Merge remote-tracking branch 'upstream/master' into fix_sge

Author: bpinsard

.coveragerc

@@ -4,6 +4,5 @@ source = nipype
 include = */nipype/*
 omit =
     */nipype/external/*
-    */nipype/workflows/*
     */nipype/fixes/*
     */setup.py

.travis.yml

@@ -33,18 +33,13 @@ install:
   conda config --add channels conda-forge &&
   conda update --yes conda &&
   conda update --all -y python=$TRAVIS_PYTHON_VERSION &&
-  conda install -y nipype &&
+  conda install -y nipype icu &&
   rm -r /home/travis/miniconda/lib/python${TRAVIS_PYTHON_VERSION}/site-packages/nipype* &&
   pip install -r requirements.txt &&
-  pip install -e .[$NIPYPE_EXTRAS] &&
-  export COVERAGE_PROCESS_START=$(pwd)/.coveragerc &&
-  export COVERAGE_DATA_FILE=$(pwd)/.coverage &&
-  echo "data_file = ${COVERAGE_DATA_FILE}" >> ${COVERAGE_PROCESS_START}; }
+  pip install -e .[$NIPYPE_EXTRAS]; }
 - travis_retry inst
 script:
-- py.test --doctest-modules --cov=nipype nipype
-after_success:
-- bash <(curl -s https://codecov.io/bash) -t ac172a50-8e66-42e5-8822-5373fcf54686 -cF unittests
+- py.test --doctest-modules nipype
 deploy:
   provider: pypi
   user: satra

CHANGES

@@ -29,6 +29,7 @@ Upcoming release 0.13
 * ENH: Added support for custom job submission check in SLURM (https://github.com/nipy/nipype/pull/1582)
 * ENH: Added ANTs interface CreateJacobianDeterminantImage; replaces deprecated JacobianDeterminant
        (https://github.com/nipy/nipype/pull/1654)
+* ENH: Update ReconAll interface for FreeSurfer v6.0.0 (https://github.com/nipy/nipype/pull/1790)
 
 Release 0.12.1 (August 3, 2016)
 ===============================

README.rst

@@ -77,21 +77,16 @@ Information specific to Nipype is located here::
 Support and Communication
 -------------------------
 
-If you have a problem or would like to ask a question about how to do something in Nipype please open an issue
-in this GitHub repository.
+If you have a problem or would like to ask a question about how to do something in Nipype please open an issue to
+`NeuroStars.org <http://neurostars.org>`_ with a *nipype* tag. `NeuroStars.org <http://neurostars.org>`_  is a 
+platform similar to StackOverflow but dedicated to neuroinformatics. 
 
 To participate in the Nipype development related discussions please use the following mailing list::
 
        http://mail.python.org/mailman/listinfo/neuroimaging
 
 Please add *[nipype]* to the subject line when posting on the mailing list.
 
-  .. warning ::
-
-    As of `Nov 23, 2016 <https://twitter.com/neuroquestion/status/801453442132754432>`_,
-    `NeuroStars <http://neurostars.org>`_ is down. We used to have all previous Nipype
-    questions available under the `nipype <http://neurostars.org/t/nipype/>`_ label.
-
 
 Nipype structure
 ----------------

circle.yml

@@ -20,43 +20,27 @@ dependencies:
     - sudo apt-get -y update && sudo apt-get install -y wget bzip2
 
