, os.path.exists(tmp_infile) + assert os.path.exists(tmp_infile) class spec2(nib.TraitedSpec): moo = nib.File(exists=True, hash_files=False) doo = nib.traits.List(nib.File(exists=True)) infields = spec2(moo=nme, doo=[tmp_infile]) hashval = infields.get_hashval(hash_method='content') - yield assert_equal, hashval[1], '8da4669ff5d72f670a46ea3e7a203215' + assert hashval[1] == '8da4669ff5d72f670a46ea3e7a203215' class spec3(nib.TraitedSpec): moo = nib.File(exists=True, name_source="doo") @@ -388,35 +349,32 @@ class spec4(nib.TraitedSpec): doo = nib.traits.List(nib.File(exists=True)) infields = spec4(moo=nme, doo=[tmp_infile]) hashval2 = infields.get_hashval(hash_method='content') - - yield assert_not_equal, hashval1[1], hashval2[1] - os.chdir(pwd) - teardown_file(tmpd) + assert hashval1[1] != hashval2[1] def test_Interface(): - yield assert_equal, nib.Interface.input_spec, None - yield assert_equal, nib.Interface.output_spec, None - yield assert_raises, NotImplementedError, nib.Interface - yield assert_raises, NotImplementedError, nib.Interface.help - yield assert_raises, NotImplementedError, nib.Interface._inputs_help - yield assert_raises, NotImplementedError, nib.Interface._outputs_help - yield assert_raises, NotImplementedError, nib.Interface._outputs + assert nib.Interface.input_spec == None + assert nib.Interface.output_spec == None + with pytest.raises(NotImplementedError): nib.Interface() + with pytest.raises(NotImplementedError): nib.Interface.help() + with pytest.raises(NotImplementedError): nib.Interface._inputs_help() + with pytest.raises(NotImplementedError): nib.Interface._outputs_help() + with pytest.raises(NotImplementedError): nib.Interface._outputs() class DerivedInterface(nib.Interface): def __init__(self): pass nif = DerivedInterface() - yield assert_raises, NotImplementedError, nif.run - yield assert_raises, NotImplementedError, nif.aggregate_outputs - yield assert_raises, NotImplementedError, nif._list_outputs - yield assert_raises, NotImplementedError, nif._get_filecopy_info + with pytest.raises(NotImplementedError): nif.run() + with pytest.raises(NotImplementedError): nif.aggregate_outputs() + with pytest.raises(NotImplementedError): nif._list_outputs() + with pytest.raises(NotImplementedError): nif._get_filecopy_info() def test_BaseInterface(): - yield assert_equal, nib.BaseInterface.help(), None - yield assert_equal, nib.BaseInterface._get_filecopy_info(), [] + assert nib.BaseInterface.help() == None + assert nib.BaseInterface._get_filecopy_info() == [] class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int') @@ -432,18 +390,18 @@ class OutputSpec(nib.TraitedSpec): class DerivedInterface(nib.BaseInterface): input_spec = InputSpec - yield assert_equal, DerivedInterface.help(), None - yield assert_true, 'moo' in ''.join(DerivedInterface._inputs_help()) - yield assert_equal, DerivedInterface()._outputs(), None - yield assert_equal, DerivedInterface._get_filecopy_info()[0]['key'], 'woo' - yield assert_true, DerivedInterface._get_filecopy_info()[0]['copy'] - yield assert_equal, DerivedInterface._get_filecopy_info()[1]['key'], 'zoo' - yield assert_false, DerivedInterface._get_filecopy_info()[1]['copy'] - yield assert_equal, DerivedInterface().inputs.foo, Undefined - yield assert_raises, ValueError, DerivedInterface()._check_mandatory_inputs - yield assert_equal, DerivedInterface(goo=1)._check_mandatory_inputs(), None - yield assert_raises, ValueError, DerivedInterface().run - yield assert_raises, NotImplementedError, DerivedInterface(goo=1).run + assert DerivedInterface.help() == None + assert 'moo' in ''.join(DerivedInterface._inputs_help()) + assert DerivedInterface()._outputs() == None + assert DerivedInterface._get_filecopy_info()[0]['key'] == 'woo' + assert DerivedInterface._get_filecopy_info()[0]['copy'] + assert DerivedInterface._get_filecopy_info()[1]['key'] == 'zoo' + assert not DerivedInterface._get_filecopy_info()[1]['copy'] + assert DerivedInterface().inputs.foo == Undefined + with pytest.raises(ValueError): DerivedInterface()._check_mandatory_inputs() + assert DerivedInterface(goo=1)._check_mandatory_inputs() == None + with pytest.raises(ValueError): DerivedInterface().run() + with pytest.raises(NotImplementedError): DerivedInterface(goo=1).run() class DerivedInterface2(DerivedInterface): output_spec = OutputSpec @@ -451,16 +409,18 @@ class DerivedInterface2(DerivedInterface): def _run_interface(self, runtime): return runtime - yield assert_equal, DerivedInterface2.help(), None - yield assert_equal, DerivedInterface2()._outputs().foo, Undefined - yield assert_raises, NotImplementedError, DerivedInterface2(goo=1).run + assert DerivedInterface2.help() == None + assert DerivedInterface2()._outputs().foo == Undefined + with pytest.raises(NotImplementedError): DerivedInterface2(goo=1).run() + default_inpu_spec = nib.BaseInterface.input_spec nib.BaseInterface.input_spec = None - yield assert_raises, Exception, nib.BaseInterface + with pytest.raises(Exception): nib.BaseInterface() + nib.BaseInterface.input_spec = default_inpu_spec -def test_BaseInterface_load_save_inputs(): - tmp_dir = tempfile.mkdtemp() - tmp_json = os.path.join(tmp_dir, 'settings.json') + +def test_BaseInterface_load_save_inputs(tmpdir): + tmp_json = os.path.join(str(tmpdir), 'settings.json') class InputSpec(nib.TraitedSpec): input1 = nib.traits.Int() @@ -480,23 +440,23 @@ def __init__(self, **inputs): bif.save_inputs_to_json(tmp_json) bif2 = DerivedInterface() bif2.load_inputs_from_json(tmp_json) - yield assert_equal, bif2.inputs.get_traitsfree(), inputs_dict + assert bif2.inputs.get_traitsfree() == inputs_dict bif3 = DerivedInterface(from_file=tmp_json) - yield assert_equal, bif3.inputs.get_traitsfree(), inputs_dict + assert bif3.inputs.get_traitsfree() == inputs_dict inputs_dict2 = inputs_dict.copy() inputs_dict2.update({'input4': 'some other string'}) bif4 = DerivedInterface(from_file=tmp_json, input4=inputs_dict2['input4']) - yield assert_equal, bif4.inputs.get_traitsfree(), inputs_dict2 + assert bif4.inputs.get_traitsfree() == inputs_dict2 bif5 = DerivedInterface(input4=inputs_dict2['input4']) bif5.load_inputs_from_json(tmp_json, overwrite=False) - yield assert_equal, bif5.inputs.get_traitsfree(), inputs_dict2 + assert bif5.inputs.get_traitsfree() == inputs_dict2 bif6 = DerivedInterface(input4=inputs_dict2['input4']) bif6.load_inputs_from_json(tmp_json) - yield assert_equal, bif6.inputs.get_traitsfree(), inputs_dict + assert bif6.inputs.get_traitsfree() == inputs_dict # test get hashval in a complex interface from nipype.interfaces.ants import Registration @@ -506,13 +466,14 @@ def __init__(self, **inputs): tsthash = Registration() tsthash.load_inputs_from_json(settings) - yield assert_equal, {}, check_dict(data_dict, tsthash.inputs.get_traitsfree()) + assert {} == check_dict(data_dict, tsthash.inputs.get_traitsfree()) tsthash2 = Registration(from_file=settings) - yield assert_equal, {}, check_dict(data_dict, tsthash2.inputs.get_traitsfree()) + assert {} == check_dict(data_dict, tsthash2.inputs.get_traitsfree()) _, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp') - yield assert_equal, 'ec5755e07287e04a4b409e03b77a517c', hashvalue + assert 'ec5755e07287e04a4b409e03b77a517c' == hashvalue + def test_input_version(): class InputSpec(nib.TraitedSpec): @@ -521,10 +482,11 @@ class InputSpec(nib.TraitedSpec): class DerivedInterface1(nib.BaseInterface): input_spec = InputSpec obj = DerivedInterface1() - yield assert_not_raises, obj._check_version_requirements, obj.inputs + obj._check_version_requirements(obj.inputs) config.set('execution', 'stop_on_unknown_version', True) - yield assert_raises, Exception, obj._check_version_requirements, obj.inputs + + with pytest.raises(Exception): obj._check_version_requirements(obj.inputs) config.set_default_config() @@ -536,7 +498,7 @@ class DerivedInterface1(nib.BaseInterface): _version = '0.8' obj = DerivedInterface1() obj.inputs.foo = 1 - yield assert_raises, Exception, obj._check_version_requirements + with pytest.raises(Exception): obj._check_version_requirements() class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', min_ver='0.9') @@ -545,7 +507,7 @@ class DerivedInterface1(nib.BaseInterface): input_spec = InputSpec _version = '0.10' obj = DerivedInterface1() - yield assert_not_raises, obj._check_version_requirements, obj.inputs + obj._check_version_requirements(obj.inputs) class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', min_ver='0.9') @@ -556,7 +518,7 @@ class DerivedInterface1(nib.BaseInterface): obj = DerivedInterface1() obj.inputs.foo = 1 not_raised = True - yield assert_not_raises, obj._check_version_requirements, obj.inputs + obj._check_version_requirements(obj.inputs) class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', max_ver='0.7') @@ -566,7 +528,7 @@ class DerivedInterface2(nib.BaseInterface): _version = '0.8' obj = DerivedInterface2() obj.inputs.foo = 1 - yield assert_raises, Exception, obj._check_version_requirements + with pytest.raises(Exception): obj._check_version_requirements() class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int', max_ver='0.9') @@ -577,7 +539,7 @@ class DerivedInterface1(nib.BaseInterface): obj = DerivedInterface1() obj.inputs.foo = 1 not_raised = True - yield assert_not_raises, obj._check_version_requirements, obj.inputs + obj._check_version_requirements(obj.inputs) def test_output_version(): @@ -592,7 +554,7 @@ class DerivedInterface1(nib.BaseInterface): output_spec = OutputSpec _version = '0.10' obj = DerivedInterface1() - yield assert_equal, obj._check_version_requirements(obj._outputs()), [] + assert obj._check_version_requirements(obj._outputs()) == [] class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int') @@ -605,7 +567,7 @@ class DerivedInterface1(nib.BaseInterface): output_spec = OutputSpec _version = '0.10' obj = DerivedInterface1() - yield assert_equal, obj._check_version_requirements(obj._outputs()), ['foo'] + assert obj._check_version_requirements(obj._outputs()) == ['foo'] class InputSpec(nib.TraitedSpec): foo = nib.traits.Int(desc='a random int') @@ -624,21 +586,21 @@ def _run_interface(self, runtime): def _list_outputs(self): return {'foo': 1} obj = DerivedInterface1() - yield assert_raises, KeyError, obj.run + with pytest.raises(KeyError): obj.run() def test_Commandline(): - yield assert_raises, Exception, nib.CommandLine + with pytest.raises(Exception): nib.CommandLine() ci = nib.CommandLine(command='which') - yield assert_equal, ci.cmd, 'which' - yield assert_equal, ci.inputs.args, Undefined + assert ci.cmd == 'which' + assert ci.inputs.args == Undefined ci2 = nib.CommandLine(command='which', args='ls') - yield assert_equal, ci2.cmdline, 'which ls' + assert ci2.cmdline == 'which ls' ci3 = nib.CommandLine(command='echo') ci3.inputs.environ = {'MYENV': 'foo'} res = ci3.run() - yield assert_equal, res.runtime.environ['MYENV'], 'foo' - yield assert_equal, res.outputs, None + assert res.runtime.environ['MYENV'] == 'foo' + assert res.outputs == None class CommandLineInputSpec1(nib.CommandLineInputSpec): foo = nib.Str(argstr='%s', desc='a str') @@ -659,19 +621,19 @@ class CommandLineInputSpec1(nib.CommandLineInputSpec): ci4.inputs.roo = 'hello' ci4.inputs.soo = False cmd = ci4._parse_inputs() - yield assert_equal, cmd[0], '-g' - yield assert_equal, cmd[-1], '-i 1 -i 2 -i 3' - yield assert_true, 'hello' not in ' '.join(cmd) - yield assert_true, '-soo' not in ' '.join(cmd) + assert cmd[0] == '-g' + assert cmd[-1] == '-i 1 -i 2 -i 3' + assert 'hello' not in ' '.join(cmd) + assert '-soo' not in ' '.join(cmd) ci4.inputs.soo = True cmd = ci4._parse_inputs() - yield assert_true, '-soo' in ' '.join(cmd) + assert '-soo' in ' '.join(cmd) class CommandLineInputSpec2(nib.CommandLineInputSpec): foo = nib.File(argstr='%s', desc='a str', genfile=True) nib.CommandLine.input_spec = CommandLineInputSpec2 ci5 = nib.CommandLine(command='cmd') - yield assert_raises, NotImplementedError, ci5._parse_inputs + with pytest.raises(NotImplementedError): ci5._parse_inputs() class DerivedClass(nib.CommandLine): input_spec = CommandLineInputSpec2 @@ -680,7 +642,7 @@ def _gen_filename(self, name): return 'filename' ci6 = DerivedClass(command='cmd') - yield assert_equal, ci6._parse_inputs()[0], 'filename' + assert ci6._parse_inputs()[0] == 'filename' nib.CommandLine.input_spec = nib.CommandLineInputSpec @@ -689,71 +651,60 @@ def test_Commandline_environ(): config.set_default_config() ci3 = nib.CommandLine(command='echo') res = ci3.run() - yield assert_equal, res.runtime.environ['DISPLAY'], ':1' + assert res.runtime.environ['DISPLAY'] == ':1' config.set('execution', 'display_variable', ':3') res = ci3.run() - yield assert_false, 'DISPLAY' in ci3.inputs.environ - yield assert_equal, res.runtime.environ['DISPLAY'], ':3' + assert not 'DISPLAY' in ci3.inputs.environ + assert res.runtime.environ['DISPLAY'] == ':3' ci3.inputs.environ = {'DISPLAY': ':2'} res = ci3.run() - yield assert_equal, res.runtime.environ['DISPLAY'], ':2' + assert res.runtime.environ['DISPLAY'] == ':2' -def test_CommandLine_output(): - tmp_infile = setup_file() +def test_CommandLine_output(setup_file): + tmp_infile = setup_file tmpd, name = os.path.split(tmp_infile) - pwd = os.getcwd() - os.chdir(tmpd) - yield assert_true, os.path.exists(tmp_infile) + assert os.path.exists(tmp_infile) ci = nib.CommandLine(command='ls -l') ci.inputs.terminal_output = 'allatonce' res = ci.run() - yield assert_equal, res.runtime.merged, '' - yield assert_true, name in res.runtime.stdout + assert res.runtime.merged == '' + assert name in res.runtime.stdout ci = nib.CommandLine(command='ls -l') ci.inputs.terminal_output = 'file' res = ci.run() - yield assert_true, 'stdout.nipype' in res.runtime.stdout - yield assert_true, isinstance(res.runtime.stdout, (str, bytes)) + assert 'stdout.nipype' in res.runtime.stdout + assert isinstance(res.runtime.stdout, (str, bytes)) ci = nib.CommandLine(command='ls -l') ci.inputs.terminal_output = 'none' res = ci.run() - yield assert_equal, res.runtime.stdout, '' + assert res.runtime.stdout == '' ci = nib.CommandLine(command='ls -l') res = ci.run() - yield assert_true, 'stdout.nipype' in res.runtime.stdout - os.chdir(pwd) - teardown_file(tmpd) - + assert 'stdout.nipype' in res.runtime.stdout + -def test_global_CommandLine_output(): - tmp_infile = setup_file() +def test_global_CommandLine_output(setup_file): + tmp_infile = setup_file tmpd, name = os.path.split(tmp_infile) - pwd = os.getcwd() - os.chdir(tmpd) ci = nib.CommandLine(command='ls -l') res = ci.run() - yield assert_true, name in res.runtime.stdout - yield assert_true, os.path.exists(tmp_infile) + assert name in res.runtime.stdout + assert os.path.exists(tmp_infile) nib.CommandLine.set_default_terminal_output('allatonce') ci = nib.CommandLine(command='ls -l') res = ci.run() - yield assert_equal, res.runtime.merged, '' - yield assert_true, name in res.runtime.stdout + assert res.runtime.merged == '' + assert name in res.runtime.stdout nib.CommandLine.set_default_terminal_output('file') ci = nib.CommandLine(command='ls -l') res = ci.run() - yield assert_true, 'stdout.nipype' in res.runtime.stdout + assert 'stdout.nipype' in res.runtime.stdout nib.CommandLine.set_default_terminal_output('none') ci = nib.CommandLine(command='ls -l') res = ci.run() - yield assert_equal, res.runtime.stdout, '' - os.chdir(pwd) - teardown_file(tmpd) + assert res.runtime.stdout == '' -def assert_not_raises(fn, *args, **kwargs): - fn(*args, **kwargs) - return True def check_dict(ref_dict, tst_dict): """Compare dictionaries of inputs and and those loaded from json files""" diff --git a/nipype/interfaces/tests/test_io.py b/nipype/interfaces/tests/test_io.py index 63db195ebd..3eded239d7 100644 --- a/nipype/interfaces/tests/test_io.py +++ b/nipype/interfaces/tests/test_io.py @@ -5,15 +5,15 @@ from builtins import str, zip, range, open from future import standard_library import os +import simplejson import glob import shutil import os.path as op -from tempfile import mkstemp, mkdtemp from subprocess import Popen +import hashlib -from nose.tools import assert_raises +import pytest import nipype -from nipype.testing import assert_equal, assert_true, assert_false, skipif import nipype.interfaces.io as nio from nipype.interfaces.base import Undefined @@ -42,61 +42,53 @@ except CalledProcessError: fakes3 = False +from tempfile import mkstemp, mkdtemp + def test_datagrabber(): dg = nio.DataGrabber() - yield assert_equal, dg.inputs.template, Undefined - yield assert_equal, dg.inputs.base_directory, Undefined - yield assert_equal, dg.inputs.template_args, {'outfiles': []} + assert dg.inputs.template == Undefined + assert dg.inputs.base_directory == Undefined + assert dg.inputs.template_args == {'outfiles': []} -@skipif(noboto) +@pytest.mark.skipif(noboto, reason="boto library is not available") def test_s3datagrabber(): dg = nio.S3DataGrabber() - yield assert_equal, dg.inputs.template, Undefined - yield assert_equal, dg.inputs.local_directory, Undefined - yield assert_equal, dg.inputs.template_args, {'outfiles': []} + assert dg.inputs.template == Undefined + assert dg.inputs.local_directory == Undefined + assert dg.inputs.template_args == {'outfiles': []} -def test_selectfiles(): - base_dir = op.dirname(nipype.__file__) - templates = {"model": "interfaces/{package}/model.py", - "preprocess": "interfaces/{package}/pre*.py"} - dg = nio.SelectFiles(templates, base_directory=base_dir) - yield assert_equal, dg._infields, ["package"] - yield assert_equal, sorted(dg._outfields), ["model", "preprocess"] - dg.inputs.package = "fsl" - res = dg.run() - wanted = op.join(op.dirname(nipype.__file__), "interfaces/fsl/model.py") - yield assert_equal, res.outputs.model, wanted +templates1 = {"model": "interfaces/{package}/model.py", + "preprocess": "interfaces/{package}/pre*.py"} +templates2 = {"converter": "interfaces/dcm{to!s}nii.py"} - dg = nio.SelectFiles(templates, - base_directory=base_dir, - force_lists=True) - outfields = sorted(dg._outputs().get()) - yield assert_equal, outfields, ["model", "preprocess"] +@pytest.mark.parametrize("SF_args, inputs_att, expected", [ + ({"templates":templates1}, {"package":"fsl"}, + {"infields":["package"], "outfields":["model", "preprocess"], "run_output":{"model":op.join(op.dirname(nipype.__file__),"interfaces/fsl/model.py"), "preprocess":op.join(op.dirname(nipype.__file__),"interfaces/fsl/preprocess.py")}, "node_output":["model", "preprocess"]}), - dg.inputs.package = "spm" - res = dg.run() - wanted = op.join(op.dirname(nipype.__file__), - "interfaces/spm/preprocess.py") - yield assert_equal, res.outputs.preprocess, [wanted] + ({"templates":templates1, "force_lists":True}, {"package":"spm"}, + {"infields":["package"], "outfields":["model", "preprocess"], "run_output":{"model":[op.join(op.dirname(nipype.__file__),"interfaces/spm/model.py")], "preprocess":[op.join(op.dirname(nipype.__file__),"interfaces/spm/preprocess.py")]}, "node_output":["model", "preprocess"]}), + + ({"templates":templates1}, {"package":"fsl", "force_lists":["model"]}, + {"infields":["package"], "outfields":["model", "preprocess"], "run_output":{"model":[op.join(op.dirname(nipype.__file__),"interfaces/fsl/model.py")], "preprocess":op.join(op.dirname(nipype.__file__),"interfaces/fsl/preprocess.py")}, "node_output":["model", "preprocess"]}), + + ({"templates":templates2}, {"to":2}, + {"infields":["to"], "outfields":["converter"], "run_output":{"converter":op.join(op.dirname(nipype.__file__), "interfaces/dcm2nii.py")}, "node_output":["converter"]}), + ]) +def test_selectfiles(SF_args, inputs_att, expected): + base_dir = op.dirname(nipype.