Merge pull request #891 from effigies/test/final_nose_purge

TEST: Final nose purge

Author: effigies

.azure-pipelines/windows.yml

@@ -36,24 +36,6 @@ jobs:
         python -m pip install .[$(CHECK_TYPE)]
         SET NIBABEL_DATA_DIR=%CD%\\nibabel-data
       displayName: 'Install nibabel'
-    - script: |
-        mkdir for_testing
-        cd for_testing
-        cp ../.coveragerc .
-        nosetests --with-doctest --with-coverage --cover-package nibabel nibabel ^
-          -I test_data ^
-          -I test_environment ^
-          -I test_euler ^
-          -I test_giftiio ^
-          -I test_netcdf ^
-          -I test_pkg_info ^
-          -I test_quaternions ^
-          -I test_scaling ^
-          -I test_scripts ^
-          -I test_spaces ^
-          -I test_testing
-      displayName: 'Nose tests'
-      condition: and(succeeded(), eq(variables['CHECK_TYPE'], 'nosetests'))
     - script: |
         mkdir for_testing
         cd for_testing

.travis.yml

@@ -27,10 +27,6 @@ python:
 
 jobs:
   include:
-    # Old nosetests - Remove soon
-    - python: 3.7
-      env:
-        - CHECK_TYPE="nosetests"
     # Basic dependencies only
     - python: 3.5
       env:
@@ -140,23 +136,6 @@ script:
           cd doc
           make html;
           make doctest;
-      elif [ "${CHECK_TYPE}" == "nosetests" ]; then
-          # Change into an innocuous directory and find tests from installation
-          mkdir for_testing
-          cd for_testing
-          cp ../.coveragerc .
-          nosetests --with-doctest --with-coverage --cover-package nibabel nibabel \
-                -I test_data \
-                -I test_environment \
-                -I test_euler \
-                -I test_giftiio \
-                -I test_netcdf \
-                -I test_pkg_info \
-                -I test_quaternions \
-                -I test_scaling \
-                -I test_scripts \
-                -I test_spaces \
-                -I test_testing
       elif [ "${CHECK_TYPE}" == "test" ]; then
           # Change into an innocuous directory and find tests from installation
           mkdir for_testing

azure-pipelines.yml

@@ -34,7 +34,3 @@ jobs:
       py38-x64:
         PYTHON_VERSION: '3.8'
         PYTHON_ARCH: 'x64'
-      nosetests:
-        PYTHON_VERSION: '3.6'
-        PYTHON_ARCH: 'x64'
-        CHECK_TYPE: 'nosetests'

dev-requirements.txt

@@ -1,4 +1,3 @@
 # Requirements for running tests
 -r requirements.txt
-nose
 pytest

doc/source/devel/advanced_testing.rst

@@ -25,7 +25,7 @@ Long-running tests
 Long-running tests are not enabled by default, and can be resource-intensive. To run these tests:
 
 * Set environment variable ``NIPY_EXTRA_TESTS=slow``;
-* Run ``nosetests``.
+* Run ``pytest nibabel``.
 
 Note that some tests may require a machine with >4GB of RAM.
 

doc/source/devel/make_release.rst

@@ -79,7 +79,7 @@ Release checklist
 
 * Make sure all tests pass (from the nibabel root directory)::
 
-    nosetests --with-doctest nibabel
+    pytest --doctest-modules nibabel
 
 * Make sure you are set up to use the ``try_branch.py`` - see
   https://github.com/nipy/nibotmi/blob/master/install.rst#trying-a-set-of-changes-on-the-buildbots

doc/source/installation.rst

@@ -90,7 +90,7 @@ Requirements
 *  h5py_ (optional, for MINC2 support)
 *  PyDICOM_ 0.9.9 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)
-*  nose_ 0.11 or greater and pytest_ (optional, to run the tests)
+*  pytest_ (optional, to run the tests)
 *  sphinx_ (optional, to build the documentation)
 
 Get the development sources
@@ -128,7 +128,7 @@ module to see if everything is fine.  It should look something like this::
     >>>
 
 
-To run the nibabel test suite, from the terminal run ``nosetests nibabel`` or
+To run the nibabel test suite, from the terminal run ``pytest nibabel`` or
 ``python -c "import nibabel; nibabel.test()``.
 
 To run an extended test suite that validates ``nibabel`` for long-running and

nibabel/__init__.py

@@ -36,29 +36,6 @@
 For more detailed information see the :ref:`manual`.
 """
 
-# Package-wide test setup and teardown
-_test_states = {
-    # Numpy changed print options in 1.14; we can update docstrings and remove
-    # these when our minimum for building docs exceeds that
-    'legacy_printopt': None,
-    }
-
-def setup_package():
-    """ Set numpy print style to legacy="1.13" for newer versions of numpy """
-    import numpy as np
-    from distutils.version import LooseVersion
-    if LooseVersion(np.__version__) >= LooseVersion('1.14'):
-        if _test_states.get('legacy_printopt') is None:
-            _test_states['legacy_printopt'] = np.get_printoptions().get('legacy')
-        np.set_printoptions(legacy="1.13")
-
-def teardown_package():
-    """ Reset print options when tests finish """
-    import numpy as np
-    if _test_states.get('legacy_printopt') is not None:
-        np.set_printoptions(legacy=_test_states.pop('legacy_printopt'))
-
-
 # module imports
 from . import analyze as ana
 from . import spm99analyze as spm99
@@ -92,13 +69,105 @@ def teardown_package():
 from . import streamlines
 from . import viewers
 