   override:
-    - mkdir -p ~/examples ~/scratch/pytest ~/scratch/logs
+    - mkdir -p ~/docker ~/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
-    - if [[ -e ~/docker/image.tar ]]; then docker load -i ~/docker/image.tar; fi
+    - if [[ -e ~/docker/image.tar ]]; then mv -n ~/docker/image.tar ~/docker/image_27.tar; fi
+    - if [[ -e ~/docker/image_27.tar ]]; then docker load -i ~/docker/image_27.tar; fi
+    - if [[ -e ~/docker/image_35.tar ]]; then docker load -i ~/docker/image_35.tar; fi
+    - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
+        timeout: 1600
     - docker build -f docker/nipype_test/Dockerfile_py35 -t nipype/nipype_test:py35 . :
         timeout: 1600
-    - docker build -f docker/nipype_test/Dockerfile_py27 -t nipype/nipype_test:py27 . :
+    - docker save nipype/nipype_test:py27 > ~/docker/image_27.tar :
         timeout: 1600
-    - mkdir -p ~/docker; docker save nipype/nipype_test:py27 > ~/docker/image.tar :
+    - docker save nipype/nipype_test:py35 > ~/docker/image_35.tar :
         timeout: 1600
 
 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" -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 -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 :
-        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 fmri_fsl_feeds Linear /root/examples/ l1pipeline
-    - 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 fmri_spm_dartel Linear /root/examples/ level1 :
-        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 fmri_spm_dartel Linear /root/examples/ l2pipeline :
-        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 fmri_fsl_reuse Linear /root/examples/ level1_workflow
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
-    - docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
-
-  post:
-    - bash docker/circleci/teardown.sh
-    - 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
+    - bash docker/circleci/tests.sh :
+        timeout: 7200
+        parallel: true
 
 general:
   artifacts:

doc/devel/interface_specs.rst

@@ -353,7 +353,7 @@ CommandLine
 	be fixed it's recommended to just use ``usedefault``.
 
 ``sep``
-	For List traits the string with witch elements of the list will be joined.
+	For List traits the string with which elements of the list will be joined.
 
 ``name_source``
     Indicates the list of input fields from which the value of the current File

doc/users/config_file.rst

@@ -55,7 +55,7 @@ Execution
 	Should the input files be checked for changes using their content (slow, but
 	100% accurate) or just their size and modification date (fast, but
 	potentially prone to errors)? (possible values: ``content`` and
-	``timestamp``; default value: ``content``)
+	``timestamp``; default value: ``timestamp``)
 
 *keep_inputs*
     Ensures that all inputs that are created in the nodes working directory are
@@ -134,7 +134,7 @@ Execution
 *poll_sleep_duration*
     This controls how long the job submission loop will sleep between submitting
     all pending jobs and checking for job completion. To be nice to cluster
-    schedulers the default is set to 60 seconds.
+    schedulers the default is set to 2 seconds.
 
 *xvfb_max_wait*
     Maximum time (in seconds) to wait for Xvfb to start, if the _redirect_x parameter of an Interface is True.

docker/circleci/tests.sh

@@ -0,0 +1,50 @@
+#!/bin/bash
+
+set -o nounset
+set -o xtrace
+
+export CODECOV_TOKEN=ac172a50-8e66-42e5-8822-5373fcf54686
+
+if [ "${CIRCLE_NODE_TOTAL:-}" != "4" ]; then
+  echo "These tests were designed to be run at 4x parallelism."
+  exit 1
+fi
+
+# These tests are manually balanced based on previous build timings. 
+# They may need to be rebalanced in the future.
+case ${CIRCLE_NODE_INDEX} in
+  0)
+    time 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 fmri_spm_dartel Linear /root/examples/ level1
+    ;;
+  1)
+    time 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 fmri_spm_dartel Linear /root/examples/ l2pipeline
+    time 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
+    time 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
+    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py27 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    ;;
+  2)
+    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ l2pipeline
+    time 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
+    time 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
+    time docker run -v /etc/localtime:/etc/localtime:ro -e NIPYPE_NUMBER_OF_CPUS=4 -v ~/examples:/root/examples:ro -v ~/scratch:/scratch -w /scratch nipype/nipype_test:py35 /usr/bin/run_examples.sh fmri_spm_nested MultiProc /root/examples/ level1
+    ;;
+  3)
+    time 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
+    time 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 fmri_fsl_feeds Linear /root/examples/ l1pipeline
+    time 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 fmri_fsl_reuse Linear /root/examples/ level1_workflow
+    ;;
+esac
+
+# Put the artifacts in place
+bash docker/circleci/teardown.sh
+
+# Send coverage data to codecov.io
+curl -so codecov.io https://codecov.io/bash
+chmod 755 codecov.io
+find "${CIRCLE_TEST_REPORTS}/pytest" -name 'coverage*.xml' -print0 | \
+  xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F unittests
+find "${CIRCLE_TEST_REPORTS}/pytest" -name 'smoketests*.xml' -print0 | \
+  xargs -0 -I file ./codecov.io -f file -t "${CODECOV_TOKEN}" -F smoketests
+
+
+