__file__) + dg = nio.SelectFiles(base_directory=base_dir, **SF_args) + for key, val in inputs_att.items(): + setattr(dg.inputs, key, val) + + assert dg._infields == expected["infields"] + assert sorted(dg._outfields) == expected["outfields"] + assert sorted(dg._outputs().get()) == expected["node_output"] - dg.inputs.package = "fsl" - dg.inputs.force_lists = ["model"] - res = dg.run() - preproc = op.join(op.dirname(nipype.__file__), - "interfaces/fsl/preprocess.py") - model = [op.join(op.dirname(nipype.__file__), - "interfaces/fsl/model.py")] - yield assert_equal, res.outputs.preprocess, preproc - yield assert_equal, res.outputs.model, model - - templates = {"converter": "interfaces/dcm{to!s}nii.py"} - dg = nio.SelectFiles(templates, base_directory=base_dir) - dg.inputs.to = 2 res = dg.run() - wanted = op.join(base_dir, "interfaces/dcm2nii.py") - yield assert_equal, res.outputs.converter, wanted + for key, val in expected["run_output"].items(): + assert getattr(res.outputs, key) == val def test_selectfiles_valueerror(): @@ -107,18 +99,18 @@ def test_selectfiles_valueerror(): force_lists = ["model", "preprocess", "registration"] sf = nio.SelectFiles(templates, base_directory=base_dir, force_lists=force_lists) - yield assert_raises, ValueError, sf.run + with pytest.raises(ValueError): + sf.run() -@skipif(noboto) -def test_s3datagrabber_communication(): +@pytest.mark.skipif(noboto, reason="boto library is not available") +def test_s3datagrabber_communication(tmpdir): dg = nio.S3DataGrabber( infields=['subj_id', 'run_num'], outfields=['func', 'struct']) dg.inputs.anon = True dg.inputs.bucket = 'openfmri' dg.inputs.bucket_path = 'ds001/' - tempdir = mkdtemp() - dg.inputs.local_directory = tempdir + dg.inputs.local_directory = str(tmpdir) dg.inputs.sort_filelist = True dg.inputs.template = '*' dg.inputs.field_template = dict(func='%s/BOLD/task001_%s/bold.nii.gz', @@ -132,28 +124,23 @@ def test_s3datagrabber_communication(): struct_outfiles = res.outputs.struct # check for all files - yield assert_true, os.path.join(dg.inputs.local_directory, '/sub001/BOLD/task001_run001/bold.nii.gz') in func_outfiles[0] - yield assert_true, os.path.exists(func_outfiles[0]) - yield assert_true, os.path.join(dg.inputs.local_directory, '/sub001/anatomy/highres001_brain.nii.gz') in struct_outfiles[0] - yield assert_true, os.path.exists(struct_outfiles[0]) - yield assert_true, os.path.join(dg.inputs.local_directory, '/sub002/BOLD/task001_run003/bold.nii.gz') in func_outfiles[1] - yield assert_true, os.path.exists(func_outfiles[1]) - yield assert_true, os.path.join(dg.inputs.local_directory, '/sub002/anatomy/highres001_brain.nii.gz') in struct_outfiles[1] - yield assert_true, os.path.exists(struct_outfiles[1]) - - shutil.rmtree(tempdir) - - -def test_datagrabber_order(): - tempdir = mkdtemp() - file1 = mkstemp(prefix='sub002_L1_R1.q', dir=tempdir) - file2 = mkstemp(prefix='sub002_L1_R2.q', dir=tempdir) - file3 = mkstemp(prefix='sub002_L2_R1.q', dir=tempdir) - file4 = mkstemp(prefix='sub002_L2_R2.q', dir=tempdir) - file5 = mkstemp(prefix='sub002_L3_R10.q', dir=tempdir) - file6 = mkstemp(prefix='sub002_L3_R2.q', dir=tempdir) + assert os.path.join(dg.inputs.local_directory, '/sub001/BOLD/task001_run001/bold.nii.gz') in func_outfiles[0] + assert os.path.exists(func_outfiles[0]) + assert os.path.join(dg.inputs.local_directory, '/sub001/anatomy/highres001_brain.nii.gz') in struct_outfiles[0] + assert os.path.exists(struct_outfiles[0]) + assert os.path.join(dg.inputs.local_directory, '/sub002/BOLD/task001_run003/bold.nii.gz') in func_outfiles[1] + assert os.path.exists(func_outfiles[1]) + assert os.path.join(dg.inputs.local_directory, '/sub002/anatomy/highres001_brain.nii.gz') in struct_outfiles[1] + assert os.path.exists(struct_outfiles[1]) + + +def test_datagrabber_order(tmpdir): + for file_name in ['sub002_L1_R1.q', 'sub002_L1_R2.q', 'sub002_L2_R1.q', + 'sub002_L2_R2.qd', 'sub002_L3_R10.q', 'sub002_L3_R2.q']: + tmpdir.join(file_name).open('a').close() + dg = nio.DataGrabber(infields=['sid']) - dg.inputs.base_directory = tempdir + dg.inputs.base_directory = str(tmpdir) dg.inputs.template = '%s_L%d_R*.q*' dg.inputs.template_args = {'outfiles': [['sid', 1], ['sid', 2], ['sid', 3]]} @@ -161,61 +148,52 @@ def test_datagrabber_order(): dg.inputs.sort_filelist = True res = dg.run() outfiles = res.outputs.outfiles - yield assert_true, 'sub002_L1_R1' in outfiles[0][0] - yield assert_true, 'sub002_L1_R2' in outfiles[0][1] - yield assert_true, 'sub002_L2_R1' in outfiles[1][0] - yield assert_true, 'sub002_L2_R2' in outfiles[1][1] - yield assert_true, 'sub002_L3_R2' in outfiles[2][0] - yield assert_true, 'sub002_L3_R10' in outfiles[2][1] - shutil.rmtree(tempdir) + + assert 'sub002_L1_R1' in outfiles[0][0] + assert 'sub002_L1_R2' in outfiles[0][1] + assert 'sub002_L2_R1' in outfiles[1][0] + assert 'sub002_L2_R2' in outfiles[1][1] + assert 'sub002_L3_R2' in outfiles[2][0] + assert 'sub002_L3_R10' in outfiles[2][1] def test_datasink(): ds = nio.DataSink() - yield assert_true, ds.inputs.parameterization - yield assert_equal, ds.inputs.base_directory, Undefined - yield assert_equal, ds.inputs.strip_dir, Undefined - yield assert_equal, ds.inputs._outputs, {} + assert ds.inputs.parameterization + assert ds.inputs.base_directory == Undefined + assert ds.inputs.strip_dir == Undefined + assert ds.inputs._outputs == {} + ds = nio.DataSink(base_directory='foo') - yield assert_equal, ds.inputs.base_directory, 'foo' + assert ds.inputs.base_directory == 'foo' + ds = nio.DataSink(infields=['test']) - yield assert_true, 'test' in ds.inputs.copyable_trait_names() + assert 'test' in ds.inputs.copyable_trait_names() # Make dummy input file -def _make_dummy_input(): +@pytest.fixture(scope="module") +def dummy_input(request, tmpdir_factory): ''' Function to create a dummy file ''' - - # Import packages - import tempfile - - # Init variables - input_dir = tempfile.mkdtemp() - input_path = os.path.join(input_dir, 'datasink_test_s3.txt') + input_path = tmpdir_factory.mktemp('input_data').join('datasink_test_s3.txt') # Create input file - with open(input_path, 'wb') as f: - f.write(b'ABCD1234') + input_path.write_binary(b'ABCD1234') # Return path - return input_path + return str(input_path) # Test datasink writes to s3 properly -@skipif(noboto3 or not fakes3) -def test_datasink_to_s3(): +@pytest.mark.skipif(noboto3 or not fakes3, reason="boto3 or fakes3 library is not available") +def test_datasink_to_s3(dummy_input, tmpdir): ''' This function tests to see if the S3 functionality of a DataSink works properly ''' - - # Import packages - import hashlib - import tempfile - # Init variables ds = nio.DataSink() bucket_name = 'test' @@ -223,8 +201,8 @@ def test_datasink_to_s3(): attr_folder = 'text_file' output_dir = 's3://' + bucket_name # Local temporary filepaths for testing - fakes3_dir = tempfile.mkdtemp() - input_path = _make_dummy_input() + fakes3_dir = str(tmpdir) + input_path = dummy_input # Start up fake-S3 server proc = Popen(['fakes3', '-r', fakes3_dir, '-p', '4567'], stdout=open(os.devnull, 'wb')) @@ -258,26 +236,17 @@ def test_datasink_to_s3(): # Kill fakes3 proc.kill() - # Delete fakes3 folder and input file - shutil.rmtree(fakes3_dir) - shutil.rmtree(os.path.dirname(input_path)) - # Make sure md5sums match - yield assert_equal, src_md5, dst_md5 + assert src_md5 == dst_md5 # Test AWS creds read from env vars -@skipif(noboto3 or not fakes3) def test_aws_keys_from_env(): ''' Function to ensure the DataSink can successfully read in AWS credentials from the environment variables ''' - # Import packages - import os - import nipype.interfaces.io as nio - # Init variables ds = nio.DataSink() aws_access_key_id = 'ABCDACCESS' @@ -291,33 +260,31 @@ def test_aws_keys_from_env(): access_key_test, secret_key_test = ds._return_aws_keys() # Assert match - yield assert_equal, aws_access_key_id, access_key_test - yield assert_equal, aws_secret_access_key, secret_key_test + assert aws_access_key_id == access_key_test + assert aws_secret_access_key == secret_key_test # Test the local copy attribute -def test_datasink_localcopy(): +def test_datasink_localcopy(dummy_input, tmpdir): ''' Function to validate DataSink will make local copy via local_copy attribute ''' - # Import packages - import hashlib - import tempfile - # Init variables - local_dir = tempfile.mkdtemp() + local_dir = str(tmpdir) container = 'outputs' attr_folder = 'text_file' # Make dummy input file and datasink - input_path = _make_dummy_input() + input_path = dummy_input + ds = nio.DataSink() # Set up datasink ds.inputs.container = container ds.inputs.local_copy = local_dir + setattr(ds.inputs, attr_folder, input_path) # Expected local copy path @@ -331,25 +298,21 @@ def test_datasink_localcopy(): src_md5 = hashlib.md5(open(input_path, 'rb').read()).hexdigest() dst_md5 = hashlib.md5(open(local_copy, 'rb').read()).hexdigest() - # Delete temp diretories - shutil.rmtree(os.path.dirname(input_path)) - shutil.rmtree(local_dir) - # Perform test - yield assert_equal, src_md5, dst_md5 + assert src_md5 == dst_md5 -def test_datasink_substitutions(): - indir = mkdtemp(prefix='-Tmp-nipype_ds_subs_in') - outdir = mkdtemp(prefix='-Tmp-nipype_ds_subs_out') +def test_datasink_substitutions(tmpdir): + indir = tmpdir.mkdir('-Tmp-nipype_ds_subs_in') + outdir = tmpdir.mkdir('-Tmp-nipype_ds_subs_out') files = [] for n in ['ababab.n', 'xabababyz.n']: - f = os.path.join(indir, n) + f = str(indir.join(n)) files.append(f) open(f, 'w') ds = nio.DataSink( parametrization=False, - base_directory=outdir, + base_directory=str(outdir), substitutions=[('ababab', 'ABABAB')], # end archoring ($) is used to assure operation on the filename # instead of possible temporary directories names matches @@ -360,12 +323,9 @@ def test_datasink_substitutions(): r'\1!\2')]) setattr(ds.inputs, '@outdir', files) ds.run() - yield assert_equal, \ - sorted([os.path.basename(x) for - x in glob.glob(os.path.join(outdir, '*'))]), \ - ['!-yz-b.n', 'ABABAB.n'] # so we got re used 2nd and both patterns - shutil.rmtree(indir) - shutil.rmtree(outdir) + assert sorted([os.path.basename(x) for + x in glob.glob(os.path.join(str(outdir), '*'))]) \ + == ['!-yz-b.n', 'ABABAB.n'] # so we got re used 2nd and both patterns def _temp_analyze_files(): @@ -388,7 +348,7 @@ def test_datasink_copydir(): file_exists = lambda: os.path.exists(os.path.join(outdir, pth.split(sep)[-1], fname)) - yield assert_true, file_exists() + assert file_exists() shutil.rmtree(pth) orig_img, orig_hdr = _temp_analyze_files() @@ -396,42 +356,16 @@ def test_datasink_copydir(): ds.inputs.remove_dest_dir = True setattr(ds.inputs, 'outdir', pth) ds.run() - yield assert_false, file_exists() + assert not file_exists() shutil.rmtree(outdir) shutil.rmtree(pth) -def test_datafinder_copydir(): - outdir = mkdtemp() - open(os.path.join(outdir, "findme.txt"), 'a').close() - open(os.path.join(outdir, "dontfindme"), 'a').close() - open(os.path.join(outdir, "dontfindmealsotxt"), 'a').close() - open(os.path.join(outdir, "findmetoo.txt"), 'a').close() - open(os.path.join(outdir, "ignoreme.txt"), 'a').close() - open(os.path.join(outdir, "alsoignore.txt"), 'a').close() - - from nipype.interfaces.io import DataFinder - df = DataFinder() - df.inputs.root_paths = outdir - df.inputs.match_regex = '.+/(?P.+)\.txt' - df.inputs.ignore_regexes = ['ignore'] - result = df.run() - expected = ["findme.txt", "findmetoo.txt"] - for path, expected_fname in zip(result.outputs.out_paths, expected): - _, fname = os.path.split(path) - yield assert_equal, fname, expected_fname - - yield assert_equal, result.outputs.basename, ["findme", "findmetoo"] - - shutil.rmtree(outdir) - - -def test_datafinder_depth(): - outdir = mkdtemp() +def test_datafinder_depth(tmpdir): + outdir = str(tmpdir) os.makedirs(os.path.join(outdir, '0', '1', '2', '3')) - from nipype.interfaces.io import DataFinder - df = DataFinder() + df = nio.DataFinder() df.inputs.root_paths = os.path.join(outdir, '0') for min_depth in range(4): for max_depth in range(min_depth, 4): @@ -441,66 +375,61 @@ def test_datafinder_depth(): expected = ['{}'.format(x) for x in range(min_depth, max_depth + 1)] for path, exp_fname in zip(result.outputs.out_paths, expected): _, fname = os.path.split(path) - yield assert_equal, fname, exp_fname - - shutil.rmtree(outdir) + assert fname == exp_fname -def test_datafinder_unpack(): - outdir = mkdtemp() +def test_datafinder_unpack(tmpdir): + outdir = str(tmpdir) single_res = os.path.join(outdir, "findme.txt") open(single_res, 'a').close() open(os.path.join(outdir, "dontfindme"), 'a').close() - from nipype.interfaces.io import DataFinder - df = DataFinder() + df = nio.DataFinder() df.inputs.root_paths = outdir df.inputs.match_regex = '.+/(?P.+)\.txt' df.inputs.unpack_single = True result = df.run() print(result.outputs.out_paths) - yield assert_equal, result.outputs.out_paths, single_res + assert result.outputs.out_paths == single_res def test_freesurfersource(): fss = nio.FreeSurferSource() - yield assert_equal, fss.inputs.hemi, 'both' - yield assert_equal, fss.inputs.subject_id, Undefined - yield assert_equal, fss.inputs.subjects_dir, Undefined + assert fss.inputs.hemi == 'both' + assert fss.inputs.subject_id == Undefined + assert fss.inputs.subjects_dir == Undefined -def test_jsonsink(): - import simplejson - import os +def test_jsonsink_input(tmpdir): ds = nio.JSONFileSink() - yield assert_equal, ds.inputs._outputs, {} + assert ds.inputs._outputs == {} + ds = nio.JSONFileSink(in_dict={'foo': 'var'}) - yield assert_equal, ds.inputs.in_dict, {'foo': 'var'} + assert ds.inputs.in_dict == {'foo': 'var'} + ds = nio.JSONFileSink(infields=['test']) - yield assert_true, 'test' in ds.inputs.copyable_trait_names() + assert 'test' in ds.inputs.copyable_trait_names() - curdir = os.getcwd() - outdir = mkdtemp() - os.chdir(outdir) + +@pytest.mark.parametrize("inputs_attributes", [ + {'new_entry' : 'someValue'}, + {'new_entry' : 'someValue', 'test' : 'testInfields'} +]) +def test_jsonsink(tmpdir, inputs_attributes): + os.chdir(str(tmpdir)) js = nio.JSONFileSink(infields=['test'], in_dict={'foo': 'var'}) - js.inputs.new_entry = 'someValue' setattr(js.inputs, 'contrasts.alt', 'someNestedValue') + expected_data = {"contrasts": {"alt": "someNestedValue"}, "foo": "var"} + for key, val in inputs_attributes.items(): + setattr(js.inputs, key, val) + expected_data[key] = val + res = js.run() - with open(res.outputs.out_file, 'r') as f: data = simplejson.load(f) - yield assert_true, data == {"contrasts": {"alt": "someNestedValue"}, "foo": "var", "new_entry": "someValue"} + + assert data == expected_data - js = nio.JSONFileSink(infields=['test'], in_dict={'foo': 'var'}) - js.inputs.new_entry = 'someValue' - js.inputs.test = 'testInfields' - setattr(js.inputs, 'contrasts.alt', 'someNestedValue') - res = js.run() - with open(res.outputs.out_file, 'r') as f: - data = simplejson.load(f) - yield assert_true, data == {"test": "testInfields", "contrasts": {"alt": "someNestedValue"}, "foo": "var", "new_entry": "someValue"} - os.chdir(curdir) - shutil.rmtree(outdir) diff --git a/nipype/interfaces/tests/test_matlab.py b/nipype/interfaces/tests/test_matlab.py index 11e95d5615..33f80c0fa1 100644 --- a/nipype/interfaces/tests/test_matlab.py +++ b/nipype/interfaces/tests/test_matlab.py @@ -5,8 +5,7 @@ from tempfile import mkdtemp from shutil import rmtree -from nipype.testing import (assert_equal, assert_true, assert_false, - assert_raises, skipif) +import pytest import nipype.interfaces.matlab as mlab matlab_cmd = mlab.get_matlab_command() @@ -23,14 +22,14 @@ def clean_workspace_and_get_default_script_file(): return default_script_file -@skipif(no_matlab) +@pytest.mark.skipif(no_matlab, reason="matlab is not available") def test_cmdline(): default_script_file = clean_workspace_and_get_default_script_file() mi = mlab.MatlabCommand(script='whos', script_file='testscript', mfile=False) - yield assert_equal, mi.cmdline, \ + assert mi.cmdline == \ matlab_cmd + (' -nodesktop -nosplash -singleCompThread -r "fprintf(1,' '\'Executing code at %s:\\n\',datestr(now));ver,try,' 'whos,catch ME,fprintf(2,\'MATLAB code threw an ' @@ -39,52 +38,54 @@ def test_cmdline(): 'Line:%d\\n\',ME.stack.file,ME.stack.name,' 'ME.stack.line);, end;end;;exit"') - yield assert_equal, mi.inputs.script, 'whos' - yield assert_equal, mi.inputs.script_file, 'testscript' - yield assert_false, os.path.exists(mi.inputs.script_file), 'scriptfile should not exist' - yield assert_false, os.path.exists(default_script_file), 'default scriptfile should not exist.' + assert mi.inputs.script == 'whos' + assert mi.inputs.script_file == 'testscript' + assert not os.path.exists(mi.inputs.script_file), 'scriptfile should not exist' + assert not os.path.exists(default_script_file), 'default scriptfile should not exist.' -@skipif(no_matlab) +@pytest.mark.skipif(no_matlab, reason="matlab is not available") def test_mlab_inputspec(): default_script_file = clean_workspace_and_get_default_script_file() spec = mlab.MatlabInputSpec() for k in ['paths', 'script', 'nosplash', 'mfile', 'logfile', 'script_file', 'nodesktop']: - yield assert_true, k in spec.copyable_trait_names() - yield assert_true, spec.nodesktop - yield assert_true, spec.nosplash - yield assert_true, spec.mfile - yield assert_equal, spec.script_file, default_script_file + assert k in spec.copyable_trait_names() + assert spec.nodesktop + assert spec.nosplash + assert spec.mfile + assert spec.script_file == default_script_file -@skipif(no_matlab) +@pytest.mark.skipif(no_matlab, reason="matlab is not available") def test_mlab_init(): default_script_file = clean_workspace_and_get_default_script_file() - yield assert_equal, mlab.MatlabCommand._cmd, 'matlab' - yield assert_equal, mlab.MatlabCommand.input_spec, mlab.MatlabInputSpec + assert mlab.MatlabCommand._cmd == 'matlab' + assert mlab.MatlabCommand.input_spec == mlab.MatlabInputSpec - yield assert_equal, mlab.MatlabCommand().cmd, matlab_cmd + assert mlab.MatlabCommand().cmd == matlab_cmd mc = mlab.MatlabCommand(matlab_cmd='foo_m') - yield assert_equal, mc.cmd, 'foo_m' + assert mc.cmd == 'foo_m' -@skipif(no_matlab) +@pytest.mark.skipif(no_matlab, reason="matlab is not available") def test_run_interface(): default_script_file = clean_workspace_and_get_default_script_file() mc = mlab.MatlabCommand(matlab_cmd='foo_m') - yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 1.' - yield assert_raises, ValueError, mc.run # script is mandatory - yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 2.' + assert not os.path.exists(default_script_file), 'scriptfile should not exist 1.' + with pytest.raises(ValueError): + mc.run() # script is mandatory + assert not os.path.exists(default_script_file), 'scriptfile should not exist 2.' if os.path.exists(default_script_file): # cleanup os.remove(default_script_file) mc.inputs.script = 'a=1;' - yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 3.' - yield assert_raises, IOError, mc.run # foo_m is not an executable - yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 3.' + assert not os.path.exists(default_script_file), 'scriptfile should not exist 3.' + with pytest.raises(IOError): + mc.run() # foo_m is not an executable + assert os.path.exists(default_script_file), 'scriptfile should exist 3.' if os.path.exists(default_script_file): # cleanup os.remove(default_script_file) @@ -94,26 +95,27 @@ def test_run_interface(): # bypasses ubuntu dash issue mc = mlab.MatlabCommand(script='foo;', paths=[basedir], mfile=True) - yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist 4.' - yield assert_raises, RuntimeError, mc.run - yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 4.' + assert not os.path.exists(default_script_file), 'scriptfile should not exist 4.' + with pytest.raises(RuntimeError): + mc.run() + assert os.path.exists(default_script_file), 'scriptfile should exist 4.' if os.path.exists(default_script_file): # cleanup