-from numpy.testing import Tester
-test = Tester().test
-bench = Tester().bench
-del Tester
-
 from .pkg_info import get_pkg_info as _get_pkg_info
 
 
 def get_info():
     return _get_pkg_info(os.path.dirname(__file__))
+
+
+def test(label=None, verbose=1, extra_argv=None,
+         doctests=False, coverage=False, raise_warnings=None,
+         timer=False):
+    """
+    Run tests for nibabel using pytest
+
+    The protocol mimics the ``numpy.testing.NoseTester.test()``.
+    Not all features are currently implemented.
+
+    Parameters
+    ----------
+    label : None
+        Unused.
+    verbose: int, optional
+        Verbosity value for test outputs. Positive values increase verbosity, and
+        negative values decrease it. Default is 1.
+    extra_argv : list, optional
+        List with any extra arguments to pass to pytest.
+    doctests: bool, optional
+        If True, run doctests in module. Default is False.
+    coverage: bool, optional
+        If True, report coverage of NumPy code. Default is False.
+        (This requires the
+        `coverage module <https://nedbatchelder.com/code/modules/coveragehtml>`_).
+    raise_warnings : None
+        Unused.
+    timer : False
+        Unused.
+
+    Returns
+    -------
+    code : ExitCode
+        Returns the result of running the tests as a ``pytest.ExitCode`` enum
+    """
+    import pytest
+    args = []
+
+    if label is not None:
+        raise NotImplementedError("Labels cannot be set at present")
+
+    try:
+        verbose = int(verbose)
+    except ValueError:
+        pass
+    else:
+        if verbose > 0:
+            args.append("-" + "v" * verbose)
+        elif verbose < 0:
+            args.append("-" + "q" * -verbose)
+
+    if extra_argv:
+        args.extend(extra_argv)
+    if doctests:
+        args.append("--doctest-modules")
+    if coverage:
+        args.extend(["--cov", "nibabel"])
+    if raise_warnings:
+        raise NotImplementedError("Warning filters are not implemented")
+    if timer:
+        raise NotImplementedError("Timing is not implemented")
+
+    args.extend(["--pyargs", "nibabel"])
+
+    pytest.main(args=args)
+
+
+def bench(label=None, verbose=1, extra_argv=None):
+    """
+    Run benchmarks for nibabel using pytest
+
+    The protocol mimics the ``numpy.testing.NoseTester.bench()``.
+    Not all features are currently implemented.
+
+    Parameters
+    ----------
+    label : None
+        Unused.
+    verbose: int, optional
+        Verbosity value for test outputs. Positive values increase verbosity, and
+        negative values decrease it. Default is 1.
+    extra_argv : list, optional
+        List with any extra arguments to pass to pytest.
+
+    Returns
+    -------
+    code : ExitCode
+        Returns the result of running the tests as a ``pytest.ExitCode`` enum
+    """
+    from pkg_resources import resource_filename
+    config = resource_filename("nibabel", "benchmarks/pytest.benchmark.ini")
+    args = []
+    if extra_argv is not None:
+        args.extend(extra_argv)
+    args.extend(["-c", config])
+    test(label, verbose, extra_argv=args)

nibabel/benchmarks/bench_array_to_file.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_load_save.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_load_save.py
 """
 
 import sys

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_arrayproxy_slicing.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_arrayproxy_slicing.py
 """
 
 from timeit import timeit

nibabel/benchmarks/bench_fileslice.py

@@ -3,13 +3,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_fileslice.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_fileslice.py
 """
 
 import sys

nibabel/benchmarks/bench_finite_range.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_finite_range
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_finite_range.py
 """
 
 import sys

nibabel/benchmarks/bench_load_save.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_load_save.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_load_save.py
 """
 
 import sys

nibabel/benchmarks/bench_streamlines.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also run
-the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_streamlines.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_streamlines.py
 """
 
 import numpy as np

nibabel/benchmarks/pytest.benchmark.ini

@@ -0,0 +1,4 @@
+[pytest]
+python_files = bench_*.py
+python_functions = bench_*
+addopts = --capture=no

nibabel/cmdline/tests/test_utils.py

@@ -5,8 +5,6 @@
 Test running scripts
 """
 
-from numpy.testing import assert_raises
-
 import pytest
 
 import nibabel as nib
@@ -196,10 +194,10 @@ def test_main():
                               -7.24879837e+00]).astype(dtype="float32")]),
         ('DATA(md5)', ['0a2576dd6badbb25bfb3b12076df986b', 'b0abbc492b4fd533b2c80d82570062cf'])])
 
-    with assert_raises(SystemExit):
+    with pytest.raises(SystemExit):
         np.testing.assert_equal(main(test_names, StringIO()), expected_difference)
 
     test_names_2 = [pjoin(data_path, f) for f in ('standard.nii.gz', 'standard.nii.gz')]
 
-    with assert_raises(SystemExit):
+    with pytest.raises(SystemExit):
         assert main(test_names_2, StringIO()) == "These files are identical."