Merge pull request #883 from effigies/test/vanilla_unittest

TEST: Prefer vanilla unittest.skip* to pytest skips

Author: effigies

.azure-pipelines/windows.yml

@@ -41,73 +41,17 @@ jobs:
         cd for_testing
         cp ../.coveragerc .
         nosetests --with-doctest --with-coverage --cover-package nibabel nibabel ^
-          -I test_array_sequence ^
-          -I test_tractogram ^
-          -I test_api_validators ^
-          -I test_arrayproxy ^
-          -I test_arraywriters ^
-          -I test_batteryrunners ^
-          -I test_brikhead ^
-          -I test_casting ^
-          -I test_cifti2io_axes ^
-          -I test_cifti2io_header ^
           -I test_data ^
-          -I test_deprecated ^
-          -I test_deprecator ^
-          -I test_dicomwrappers ^
-          -I test_dft ^
-          -I test_ecat ^
-          -I test_ecat_data ^
-          -I test_endiancodes ^
           -I test_environment ^
           -I test_euler ^
-          -I test_filebasedimages ^
-          -I test_filehandles ^
-          -I test_fileholders ^
-          -I test_filename_parser ^
-          -I test_files_interface ^
-          -I test_fileslice ^
-          -I test_fileutils ^
-          -I test_floating ^
-          -I test_funcs ^
           -I test_giftiio ^
-          -I test_h5py_compat ^
-          -I test_image_api ^
-          -I test_image_load_save ^
-          -I test_image_types ^
-          -I test_imageclasses ^
-          -I test_imageglobals ^
-          -I test_io ^
-          -I test_keywordonly ^
-          -I test_loadsave ^
-          -I test_minc1 ^
-          -I test_minc2 ^
-          -I test_minc2_data ^
-          -I test_mriutils ^
           -I test_netcdf ^
-          -I test_nibabel_data ^
-          -I test_nifti1 ^
-          -I test_nifti2 ^
-          -I test_openers ^
-          -I test_optpkg ^
-          -I test_orientations ^
-          -I test_parrec ^
-          -I test_parrec_data ^
           -I test_pkg_info ^
-          -I test_processing ^
-          -I test_proxy_api ^
           -I test_quaternions ^
-          -I test_recoder ^
-          -I test_remmovalschedule ^
-          -I test_round_trip ^
-          -I test_rstutils ^
           -I test_scaling ^
-          -I test_wrapstruct ^
-          -I test_io ^
           -I test_scripts ^
           -I test_spaces ^
-          -I test_testing ^
-          -I test_wrapstruct
+          -I test_testing
       displayName: 'Nose tests'
       condition: and(succeeded(), eq(variables['CHECK_TYPE'], 'nosetests'))
     - script: |

.travis.yml

@@ -134,73 +134,17 @@ script:
           cd for_testing
           cp ../.coveragerc .
           nosetests --with-doctest --with-coverage --cover-package nibabel nibabel \
-                -I test_array_sequence \
-                -I test_tractogram \
-                -I test_api_validators \
-                -I test_arrayproxy \
-                -I test_arraywriters \
-                -I test_batteryrunners \
-                -I test_brikhead \
-                -I test_casting \
-                -I test_cifti2io_axes \
-                -I test_cifti2io_header \
                 -I test_data \
-                -I test_deprecated \
-                -I test_deprecator \
-                -I test_dicomwrappers \
-                -I test_dft \
-                -I test_ecat \
-                -I test_ecat_data \
-                -I test_endiancodes \
                 -I test_environment \
                 -I test_euler \
-                -I test_filebasedimages \
-                -I test_filehandles \
-                -I test_fileholders \
-                -I test_filename_parser \
-                -I test_files_interface \
-                -I test_fileslice \
-                -I test_fileutils \
-                -I test_floating \
-                -I test_funcs \
                 -I test_giftiio \
-                -I test_h5py_compat \
-                -I test_image_api \
-                -I test_image_load_save \
-                -I test_image_types \
-                -I test_imageclasses \
-                -I test_imageglobals \
-                -I test_io \
-                -I test_keywordonly \
-                -I test_loadsave \
-                -I test_minc1 \
-                -I test_minc2 \
-                -I test_minc2_data \
-                -I test_mriutils \
                 -I test_netcdf \
-                -I test_nibabel_data \
-                -I test_nifti1 \
-                -I test_nifti2 \
-                -I test_openers \
-                -I test_optpkg \
-                -I test_orientations \
-                -I test_parrec \
-                -I test_parrec_data \
                 -I test_pkg_info \
-                -I test_processing \
-                -I test_proxy_api \
                 -I test_quaternions \
-                -I test_recoder \
-                -I test_remmovalschedule \
-                -I test_round_trip \
-                -I test_rstutils \
                 -I test_scaling \
-                -I test_wrapstruct \
-                -I test_io \
                 -I test_scripts \
                 -I test_spaces \
-                -I test_testing \
-                -I test_wrapstruct
+                -I test_testing
       elif [ "${CHECK_TYPE}" == "test" ]; then
           # Change into an innocuous directory and find tests from installation
           mkdir for_testing