os.remove(default_script_file) # bypasses ubuntu dash issue res = mlab.MatlabCommand(script='a=1;', paths=[basedir], mfile=True).run() - yield assert_equal, res.runtime.returncode, 0 - yield assert_true, os.path.exists(default_script_file), 'scriptfile should exist 5.' + assert res.runtime.returncode == 0 + assert os.path.exists(default_script_file), 'scriptfile should exist 5.' os.chdir(cwd) rmtree(basedir) -@skipif(no_matlab) +@pytest.mark.skipif(no_matlab, reason="matlab is not available") def test_set_matlabcmd(): default_script_file = clean_workspace_and_get_default_script_file() mi = mlab.MatlabCommand() mi.set_default_matlab_cmd('foo') - yield assert_false, os.path.exists(default_script_file), 'scriptfile should not exist.' - yield assert_equal, mi._default_matlab_cmd, 'foo' + assert not os.path.exists(default_script_file), 'scriptfile should not exist.' + assert mi._default_matlab_cmd == 'foo' mi.set_default_matlab_cmd(matlab_cmd) diff --git a/nipype/interfaces/tests/test_nilearn.py b/nipype/interfaces/tests/test_nilearn.py index 94a39c82de..7558b9d0bf 100644 --- a/nipype/interfaces/tests/test_nilearn.py +++ b/nipype/interfaces/tests/test_nilearn.py @@ -1,17 +1,19 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import unittest import os import tempfile import shutil import numpy as np -from ...testing import (assert_equal, utils, assert_almost_equal, raises, - skipif) +from ...testing import utils + from .. import nilearn as iface from ...pipeline import engine as pe +import pytest +import numpy.testing as npt + no_nilearn = True try: __import__('nilearn') @@ -19,7 +21,8 @@ except ImportError: pass -class TestSignalExtraction(unittest.TestCase): +@pytest.mark.skipif(no_nilearn, reason="the nilearn library is not available") +class TestSignalExtraction(): filenames = { 'in_file': 'fmri.nii', @@ -30,15 +33,13 @@ class TestSignalExtraction(unittest.TestCase): labels = ['CSF', 'GrayMatter', 'WhiteMatter'] global_labels = ['GlobalSignal'] + labels - def setUp(self): + def setup_class(self): self.orig_dir = os.getcwd() self.temp_dir = tempfile.mkdtemp() os.chdir(self.temp_dir) - utils.save_toy_nii(self.fake_fmri_data, self.filenames['in_file']) utils.save_toy_nii(self.fake_label_data, self.filenames['label_files']) - @skipif(no_nilearn) def test_signal_extract_no_shared(self): # run iface.SignalExtraction(in_file=self.filenames['in_file'], @@ -49,26 +50,22 @@ def test_signal_extract_no_shared(self): self.assert_expected_output(self.labels, self.base_wanted) - @skipif(no_nilearn) - @raises(ValueError) def test_signal_extr_bad_label_list(self): # run - iface.SignalExtraction(in_file=self.filenames['in_file'], - label_files=self.filenames['label_files'], - class_labels=['bad'], - incl_shared_variance=False).run() + with pytest.raises(ValueError): + iface.SignalExtraction(in_file=self.filenames['in_file'], + label_files=self.filenames['label_files'], + class_labels=['bad'], + incl_shared_variance=False).run() - @skipif(no_nilearn) def test_signal_extr_equiv_4d_no_shared(self): self._test_4d_label(self.base_wanted, self.fake_equiv_4d_label_data, incl_shared_variance=False) - @skipif(no_nilearn) def test_signal_extr_4d_no_shared(self): # set up & run & assert self._test_4d_label(self.fourd_wanted, self.fake_4d_label_data, incl_shared_variance=False) - @skipif(no_nilearn) def test_signal_extr_global_no_shared(self): # set up wanted_global = [[-4./6], [-1./6], [3./6], [-1./6], [-7./6]] @@ -85,7 +82,6 @@ def test_signal_extr_global_no_shared(self): # assert self.assert_expected_output(self.global_labels, wanted_global) - @skipif(no_nilearn) def test_signal_extr_4d_global_no_shared(self): # set up wanted_global = [[3./8], [-3./8], [1./8], [-7./8], [-9./8]] @@ -96,7 +92,6 @@ def test_signal_extr_4d_global_no_shared(self): self._test_4d_label(wanted_global, self.fake_4d_label_data, include_global=True, incl_shared_variance=False) - @skipif(no_nilearn) def test_signal_extr_shared(self): # set up wanted = [] @@ -111,7 +106,7 @@ def test_signal_extr_shared(self): # run & assert self._test_4d_label(wanted, self.fake_4d_label_data) - @skipif(no_nilearn) + def test_signal_extr_traits_valid(self): ''' Test a node using the SignalExtraction interface. Unlike interface.run(), node.run() checks the traits @@ -147,21 +142,21 @@ def assert_expected_output(self, labels, wanted): with open(self.filenames['out_file'], 'r') as output: got = [line.split() for line in output] labels_got = got.pop(0) # remove header - assert_equal(labels_got, labels) - assert_equal(len(got), self.fake_fmri_data.shape[3], - 'num rows and num volumes') + assert labels_got == labels + assert len(got) == self.fake_fmri_data.shape[3],'num rows and num volumes' # convert from string to float got = [[float(num) for num in row] for row in got] for i, time in enumerate(got): - assert_equal(len(labels), len(time)) + assert len(labels) == len(time) for j, segment in enumerate(time): - assert_almost_equal(segment, wanted[i][j], decimal=1) + npt.assert_almost_equal(segment, wanted[i][j], decimal=1) - def tearDown(self): + def teardown_class(self): os.chdir(self.orig_dir) shutil.rmtree(self.temp_dir) + fake_fmri_data = np.array([[[[2, -1, 4, -2, 3], [4, -2, -5, -1, 0]], diff --git a/nipype/interfaces/tests/test_runtime_profiler.py b/nipype/interfaces/tests/test_runtime_profiler.py index 8797eeafce..1672bae0d8 100644 --- a/nipype/interfaces/tests/test_runtime_profiler.py +++ b/nipype/interfaces/tests/test_runtime_profiler.py @@ -11,9 +11,10 @@ from builtins import open, str # Import packages -import unittest from nipype.interfaces.base import (traits, CommandLine, CommandLineInputSpec, runtime_profile) +import pytest +import sys run_profile = runtime_profile @@ -118,31 +119,21 @@ def _use_gb_ram(num_gb): # Test case for the run function -class RuntimeProfilerTestCase(unittest.TestCase): +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") +class TestRuntimeProfiler(): ''' This class is a test case for the runtime profiler - - Inherits - -------- - unittest.TestCase class - - Attributes (class): - ------------------ - see unittest.TestCase documentation - - Attributes (instance): - ---------------------- ''' - # setUp method for the necessary arguments to run cpac_pipeline.run - def setUp(self): + # setup method for the necessary arguments to run cpac_pipeline.run + def setup_class(self): ''' - Method to instantiate TestCase + Method to instantiate TestRuntimeProfiler Parameters ---------- - self : RuntimeProfileTestCase - a unittest.TestCase-inherited class + self : TestRuntimeProfile ''' # Init parameters @@ -227,8 +218,7 @@ def _run_cmdline_workflow(self, num_gb, num_threads): Parameters ---------- - self : RuntimeProfileTestCase - a unittest.TestCase-inherited class + self : TestRuntimeProfile Returns ------- @@ -303,8 +293,7 @@ def _run_function_workflow(self, num_gb, num_threads): Parameters ---------- - self : RuntimeProfileTestCase - a unittest.TestCase-inherited class + self : TestRuntimeProfile Returns ------- @@ -376,7 +365,7 @@ def _run_function_workflow(self, num_gb, num_threads): return start_str, finish_str # Test resources were used as expected in cmdline interface - @unittest.skipIf(run_profile == False, skip_profile_msg) + @pytest.mark.skipif(run_profile == False, reason=skip_profile_msg) def test_cmdline_profiling(self): ''' Test runtime profiler correctly records workflow RAM/CPUs consumption @@ -413,13 +402,12 @@ def test_cmdline_profiling(self): % (expected_runtime_threads, runtime_threads) # Assert runtime stats are what was input - self.assertLessEqual(runtime_gb_err, allowed_gb_err, msg=mem_err) - self.assertTrue(abs(expected_runtime_threads - runtime_threads) <= 1, - msg=threads_err) + assert runtime_gb_err <= allowed_gb_err, mem_err + assert abs(expected_runtime_threads - runtime_threads) <= 1, threads_err # Test resources were used as expected - @unittest.skipIf(True, "https://github.com/nipy/nipype/issues/1663") - @unittest.skipIf(run_profile == False, skip_profile_msg) + @pytest.mark.skipif(True, reason="https://github.com/nipy/nipype/issues/1663") + @pytest.mark.skipif(run_profile == False, reason=skip_profile_msg) def test_function_profiling(self): ''' Test runtime profiler correctly records workflow RAM/CPUs consumption @@ -456,11 +444,7 @@ def test_function_profiling(self): % (expected_runtime_threads, runtime_threads) # Assert runtime stats are what was input - self.assertLessEqual(runtime_gb_err, allowed_gb_err, msg=mem_err) - self.assertTrue(abs(expected_runtime_threads - runtime_threads) <= 1, - msg=threads_err) + assert runtime_gb_err <= allowed_gb_err, mem_err + assert abs(expected_runtime_threads - runtime_threads) <= 1, threads_err -# Command-line run-able unittest module -if __name__ == '__main__': - unittest.main() diff --git a/nipype/interfaces/tests/test_utility.py b/nipype/interfaces/tests/test_utility.py index 208026a72d..b08f7da768 100644 --- a/nipype/interfaces/tests/test_utility.py +++ b/nipype/interfaces/tests/test_utility.py @@ -1,53 +1,42 @@ -# -*- coding: utf-8 -*- +# -*- coding: utf-8 -*- from __future__ import print_function, unicode_literals -from builtins import range, open, str, bytes -# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- -# vi: set ft=python sts=4 ts=4 sw=4 et: +# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- +# vi: set ft=python sts=4 ts=4 sw=4 et: import os -import shutil -from tempfile import mkdtemp, mkstemp +import pytest -import numpy as np -from nipype.testing import assert_equal, assert_true, assert_raises from nipype.interfaces import utility import nipype.pipeline.engine as pe -def test_rename(): - tempdir = os.path.realpath(mkdtemp()) - origdir = os.getcwd() - os.chdir(tempdir) +def test_rename(tmpdir): + os.chdir(str(tmpdir)) # Test very simple rename _ = open("file.txt", "w").close() rn = utility.Rename(in_file="file.txt", format_string="test_file1.txt") res = rn.run() - outfile = os.path.join(tempdir, "test_file1.txt") - yield assert_equal, res.outputs.out_file, outfile - yield assert_true, os.path.exists(outfile) + outfile = str(tmpdir.join("test_file1.txt")) + assert res.outputs.out_file == outfile + assert os.path.exists(outfile) # Now a string-formatting version rn = utility.Rename(in_file="file.txt", format_string="%(field1)s_file%(field2)d", keep_ext=True) # Test .input field creation - yield assert_true, hasattr(rn.inputs, "field1") - yield assert_true, hasattr(rn.inputs, "field2") + assert hasattr(rn.inputs, "field1") + assert hasattr(rn.inputs, "field2") + # Set the inputs rn.inputs.field1 = "test" rn.inputs.field2 = 2 res = rn.run() - outfile = os.path.join(tempdir, "test_file2.txt") - yield assert_equal, res.outputs.out_file, outfile - yield assert_true, os.path.exists(outfile) - - # Clean up - os.chdir(origdir) - shutil.rmtree(tempdir) + outfile = str(tmpdir.join("test_file2.txt")) + assert res.outputs.out_file == outfile + assert os.path.exists(outfile) -def test_function(): - tempdir = os.path.realpath(mkdtemp()) - origdir = os.getcwd() - os.chdir(tempdir) +def test_function(tmpdir): + os.chdir(str(tmpdir)) def gen_random_array(size): import numpy as np @@ -66,42 +55,29 @@ def increment_array(in_array): wf.connect(f1, 'random_array', f2, 'in_array') wf.run() - # Clean up - os.chdir(origdir) - shutil.rmtree(tempdir) - def make_random_array(size): - return np.random.randn(size, size) -def should_fail(): - - tempdir = os.path.realpath(mkdtemp()) - origdir = os.getcwd() - os.chdir(tempdir) +def should_fail(tmpdir): + os.chdir(tmpdir) node = pe.Node(utility.Function(input_names=["size"], output_names=["random_array"], function=make_random_array), name="should_fail") - try: - node.inputs.size = 10 - node.run() - finally: - os.chdir(origdir) - shutil.rmtree(tempdir) - + node.inputs.size = 10 + node.run() -assert_raises(NameError, should_fail) + +def test_should_fail(tmpdir): + with pytest.raises(NameError): + should_fail(str(tmpdir)) -def test_function_with_imports(): - - tempdir = os.path.realpath(mkdtemp()) - origdir = os.getcwd() - os.chdir(tempdir) +def test_function_with_imports(tmpdir): + os.chdir(str(tmpdir)) node = pe.Node(utility.Function(input_names=["size"], output_names=["random_array"], @@ -109,46 +85,33 @@ def test_function_with_imports(): imports=["import numpy as np"]), name="should_not_fail") print(node.inputs.function_str) - try: - node.inputs.size = 10 - node.run() - finally: - os.chdir(origdir) - shutil.rmtree(tempdir) - - -def test_split(): - tempdir = os.path.realpath(mkdtemp()) - origdir = os.getcwd() - os.chdir(tempdir) - - try: - node = pe.Node(utility.Split(inlist=list(range(4)), - splits=[1, 3]), - name='split_squeeze') - res = node.run() - yield assert_equal, res.outputs.out1, [0] - yield assert_equal, res.outputs.out2, [1, 2, 3] - - node = pe.Node(utility.Split(inlist=list(range(4)), - splits=[1, 3], - squeeze=True), - name='split_squeeze') - res = node.run() - yield assert_equal, res.outputs.out1, 0 - yield assert_equal, res.outputs.out2, [1, 2, 3] - finally: - os.chdir(origdir) - shutil.rmtree(tempdir) - - -def test_csvReader(): + node.inputs.size = 10 + node.run() + + +@pytest.mark.parametrize("args, expected", [ + ({} , ([0], [1,2,3])), + ({"squeeze" : True}, (0 , [1,2,3])) + ]) +def test_split(tmpdir, args, expected): + os.chdir(str(tmpdir)) + + node = pe.Node(utility.Split(inlist=list(range(4)), + splits=[1, 3], + **args), + name='split_squeeze') + res = node.run() + assert res.outputs.out1 == expected[0] + assert res.outputs.out2 == expected[1] + + +def test_csvReader(tmpdir): header = "files,labels,erosion\n" lines = ["foo,hello,300.1\n", "bar,world,5\n", "baz,goodbye,0.3\n"] for x in range(2): - fd, name = mkstemp(suffix=".csv") + name = str(tmpdir.join("testfile.csv")) with open(name, 'w') as fid: reader = utility.CSVReader() if x % 2 == 0: @@ -159,23 +122,20 @@ def test_csvReader(): reader.inputs.in_file = name out = reader.run() if x % 2 == 0: - yield assert_equal, out.outputs.files, ['foo', 'bar', 'baz'] - yield assert_equal, out.outputs.labels, ['hello', 'world', 'goodbye'] - yield assert_equal, out.outputs.erosion, ['300.1', '5', '0.3'] + assert out.outputs.files == ['foo', 'bar', 'baz'] + assert out.outputs.labels == ['hello', 'world', 'goodbye'] + assert out.outputs.erosion == ['300.1', '5', '0.3'] else: - yield assert_equal, out.outputs.column_0, ['foo', 'bar', 'baz'] - yield assert_equal, out.outputs.column_1, ['hello', 'world', 'goodbye'] - yield assert_equal, out.outputs.column_2, ['300.1', '5', '0.3'] - os.unlink(name) + assert out.outputs.column_0 == ['foo', 'bar', 'baz'] + assert out.outputs.column_1 == ['hello', 'world', 'goodbye'] + assert out.outputs.column_2 == ['300.1', '5', '0.3'] + - -def test_aux_connect_function(): +def test_aux_connect_function(tmpdir): """ This tests excution nodes with multiple inputs and auxiliary function inside the Workflow connect function. """ - tempdir = os.path.realpath(mkdtemp()) - origdir = os.getcwd() - os.chdir(tempdir) + os.chdir(str(tmpdir)) wf = pe.Workflow(name="test_workflow") @@ -206,7 +166,6 @@ def _inc(x): squeeze=True), name='split') - wf.connect([ (params, gen_tuple, [(("size", _inc), "size")]), (params, ssm, [(("num", _inc), "c")]), @@ -217,7 +176,3 @@ def _inc(x): ]) wf.run() - - # Clean up - os.chdir(origdir) - shutil.rmtree(tempdir) diff --git a/nipype/interfaces/utility.py b/nipype/interfaces/utility.py index 8423c64301..7ef2d1bad3 100644 --- a/nipype/interfaces/utility.py +++ b/nipype/interfaces/utility.py @@ -54,7 +54,7 @@ class IdentityInterface(IOBase): >>> out = ii.run() - >>> out.outputs.a # doctest: +IGNORE_UNICODE + >>> out.outputs.a # doctest: +ALLOW_UNICODE 'foo' >>> ii2 = IdentityInterface(fields=['a', 'b'], mandatory_inputs=True) diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 2fd2ad4407..a7f7833ce6 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..vista import Vnifti2Image @@ -33,7 +32,7 @@ def test_Vnifti2Image_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_Vnifti2Image_outputs(): @@ -43,4 +42,4 @@ def test_Vnifti2Image_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index 6a55d5e69c..a4bec6f193 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -1,5 +1,4 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ....testing import assert_equal from ..vista import VtoMat @@ -30,7 +29,7 @@ def test_VtoMat_inputs(): for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value + assert getattr(inputs.traits()[key], metakey) == value def test_VtoMat_outputs(): @@ -40,4 +39,4 @@ def test_VtoMat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value + assert getattr(outputs.traits()[key], metakey) == value diff --git a/nipype/interfaces/vista/vista.py b/nipype/interfaces/vista/vista.py index 0329404232..e898956d65 100644 --- a/nipype/interfaces/vista/vista.py +++ b/nipype/interfaces/vista/vista.py @@ -34,7 +34,7 @@ class Vnifti2Image(CommandLine): >>> vimage = Vnifti2Image() >>> vimage.inputs.in_file = 'image.nii' - >>> vimage.cmdline # doctest: +IGNORE_UNICODE + >>> vimage.cmdline # doctest: +ALLOW_UNICODE 'vnifti2image -in image.nii -out image.v' >>> vimage.run() # doctest: +SKIP """ @@ -63,7 +63,7 @@ class VtoMat(CommandLine): >>> vimage = VtoMat() >>> vimage.inputs.in_file = 'image.v' - >>> vimage.cmdline # doctest: +IGNORE_UNICODE + >>> vimage.cmdline # doctest: +ALLOW_UNICODE 'vtomat -in image.v -out image.mat' >>> vimage.run() # doctest: +SKIP """ diff --git a/nipype/pipeline/engine/nodes.py b/nipype/pipeline/engine/nodes.py index 6391b2ac5a..699b9e470e 100644 --- a/nipype/pipeline/engine/nodes.py +++ b/nipype/pipeline/engine/nodes.py @@ -845,7 +845,7 @@ def _add_join_item_fields(self): ... name='inputspec'), >>> join = JoinNode(IdentityInterface(fields=['images', 'mask']), ... joinsource='inputspec', joinfield='images', name='join') - >>> join._add_join_item_fields() # doctest: +IGNORE_UNICODE + >>> join._add_join_item_fields() # doctest: +ALLOW_UNICODE {'images': 'imagesJ1'} Return the {base field: slot field} dictionary diff --git a/nipype/pipeline/engine/tests/test_engine.py b/nipype/pipeline/engine/tests/test_engine.py index 35e1a6431b..e5a8f58baa 100644 --- a/nipype/pipeline/engine/tests/test_engine.py +++ b/nipype/pipeline/engine/tests/test_engine.py @@ -10,13 +10,11 @@ from builtins import open from copy import deepcopy from glob import glob -import os -from shutil import rmtree -from tempfile import mkdtemp +import os, sys import networkx as nx -from ....testing import (assert_raises, assert_equal, assert_true, assert_false) +import pytest from ... import engine as pe from ....interfaces import base as nib @@ -30,7 +28,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class EngineTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -45,162 +43,114 @@ def _list_outputs(self): def test_init(): - yield assert_raises, Exception, pe.Workflow + with pytest.raises(Exception): pe.Workflow() pipe = pe.Workflow(name='pipe') - yield assert_equal, type(pipe._graph), nx.DiGraph + assert type(pipe._graph) == nx.DiGraph def test_connect(): pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') + mod2 = pe.Node(interface=EngineTestInterface(), name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) - yield assert_true, mod1 in pipe._graph.nodes() - yield assert_true, mod2 in pipe._graph.nodes() - yield assert_equal, pipe._graph.get_edge_data(mod1, mod2), {'connect': [('output1', 'input1')]} + assert mod1 in pipe._graph.nodes() + assert mod2 in pipe._graph.nodes() + assert pipe._graph.get_edge_data(mod1, mod2) == {'connect': [('output1', 'input1')]} def test_add_nodes(): pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') + mod2 = pe.Node(interface=EngineTestInterface(), name='mod2') pipe.add_nodes([mod1, mod2]) - yield assert_true, mod1 in pipe._graph.nodes() - yield