nipype/__init__.py

@@ -11,9 +11,9 @@
                    STATUS as __status__,
                    __version__)
 from .utils.config import NipypeConfig
-from .fixes.numpy.testing import nosetester
 from .utils.logger import Logging
 from .refs import due
+from .pkg_info import get_pkg_info as _get_pkg_info
 
 try:
     import faulthandler
@@ -25,48 +25,26 @@
 logging = Logging(config)
 
 
-class _NoseTester(nosetester.NoseTester):
-    """ Subclass numpy's NoseTester to add doctests by default
-    """
-
-    def _get_custom_doctester(self):
-        return None
-
-    def test(self, label='fast', verbose=1, extra_argv=['--exe'],
-             doctests=True, coverage=False):
-        """Run the full test suite
+class NipypeTester(object):
+    def __call__(self, doctests=True):
+        try:
+            import pytest
+        except:
+            raise RuntimeError('py.test not installed, run: pip install pytest')
+        params = {'args': []}
+        if doctests:
+            params['args'].append('--doctest-modules')
+        nipype_path = os.path.dirname(__file__)
+        params['args'].extend(['-x', '--ignore={}/external'.format(nipype_path),
+                               nipype_path])
+        pytest.main(**params)
 
-        Examples
-        --------
-        This will run the test suite and stop at the first failing
-        example
-        >>> from nipype import test
-        >>> test(extra_argv=['--exe', '-sx'])  # doctest: +SKIP
-        """
-        return super(_NoseTester, self).test(label=label,
-                                             verbose=verbose,
-                                             extra_argv=extra_argv,
-                                             doctests=doctests,
-                                             coverage=coverage)
-
-try:
-    test = _NoseTester(raise_warnings="release").test
-except TypeError:
-    # Older versions of numpy do not have a raise_warnings argument
-    test = _NoseTester().test
-del nosetester
+test = NipypeTester()
 
-# Set up package information function
-from .pkg_info import get_pkg_info as _get_pkg_info
-get_info = lambda: _get_pkg_info(os.path.dirname(__file__))
-
-# If this file is exec after being imported, the following lines will
-# fail
-try:
-    del Tester
-except:
-    pass
 
+def get_info():
+    """Returns package information"""
+    return _get_pkg_info(os.path.dirname(__file__))
 
 from .pipeline import Node, MapNode, JoinNode, Workflow
 from .interfaces import (DataGrabber, DataSink, SelectFiles,

nipype/algorithms/confounds.py

@@ -127,9 +127,9 @@ def _run_interface(self, runtime):
         dvars = compute_dvars(self.inputs.in_file, self.inputs.in_mask,
                               remove_zerovariance=self.inputs.remove_zerovariance)
 
-        self._results['avg_std'] = dvars[0].mean()
-        self._results['avg_nstd'] = dvars[1].mean()
-        self._results['avg_vxstd'] = dvars[2].mean()
+        self._results['avg_std'] = float(dvars[0].mean())
+        self._results['avg_nstd'] = float(dvars[1].mean())
+        self._results['avg_vxstd'] = float(dvars[2].mean())
 
         tr = None
         if isdefined(self.inputs.series_tr):