nibabel/freesurfer/tests/test_io.py

@@ -6,10 +6,9 @@
 import hashlib
 import warnings
 
-
 from ...tmpdirs import InTemporaryDirectory
 
-
+import unittest
 import pytest
 import numpy as np
 from numpy.testing import assert_allclose, assert_array_equal
@@ -36,8 +35,8 @@
         data_path = pjoin(nib_data, 'nitest-freesurfer', DATA_SDIR)
         have_freesurfer = isdir(data_path)
 
-freesurfer_test = pytest.mark.skipif(not have_freesurfer,
-                                     reason='cannot find freesurfer {0} directory'.format(DATA_SDIR))
+freesurfer_test = unittest.skipUnless(have_freesurfer,
+                                      'cannot find freesurfer {0} directory'.format(DATA_SDIR))
 
 def _hash_file_content(fname):
     hasher = hashlib.md5()

nibabel/testing_pytest/__init__.py

@@ -13,17 +13,12 @@
 import sys
 import warnings
 from pkg_resources import resource_filename
-from os.path import dirname, abspath, join as pjoin
 
 import unittest
 
 import numpy as np
-from numpy.testing import assert_array_equal, assert_warns
-from numpy.testing import dec
-skipif = dec.skipif
-slow = dec.slow
+from numpy.testing import assert_array_equal
 
-from ..deprecated import deprecate_with_version as _deprecate_with_version
 from .np_features import memmap_after_ufunc
 from .helpers import bytesio_filemap, bytesio_round_trip, assert_data_similar
 
@@ -63,7 +58,7 @@ def assert_allclose_safely(a, b, match_nans=True, rtol=1e-5, atol=1e-8):
     a, b = np.broadcast_arrays(a, b)
     if match_nans:
         nans = np.isnan(a)
-        np.testing.assert_array_equal(nans, np.isnan(b))
+        assert_array_equal(nans, np.isnan(b))
         to_test = ~nans
     else:
         to_test = np.ones(a.shape, dtype=bool)
@@ -199,20 +194,12 @@ class suppress_warnings(error_warnings):
     filter = 'ignore'
 
 
-@_deprecate_with_version('catch_warn_reset is deprecated; use '
-                         'nibabel.testing.clear_and_catch_warnings.',
-                         since='2.1.0', until='3.0.0')
-class catch_warn_reset(clear_and_catch_warnings):
-    pass
-
-
 EXTRA_SET = os.environ.get('NIPY_EXTRA_TESTS', '').split(',')
 
 
 def runif_extra_has(test_str):
     """Decorator checks to see if NIPY_EXTRA_TESTS env var contains test_str"""
-    return skipif(test_str not in EXTRA_SET,
-                  "Skip {0} tests.".format(test_str))
+    return unittest.skipUnless(test_str in EXTRA_SET, "Skip {0} tests.".format(test_str))
 
 
 def assert_arr_dict_equal(dict1, dict2):

nibabel/tests/nibabel_data.py

@@ -4,7 +4,7 @@
 from os import environ, listdir
 from os.path import dirname, realpath, join as pjoin, isdir, exists
 
-import pytest
+import unittest
 
 
 def get_nibabel_data():
@@ -39,11 +39,11 @@ def needs_nibabel_data(subdir=None):
     """
     nibabel_data = get_nibabel_data()
     if nibabel_data == '':
-        return pytest.mark.skipif(True, reason="Need nibabel-data directory for this test")
+        return unittest.skip("Need nibabel-data directory for this test")
     if subdir is None:
-        return pytest.mark.skipif(False, reason="Don't skip")
+        return lambda x: x
     required_path = pjoin(nibabel_data, subdir)
     # Path should not be empty (as is the case for not-updated submodules)
     have_files = exists(required_path) and len(listdir(required_path)) > 0
-    return pytest.mark.skipif(not have_files,
-                              reason="Need files in {0} for these tests".format(required_path))
+    return unittest.skipUnless(have_files,
+                               "Need files in {0} for these tests".format(required_path))

nibabel/tests/test_dft.py

@@ -10,6 +10,7 @@
     from .. import dft
 from .. import nifti1
 
+import unittest
 import pytest
 
 # Shield optional package imports
@@ -22,10 +23,12 @@
 data_dir = pjoin(dirname(__file__), 'data')
 
 
-pytestmark = [
-    pytest.mark.skipif(os.name == 'nt', reason='FUSE not available for windows, skipping dft tests'),
-    pytest.mark.skipif(not have_dicom, reason='Need pydicom for dft tests, skipping')
-]
+def setUpModule():
+    if os.name == 'nt':
+        raise unittest.SkipTest('FUSE not available for windows, skipping dft tests')
+    if not have_dicom:
+        raise unittest.SkipTest('Need pydicom for dft tests, skipping')
+
 
 def test_init():
     dft.clear_cache()
@@ -76,7 +79,7 @@ def test_storage_instance():
     pass
 