assert_true, mod2 in pipe._graph.nodes() + assert mod1 in pipe._graph.nodes() + assert mod2 in pipe._graph.nodes() # Test graph expansion. The following set tests the building blocks # of the graph expansion routine. # XXX - SG I'll create a graphical version of these tests and actually # ensure that all connections are tested later - -def test1(): +@pytest.mark.parametrize("iterables, expected", [ + ({"1": None}, (1,0)), #test1 + ({"1": dict(input1=lambda: [1, 2], input2=lambda: [1, 2])}, (4,0)) #test2 + ]) +def test_1mod(iterables, expected): pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') + setattr(mod1, "iterables", iterables["1"]) pipe.add_nodes([mod1]) pipe._flatgraph = pipe._create_flat_graph() pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 1 - yield assert_equal, len(pipe._execgraph.edges()), 0 - - -def test2(): - pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod1.iterables = dict(input1=lambda: [1, 2], input2=lambda: [1, 2]) - pipe.add_nodes([mod1]) - pipe._flatgraph = pipe._create_flat_graph() - pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 4 - yield assert_equal, len(pipe._execgraph.edges()), 0 - - -def test3(): - pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod1.iterables = {} - mod2 = pe.Node(interface=TestInterface(), name='mod2') - mod2.iterables = dict(input1=lambda: [1, 2]) - pipe.connect([(mod1, mod2, [('output1', 'input2')])]) - pipe._flatgraph = pipe._create_flat_graph() - pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 3 - yield assert_equal, len(pipe._execgraph.edges()), 2 - - -def test4(): - pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') - mod1.iterables = dict(input1=lambda: [1, 2]) - mod2.iterables = {} - pipe.connect([(mod1, mod2, [('output1', 'input2')])]) - pipe._flatgraph = pipe._create_flat_graph() - pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 4 - yield assert_equal, len(pipe._execgraph.edges()), 2 + assert len(pipe._execgraph.nodes()) == expected[0] + assert len(pipe._execgraph.edges()) == expected[1] -def test5(): +@pytest.mark.parametrize("iterables, expected", [ + ({"1": {}, "2": dict(input1=lambda: [1, 2])}, (3,2)), #test3 + ({"1": dict(input1=lambda: [1, 2]), "2": {}}, (4,2)), #test4 + ({"1": dict(input1=lambda: [1, 2]), "2": dict(input1=lambda: [1, 2])}, (6,4)) #test5 + ]) +def test_2mods(iterables, expected): pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') - mod1.iterables = dict(input1=lambda: [1, 2]) - mod2.iterables = dict(input1=lambda: [1, 2]) + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') + mod2 = pe.Node(interface=EngineTestInterface(), name='mod2') + for nr in ["1", "2"]: + setattr(eval("mod"+nr), "iterables", iterables[nr]) pipe.connect([(mod1, mod2, [('output1', 'input2')])]) pipe._flatgraph = pipe._create_flat_graph() pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 6 - yield assert_equal, len(pipe._execgraph.edges()), 4 + assert len(pipe._execgraph.nodes()) == expected[0] + assert len(pipe._execgraph.edges()) == expected[1] -def test6(): +@pytest.mark.parametrize("iterables, expected, connect", [ + ({"1": {}, "2": dict(input1=lambda: [1, 2]), "3": {}}, (5,4), ("1-2","2-3")), #test6 + ({"1": dict(input1=lambda: [1, 2]), "2": {}, "3": {}}, (5,4), ("1-3","2-3")), #test7 + ({"1": dict(input1=lambda: [1, 2]), "2": dict(input1=lambda: [1, 2]), "3": {}}, + (8,8), ("1-3","2-3")), #test8 + ]) +def test_3mods(iterables, expected, connect): pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') - mod3 = pe.Node(interface=TestInterface(), name='mod3') - mod1.iterables = {} - mod2.iterables = dict(input1=lambda: [1, 2]) - mod3.iterables = {} - pipe.connect([(mod1, mod2, [('output1', 'input2')]), - (mod2, mod3, [('output1', 'input2')])]) - pipe._flatgraph = pipe._create_flat_graph() - pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 5 - yield assert_equal, len(pipe._execgraph.edges()), 4 - - -def test7(): - pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') - mod3 = pe.Node(interface=TestInterface(), name='mod3') - mod1.iterables = dict(input1=lambda: [1, 2]) - mod2.iterables = {} - mod3.iterables = {} - pipe.connect([(mod1, mod3, [('output1', 'input1')]), - (mod2, mod3, [('output1', 'input2')])]) + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') + mod2 = pe.Node(interface=EngineTestInterface(), name='mod2') + mod3 = pe.Node(interface=EngineTestInterface(), name='mod3') + for nr in ["1", "2", "3"]: + setattr(eval("mod"+nr), "iterables", iterables[nr]) + if connect == ("1-2","2-3"): + pipe.connect([(mod1, mod2, [('output1', 'input2')]), + (mod2, mod3, [('output1', 'input2')])]) + elif connect == ("1-3","2-3"): + pipe.connect([(mod1, mod3, [('output1', 'input1')]), + (mod2, mod3, [('output1', 'input2')])]) + else: + raise Exception("connect pattern is not implemented yet within the test function") pipe._flatgraph = pipe._create_flat_graph() pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 5 - yield assert_equal, len(pipe._execgraph.edges()), 4 - + assert len(pipe._execgraph.nodes()) == expected[0] + assert len(pipe._execgraph.edges()) == expected[1] -def test8(): - pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') - mod3 = pe.Node(interface=TestInterface(), name='mod3') - mod1.iterables = dict(input1=lambda: [1, 2]) - mod2.iterables = dict(input1=lambda: [1, 2]) - mod3.iterables = {} - pipe.connect([(mod1, mod3, [('output1', 'input1')]), - (mod2, mod3, [('output1', 'input2')])]) - pipe._flatgraph = pipe._create_flat_graph() - pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) - yield assert_equal, len(pipe._execgraph.nodes()), 8 - yield assert_equal, len(pipe._execgraph.edges()), 8 edgenum = sorted([(len(pipe._execgraph.in_edges(node)) + len(pipe._execgraph.out_edges(node))) for node in pipe._execgraph.nodes()]) - yield assert_true, edgenum[0] > 0 + assert edgenum[0] > 0 def test_expansion(): pipe1 = pe.Workflow(name='pipe1') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') + mod2 = pe.Node(interface=EngineTestInterface(), name='mod2') pipe1.connect([(mod1, mod2, [('output1', 'input2')])]) pipe2 = pe.Workflow(name='pipe2') - mod3 = pe.Node(interface=TestInterface(), name='mod3') - mod4 = pe.Node(interface=TestInterface(), name='mod4') + mod3 = pe.Node(interface=EngineTestInterface(), name='mod3') + mod4 = pe.Node(interface=EngineTestInterface(), name='mod4') pipe2.connect([(mod3, mod4, [('output1', 'input2')])]) pipe3 = pe.Workflow(name="pipe3") pipe3.connect([(pipe1, pipe2, [('mod2.output1', 'mod4.input1')])]) pipe4 = pe.Workflow(name="pipe4") - mod5 = pe.Node(interface=TestInterface(), name='mod5') + mod5 = pe.Node(interface=EngineTestInterface(), name='mod5') pipe4.add_nodes([mod5]) pipe5 = pe.Workflow(name="pipe5") pipe5.add_nodes([pipe4]) @@ -211,30 +161,28 @@ def test_expansion(): pipe6._flatgraph = pipe6._create_flat_graph() except: error_raised = True - yield assert_false, error_raised + assert not error_raised def test_iterable_expansion(): - import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(), name='node1') - node2 = pe.Node(TestInterface(), name='node2') + node1 = pe.Node(EngineTestInterface(), name='node1') + node2 = pe.Node(EngineTestInterface(), name='node2') node1.iterables = ('input1', [1, 2]) wf1.connect(node1, 'output1', node2, 'input2') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: wf3.add_nodes([wf1.clone(name='test%d' % i)]) wf3._flatgraph = wf3._create_flat_graph() - yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 12 + assert len(pe.generate_expanded_graph(wf3._flatgraph).nodes()) == 12 def test_synchronize_expansion(): - import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(), name='node1') + node1 = pe.Node(EngineTestInterface(), name='node1') node1.iterables = [('input1', [1, 2]), ('input2', [3, 4, 5])] node1.synchronize = True - node2 = pe.Node(TestInterface(), name='node2') + node2 = pe.Node(EngineTestInterface(), name='node2') wf1.connect(node1, 'output1', node2, 'input2') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: @@ -245,15 +193,14 @@ def test_synchronize_expansion(): # 1 node2 replicate per node1 replicate # => 2 * 3 = 6 nodes per expanded subgraph # => 18 nodes in the group - yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 18 + assert len(pe.generate_expanded_graph(wf3._flatgraph).nodes()) == 18 def test_synchronize_tuples_expansion(): - import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(), name='node1') - node2 = pe.Node(TestInterface(), name='node2') + node1 = pe.Node(EngineTestInterface(), name='node1') + node2 = pe.Node(EngineTestInterface(), name='node2') node1.iterables = [('input1', 'input2'), [(1, 3), (2, 4), (None, 5)]] node1.synchronize = True @@ -266,25 +213,24 @@ def test_synchronize_tuples_expansion(): wf3._flatgraph = wf3._create_flat_graph() # Identical to test_synchronize_expansion - yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 18 + assert len(pe.generate_expanded_graph(wf3._flatgraph).nodes()) == 18 def test_itersource_expansion(): - import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(), name='node1') + node1 = pe.Node(EngineTestInterface(), name='node1') node1.iterables = ('input1', [1, 2]) - node2 = pe.Node(TestInterface(), name='node2') + node2 = pe.Node(EngineTestInterface(), name='node2') wf1.connect(node1, 'output1', node2, 'input1') - node3 = pe.Node(TestInterface(), name='node3') + node3 = pe.Node(EngineTestInterface(), name='node3') node3.itersource = ('node1', 'input1') node3.iterables = [('input1', {1: [3, 4], 2: [5, 6, 7]})] wf1.connect(node2, 'output1', node3, 'input1') - node4 = pe.Node(TestInterface(), name='node4') + node4 = pe.Node(EngineTestInterface(), name='node4') wf1.connect(node3, 'output1', node4, 'input1') @@ -302,23 +248,22 @@ def test_itersource_expansion(): # 1 node4 successor per node3 replicate # => 2 + 2 + (2 + 3) + 5 = 14 nodes per expanded graph clone # => 3 * 14 = 42 nodes in the group - yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 42 + assert len(pe.generate_expanded_graph(wf3._flatgraph).nodes()) == 42 def test_itersource_synchronize1_expansion(): - import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(), name='node1') + node1 = pe.Node(EngineTestInterface(), name='node1') node1.iterables = [('input1', [1, 2]), ('input2', [3, 4])] node1.synchronize = True - node2 = pe.Node(TestInterface(), name='node2') + node2 = pe.Node(EngineTestInterface(), name='node2') wf1.connect(node1, 'output1', node2, 'input1') - node3 = pe.Node(TestInterface(), name='node3') + node3 = pe.Node(EngineTestInterface(), name='node3') node3.itersource = ('node1', ['input1', 'input2']) node3.iterables = [('input1', {(1, 3): [5, 6]}), ('input2', {(1, 3): [7, 8], (2, 4): [9]})] wf1.connect(node2, 'output1', node3, 'input1') - node4 = pe.Node(TestInterface(), name='node4') + node4 = pe.Node(EngineTestInterface(), name='node4') wf1.connect(node3, 'output1', node4, 'input1') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: @@ -333,25 +278,24 @@ def test_itersource_synchronize1_expansion(): # 1 node4 successor per node3 replicate # => 2 + 2 + (2 + 3) + 5 = 14 nodes per expanded graph clone # => 3 * 14 = 42 nodes in the group - yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 42 + assert len(pe.generate_expanded_graph(wf3._flatgraph).nodes()) == 42 def test_itersource_synchronize2_expansion(): - import nipype.pipeline.engine as pe wf1 = pe.Workflow(name='test') - node1 = pe.Node(TestInterface(), name='node1') + node1 = pe.Node(EngineTestInterface(), name='node1') node1.iterables = [('input1', [1, 2]), ('input2', [3, 4])] node1.synchronize = True - node2 = pe.Node(TestInterface(), name='node2') + node2 = pe.Node(EngineTestInterface(), name='node2') wf1.connect(node1, 'output1', node2, 'input1') - node3 = pe.Node(TestInterface(), name='node3') + node3 = pe.Node(EngineTestInterface(), name='node3') node3.itersource = ('node1', ['input1', 'input2']) node3.synchronize = True node3.iterables = [('input1', 'input2'), {(1, 3): [(5, 7), (6, 8)], (2, 4):[(None, 9)]}] wf1.connect(node2, 'output1', node3, 'input1') - node4 = pe.Node(TestInterface(), name='node4') + node4 = pe.Node(EngineTestInterface(), name='node4') wf1.connect(node3, 'output1', node4, 'input1') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: @@ -366,33 +310,31 @@ def test_itersource_synchronize2_expansion(): # 1 node4 successor per node3 replicate # => 2 + 2 + (2 + 1) + 3 = 10 nodes per expanded graph clone # => 3 * 10 = 30 nodes in the group - yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 30 + assert len(pe.generate_expanded_graph(wf3._flatgraph).nodes()) == 30 def test_disconnect(): - import nipype.pipeline.engine as pe from nipype.interfaces.utility import IdentityInterface a = pe.Node(IdentityInterface(fields=['a', 'b']), name='a') b = pe.Node(IdentityInterface(fields=['a', 'b']), name='b') flow1 = pe.Workflow(name='test') flow1.connect(a, 'a', b, 'a') flow1.disconnect(a, 'a', b, 'a') - yield assert_equal, flow1._graph.edges(), [] + assert flow1._graph.edges() == [] def test_doubleconnect(): - import nipype.pipeline.engine as pe from nipype.interfaces.utility import IdentityInterface a = pe.Node(IdentityInterface(fields=['a', 'b']), name='a') b = pe.Node(IdentityInterface(fields=['a', 'b']), name='b') flow1 = pe.Workflow(name='test') flow1.connect(a, 'a', b, 'a') x = lambda: flow1.connect(a, 'b', b, 'a') - yield assert_raises, Exception, x + with pytest.raises(Exception): x() c = pe.Node(IdentityInterface(fields=['a', 'b']), name='c') flow1 = pe.Workflow(name='test2') x = lambda: flow1.connect([(a, c, [('b', 'b')]), (b, c, [('a', 'b')])]) - yield assert_raises, Exception, x + with pytest.raises(Exception): x() ''' @@ -469,14 +411,14 @@ def test_doubleconnect(): def test_node_init(): - yield assert_raises, Exception, pe.Node + with pytest.raises(Exception): pe.Node() try: - node = pe.Node(TestInterface, name='test') + node = pe.Node(EngineTestInterface, name='test') except IOError: exception = True else: exception = False - yield assert_true, exception + assert exception def test_workflow_add(): @@ -486,38 +428,35 @@ def test_workflow_add(): n3 = pe.Node(ii(fields=['c', 'd']), name='n1') w1 = pe.Workflow(name='test') w1.connect(n1, 'a', n2, 'c') - yield assert_raises, IOError, w1.add_nodes, [n1] - yield assert_raises, IOError, w1.add_nodes, [n2] - yield assert_raises, IOError, w1.add_nodes, [n3] - yield assert_raises, IOError, w1.connect, [(w1, n2, [('n1.a', 'd')])] + for node in [n1, n2, n3]: + with pytest.raises(IOError): w1.add_nodes([node]) + with pytest.raises(IOError): w1.connect([(w1, n2, [('n1.a', 'd')])]) def test_node_get_output(): - mod1 = pe.Node(interface=TestInterface(), name='mod1') + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') mod1.inputs.input1 = 1 mod1.run() - yield assert_equal, mod1.get_output('output1'), [1, 1] + assert mod1.get_output('output1') == [1, 1] mod1._result = None - yield assert_equal, mod1.get_output('output1'), [1, 1] + assert mod1.get_output('output1') == [1, 1] def test_mapnode_iterfield_check(): - mod1 = pe.MapNode(TestInterface(), + mod1 = pe.MapNode(EngineTestInterface(), iterfield=['input1'], name='mod1') - yield assert_raises, ValueError, mod1._check_iterfield - mod1 = pe.MapNode(TestInterface(), + with pytest.raises(ValueError): mod1._check_iterfield() + mod1 = pe.MapNode(EngineTestInterface(), iterfield=['input1', 'input2'], name='mod1') mod1.inputs.input1 = [1, 2] mod1.inputs.input2 = 3 - yield assert_raises, ValueError, mod1._check_iterfield + with pytest.raises(ValueError): mod1._check_iterfield() -def test_mapnode_nested(): - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) +def test_mapnode_nested(tmpdir): + os.chdir(str(tmpdir)) from nipype import MapNode, Function def func1(in1): @@ -531,7 +470,7 @@ def func1(in1): n1.inputs.in1 = [[1, [2]], 3, [4, 5]] n1.run() print(n1.get_output('out')) - yield assert_equal, n1.get_output('out'), [[2, [3]], 4, [5, 6]] + assert n1.get_output('out') == [[2, [3]], 4, [5, 6]] n2 = MapNode(Function(input_names=['in1'], output_names=['out'], @@ -547,12 +486,11 @@ def func1(in1): from nipype.pipeline.engine.base import logger logger.info('Exception: %s' % str(e)) error_raised = True - yield assert_true, error_raised + assert error_raised -def test_node_hash(): - cwd = os.getcwd() - wd = mkdtemp() +def test_node_hash(tmpdir): + wd = str(tmpdir) os.chdir(wd) from nipype.interfaces.utility import Function @@ -593,8 +531,7 @@ def _submit_job(self, node, updatehash=False): from nipype.pipeline.engine.base import logger logger.info('Exception: %s' % str(e)) error_raised = True - yield assert_true, error_raised - # yield assert_true, 'Submit called' in e + assert error_raised # rerun to ensure we have outputs w1.run(plugin='Linear') # set local check @@ -608,14 +545,11 @@ def _submit_job(self, node, updatehash=False): from nipype.pipeline.engine.base import logger logger.info('Exception: %s' % str(e)) error_raised = True - yield assert_false, error_raised - os.chdir(cwd) - rmtree(wd) + assert not error_raised -def test_old_config(): - cwd = os.getcwd() - wd = mkdtemp() +def test_old_config(tmpdir): + wd = str(tmpdir) os.chdir(wd) from nipype.interfaces.utility import Function @@ -647,16 +581,13 @@ def func2(a): from nipype.pipeline.engine.base import logger logger.info('Exception: %s' % str(e)) error_raised = True - yield assert_false, error_raised - os.chdir(cwd) - rmtree(wd) - + assert not error_raised + -def test_mapnode_json(): +def test_mapnode_json(tmpdir): """Tests that mapnodes don't generate excess jsons """ - cwd = os.getcwd() - wd = mkdtemp() + wd = str(tmpdir) os.chdir(wd) from nipype import MapNode, Function, Workflow @@ -681,7 +612,7 @@ def func1(in1): node = eg.nodes()[0] outjson = glob(os.path.join(node.output_dir(), '_0x*.json')) - yield assert_equal, len(outjson), 1 + assert len(outjson) == 1 # check that multiple json's don't trigger rerun with open(os.path.join(node.output_dir(), 'test.json'), 'wt') as fp: @@ -692,14 +623,13 @@ def func1(in1): w1.run() except: error_raised = True - yield assert_false, error_raised - os.chdir(cwd) - rmtree(wd) + assert not error_raised -def test_serial_input(): - cwd = os.getcwd() - wd = mkdtemp() +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") +def test_serial_input(tmpdir): + wd = str(tmpdir) os.chdir(wd) from nipype import MapNode, Function, Workflow @@ -722,7 +652,7 @@ def func1(in1): 'poll_sleep_duration': 2} # test output of num_subnodes method when serial is default (False) - yield assert_equal, n1.num_subnodes(), len(n1.inputs.in1) + assert n1.num_subnodes() == len(n1.inputs.in1) # test running the workflow on default conditions error_raised = False @@ -732,11 +662,11 @@ def func1(in1): from nipype.pipeline.engine.base import logger logger.info('Exception: %s' % str(e)) error_raised = True - yield assert_false, error_raised + assert not error_raised # test output of num_subnodes method when serial is True n1._serial = True - yield assert_equal, n1.num_subnodes(), 1 + assert n1.num_subnodes() == 1 # test running the workflow on serial conditions error_raised = False @@ -746,31 +676,27 @@ def func1(in1): from nipype.pipeline.engine.base import logger logger.info('Exception: %s' % str(e)) error_raised = True - yield assert_false, error_raised - os.chdir(cwd) - rmtree(wd) + assert not error_raised + - -def test_write_graph_runs(): - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) +def test_write_graph_runs(tmpdir): + os.chdir(str(tmpdir)) for graph in ('orig', 'flat', 'exec', 'hierarchical', 'colored'): for simple in (True, False): pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.Node(interface=TestInterface(), name='mod2') + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') + mod2 = pe.Node(interface=EngineTestInterface(), name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) try: pipe.write_graph(graph2use=graph, simple_form=simple) except Exception: - yield assert_true, False, \ - 'Failed to plot {} {} graph'.format( + assert False, \ + 'Failed to plot {} {} graph'.format( 'simple' if simple else 'detailed', graph) - yield assert_true, os.path.exists('graph.dot') or os.path.exists('graph_detailed.dot') + assert os.path.exists('graph.dot') or os.path.exists('graph_detailed.dot') try: os.remove('graph.dot') except OSError: @@ -780,13 +706,9 @@ def test_write_graph_runs(): except OSError: pass - os.chdir(cwd) - rmtree(wd) -def test_deep_nested_write_graph_runs(): - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) +def test_deep_nested_write_graph_runs(tmpdir): + os.chdir(str(tmpdir)) for graph in ('orig', 'flat', 'exec', 'hierarchical', 'colored'): for simple in (True, False): @@ -796,16 +718,16 @@ def test_deep_nested_write_graph_runs(): sub = pe.Workflow(name='pipe_nest_{}'.format(depth)) parent.add_nodes([sub]) parent = sub - mod1 = pe.Node(interface=TestInterface(), name='mod1') + mod1 = pe.Node(interface=EngineTestInterface(), name='mod1') parent.add_nodes([mod1]) try: pipe.write_graph(graph2use=graph, simple_form=simple) except Exception as e: - yield assert_true, False, \ - 'Failed to plot {} {} deep graph: {!s}'.format( + assert False, \ + 'Failed to plot {} {} deep graph: {!s}'.format( 'simple' if simple else 'detailed', graph, e) - yield assert_true, os.path.exists('graph.dot') or os.path.exists('graph_detailed.dot') + assert os.path.exists('graph.dot') or os.path.exists('graph_detailed.dot') try: os.remove('graph.dot') except OSError: @@ -814,6 +736,3 @@ def test_deep_nested_write_graph_runs(): os.remove('graph_detailed.dot') except OSError: pass - - os.chdir(cwd) - rmtree(wd) diff --git a/nipype/pipeline/engine/tests/test_join.py b/nipype/pipeline/engine/tests/test_join.py index cefb53acd9..dc4c74361d 100644 --- a/nipype/pipeline/engine/tests/test_join.py +++ b/nipype/pipeline/engine/tests/test_join.py @@ -7,10 +7,7 @@ from builtins import open import os -from shutil import rmtree -from tempfile import mkdtemp -from ....testing import (assert_equal, assert_true) from ... import engine as pe from ....interfaces import base as nib from ....interfaces.utility import IdentityInterface @@ -151,10 +148,8 @@ def _list_outputs(self): return outputs -def test_join_expansion(): - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) +def test_join_expansion(tmpdir): + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -183,31 +178,25 @@ def test_join_expansion(): # the two expanded pre-join predecessor nodes feed into one join node joins = [node for node in result.nodes() if node.name == 'join'] - assert_equal(len(joins), 1, "The number of join result nodes is incorrect.") + assert len(joins) == 1, "The number of join result nodes is incorrect." # the expanded graph contains 2 * 2 = 4 iteration pre-join nodes, 1 join # node, 1 non-iterated post-join node and 2 * 1 iteration post-join nodes. # Nipype factors away the IdentityInterface. - assert_equal(len(result.nodes()), 8, "The number of expanded nodes is incorrect.") + assert len(result.nodes()) == 8, "The number of expanded nodes is incorrect." # the join Sum result is (1 + 1 + 1) + (2 + 1 + 1) - assert_equal(len(_sums), 1, - "The number of join outputs is incorrect") - assert_equal(_sums[0], 7, "The join Sum output value is incorrect: %s." % _sums[0]) + assert len(_sums) == 1, "The number of join outputs is incorrect" + assert _sums[0] == 7, "The join Sum output value is incorrect: %s." % _sums[0] # the join input preserves the iterables input order - assert_equal(_sum_operands[0], [3, 4], - "The join Sum input is incorrect: %s." % _sum_operands[0]) + assert _sum_operands[0] == [3, 4], \ + "The join Sum input is incorrect: %s." % _sum_operands[0] # there are two iterations of the post-join node in the iterable path - assert_equal(len(_products), 2, - "The number of iterated post-join outputs is incorrect") - - os.chdir(cwd) - rmtree(wd) + assert len(_products) == 2,\ + "The number of iterated post-join outputs is incorrect" -def test_node_joinsource(): +def test_node_joinsource(tmpdir): """Test setting the joinsource to a Node.""" - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -219,18 +208,13 @@ def test_node_joinsource(): joinfield='input1', name='join') # the joinsource is the inputspec name - assert_equal(join.joinsource, inputspec.name, - "The joinsource is not set to the node name.") + assert join.joinsource == inputspec.name, \ + "The joinsource is not set to the node name." - os.chdir(cwd) - rmtree(wd) - -def test_set_join_node(): +def test_set_join_node(tmpdir): """Test collecting join inputs to a set.""" - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -248,20 +232,15 @@ def test_set_join_node(): wf.run() # the join length is the number of unique inputs - assert_equal(_set_len, 3, - "The join Set output value is incorrect: %s." % _set_len) - - os.chdir(cwd) - rmtree(wd) + assert _set_len == 3, \ + "The join Set output value is incorrect: %s." % _set_len -def test_unique_join_node(): +def test_unique_join_node(tmpdir): """Test join with the ``unique`` flag set to True.""" global _sum_operands _sum_operands = [] - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -278,20 +257,15 @@ def test_unique_join_node(): wf.run() - assert_equal(_sum_operands[0], [4, 2, 3], - "The unique join output value is incorrect: %s." % _sum_operands[0]) - - os.chdir(cwd) - rmtree(wd) + assert _sum_operands[0] == [4, 2, 3], \ + "The unique join output value is incorrect: %s." % _sum_operands[0] -def test_multiple_join_nodes(): +def test_multiple_join_nodes(tmpdir): """Test two join nodes, one downstream of the other.""" global _products _products = [] - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -329,27 +303,22 @@ def test_multiple_join_nodes(): # The expanded graph contains one pre_join1 replicate per inputspec # replicate and one of each remaining node = 3 + 5 = 8 nodes. # The replicated inputspec nodes are factored out of the expansion. - assert_equal(len(result.nodes()), 8, - "The number of expanded nodes is incorrect.") + assert len(result.nodes()) == 8, \ + "The number of expanded nodes is incorrect." # The outputs are: # pre_join1: [2, 3, 4] # post_join1: 9 # join2: [2, 3, 4] and 9 # post_join2: 9 # post_join3: 9 * 9 = 81 - assert_equal(_products, [81], "The post-join product is incorrect") + assert _products == [81], "The post-join product is incorrect" - os.chdir(cwd) - rmtree(wd) - -def test_identity_join_node(): +def test_identity_join_node(tmpdir): """Test an IdentityInterface join.""" global _sum_operands _sum_operands = [] - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -374,22 +343,17 @@ def test_identity_join_node(): # the expanded graph contains 1 * 3 iteration pre-join nodes, 1 join # node and 1 post-join node. Nipype factors away the iterable input # IdentityInterface but keeps the join IdentityInterface. - assert_equal(len(result.nodes()), 5, - "The number of expanded nodes is incorrect.") - assert_equal(_sum_operands[0], [2, 3, 4], - "The join Sum input is incorrect: %s." % _sum_operands[0]) + assert len(result.nodes()) == 5, \ + "The number of expanded nodes is incorrect." + assert _sum_operands[0] == [2, 3, 4], \ + "The join Sum input is incorrect: %s." % _sum_operands[0] - os.chdir(cwd) - rmtree(wd) - -def test_multifield_join_node(): +def test_multifield_join_node(tmpdir): """Test join on several fields.""" global _products _products = [] - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -418,23 +382,18 @@ def test_multifield_join_node(): # the iterables are expanded as the cartesian product of the iterables values. # thus, the expanded graph contains 2 * (2 * 2) iteration pre-join nodes, 1 join # node and 1 post-join node. - assert_equal(len(result.nodes()), 10, - "The number of expanded nodes is incorrect.") + assert len(result.nodes()) == 10, \ + "The number of expanded nodes is incorrect." # the product inputs are [2, 4], [2, 5], [3, 4], [3, 5] - assert_equal(set(_products), set([8, 10, 12, 15]), - "The post-join products is incorrect: %s." % _products) - - os.chdir(cwd) - rmtree(wd) + assert set(_products) == set([8, 10, 12, 15]), \ + "The post-join products is incorrect: %s." % _products -def test_synchronize_join_node(): +def test_synchronize_join_node(tmpdir): """Test join on an input node which has the ``synchronize`` flag set to True.""" global _products _products = [] - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -462,21 +421,16 @@ def test_synchronize_join_node(): # there are 3 iterables expansions. # thus, the expanded graph contains 2 * 2 iteration pre-join nodes, 1 join # node and 1 post-join node. - assert_equal(len(result.nodes()), 6, - "The number of expanded nodes is incorrect.") + assert len(result.nodes()) == 6, \ + "The number of expanded nodes is incorrect." # the product inputs are [2, 3] and [4, 5] - assert_equal(_products, [8, 15], - "The post-join products is incorrect: %s." % _products) - - os.chdir(cwd) - rmtree(wd) + assert _products == [8, 15], \ + "The post-join products is incorrect: %s." % _products -def test_itersource_join_source_node(): +def test_itersource_join_source_node(tmpdir): """Test join on an input node which has an ``itersource``.""" - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -513,29 +467,24 @@ def test_itersource_join_source_node(): # 2 + (2 * 2) + 4 + 2 + 2 = 14 expansion graph nodes. # Nipype factors away the iterable input # IdentityInterface but keeps the join IdentityInterface. - assert_equal(len(result.nodes()), 14, - "The number of expanded nodes is incorrect.") + assert len(result.nodes()) == 14, \ + "The number of expanded nodes is incorrect." # The first join inputs are: # 1 + (3 * 2) and 1 + (4 * 2) # The second join inputs are: # 1 + (5 * 3) and 1 + (6 * 3) # the post-join nodes execution order is indeterminate; # therefore, compare the lists item-wise. - assert_true([16, 19] in _sum_operands, - "The join Sum input is incorrect: %s." % _sum_operands) - assert_true([7, 9] in _sum_operands, - "The join Sum input is incorrect: %s." % _sum_operands) + assert [16, 19] in _sum_operands, \ + "The join Sum input is incorrect: %s." % _sum_operands + assert [7, 9] in _sum_operands, \ + "The join Sum input is incorrect: %s." % _sum_operands - os.chdir(cwd) - rmtree(wd) - -def test_itersource_two_join_nodes(): +def test_itersource_two_join_nodes(tmpdir): """Test join with a midstream ``itersource`` and an upstream iterable.""" - cwd = os.getcwd() - wd = mkdtemp() - os.chdir(wd) + os.chdir(str(tmpdir)) # Make the workflow. wf = pe.Workflow(name='test') @@ -569,17 +518,13 @@ def test_itersource_two_join_nodes(): # the expanded graph contains the 14 test_itersource_join_source_node # nodes plus the summary join node. - assert_equal(len(result.nodes()), 15, - "The number of expanded nodes is incorrect.") - - os.chdir(cwd) - rmtree(wd) + assert len(result.nodes()) == 15, \ + "The number of expanded nodes is incorrect." -def test_set_join_node_file_input(): +def test_set_join_node_file_input(tmpdir): """Test collecting join inputs to a set.""" - cwd = os.getcwd() - wd = mkdtemp() + wd = str(tmpdir) os.chdir(wd) open('test.nii', 'w+').close() open('test2.nii', 'w+').close() @@ -599,13 +544,10 @@ def test_set_join_node_file_input(): wf.run() - os.chdir(cwd) - rmtree(wd) -def test_nested_workflow_join(): +def test_nested_workflow_join(tmpdir): """Test collecting join inputs within a nested workflow""" - cwd = os.getcwd() - wd = mkdtemp() + wd = str(tmpdir) os.chdir(wd) # Make the nested workflow @@ -636,14 +578,7 @@ def nested_wf(i, name='smallwf'): result = meta_wf.run() # there should be six nodes in total - assert_equal(len(result.nodes()), 6, - "The number of expanded nodes is incorrect.") + assert len(result.nodes()) == 6, \ + "The number of expanded nodes is incorrect." - os.chdir(cwd) - rmtree(wd) - - -if __name__ == "__main__": - import nose - nose.main(defaultTest=__name__) diff --git a/nipype/pipeline/engine/tests/test_utils.py b/nipype/pipeline/engine/tests/test_utils.py index 4d37beef4d..f14fe25916 100644 --- a/nipype/pipeline/engine/tests/test_utils.py +++ b/nipype/pipeline/engine/tests/test_utils.py @@ -8,10 +8,8 @@ import os from copy import deepcopy -from tempfile import mkdtemp from shutil import rmtree -from ....testing import (assert_equal, assert_true, assert_false) from ... import engine as pe from ....interfaces import base as nib from ....interfaces import utility as niu @@ -46,10 +44,10 @@ def test_function(arg1, arg2, arg3): fg = wf._create_flat_graph() wf._set_needed_outputs(fg) eg = pe.generate_expanded_graph(deepcopy(fg)) - yield assert_equal, len(eg.nodes()), 8 + assert len(eg.nodes()) == 8 -def test_clean_working_directory(): +def test_clean_working_directory(tmpdir): class OutputSpec(nib.TraitedSpec): files = nib.traits.List(nib.File) others = nib.File() @@ -59,7 +57,7 @@ class InputSpec(nib.TraitedSpec): outputs = OutputSpec() inputs = InputSpec() - wd = mkdtemp() + wd = str(tmpdir) filenames = ['file.hdr', 'file.img', 'file.BRIK', 'file.HEAD', '_0x1234.json', 'foo.txt'] outfiles = [] @@ -73,27 +71,26 @@ class InputSpec(nib.TraitedSpec): inputs.infile = outfiles[-1] needed_outputs = ['files'] config.set_default_config() - yield assert_true, os.path.exists(outfiles[5]) + assert os.path.exists(outfiles[5]) config.set_default_config() config.set('execution', 'remove_unnecessary_outputs', False) out = clean_working_directory(outputs, wd, inputs, needed_outputs, deepcopy(config._sections)) - yield assert_true, os.path.exists(outfiles[5]) - yield assert_equal, out.others, outfiles[5] + assert os.path.exists(outfiles[5]) + assert out.others == outfiles[5] config.set('execution', 'remove_unnecessary_outputs', True) out = clean_working_directory(outputs, wd, inputs, needed_outputs, deepcopy(config._sections)) - yield assert_true, os.path.exists(outfiles[1]) - yield assert_true, os.path.exists(outfiles[3]) - yield assert_true, os.path.exists(outfiles[4]) - yield assert_false, os.path.exists(outfiles[5]) - yield assert_equal, out.others, nib.Undefined - yield assert_equal, len(out.files), 2 + assert os.path.exists(outfiles[1]) + assert os.path.exists(outfiles[3]) + assert os.path.exists(outfiles[4]) + assert not os.path.exists(outfiles[5]) + assert out.others == nib.Undefined + assert len(out.files) == 2 config.set_default_config() - rmtree(wd) -def test_outputs_removal(): +def test_outputs_removal(tmpdir): def test_function(arg1): import os @@ -107,7 +104,7 @@ def test_function(arg1): fp.close() return file1, file2 - out_dir = mkdtemp() + out_dir = str(tmpdir) n1 = pe.Node(niu.Function(input_names=['arg1'], output_names=['file1', 'file2'], function=test_function), @@ -117,21 +114,20 @@ def test_function(arg1): n1.config = {'execution': {'remove_unnecessary_outputs': True}} n1.config = merge_dict(deepcopy(config._sections), n1.config) n1.run() - yield assert_true, os.path.exists(os.path.join(out_dir, - n1.name, - 'file1.txt')) - yield assert_true, os.path.exists(os.path.join(out_dir, - n1.name, - 'file2.txt')) + assert os.path.exists(os.path.join(out_dir, + n1.name, + 'file1.txt')) + assert os.path.exists(os.path.join(out_dir, + n1.name, + 'file2.txt')) n1.needed_outputs = ['file2'] n1.run() - yield assert_false, os.path.exists(os.path.join(out_dir, - n1.name, - 'file1.txt')) - yield assert_true, os.path.exists(os.path.join(out_dir, - n1.name, - 'file2.txt')) - rmtree(out_dir) + assert not os.path.exists(os.path.join(out_dir, + n1.name, + 'file1.txt')) + assert os.path.exists(os.path.join(out_dir, + n1.name, + 'file2.txt')) class InputSpec(nib.TraitedSpec): @@ -142,7 +138,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class UtilsTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -156,34 +152,33 @@ def _list_outputs(self): return outputs -def test_inputs_removal(): - out_dir = mkdtemp() +def test_inputs_removal(tmpdir): + out_dir = str(tmpdir) file1 = os.path.join(out_dir, 'file1.txt') fp = open(file1, 'wt') fp.write('dummy_file') fp.close() - n1 = pe.Node(TestInterface(), + n1 = pe.Node(UtilsTestInterface(), base_dir=out_dir, name='testinputs') n1.inputs.in_file = file1 n1.config = {'execution': {'keep_inputs': True}} n1.config = merge_dict(deepcopy(config._sections), n1.config) n1.run() - yield assert_true, os.path.exists(os.path.join(out_dir, - n1.name, - 'file1.txt')) + assert os.path.exists(os.path.join(out_dir, + n1.name, + 'file1.txt')) n1.inputs.in_file = file1 n1.config = {'execution': {'keep_inputs': False}} n1.config = merge_dict(deepcopy(config._sections), n1.config) n1.overwrite = True n1.run() - yield assert_false, os.path.exists(os.path.join(out_dir, - n1.name, - 'file1.txt')) - rmtree(out_dir) + assert not os.path.exists(os.path.join(out_dir, + n1.name, + 'file1.txt')) -def test_outputs_removal_wf(): +def test_outputs_removal_wf(tmpdir): def test_function(arg1): import os @@ -214,7 +209,7 @@ def test_function3(arg): import os return arg - out_dir = mkdtemp() + out_dir = str(tmpdir) for plugin in ('Linear',): # , 'MultiProc'): n1 = pe.Node(niu.Function(input_names=['arg1'], @@ -245,37 +240,37 @@ def test_function3(arg): rmtree(os.path.join(wf.base_dir, wf.name)) wf.run(plugin=plugin) - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n1.name, - 'file2.txt')) != remove_unnecessary_outputs - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n1.name, - "subdir", - 'file1.txt')) != remove_unnecessary_outputs - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n1.name, - 'file1.txt')) - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n1.name, - 'file3.txt')) != remove_unnecessary_outputs - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n2.name, - 'file1.txt')) - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n2.name, - 'file2.txt')) - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n2.name, - 'file3.txt')) != remove_unnecessary_outputs - - n4 = pe.Node(TestInterface(), name='n4') + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n1.name, + 'file2.txt')) != remove_unnecessary_outputs + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n1.name, + "subdir", + 'file1.txt')) != remove_unnecessary_outputs + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n1.name, + 'file1.txt')) + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n1.name, + 'file3.txt')) != remove_unnecessary_outputs + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n2.name, + 'file1.txt')) + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n2.name, + 'file2.txt')) + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n2.name, + 'file3.txt')) != remove_unnecessary_outputs + + n4 = pe.Node(UtilsTestInterface(), name='n4') wf.connect(n2, "out_file1", n4, "in_file") def pick_first(l): @@ -288,20 +283,18 @@ def pick_first(l): wf.config = {'execution': {'keep_inputs': keep_inputs, 'remove_unnecessary_outputs': remove_unnecessary_outputs}} rmtree(os.path.join(wf.base_dir, wf.name)) wf.run(plugin=plugin) - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n2.name, - 'file1.txt')) - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n2.name, - 'file2.txt')) != remove_unnecessary_outputs - yield assert_true, os.path.exists(os.path.join(wf.base_dir, - wf.name, - n4.name, - 'file1.txt')) == keep_inputs - - rmtree(out_dir) + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n2.name, + 'file1.txt')) + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n2.name, + 'file2.txt')) != remove_unnecessary_outputs + assert os.path.exists(os.path.join(wf.base_dir, + wf.name, + n4.name, + 'file1.txt')) == keep_inputs def fwhm(fwhm): @@ -324,17 +317,16 @@ def create_wf(name): return pipe -def test_multi_disconnected_iterable(): - out_dir = mkdtemp() +def test_multi_disconnected_iterable(tmpdir): metawf = pe.Workflow(name='meta') - metawf.base_dir = out_dir + metawf.base_dir = str(tmpdir) metawf.add_nodes([create_wf('wf%d' % i) for i in range(30)]) eg = metawf.run(plugin='Linear') - yield assert_equal, len(eg.nodes()), 60 - rmtree(out_dir) + assert len(eg.nodes()) == 60 + -def test_provenance(): - out_dir = mkdtemp() +def test_provenance(tmpdir): + out_dir = str(tmpdir) metawf = pe.Workflow(name='meta') metawf.base_dir = out_dir metawf.add_nodes([create_wf('wf%d' % i) for i in range(1)]) @@ -342,6 +334,6 @@ def test_provenance(): prov_base = os.path.join(out_dir, 'workflow_provenance_test') psg = write_workflow_prov(eg, prov_base, format='all') - yield assert_equal, len(psg.bundles), 2 - yield assert_equal, len(psg.get_records()), 7 - rmtree(out_dir) + assert len(psg.bundles) == 2 + assert len(psg.get_records()) == 7 + diff --git a/nipype/pipeline/plugins/sge.py b/nipype/pipeline/plugins/sge.py index f27ffc4b7a..8db4461cba 100644 --- a/nipype/pipeline/plugins/sge.py +++ b/nipype/pipeline/plugins/sge.py @@ -312,9 +312,9 @@ def qsub_sanitize_job_name(testjobname): Numbers and punctuation are not allowed. - >>> qsub_sanitize_job_name('01') # doctest: +IGNORE_UNICODE + >>> qsub_sanitize_job_name('01') # doctest: +ALLOW_UNICODE 'J01' - >>> qsub_sanitize_job_name('a01') # doctest: +IGNORE_UNICODE + >>> qsub_sanitize_job_name('a01') # doctest: +ALLOW_UNICODE 'a01' """ if testjobname[0].isalpha(): diff --git a/nipype/pipeline/plugins/tests/test_base.py b/nipype/pipeline/plugins/tests/test_base.py index 3e22019816..5974f93c49 100644 --- a/nipype/pipeline/plugins/tests/test_base.py +++ b/nipype/pipeline/plugins/tests/test_base.py @@ -9,15 +9,14 @@ import mock -from nipype.testing import (assert_raises, assert_equal, assert_true, - assert_false, skipif, assert_regexp_matches) import nipype.pipeline.plugins.base as pb + def test_scipy_sparse(): foo = ssp.lil_matrix(np.eye(3, k=1)) goo = foo.getrowview(0) goo[goo.nonzero()] = 0 - yield assert_equal, foo[0, 1], 0 + assert foo[0, 1] == 0 def test_report_crash(): with mock.patch('pickle.dump', mock.MagicMock()) as mock_pickle_dump: @@ -34,9 +33,9 @@ def test_report_crash(): actual_crashfile = pb.report_crash(mock_node) expected_crashfile = re.compile('.