 
-@pytest.mark.skipif(not have_pil, reason='could not import PIL.Image')
+@unittest.skipUnless(have_pil, 'could not import PIL.Image')
 def test_png():
     studies = dft.get_studies(data_dir)
     data = studies[0].series[0].as_png()

nibabel/tests/test_image_api.py

@@ -41,6 +41,7 @@
 from ..spatialimages import SpatialImage
 from .. import minc1, minc2, parrec, brikhead
 
+import unittest
 import pytest
 
 from numpy.testing import assert_almost_equal, assert_array_equal, assert_warns, assert_allclose
@@ -121,7 +122,7 @@ def validate_filenames(self, imaker, params):
         # Validate the filename, file_map interface
 
         if not self.can_save:
-            pytest.skip()
+            raise unittest.SkipTest
         img = imaker()
         img.set_data_dtype(np.float32)  # to avoid rounding in load / save
         # Make sure the object does not have a file_map
@@ -706,8 +707,12 @@ class TestMinc1API(ImageHeaderAPI):
     example_images = MINC1_EXAMPLE_IMAGES
 
 
-@pytest.mark.skipif(not have_h5py, reason="Need h5py for Minc2 tests")
 class TestMinc2API(TestMinc1API):
+
+    def __init__(self):
+        if not have_h5py:
+            raise unittest.SkipTest('Need h5py for these tests')
+
     klass = image_maker = Minc2Image
     loader = minc2.load
     example_images = MINC2_EXAMPLE_IMAGES

nibabel/tests/test_parrec_data.py

@@ -12,6 +12,7 @@
 
 from .nibabel_data import get_nibabel_data, needs_nibabel_data
 
+import unittest
 import pytest
 from numpy.testing import assert_almost_equal
 
@@ -60,7 +61,7 @@ def test_fieldmap():
     fieldmap_nii = pjoin(BALLS, 'NIFTI', 'fieldmap.nii.gz')
     load(fieldmap_par)
     top_load(fieldmap_nii)
-    raise pytest.skip('Fieldmap remains puzzling')
+    raise unittest.SkipTest('Fieldmap remains puzzling')
 
 
 @needs_nibabel_data('parrec_oblique')

nibabel/tests/test_processing.py

@@ -27,14 +27,14 @@
                              voxel_sizes)
 from nibabel.eulerangles import euler2mat
 
-from numpy.testing import (assert_almost_equal,
-                           assert_array_equal)
+from numpy.testing import assert_almost_equal, assert_array_equal
+import unittest
 import pytest
 
 from nibabel.tests.test_spaces import assert_all_in, get_outspace_params
 from nibabel.testing import assert_allclose_safely
 
-needs_scipy = pytest.mark.skipif(not have_scipy, reason='These tests need scipy')
+needs_scipy = unittest.skipUnless(have_scipy, 'These tests need scipy')
 
 DATA_DIR = pjoin(dirname(__file__), 'data')
 

nibabel/tests/test_proxy_api.py

@@ -51,6 +51,7 @@
 
 from ..arrayproxy import ArrayProxy, is_proxy
 
+import unittest
 import pytest
 from numpy.testing import assert_almost_equal, assert_array_equal, assert_allclose
 
@@ -428,7 +429,7 @@ def eg_func():
                     arr_out=arr_out))
 
     def validate_header_isolated(self, pmaker, params):
-        raise pytest.skip('ECAT header does not support dtype get')
+        raise unittest.SkipTest('ECAT header does not support dtype get')
 
 
 class TestPARRECAPI(_TestProxyAPI):

nibabel/tests/test_scripts.py

@@ -20,6 +20,7 @@
 from ..loadsave import load
 from ..orientations import flip_axis, aff2axcodes, inv_ornt_aff
 
+import unittest
 import pytest
 from numpy.testing import assert_almost_equal
 
@@ -120,7 +121,7 @@ def test_nib_ls(args):
     check_nib_ls_example4d(*args)
 
 
-@pytest.mark.skipif(not load_small_file(), reason="can't load the small.mnc file")
+@unittest.skipUnless(load_small_file(), "Can't load the small.mnc file")
 @script_test
 def test_nib_ls_multiple():
     # verify that correctly lists/formats for multiple files