*/crash-.*-an_id-[0-9a-f\-]*.pklz') - - yield assert_regexp_matches, actual_crashfile, expected_crashfile - yield assert_true, mock_pickle_dump.call_count == 1 + + assert expected_crashfile.match(actual_crashfile).group() == actual_crashfile + assert mock_pickle_dump.call_count == 1 ''' Can use the following code to test that a mapnode crash continues successfully diff --git a/nipype/pipeline/plugins/tests/test_callback.py b/nipype/pipeline/plugins/tests/test_callback.py index 78b48f6b32..7f165d1f2c 100644 --- a/nipype/pipeline/plugins/tests/test_callback.py +++ b/nipype/pipeline/plugins/tests/test_callback.py @@ -6,10 +6,9 @@ """ from builtins import object -from tempfile import mkdtemp -from shutil import rmtree -from nipype.testing import assert_equal +import pytest +import sys import nipype.interfaces.utility as niu import nipype.pipeline.engine as pe @@ -31,26 +30,25 @@ def callback(self, node, status, result=None): self.statuses.append((node, status)) -def test_callback_normal(): +def test_callback_normal(tmpdir): so = Status() - wf = pe.Workflow(name='test', base_dir=mkdtemp()) + wf = pe.Workflow(name='test', base_dir=str(tmpdir)) f_node = pe.Node(niu.Function(function=func, input_names=[], output_names=[]), name='f_node') wf.add_nodes([f_node]) wf.config['execution'] = {'crashdump_dir': wf.base_dir} wf.run(plugin="Linear", plugin_args={'status_callback': so.callback}) - assert_equal(len(so.statuses), 2) + assert len(so.statuses) == 2 for (n, s) in so.statuses: - yield assert_equal, n.name, 'f_node' - yield assert_equal, so.statuses[0][1], 'start' - yield assert_equal, so.statuses[1][1], 'end' - rmtree(wf.base_dir) + assert n.name == 'f_node' + assert so.statuses[0][1] == 'start' + assert so.statuses[1][1] == 'end' -def test_callback_exception(): +def test_callback_exception(tmpdir): so = Status() - wf = pe.Workflow(name='test', base_dir=mkdtemp()) + wf = pe.Workflow(name='test', base_dir=str(tmpdir)) f_node = pe.Node(niu.Function(function=bad_func, input_names=[], output_names=[]), name='f_node') @@ -60,17 +58,18 @@ def test_callback_exception(): wf.run(plugin="Linear", plugin_args={'status_callback': so.callback}) except: pass - assert_equal(len(so.statuses), 2) + assert len(so.statuses) == 2 for (n, s) in so.statuses: - yield assert_equal, n.name, 'f_node' - yield assert_equal, so.statuses[0][1], 'start' - yield assert_equal, so.statuses[1][1], 'exception' - rmtree(wf.base_dir) - - -def test_callback_multiproc_normal(): + assert n.name == 'f_node' + assert so.statuses[0][1] == 'start' + assert so.statuses[1][1] == 'exception' + + +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") +def test_callback_multiproc_normal(tmpdir): so = Status() - wf = pe.Workflow(name='test', base_dir=mkdtemp()) + wf = pe.Workflow(name='test', base_dir=str(tmpdir)) f_node = pe.Node(niu.Function(function=func, input_names=[], output_names=[]), name='f_node') @@ -78,17 +77,18 @@ def test_callback_multiproc_normal(): wf.config['execution']['crashdump_dir'] = wf.base_dir wf.config['execution']['poll_sleep_duration'] = 2 wf.run(plugin='MultiProc', plugin_args={'status_callback': so.callback}) - assert_equal(len(so.statuses), 2) + assert len(so.statuses) == 2 for (n, s) in so.statuses: - yield assert_equal, n.name, 'f_node' - yield assert_equal, so.statuses[0][1], 'start' - yield assert_equal, so.statuses[1][1], 'end' - rmtree(wf.base_dir) - - -def test_callback_multiproc_exception(): + assert n.name == 'f_node' + assert so.statuses[0][1] == 'start' + assert so.statuses[1][1] == 'end' + + +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") +def test_callback_multiproc_exception(tmpdir): so = Status() - wf = pe.Workflow(name='test', base_dir=mkdtemp()) + wf = pe.Workflow(name='test', base_dir=str(tmpdir)) f_node = pe.Node(niu.Function(function=bad_func, input_names=[], output_names=[]), name='f_node') @@ -99,9 +99,9 @@ def test_callback_multiproc_exception(): plugin_args={'status_callback': so.callback}) except: pass - assert_equal(len(so.statuses), 2) + assert len(so.statuses) == 2 for (n, s) in so.statuses: - yield assert_equal, n.name, 'f_node' - yield assert_equal, so.statuses[0][1], 'start' - yield assert_equal, so.statuses[1][1], 'exception' - rmtree(wf.base_dir) + assert n.name == 'f_node' + assert so.statuses[0][1] == 'start' + assert so.statuses[1][1] == 'exception' + diff --git a/nipype/pipeline/plugins/tests/test_debug.py b/nipype/pipeline/plugins/tests/test_debug.py index 115d40c5d4..2bd2003492 100644 --- a/nipype/pipeline/plugins/tests/test_debug.py +++ b/nipype/pipeline/plugins/tests/test_debug.py @@ -1,10 +1,8 @@ # -*- coding: utf-8 -*- import os import nipype.interfaces.base as nib -from tempfile import mkdtemp -from shutil import rmtree -from nipype.testing import assert_raises, assert_false +import pytest import nipype.pipeline.engine as pe @@ -17,7 +15,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class DebugTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -35,26 +33,22 @@ def callme(node, graph): pass -def test_debug(): - cur_dir = os.getcwd() - temp_dir = mkdtemp(prefix='test_engine_') - os.chdir(temp_dir) +def test_debug(tmpdir): + os.chdir(str(tmpdir)) pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.MapNode(interface=TestInterface(), + mod1 = pe.Node(interface=DebugTestInterface(), name='mod1') + mod2 = pe.MapNode(interface=DebugTestInterface(), iterfield=['input1'], name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) pipe.base_dir = os.getcwd() mod1.inputs.input1 = 1 run_wf = lambda: pipe.run(plugin="Debug") - yield assert_raises, ValueError, run_wf + with pytest.raises(ValueError): run_wf() try: pipe.run(plugin="Debug", plugin_args={'callable': callme}) exception_raised = False except Exception: exception_raised = True - yield assert_false, exception_raised - os.chdir(cur_dir) - rmtree(temp_dir) + assert not exception_raised diff --git a/nipype/pipeline/plugins/tests/test_linear.py b/nipype/pipeline/plugins/tests/test_linear.py index 9c2568a89c..e4df3f7db3 100644 --- a/nipype/pipeline/plugins/tests/test_linear.py +++ b/nipype/pipeline/plugins/tests/test_linear.py @@ -1,10 +1,7 @@ # -*- coding: utf-8 -*- import os import nipype.interfaces.base as nib -from tempfile import mkdtemp -from shutil import rmtree -from nipype.testing import assert_equal import nipype.pipeline.engine as pe @@ -17,7 +14,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class LinearTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -31,14 +28,12 @@ def _list_outputs(self): return outputs -def test_run_in_series(): - cur_dir = os.getcwd() - temp_dir = mkdtemp(prefix='test_engine_') - os.chdir(temp_dir) +def test_run_in_series(tmpdir): + os.chdir(str(tmpdir)) pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.MapNode(interface=TestInterface(), + mod1 = pe.Node(interface=LinearTestInterface(), name='mod1') + mod2 = pe.MapNode(interface=LinearTestInterface(), iterfield=['input1'], name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) @@ -48,6 +43,4 @@ def test_run_in_series(): names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()] node = execgraph.nodes()[names.index('pipe.mod1')] result = node.get_output('output1') - yield assert_equal, result, [1, 1] - os.chdir(cur_dir) - rmtree(temp_dir) + assert result == [1, 1] diff --git a/nipype/pipeline/plugins/tests/test_multiproc.py b/nipype/pipeline/plugins/tests/test_multiproc.py index 3289ef58fe..ba98f5adf7 100644 --- a/nipype/pipeline/plugins/tests/test_multiproc.py +++ b/nipype/pipeline/plugins/tests/test_multiproc.py @@ -1,13 +1,11 @@ # -*- coding: utf-8 -*- import logging -import os -from tempfile import mkdtemp -from shutil import rmtree +import os, sys from multiprocessing import cpu_count import nipype.interfaces.base as nib from nipype.utils import draw_gantt_chart -from nipype.testing import assert_equal, skipif +import pytest import nipype.pipeline.engine as pe from nipype.pipeline.plugins.callback_log import log_nodes_cb from nipype.pipeline.plugins.multiproc import get_system_total_memory_gb @@ -21,7 +19,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class MultiprocTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -34,16 +32,15 @@ def _list_outputs(self): outputs['output1'] = [1, self.inputs.input1] return outputs -# Disabled until https://github.com/nipy/nipype/issues/1692 is resolved -@skipif(os.environ.get('TRAVIS_PYTHON_VERSION', '') == '2.7') -def test_run_multiproc(): - cur_dir = os.getcwd() - temp_dir = mkdtemp(prefix='test_engine_') - os.chdir(temp_dir) + +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") +def test_run_multiproc(tmpdir): + os.chdir(str(tmpdir)) pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.MapNode(interface=TestInterface(), + mod1 = pe.Node(interface=MultiprocTestInterface(), name='mod1') + mod2 = pe.MapNode(interface=MultiprocTestInterface(), iterfield=['input1'], name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) @@ -54,9 +51,7 @@ def test_run_multiproc(): names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()] node = execgraph.nodes()[names.index('pipe.mod1')] result = node.get_output('output1') - yield assert_equal, result, [1, 1] - os.chdir(cur_dir) - rmtree(temp_dir) + assert result == [1, 1] class InputSpecSingleNode(nib.TraitedSpec): @@ -68,7 +63,7 @@ class OutputSpecSingleNode(nib.TraitedSpec): output1 = nib.traits.Int(desc='a random int') -class TestInterfaceSingleNode(nib.BaseInterface): +class SingleNodeTestInterface(nib.BaseInterface): input_spec = InputSpecSingleNode output_spec = OutputSpecSingleNode @@ -123,8 +118,9 @@ def find_metrics(nodes, last_node): return total_memory, total_threads -# Disabled until https://github.com/nipy/nipype/issues/1692 is resolved -@skipif(os.environ.get('TRAVIS_PYTHON_VERSION') == '2.7') + +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") def test_no_more_memory_than_specified(): LOG_FILENAME = 'callback.log' my_logger = logging.getLogger('callback') @@ -136,10 +132,10 @@ def test_no_more_memory_than_specified(): max_memory = 1 pipe = pe.Workflow(name='pipe') - n1 = pe.Node(interface=TestInterfaceSingleNode(), name='n1') - n2 = pe.Node(interface=TestInterfaceSingleNode(), name='n2') - n3 = pe.Node(interface=TestInterfaceSingleNode(), name='n3') - n4 = pe.Node(interface=TestInterfaceSingleNode(), name='n4') + n1 = pe.Node(interface=SingleNodeTestInterface(), name='n1') + n2 = pe.Node(interface=SingleNodeTestInterface(), name='n2') + n3 = pe.Node(interface=SingleNodeTestInterface(), name='n3') + n4 = pe.Node(interface=SingleNodeTestInterface(), name='n4') n1.interface.estimated_memory_gb = 1 n2.interface.estimated_memory_gb = 1 @@ -168,7 +164,7 @@ def test_no_more_memory_than_specified(): result = False break - yield assert_equal, result, True + assert result max_threads = cpu_count() @@ -178,14 +174,15 @@ def test_no_more_memory_than_specified(): result = False break - yield assert_equal, result, True,\ - "using more threads than system has (threads is not specified by user)" + assert result,\ + "using more threads than system has (threads is not specified by user)" os.remove(LOG_FILENAME) -# Disabled until https://github.com/nipy/nipype/issues/1692 is resolved -@skipif(os.environ.get('TRAVIS_PYTHON_VERSION') == '2.7') -@skipif(nib.runtime_profile == False) + +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") +@pytest.mark.skipif(nib.runtime_profile == False, reason="runtime_profile=False") def test_no_more_threads_than_specified(): LOG_FILENAME = 'callback.log' my_logger = logging.getLogger('callback') @@ -197,10 +194,10 @@ def test_no_more_threads_than_specified(): max_threads = 4 pipe = pe.Workflow(name='pipe') - n1 = pe.Node(interface=TestInterfaceSingleNode(), name='n1') - n2 = pe.Node(interface=TestInterfaceSingleNode(), name='n2') - n3 = pe.Node(interface=TestInterfaceSingleNode(), name='n3') - n4 = pe.Node(interface=TestInterfaceSingleNode(), name='n4') + n1 = pe.Node(interface=SingleNodeTestInterface(), name='n1') + n2 = pe.Node(interface=SingleNodeTestInterface(), name='n2') + n3 = pe.Node(interface=SingleNodeTestInterface(), name='n3') + n4 = pe.Node(interface=SingleNodeTestInterface(), name='n4') n1.interface.num_threads = 1 n2.interface.num_threads = 1 @@ -227,15 +224,15 @@ def test_no_more_threads_than_specified(): result = False break - yield assert_equal, result, True, "using more threads than specified" - + assert result, "using more threads than specified" + max_memory = get_system_total_memory_gb() result = True for m in memory: if m > max_memory: result = False break - yield assert_equal, result, True,\ - "using more memory than system has (memory is not specified by user)" + assert result,\ + "using more memory than system has (memory is not specified by user)" os.remove(LOG_FILENAME) diff --git a/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py b/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py index 6d5c0797af..244ecb5d9c 100644 --- a/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py +++ b/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py @@ -7,11 +7,11 @@ from builtins import range, open # Import packages -import os +import os, sys from tempfile import mkdtemp from shutil import rmtree +import pytest -from nipype.testing import assert_equal, assert_true, skipif import nipype.pipeline.engine as pe from nipype.interfaces.utility import Function @@ -90,8 +90,8 @@ def dummyFunction(filename): return total -# Disabled until https://github.com/nipy/nipype/issues/1692 is resolved -@skipif(os.environ.get('TRAVIS_PYTHON_VERSION', '') == '2.7') +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") def run_multiproc_nondaemon_with_flag(nondaemon_flag): ''' Start a pipe with two nodes using the resource multiproc plugin and @@ -133,8 +133,8 @@ def run_multiproc_nondaemon_with_flag(nondaemon_flag): return result -# Disabled until https://github.com/nipy/nipype/issues/1692 is resolved -@skipif(os.environ.get('TRAVIS_PYTHON_VERSION', '') == '2.7') +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") def test_run_multiproc_nondaemon_false(): ''' This is the entry point for the test. Two times a pipe of several multiprocessing jobs gets @@ -149,12 +149,12 @@ def test_run_multiproc_nondaemon_false(): run_multiproc_nondaemon_with_flag(False) except: shouldHaveFailed = True - yield assert_true, shouldHaveFailed + assert shouldHaveFailed -# Disabled until https://github.com/nipy/nipype/issues/1692 is resolved -@skipif(os.environ.get('TRAVIS_PYTHON_VERSION', '') == '2.7') +@pytest.mark.skipif(sys.version_info < (3, 0), + reason="Disabled until https://github.com/nipy/nipype/issues/1692 is resolved") def test_run_multiproc_nondaemon_true(): # with nondaemon_flag = True, the execution should succeed result = run_multiproc_nondaemon_with_flag(True) - yield assert_equal, result, 180 # n_procs (2) * numberOfThreads (2) * 45 == 180 + assert result == 180 # n_procs (2) * numberOfThreads (2) * 45 == 180 diff --git a/nipype/pipeline/plugins/tests/test_oar.py b/nipype/pipeline/plugins/tests/test_oar.py index faf62e9d6d..68dc98c344 100644 --- a/nipype/pipeline/plugins/tests/test_oar.py +++ b/nipype/pipeline/plugins/tests/test_oar.py @@ -4,7 +4,7 @@ from tempfile import mkdtemp import nipype.interfaces.base as nib -from nipype.testing import assert_equal, skipif +import pytest import nipype.pipeline.engine as pe @@ -17,7 +17,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class OarTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -31,15 +31,15 @@ def _list_outputs(self): return outputs -@skipif(True) +@pytest.mark.xfail(reason="not known") def test_run_oar(): cur_dir = os.getcwd() temp_dir = mkdtemp(prefix='test_engine_', dir=os.getcwd()) os.chdir(temp_dir) pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.MapNode(interface=TestInterface(), + mod1 = pe.Node(interface=OarTestInterface(), name='mod1') + mod2 = pe.MapNode(interface=OarTestInterface(), iterfield=['input1'], name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) @@ -52,6 +52,6 @@ def test_run_oar(): ] node = execgraph.nodes()[names.index('pipe.mod1')] result = node.get_output('output1') - yield assert_equal, result, [1, 1] + assert result == [1, 1] os.chdir(cur_dir) rmtree(temp_dir) diff --git a/nipype/pipeline/plugins/tests/test_pbs.py b/nipype/pipeline/plugins/tests/test_pbs.py index ed6be64519..d7b5a83528 100644 --- a/nipype/pipeline/plugins/tests/test_pbs.py +++ b/nipype/pipeline/plugins/tests/test_pbs.py @@ -5,7 +5,7 @@ from time import sleep import nipype.interfaces.base as nib -from nipype.testing import assert_equal, skipif +import pytest import nipype.pipeline.engine as pe @@ -18,7 +18,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class PbsTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -32,15 +32,15 @@ def _list_outputs(self): return outputs -@skipif(True) +@pytest.mark.xfail(reason="not known") def test_run_pbsgraph(): cur_dir = os.getcwd() temp_dir = mkdtemp(prefix='test_engine_') os.chdir(temp_dir) pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.MapNode(interface=TestInterface(), + mod1 = pe.Node(interface=PbsTestInterface(), name='mod1') + mod2 = pe.MapNode(interface=PbsTestInterface(), iterfield=['input1'], name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) @@ -50,6 +50,6 @@ def test_run_pbsgraph(): names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()] node = execgraph.nodes()[names.index('pipe.mod1')] result = node.get_output('output1') - yield assert_equal, result, [1, 1] + assert result == [1, 1] os.chdir(cur_dir) rmtree(temp_dir) diff --git a/nipype/pipeline/plugins/tests/test_somaflow.py b/nipype/pipeline/plugins/tests/test_somaflow.py index 36aa050a43..f8309bf826 100644 --- a/nipype/pipeline/plugins/tests/test_somaflow.py +++ b/nipype/pipeline/plugins/tests/test_somaflow.py @@ -1,11 +1,9 @@ # -*- coding: utf-8 -*- import os -from shutil import rmtree -from tempfile import mkdtemp from time import sleep import nipype.interfaces.base as nib -from nipype.testing import assert_equal, skipif +import pytest import nipype.pipeline.engine as pe from nipype.pipeline.plugins.somaflow import soma_not_loaded @@ -20,7 +18,7 @@ class OutputSpec(nib.TraitedSpec): output1 = nib.traits.List(nib.traits.Int, desc='outputs') -class TestInterface(nib.BaseInterface): +class SomaTestInterface(nib.BaseInterface): input_spec = InputSpec output_spec = OutputSpec @@ -34,15 +32,13 @@ def _list_outputs(self): return outputs -@skipif(soma_not_loaded) -def test_run_somaflow(): - cur_dir = os.getcwd() - temp_dir = mkdtemp(prefix='test_engine_') - os.chdir(temp_dir) +@pytest.mark.skipif(soma_not_loaded, reason="soma not loaded") +def test_run_somaflow(tmpdir): + os.chdir(str(tmpdir)) pipe = pe.Workflow(name='pipe') - mod1 = pe.Node(interface=TestInterface(), name='mod1') - mod2 = pe.MapNode(interface=TestInterface(), + mod1 = pe.Node(interface=SomaTestInterface(), name='mod1') + mod2 = pe.MapNode(interface=SomaTestInterface(), iterfield=['input1'], name='mod2') pipe.connect([(mod1, mod2, [('output1', 'input1')])]) @@ -52,6 +48,4 @@ def test_run_somaflow(): names = ['.'.join((node._hierarchy, node.name)) for node in execgraph.nodes()] node = execgraph.nodes()[names.index('pipe.mod1')] result = node.get_output('output1') - yield assert_equal, result, [1, 1] - os.chdir(cur_dir) - rmtree(temp_dir) + assert result == [1, 1] diff --git a/nipype/testing/__init__.py b/nipype/testing/__init__.py index e2f1e528fb..996fb0ac01 100644 --- a/nipype/testing/__init__.py +++ b/nipype/testing/__init__.py @@ -26,8 +26,6 @@ template = funcfile transfm = funcfile -from nose.tools import * -from numpy.testing import * from . import decorators as dec from .utils import skip_if_no_package, package_check, TempFATFS diff --git a/nipype/testing/decorators.py b/nipype/testing/decorators.py index e4cdf29529..35de0cbf00 100644 --- a/nipype/testing/decorators.py +++ b/nipype/testing/decorators.py @@ -32,7 +32,7 @@ def make_label_dec(label, ds=None): -------- >>> slow = make_label_dec('slow') >>> slow.__doc__ - Labels a test as 'slow' + "Labels a test as 'slow'" >>> rare = make_label_dec(['slow','hard'], ... "Mix labels 'slow' and 'hard' for rare tests") diff --git a/nipype/testing/tests/test_utils.py b/nipype/testing/tests/test_utils.py index f62389dd95..e2ca3a32de 100644 --- a/nipype/testing/tests/test_utils.py +++ b/nipype/testing/tests/test_utils.py @@ -9,7 +9,6 @@ import subprocess from mock import patch, MagicMock from nipype.testing.utils import TempFATFS -from nose.tools import assert_true, assert_raises def test_tempfatfs(): @@ -19,7 +18,7 @@ def test_tempfatfs(): warnings.warn("Cannot mount FAT filesystems with FUSE") else: with fatfs as tmpdir: - yield assert_true, os.path.exists(tmpdir) + assert os.path.exists(tmpdir) @patch('subprocess.check_call', MagicMock( side_effect=subprocess.CalledProcessError('',''))) @@ -27,10 +26,10 @@ def test_tempfatfs_calledprocesserror(): try: TempFATFS() except IOError as e: - assert_true(isinstance(e, IOError)) - assert_true(isinstance(e.__cause__, subprocess.CalledProcessError)) + assert isinstance(e, IOError) + assert isinstance(e.__cause__, subprocess.CalledProcessError) else: - assert_true(False) + assert False @patch('subprocess.check_call', MagicMock()) @patch('subprocess.Popen', MagicMock(side_effect=OSError())) @@ -38,7 +37,7 @@ def test_tempfatfs_oserror(): try: TempFATFS() except IOError as e: - assert_true(isinstance(e, IOError)) - assert_true(isinstance(e.__cause__, OSError)) + assert isinstance(e, IOError) + assert isinstance(e.__cause__, OSError) else: - assert_true(False) + assert False diff --git a/nipype/testing/utils.py b/nipype/testing/utils.py index 092f53ea8e..95d8045b78 100644 --- a/nipype/testing/utils.py +++ b/nipype/testing/utils.py @@ -43,7 +43,7 @@ def __init__(self, size_in_mbytes=8, delay=0.5): with TempFATFS() as fatdir: target = os.path.join(fatdir, 'target') copyfile(file1, target, copy=False) - assert_false(os.path.islink(target)) + assert not os.path.islink(target) Arguments --------- diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index 7cf81c0649..3f7f7462f9 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -60,13 +60,13 @@ def split_filename(fname): -------- >>> from nipype.utils.filemanip import split_filename >>> pth, fname, ext = split_filename('/home/data/subject.nii.gz') - >>> pth # doctest: +IGNORE_UNICODE + >>> pth # doctest: +ALLOW_UNICODE '/home/data' - >>> fname # doctest: +IGNORE_UNICODE + >>> fname # doctest: +ALLOW_UNICODE 'subject' - >>> ext # doctest: +IGNORE_UNICODE + >>> ext # doctest: +ALLOW_UNICODE '.nii.gz' """ @@ -167,7 +167,7 @@ def fname_presuffix(fname, prefix='', suffix='', newpath=None, use_ext=True): >>> from nipype.utils.filemanip import fname_presuffix >>> fname = 'foo.nii.gz' - >>> fname_presuffix(fname,'pre','post','/tmp') # doctest: +IGNORE_UNICODE + >>> fname_presuffix(fname,'pre','post','/tmp') # doctest: +ALLOW_UNICODE '/tmp/prefoopost.nii.gz' """ diff --git a/nipype/utils/tests/test_cmd.py b/nipype/utils/tests/test_cmd.py index 09f07c1862..b1b87cc8a7 100644 --- a/nipype/utils/tests/test_cmd.py +++ b/nipype/utils/tests/test_cmd.py @@ -4,7 +4,7 @@ from future import standard_library standard_library.install_aliases() -import unittest +import pytest import sys from contextlib import contextmanager @@ -25,41 +25,41 @@ def capture_sys_output(): sys.stdout, sys.stderr = current_out, current_err -class TestNipypeCMD(unittest.TestCase): +class TestNipypeCMD(): maxDiff = None def test_main_returns_2_on_empty(self): - with self.assertRaises(SystemExit) as cm: + with pytest.raises(SystemExit) as cm: with capture_sys_output() as (stdout, stderr): nipype_cmd.main(['nipype_cmd']) - - exit_exception = cm.exception - self.assertEqual(exit_exception.code, 2) + + exit_exception = cm.value + assert exit_exception.code == 2 if PY2: - self.assertEqual(stderr.getvalue(), - """usage: nipype_cmd [-h] module interface + assert stderr.getvalue() == \ + """usage: nipype_cmd [-h] module interface nipype_cmd: error: too few arguments -""") +""" elif PY3: - self.assertEqual(stderr.getvalue(), - """usage: nipype_cmd [-h] module interface + assert stderr.getvalue() == \ + """usage: nipype_cmd [-h] module interface nipype_cmd: error: the following arguments are required: module, interface -""") +""" - self.assertEqual(stdout.getvalue(), '') + assert stdout.getvalue() == '' def test_main_returns_0_on_help(self): - with self.assertRaises(SystemExit) as cm: + with pytest.raises(SystemExit) as cm: with capture_sys_output() as (stdout, stderr): nipype_cmd.main(['nipype_cmd', '-h']) - exit_exception = cm.exception - self.assertEqual(exit_exception.code, 0) + exit_exception = cm.value + assert exit_exception.code == 0 - self.assertEqual(stderr.getvalue(), '') - self.assertEqual(stdout.getvalue(), - """usage: nipype_cmd [-h] module interface + assert stderr.getvalue() == '' + assert stdout.getvalue() == \ + """usage: nipype_cmd [-h] module interface Nipype interface runner @@ -69,38 +69,39 @@ def test_main_returns_0_on_help(self): optional arguments: -h, --help show this help message and exit -""") +""" + def test_list_nipy_interfacesp(self): - with self.assertRaises(SystemExit) as cm: + with pytest.raises(SystemExit) as cm: with capture_sys_output() as (stdout, stderr): nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy']) # repeat twice in case nipy raises warnings - with self.assertRaises(SystemExit) as cm: + with pytest.raises(SystemExit) as cm: with capture_sys_output() as (stdout, stderr): nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy']) - exit_exception = cm.exception - self.assertEqual(exit_exception.code, 0) + exit_exception = cm.value + assert exit_exception.code == 0 - self.assertEqual(stderr.getvalue(), '') - self.assertEqual(stdout.getvalue(), - """Available Interfaces: + assert stderr.getvalue() == '' + assert stdout.getvalue() == \ + """Available Interfaces: ComputeMask EstimateContrast FitGLM FmriRealign4d Similarity SpaceTimeRealigner -""") +""" def test_run_4d_realign_without_arguments(self): - with self.assertRaises(SystemExit) as cm: + with pytest.raises(SystemExit) as cm: with capture_sys_output() as (stdout, stderr): nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy', 'FmriRealign4d']) - exit_exception = cm.exception - self.assertEqual(exit_exception.code, 2) + exit_exception = cm.value + assert exit_exception.code == 2 error_message = """usage: nipype_cmd nipype.interfaces.nipy FmriRealign4d [-h] [--between_loops [BETWEEN_LOOPS [BETWEEN_LOOPS ...]]] @@ -123,19 +124,17 @@ def test_run_4d_realign_without_arguments(self): nipype_cmd nipype.interfaces.nipy FmriRealign4d: error: too few arguments """ - self.assertEqual(stderr.getvalue(), error_message) - self.assertEqual(stdout.getvalue(), '') + assert stderr.getvalue() == error_message + assert stdout.getvalue() == '' def test_run_4d_realign_help(self): - with self.assertRaises(SystemExit) as cm: + with pytest.raises(SystemExit) as cm: with capture_sys_output() as (stdout, stderr): nipype_cmd.main(['nipype_cmd', 'nipype.interfaces.nipy', 'FmriRealign4d', '-h']) - exit_exception = cm.exception - self.assertEqual(exit_exception.code, 0) + exit_exception = cm.value + assert exit_exception.code == 0 - self.assertEqual(stderr.getvalue(), '') - self.assertTrue("Run FmriRealign4d" in stdout.getvalue()) + assert stderr.getvalue() == '' + assert "Run FmriRealign4d" in stdout.getvalue() -if __name__ == '__main__': - unittest.main() diff --git a/nipype/utils/tests/test_docparse.py b/nipype/utils/tests/test_docparse.py index ff659cecb8..2b7e2a7571 100644 --- a/nipype/utils/tests/test_docparse.py +++ b/nipype/utils/tests/test_docparse.py @@ -1,14 +1,11 @@ # -*- coding: utf-8 -*- -from builtins import object # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -from nipype.testing import * from nipype.utils.docparse import reverse_opt_map, build_doc, insert_doc -class Foo(object): - opt_map = {'outline': '-o', 'fun': '-f %.2f', 'flags': '%s'} +foo_opt_map = {'outline': '-o', 'fun': '-f %.2f', 'flags': '%s'} foo_doc = """Usage: foo infile outfile [opts] @@ -36,14 +33,14 @@ class Foo(object): def test_rev_opt_map(): map = {'-f': 'fun', '-o': 'outline'} - rev_map = reverse_opt_map(Foo.opt_map) - assert_equal(rev_map, map) + rev_map = reverse_opt_map(foo_opt_map) + assert rev_map == map def test_build_doc(): - opts = reverse_opt_map(Foo.opt_map) + opts = reverse_opt_map(foo_opt_map) doc = build_doc(foo_doc, opts) - assert_equal(doc, fmtd_doc) + assert doc == fmtd_doc inserted_doc = """Parameters ---------- @@ -65,4 +62,4 @@ def test_insert_doc(): new_items = ['infile : str', ' The name of the input file'] new_items.extend(['outfile : str', ' The name of the output file']) newdoc = insert_doc(fmtd_doc, new_items) - assert_equal(newdoc, inserted_doc) + assert newdoc == inserted_doc diff --git a/nipype/utils/tests/test_filemanip.py b/nipype/utils/tests/test_filemanip.py index 95b7e0a1aa..dd4ec07d9e 100644 --- a/nipype/utils/tests/test_filemanip.py +++ b/nipype/utils/tests/test_filemanip.py @@ -5,11 +5,11 @@ from builtins import open import os -from tempfile import mkstemp, mkdtemp +from tempfile import mkstemp import warnings -from ...testing import (assert_equal, assert_true, assert_false, - assert_in, assert_not_in, TempFATFS) +import pytest +from ...testing import TempFATFS from ...utils.filemanip import (save_json, load_json, fname_presuffix, fnames_presuffix, hash_rename, check_forhash, @@ -23,101 +23,99 @@ def _ignore_atime(stat): return stat[:7] + stat[8:] - -def test_split_filename(): - res = split_filename('foo.nii') - yield assert_equal, res, ('', 'foo', '.nii') - res = split_filename('foo.nii.gz') - yield assert_equal, res, ('', 'foo', '.nii.gz') - res = split_filename('/usr/local/foo.nii.gz') - yield assert_equal, res, ('/usr/local', 'foo', '.nii.gz') - res = split_filename('../usr/local/foo.nii') - yield assert_equal, res, ('../usr/local', 'foo', '.nii') - res = split_filename('/usr/local/foo.a.b.c.d') - yield assert_equal, res, ('/usr/local', 'foo.a.b.c', '.d') - res = split_filename('/usr/local/') - yield assert_equal, res, ('/usr/local', '', '') +@pytest.mark.parametrize("filename, split",[ + ('foo.nii', ('', 'foo', '.nii')), + ('foo.nii.gz', ('', 'foo', '.nii.gz')), + ('/usr/local/foo.nii.gz', ('/usr/local', 'foo', '.nii.gz')), + ('../usr/local/foo.nii', ('../usr/local', 'foo', '.nii')), + ('/usr/local/foo.a.b.c.d', ('/usr/local', 'foo.a.b.c', '.d')), + ('/usr/local/', ('/usr/local', '', '')) + ]) +def test_split_filename(filename, split): + res = split_filename(filename) + assert res == split def test_fname_presuffix(): fname = 'foo.nii' pth = fname_presuffix(fname, 'pre_', '_post', '/tmp') - yield assert_equal, pth, '/tmp/pre_foo_post.nii' + assert pth == '/tmp/pre_foo_post.nii' fname += '.gz' pth = fname_presuffix(fname, 'pre_', '_post', '/tmp') - yield assert_equal, pth, '/tmp/pre_foo_post.nii.gz' + assert pth == '/tmp/pre_foo_post.nii.gz' pth = fname_presuffix(fname, 'pre_', '_post', '/tmp', use_ext=False) - yield assert_equal, pth, '/tmp/pre_foo_post' + assert pth == '/tmp/pre_foo_post' def test_fnames_presuffix(): fnames = ['foo.nii', 'bar.nii'] pths = fnames_presuffix(fnames, 'pre_', '_post', '/tmp') - yield assert_equal, pths, ['/tmp/pre_foo_post.nii', '/tmp/pre_bar_post.nii'] - - -def test_hash_rename(): - new_name = hash_rename('foobar.nii', 'abc123') - yield assert_equal, new_name, 'foobar_0xabc123.nii' - new_name = hash_rename('foobar.nii.gz', 'abc123') - yield assert_equal, new_name, 'foobar_0xabc123.nii.gz' + assert pths == ['/tmp/pre_foo_post.nii', '/tmp/pre_bar_post.nii'] +@pytest.mark.parametrize("filename, newname",[ + ('foobar.nii', 'foobar_0xabc123.nii'), + ('foobar.nii.gz', 'foobar_0xabc123.nii.gz') + ]) +def test_hash_rename(filename, newname): + new_name = hash_rename(filename, 'abc123') + assert new_name == newname + def test_check_forhash(): fname = 'foobar' orig_hash = '_0x4323dbcefdc51906decd8edcb3327943' hashed_name = ''.join((fname, orig_hash, '.nii')) result, hash = check_forhash(hashed_name) - yield assert_true, result - yield assert_equal, hash, [orig_hash] + assert result + assert hash == [orig_hash] result, hash = check_forhash('foobar.nii') - yield assert_false, result - yield assert_equal, hash, None + assert not result + assert hash == None + +@pytest.fixture() +def _temp_analyze_files(tmpdir): + """Generate temporary analyze file pair.""" + orig_img = tmpdir.join("orig.img") + orig_hdr = tmpdir.join("orig.hdr") + orig_img.open('w+').close() + orig_hdr.open('w+').close() + return str(orig_img), str(orig_hdr) -def _temp_analyze_files(): +@pytest.fixture() +def _temp_analyze_files_prime(tmpdir): """Generate temporary analyze file pair.""" - fd, orig_img = mkstemp(suffix='.img') - orig_hdr = orig_img[:-4] + '.hdr' - fp = open(orig_hdr, 'w+') - fp.close() - return orig_img, orig_hdr + orig_img = tmpdir.join("orig_prime.img") + orig_hdr = tmpdir.join("orig_prime.hdr") + orig_img.open('w+').close() + orig_hdr.open('w+').close() + return str(orig_img), str(orig_hdr) -def test_copyfile(): - orig_img, orig_hdr = _temp_analyze_files() +def test_copyfile(_temp_analyze_files): + orig_img, orig_hdr = _temp_analyze_files pth, fname = os.path.split(orig_img) new_img = os.path.join(pth, 'newfile.img') new_hdr = os.path.join(pth, 'newfile.hdr') copyfile(orig_img, new_img) - yield assert_true, os.path.exists(new_img) - yield assert_true, os.path.exists(new_hdr) - os.unlink(new_img) - os.unlink(new_hdr) - # final cleanup - os.unlink(orig_img) - os.unlink(orig_hdr) + assert os.path.exists(new_img) + assert os.path.exists(new_hdr) -def test_copyfile_true(): - orig_img, orig_hdr = _temp_analyze_files() +def test_copyfile_true(_temp_analyze_files): + orig_img, orig_hdr = _temp_analyze_files pth, fname = os.path.split(orig_img) new_img = os.path.join(pth, 'newfile.img') new_hdr = os.path.join(pth, 'newfile.hdr') # Test with copy=True copyfile(orig_img, new_img, copy=True) - yield assert_true, os.path.exists(new_img) - yield assert_true, os.path.exists(new_hdr) - os.unlink(new_img) - os.unlink(new_hdr) - # final cleanup - os.unlink(orig_img) - os.unlink(orig_hdr) - - -def test_copyfiles(): - orig_img1, orig_hdr1 = _temp_analyze_files() - orig_img2, orig_hdr2 = _temp_analyze_files() + assert os.path.exists(new_img) + assert os.path.exists(new_hdr) + + +def test_copyfiles(_temp_analyze_files, _temp_analyze_files_prime): + orig_img1, orig_hdr1 = _temp_analyze_files + orig_img2, orig_hdr2 = _temp_analyze_files_prime pth, fname = os.path.split(orig_img1) new_img1 = os.path.join(pth, 'newfile.img') new_hdr1 = os.path.join(pth, 'newfile.hdr') @@ -125,25 +123,16 @@ def test_copyfiles(): new_img2 = os.path.join(pth, 'secondfile.img') new_hdr2 = os.path.join(pth, 'secondfile.hdr') newfiles = copyfiles([orig_img1, orig_img2], [new_img1, new_img2]) - yield assert_true, os.path.exists(new_img1) - yield assert_true, os.path.exists(new_hdr1) - yield assert_true, os.path.exists(new_img2) - yield assert_true, os.path.exists(new_hdr2) - # cleanup - os.unlink(orig_img1) - os.unlink(orig_hdr1) - os.unlink(orig_img2) - os.unlink(orig_hdr2) - os.unlink(new_img1) - os.unlink(new_hdr1) - os.unlink(new_img2) - os.unlink(new_hdr2) - - -def test_linkchain(): + assert os.path.exists(new_img1) + assert os.path.exists(new_hdr1) + assert os.path.exists(new_img2) + assert os.path.exists(new_hdr2) + + +def test_linkchain(_temp_analyze_files): if os.name is not 'posix': return - orig_img, orig_hdr = _temp_analyze_files() + orig_img, orig_hdr = _temp_analyze_files pth, fname = os.path.split(orig_img) new_img1 = os.path.join(pth, 'newfile1.img') new_hdr1 = os.path.join(pth, 'newfile1.hdr') @@ -152,35 +141,26 @@ def test_linkchain(): new_img3 = os.path.join(pth, 'newfile3.img') new_hdr3 = os.path.join(pth, 'newfile3.hdr') copyfile(orig_img, new_img1) - yield assert_true, os.path.islink(new_img1) - yield assert_true, os.path.islink(new_hdr1) + assert os.path.islink(new_img1) + assert os.path.islink(new_hdr1) copyfile(new_img1, new_img2, copy=True) - yield assert_false, os.path.islink(new_img2) - yield assert_false, os.path.islink(new_hdr2) - yield assert_false, os.path.samefile(orig_img, new_img2) - yield assert_false, os.path.samefile(orig_hdr, new_hdr2) + assert not os.path.islink(new_img2) + assert not os.path.islink(new_hdr2) + assert not os.path.samefile(orig_img, new_img2) + assert not os.path.samefile(orig_hdr, new_hdr2) copyfile(new_img1, new_img3, copy=True, use_hardlink=True) - yield assert_false, os.path.islink(new_img3) - yield assert_false, os.path.islink(new_hdr3) - yield assert_true, os.path.samefile(orig_img, new_img3) - yield assert_true, os.path.samefile(orig_hdr, new_hdr3) - - os.unlink(new_img1) - os.unlink(new_hdr1) - os.unlink(new_img2) - os.unlink(new_hdr2) - os.unlink(new_img3) - os.unlink(new_hdr3) - # final cleanup - os.unlink(orig_img) - os.unlink(orig_hdr) - -def test_recopy(): + assert not os.path.islink(new_img3) + assert not os.path.islink(new_hdr3) + assert os.path.samefile(orig_img, new_img3) + assert os.path.samefile(orig_hdr, new_hdr3) + + +def test_recopy(_temp_analyze_files): # Re-copying with the same parameters on an unchanged file should be # idempotent # # Test for copying from regular files and symlinks - orig_img, orig_hdr = _temp_analyze_files() + orig_img, orig_hdr = _temp_analyze_files pth, fname = os.path.split(orig_img) img_link = os.path.join(pth, 'imglink.img') hdr_link = os.path.join(pth, 'imglink.hdr') @@ -204,10 +184,8 @@ def test_recopy(): copyfile(orig_img, new_img, **kwargs) err_msg = "Regular - OS: {}; Copy: {}; Hardlink: {}".format( os.name, copy, use_hardlink) - yield (assert_equal, img_stat, _ignore_atime(os.stat(new_img)), - err_msg) - yield (assert_equal, hdr_stat, _ignore_atime(os.stat(new_hdr)), - err_msg) + assert img_stat == _ignore_atime(os.stat(new_img)), err_msg + assert hdr_stat == _ignore_atime(os.stat(new_hdr)), err_msg os.unlink(new_img) os.unlink(new_hdr) @@ -217,22 +195,16 @@ def test_recopy(): copyfile(img_link, new_img, **kwargs) err_msg = "Symlink - OS: {}; Copy: {}; Hardlink: {}".format( os.name, copy, use_hardlink) - yield (assert_equal, img_stat, _ignore_atime(os.stat(new_img)), - err_msg) - yield (assert_equal, hdr_stat, _ignore_atime(os.stat(new_hdr)), - err_msg) + assert img_stat == _ignore_atime(os.stat(new_img)), err_msg + assert hdr_stat == _ignore_atime(os.stat(new_hdr)), err_msg os.unlink(new_img) os.unlink(new_hdr) - os.unlink(img_link) - os.unlink(hdr_link) - os.unlink(orig_img) - os.unlink(orig_hdr) -def test_copyfallback(): +def test_copyfallback(_temp_analyze_files): if os.name is not 'posix': return - orig_img, orig_hdr = _temp_analyze_files() + orig_img, orig_hdr = _temp_analyze_files pth, imgname = os.path.split(orig_img) pth, hdrname = os.path.split(orig_hdr) try: @@ -247,59 +219,56 @@ def test_copyfallback(): for use_hardlink in (True, False): copyfile(orig_img, tgt_img, copy=copy, use_hardlink=use_hardlink) - yield assert_true, os.path.exists(tgt_img) - yield assert_true, os.path.exists(tgt_hdr) - yield assert_false, os.path.islink(tgt_img) - yield assert_false, os.path.islink(tgt_hdr) - yield assert_false, os.path.samefile(orig_img, tgt_img) - yield assert_false, os.path.samefile(orig_hdr, tgt_hdr) + assert os.path.exists(tgt_img) + assert os.path.exists(tgt_hdr) + assert not os.path.islink(tgt_img) + assert not os.path.islink(tgt_hdr) + assert not os.path.samefile(orig_img, tgt_img) + assert not os.path.samefile(orig_hdr, tgt_hdr) os.unlink(tgt_img) os.unlink(tgt_hdr) - finally: - os.unlink(orig_img) - os.unlink(orig_hdr) -def test_get_related_files(): - orig_img, orig_hdr = _temp_analyze_files() +def test_get_related_files(_temp_analyze_files): + orig_img, orig_hdr = _temp_analyze_files related_files = get_related_files(orig_img) - yield assert_in, orig_img, related_files - yield assert_in, orig_hdr, related_files + assert orig_img in related_files + assert orig_hdr in related_files related_files = get_related_files(orig_hdr) - yield assert_in, orig_img, related_files - yield assert_in, orig_hdr, related_files + assert orig_img in related_files + assert orig_hdr in related_files -def test_get_related_files_noninclusive(): - orig_img, orig_hdr = _temp_analyze_files() +def test_get_related_files_noninclusive(_temp_analyze_files): + orig_img, orig_hdr = _temp_analyze_files related_files = get_related_files(orig_img, include_this_file=False) - yield assert_not_in, orig_img, related_files - yield assert_in, orig_hdr, related_files + assert orig_img not in related_files + assert orig_hdr in related_files related_files = get_related_files(orig_hdr, include_this_file=False) - yield assert_in, orig_img, related_files - yield assert_not_in, orig_hdr, related_files - - -def test_filename_to_list(): - x = filename_to_list('foo.nii') - yield assert_equal, x, ['foo.nii'] - x = filename_to_list(['foo.nii']) - yield assert_equal, x, ['foo.nii'] - x = filename_to_list(('foo', 'bar')) - yield assert_equal, x, ['foo', 'bar'] - x = filename_to_list(12.34) - yield assert_equal, x, None - - -def test_list_to_filename(): - x = list_to_filename(['foo.nii']) - yield assert_equal, x, 'foo.nii' - x = list_to_filename(['foo', 'bar']) - yield assert_equal, x, ['foo', 'bar'] + assert orig_img in related_files + assert orig_hdr not in related_files + +@pytest.mark.parametrize("filename, expected", [ + ('foo.nii', ['foo.nii']), + (['foo.nii'], ['foo.nii']), + (('foo', 'bar'), ['foo', 'bar']), + (12.34, None) + ]) +def test_filename_to_list(filename, expected): + x = filename_to_list(filename) + assert x == expected + +@pytest.mark.parametrize("list, expected", [ + (['foo.nii'], 'foo.nii'), + (['foo', 'bar'], ['foo', 'bar']), + ]) +def test_list_to_filename(list, expected): + x = list_to_filename(list) + assert x == expected def test_json(): @@ -309,33 +278,21 @@ def test_json(): save_json(name, adict) # save_json closes the file new_dict = load_json(name) os.unlink(name) - yield assert_equal, sorted(adict.items()), sorted(new_dict.items()) - - -def test_related_files(): - file1 = '/path/test.img' - file2 = '/path/test.hdr' - file3 = '/path/test.BRIK' - file4 = '/path/test.HEAD' - file5 = '/path/foo.nii' - - spm_files1 = get_related_files(file1) - spm_files2 = get_related_files(file2) - afni_files1 = get_related_files(file3) - afni_files2 = get_related_files(file4) - yield assert_equal, len(spm_files1), 3 - yield assert_equal, len(spm_files2), 3 - yield assert_equal, len(afni_files1), 2 - yield assert_equal, len(afni_files2), 2 - yield assert_equal, len(get_related_files(file5)), 1 - - yield assert_true, '/path/test.hdr' in spm_files1 - yield assert_true, '/path/test.img' in spm_files1 - yield assert_true, '/path/test.mat' in spm_files1 - yield assert_true, '/path/test.hdr' in spm_files2 - yield assert_true, '/path/test.img' in spm_files2 - yield assert_true, '/path/test.mat' in spm_files2 - yield assert_true, '/path/test.BRIK' in afni_files1 - yield assert_true, '/path/test.HEAD' in afni_files1 - yield assert_true, '/path/test.BRIK' in afni_files2 - yield assert_true, '/path/test.HEAD' in afni_files2 + assert sorted(adict.items()) == sorted(new_dict.items()) + + +@pytest.mark.parametrize("file, length, expected_files", [ + ('/path/test.img', 3, ['/path/test.hdr', '/path/test.img', '/path/test.mat']), + ('/path/test.hdr', 3, ['/path/test.hdr', '/path/test.img', '/path/test.mat']), + ('/path/test.BRIK', 2, ['/path/test.BRIK', '/path/test.HEAD']), + ('/path/test.HEAD', 2, ['/path/test.BRIK', '/path/test.HEAD']), + ('/path/foo.nii', 1, []) + ]) +def test_related_files(file, length, expected_files): + related_files = get_related_files(file) + + assert len(related_files) == length + + for ef in expected_files: + assert ef in related_files + diff --git a/nipype/utils/tests/test_misc.py b/nipype/utils/tests/test_misc.py index cf92bbb537..f2780a584f 100644 --- a/nipype/utils/tests/test_misc.py +++ b/nipype/utils/tests/test_misc.py @@ -6,8 +6,7 @@ from builtins import next -from nipype.testing import (assert_equal, assert_true, assert_false, - assert_raises) +import pytest from nipype.utils.misc import (container_to_string, getsource, create_function_from_source, str2bool, flatten, @@ -17,23 +16,23 @@ def test_cont_to_str(): # list x = ['a', 'b'] - yield assert_true, container_to_string(x) == 'a b' + assert container_to_string(x) == 'a b' # tuple x = tuple(x) - yield assert_true, container_to_string(x) == 'a b' + assert container_to_string(x) == 'a b' # set x = set(x) y = container_to_string(x) - yield assert_true, (y == 'a b') or (y == 'b a') + assert (y == 'a b') or (y == 'b a') # dict x = dict(a='a', b='b') y = container_to_string(x) - yield assert_true, (y == 'a b') or (y == 'b a') + assert (y == 'a b') or (y == 'b a') # string - yield assert_true, container_to_string('foobar') == 'foobar' + assert container_to_string('foobar') == 'foobar' # int. Integers are not the main intent of this function, but see # no reason why they shouldn't work. - yield assert_true, (container_to_string(123) == '123') + assert (container_to_string(123) == '123') def _func1(x): @@ -49,39 +48,36 @@ def func1(x): for f in _func1, func1: f_src = getsource(f) f_recreated = create_function_from_source(f_src) - yield assert_equal, f(2.3), f_recreated(2.3) + assert f(2.3) == f_recreated(2.3) def test_func_to_str_err(): bad_src = "obbledygobbledygook" - yield assert_raises, RuntimeError, create_function_from_source, bad_src + with pytest.raises(RuntimeError): create_function_from_source(bad_src) -def test_str2bool(): - yield assert_true, str2bool("yes") - yield assert_true, str2bool("true") - yield assert_true, str2bool("t") - yield assert_true, str2bool("1") - yield assert_false, str2bool("no") - yield assert_false, str2bool("false") - yield assert_false, str2bool("n") - yield assert_false, str2bool("f") - yield assert_false, str2bool("0") + +@pytest.mark.parametrize("string, expected", [ + ("yes", True), ("true", True), ("t", True), ("1", True), + ("no", False), ("false", False), ("n", False), ("f", False), ("0", False) + ]) +def test_str2bool(string, expected): + assert str2bool(string) == expected def test_flatten(): in_list = [[1, 2, 3], [4], [[5, 6], 7], 8] flat = flatten(in_list) - yield assert_equal, flat, [1, 2, 3, 4, 5, 6, 7, 8] + assert flat == [1, 2, 3, 4, 5, 6, 7, 8] back = unflatten(flat, in_list) - yield assert_equal, in_list, back + assert in_list == back new_list = [2, 3, 4, 5, 6, 7, 8, 9] back = unflatten(new_list, in_list) - yield assert_equal, back, [[2, 3, 4], [5], [[6, 7], 8], 9] + assert back == [[2, 3, 4], [5], [[6, 7], 8], 9] flat = flatten([]) - yield assert_equal, flat, [] + assert flat == [] back = unflatten([], []) - yield assert_equal, back, [] + assert back == [] diff --git a/nipype/utils/tests/test_provenance.py b/nipype/utils/tests/test_provenance.py index 85f6e032f6..270774dcf5 100644 --- a/nipype/utils/tests/test_provenance.py +++ b/nipype/utils/tests/test_provenance.py @@ -8,9 +8,7 @@ import os -from tempfile import mkdtemp -from nipype.testing import assert_equal, assert_true, assert_false from nipype.utils.provenance import ProvStore, safe_encode def test_provenance(): @@ -20,11 +18,10 @@ def test_provenance(): ps.add_results(results) provn = ps.g.get_provn() prov_json = ps.g.serialize(format='json') - yield assert_true, 'echo hello' in provn + assert 'echo hello' in provn -def test_provenance_exists(): - tempdir = mkdtemp() - cwd = os.getcwd() +def test_provenance_exists(tmpdir): + tempdir = str(tmpdir) os.chdir(tempdir) from nipype import config from nipype.interfaces.base import CommandLine @@ -35,10 +32,9 @@ def test_provenance_exists(): config.set('execution', 'write_provenance', provenance_state) config.set('execution', 'hash_method', hash_state) provenance_exists = os.path.exists(os.path.join(tempdir, 'provenance.provn')) - os.chdir(cwd) - yield assert_true, provenance_exists + assert provenance_exists def test_safe_encode(): a = '\xc3\xa9lg' out = safe_encode(a) - yield assert_equal, out.value, a + assert out.value == a diff --git a/nipype/workflows/dmri/fsl/tests/test_dti.py b/nipype/workflows/dmri/fsl/tests/test_dti.py index 9157b04947..9a8ed4ca13 100644 --- a/nipype/workflows/dmri/fsl/tests/test_dti.py +++ b/nipype/workflows/dmri/fsl/tests/test_dti.py @@ -2,7 +2,7 @@ from __future__ import unicode_literals, print_function, absolute_import import os -from nipype.testing import skipif +import pytest import nipype.interfaces.fsl as fsl import nipype.interfaces.utility as util from nipype.interfaces.fsl import no_fsl, no_fsl_course_data @@ -15,8 +15,8 @@ from nipype.utils.filemanip import list_to_filename -@skipif(no_fsl) -@skipif(no_fsl_course_data) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +@pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def test_create_bedpostx_pipeline(): fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA']) diff --git a/nipype/workflows/dmri/fsl/tests/test_epi.py b/nipype/workflows/dmri/fsl/tests/test_epi.py index f622b8304a..f7b349b442 100644 --- a/nipype/workflows/dmri/fsl/tests/test_epi.py +++ b/nipype/workflows/dmri/fsl/tests/test_epi.py @@ -1,7 +1,7 @@ # -*- coding: utf-8 -*- import os -from nipype.testing import (skipif) +import pytest import nipype.workflows.fmri.fsl as fsl_wf import nipype.interfaces.fsl as fsl import nipype.interfaces.utility as util @@ -14,8 +14,8 @@ from nipype.workflows.dmri.fsl.epi import create_eddy_correct_pipeline -@skipif(no_fsl) -@skipif(no_fsl_course_data) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +@pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def test_create_eddy_correct_pipeline(): fsl_course_dir = os.path.abspath(os.environ['FSL_COURSE_DATA']) diff --git a/nipype/workflows/dmri/fsl/tests/test_tbss.py b/nipype/workflows/dmri/fsl/tests/test_tbss.py index 1900629d49..20f7331fda 100644 --- a/nipype/workflows/dmri/fsl/tests/test_tbss.py +++ b/nipype/workflows/dmri/fsl/tests/test_tbss.py @@ -6,7 +6,7 @@ from nipype.interfaces.fsl.base import no_fsl, no_fsl_course_data import nipype.pipeline.engine as pe import nipype.interfaces.utility as util -from nipype.testing import skipif +import pytest import tempfile import shutil from subprocess import call @@ -124,15 +124,15 @@ def _tbss_test_helper(estimate_skeleton): # this test is disabled until we figure out what is wrong with TBSS in 5.0.9 -@skipif(no_fsl) -@skipif(no_fsl_course_data) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +@pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def disabled_tbss_est_skeleton(): _tbss_test_helper(True) # this test is disabled until we figure out what is wrong with TBSS in 5.0.9 -@skipif(no_fsl) -@skipif(no_fsl_course_data) +@pytest.mark.skipif(no_fsl(), reason="fsl is not installed") +@pytest.mark.skipif(no_fsl_course_data(), reason="fsl data not available") def disabled_tbss_est_skeleton_use_precomputed_skeleton(): _tbss_test_helper(False) diff --git a/nipype/workflows/rsfmri/fsl/tests/test_resting.py b/nipype/workflows/rsfmri/fsl/tests/test_resting.py index 303eef00d0..7ae4483b55 100644 --- a/nipype/workflows/rsfmri/fsl/tests/test_resting.py +++ b/nipype/workflows/rsfmri/fsl/tests/test_resting.py @@ -1,15 +1,12 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -import unittest +import pytest import os -import tempfile -import shutil - import mock import numpy as np -from .....testing import (assert_equal, assert_true, utils) +from .....testing import utils from .....interfaces import IdentityInterface from .....pipeline.engine import Node, Workflow @@ -38,7 +35,7 @@ def stub_wf(*args, **kwargs): wflow.connect(inputnode, 'func', outputnode, 'realigned_file') return wflow -class TestResting(unittest.TestCase): +class TestResting(): in_filenames = { 'realigned_file': 'rsfmrifunc.nii', @@ -51,11 +48,10 @@ class TestResting(unittest.TestCase): num_noise_components = 6 - def setUp(self): + @pytest.fixture(autouse=True) + def setup_class(self, tmpdir): # setup temp folder - self.orig_dir = os.getcwd() - self.temp_dir = tempfile.mkdtemp() - os.chdir(self.temp_dir) + os.chdir(str(tmpdir)) self.in_filenames = {key: os.path.abspath(value) for key, value in self.in_filenames.items()} @@ -87,18 +83,15 @@ def test_create_resting_preproc(self, mock_node, mock_realign_wf): with open(expected_file, 'r') as components_file: components_data = [line.split() for line in components_file] num_got_components = len(components_data) - assert_true(num_got_components == self.num_noise_components - or num_got_components == self.fake_data.shape[3]) + assert (num_got_components == self.num_noise_components + or num_got_components == self.fake_data.shape[3]) first_two = [row[:2] for row in components_data[1:]] - assert_equal(first_two, [['-0.5172356654', '-0.6973053243'], - ['0.2574722644', '0.1645270737'], - ['-0.0806469590', '0.5156853779'], - ['0.7187176051', '-0.3235820287'], - ['-0.3783072450', '0.3406749013']]) - - def tearDown(self): - os.chdir(self.orig_dir) - shutil.rmtree(self.temp_dir) + assert first_two == [['-0.5172356654', '-0.6973053243'], + ['0.2574722644', '0.1645270737'], + ['-0.0806469590', '0.5156853779'], + ['0.7187176051', '-0.3235820287'], + ['-0.3783072450', '0.3406749013']] + fake_data = np.array([[[[2, 4, 3, 9, 1], [3, 6, 4, 7, 4]], diff --git a/requirements.txt b/requirements.txt index c9156b5289..4da64e8f98 100644 --- a/requirements.txt +++ b/requirements.txt @@ -4,7 +4,6 @@ networkx>=1.7 traits>=4.3 python-dateutil>=1.5 nibabel>=2.0.1 -nose>=1.2 future==0.15.2 simplejson>=3.8.0 prov>=1.4.0 @@ -13,4 +12,6 @@ xvfbwrapper psutil funcsigs configparser -doctest-ignore-unicode \ No newline at end of file +pytest>=3.0 +pytest-raisesregexp +pytest-cov diff --git a/rtd_requirements.txt b/rtd_requirements.txt index 10e0d8189c..11b7fcfad1 100644 --- a/rtd_requirements.txt +++ b/rtd_requirements.txt @@ -4,7 +4,9 @@ networkx>=1.7 traits>=4.3 python-dateutil>=1.5 nibabel>=2.0.1 -nose>=1.2 +pytest>=3.0 +pytest-raisesregexp +pytest-cov future==0.15.2 simplejson>=3.8.0 prov>=1.4.0 @@ -12,5 +14,4 @@ xvfbwrapper psutil funcsigs configparser -doctest-ignore-unicode matplotlib diff --git a/tools/apigen.py b/tools/apigen.py index 48b11fff66..d3a732d881 100644 --- a/tools/apigen.py +++ b/tools/apigen.py @@ -103,11 +103,11 @@ def set_package_name(self, package_name): def _get_object_name(self, line): ''' Get second token in line >>> docwriter = ApiDocWriter('sphinx') - >>> docwriter._get_object_name(" def func(): ") # doctest: +IGNORE_UNICODE + >>> docwriter._get_object_name(" def func(): ") # doctest: +ALLOW_UNICODE u'func' - >>> docwriter._get_object_name(" class Klass(object): ") # doctest: +IGNORE_UNICODE + >>> docwriter._get_object_name(" class Klass(object): ") # doctest: +ALLOW_UNICODE 'Klass' - >>> docwriter._get_object_name(" class Klass: ") # doctest: +IGNORE_UNICODE + >>> docwriter._get_object_name(" class Klass: ") # doctest: +ALLOW_UNICODE 'Klass' ''' name = line.split()[1].split('(')[0].strip() diff --git a/tools/checkspecs.py b/tools/checkspecs.py index c284ee8b42..243b7419ae 100644 --- a/tools/checkspecs.py +++ b/tools/checkspecs.py @@ -206,8 +206,6 @@ def test_specs(self, uri): if not os.path.exists(nonautotest): with open(testfile, 'wt') as fp: cmd = ['# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT', - 'from %stesting import assert_equal' % - ('.' * len(uri.split('.'))), 'from ..%s import %s' % (uri.split('.')[-1], c), ''] cmd.append('\ndef test_%s_inputs():' % c) @@ -231,7 +229,7 @@ def test_specs(self, uri): cmd += [""" for key, metadata in list(input_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(inputs.traits()[key], metakey), value"""] + assert getattr(inputs.traits()[key], metakey) == value"""] fp.writelines('\n'.join(cmd) + '\n\n') else: print('%s has nonautotest' % c) @@ -275,7 +273,7 @@ def test_specs(self, uri): cmd += [""" for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): - yield assert_equal, getattr(outputs.traits()[key], metakey), value"""] + assert getattr(outputs.traits()[key], metakey) == value"""] fp.writelines('\n'.join(cmd) + '\n') for traitname, trait in sorted(classinst.output_spec().traits(transient=None).items()): diff --git a/tools/interfacedocgen.py b/tools/interfacedocgen.py index 43f61d268e..03ef31eaf8 100644 --- a/tools/interfacedocgen.py +++ b/tools/interfacedocgen.py @@ -124,11 +124,11 @@ def set_package_name(self, package_name): def _get_object_name(self, line): ''' Get second token in line >>> docwriter = ApiDocWriter('sphinx') - >>> docwriter._get_object_name(" def func(): ") # doctest: +IGNORE_UNICODE + >>> docwriter._get_object_name(" def func(): ") # doctest: +ALLOW_UNICODE u'func' - >>> docwriter._get_object_name(" class Klass(object): ") # doctest: +IGNORE_UNICODE + >>> docwriter._get_object_name(" class Klass(object): ") # doctest: +ALLOW_UNICODE 'Klass' - >>> docwriter._get_object_name(" class Klass: ") # doctest: +IGNORE_UNICODE + >>> docwriter._get_object_name(" class Klass: ") # doctest: +ALLOW_UNICODE 'Klass' ''' name = line.split()[1].split('(')[0].strip()