Merge pull request #876 from djarecka/pytest_updates

updates for nibabel.tests

Author: effigies

.azure-pipelines/windows.yml

@@ -49,10 +49,12 @@ jobs:
           -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 ^
@@ -75,6 +77,7 @@ jobs:
           -I test_image_types ^
           -I test_imageclasses ^
           -I test_imageglobals ^
+          -I test_io ^
           -I test_keywordonly ^
           -I test_loadsave ^
           -I test_minc1 ^
@@ -99,6 +102,9 @@ jobs:
           -I test_round_trip ^
           -I test_rstutils ^
           -I test_scaling ^
+          -I test_scripts ^
+          -I test_spaces ^
+          -I test_testing ^
           -I test_wrapstruct
       displayName: 'Nose tests'
       condition: and(succeeded(), eq(variables['CHECK_TYPE'], 'nosetests'))

.travis.yml

@@ -142,10 +142,12 @@ script:
                 -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 \
@@ -168,6 +170,7 @@ script:
                 -I test_image_types \
                 -I test_imageclasses \
                 -I test_imageglobals \
+                -I test_io \
                 -I test_keywordonly \
                 -I test_loadsave \
                 -I test_minc1 \
@@ -192,6 +195,9 @@ script:
                 -I test_round_trip \
                 -I test_rstutils \
                 -I test_scaling \
+                -I test_scripts \
+                -I test_spaces \
+                -I test_testing \
                 -I test_wrapstruct
       elif [ "${CHECK_TYPE}" == "test" ]; then
           # Change into an innocuous directory and find tests from installation

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
 
-from ..testing import skipif
+import pytest
 
 
 def get_nibabel_data():
@@ -39,11 +39,11 @@ def needs_nibabel_data(subdir=None):
     """
     nibabel_data = get_nibabel_data()
     if nibabel_data == '':
-        return skipif(True, "Need nibabel-data directory for this test")
+        return pytest.mark.skipif(True, reason="Need nibabel-data directory for this test")
     if subdir is None:
-        return skipif(False)
+        return pytest.mark.skipif(False, reason="Don't skip")
     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 skipif(not have_files,
-                  "Need files in {0} for these tests".format(required_path))
+    return pytest.mark.skipif(not have_files,
+                              reason="Need files in {0} for these tests".format(required_path))

nibabel/tests/scriptrunner.py

@@ -135,7 +135,7 @@ def run_command(self, cmd, check_code=True):
                 env['PYTHONPATH'] = self.local_module_dir + pathsep + pypath
         proc = Popen(cmd, stdout=PIPE, stderr=PIPE, env=env)
         stdout, stderr = proc.communicate()
-        if proc.poll() == None:
+        if proc.poll() is None:
             proc.terminate()
         if check_code and proc.returncode != 0:
             raise RuntimeError(

nibabel/tests/test_analyze.py

@@ -512,7 +512,7 @@ def test_from_header(self):
         for check in (True, False):
             copy = klass.from_header(hdr, check=check)
             assert hdr == copy
-            assert not hdr is copy
+            assert hdr is not copy
 
         class C(object):
 

nibabel/tests/test_arraywriters.py

@@ -508,9 +508,9 @@ def test_nan2zero():
         assert_array_equal(np.isnan(data_back), [True, False])
         # Deprecation warning for nan2zero as argument to `to_fileobj`
         with error_warnings():
-            with pytest.raises(DeprecationWarning):
+            with pytest.deprecated_call():
                 aw.to_fileobj(BytesIO(), 'F', True)
-            with pytest.raises(DeprecationWarning):
+            with pytest.deprecated_call():
                 aw.to_fileobj(BytesIO(), 'F', nan2zero=True)
         # Error if nan2zero is not the value set at initialization
         with pytest.raises(WriterError):
@@ -530,9 +530,9 @@ def test_nan2zero():
         assert_array_equal(data_back, [astype_res, 99])
         # Deprecation warning for nan2zero as argument to `to_fileobj`
         with error_warnings():
-            with pytest.raises(DeprecationWarning):
+            with pytest.deprecated_call():
                 aw.to_fileobj(BytesIO(), 'F', False)
-            with pytest.raises(DeprecationWarning):
+            with pytest.deprecated_call():
                 aw.to_fileobj(BytesIO(), 'F', nan2zero=False)
         # Error if nan2zero is not the value set at initialization
         with pytest.raises(WriterError):

nibabel/tests/test_casting.py

@@ -155,7 +155,7 @@ def test_floor_log2():
     assert floor_log2(0.75) == -1
     assert floor_log2(0.25) == -2
     assert floor_log2(0.24) == -3
-    assert floor_log2(0) == None
+    assert floor_log2(0) is None
 
 
 def test_able_int_type():

nibabel/tests/test_deprecator.py

@@ -34,9 +34,9 @@ def test__add_dep_doc():
     assert _add_dep_doc('bar\n\n', 'foo') == 'bar\n\nfoo\n'
     assert _add_dep_doc('bar\n    \n', 'foo') == 'bar\n\nfoo\n'
     assert (_add_dep_doc(' bar\n\nSome explanation', 'foo\nbaz') ==
-                 ' bar\n\nfoo\nbaz\n\nSome explanation\n')
+            ' bar\n\nfoo\nbaz\n\nSome explanation\n')
     assert (_add_dep_doc(' bar\n\n  Some explanation', 'foo\nbaz') ==
-                 ' bar\n  \n  foo\n  baz\n  \n  Some explanation\n')
+            ' bar\n  \n  foo\n  baz\n  \n  Some explanation\n')
 
 
 class CustomError(Exception):
@@ -69,36 +69,29 @@ def test_dep_func(self):
         # Test function deprecation
         dec = self.dep_func
         func = dec('foo')(func_no_doc)
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func() == None
-            assert len(w) == 1
-            assert w[0].category is DeprecationWarning
+        with pytest.deprecated_call():
+            assert func() is None
         assert func.__doc__ == 'foo\n'
         func = dec('foo')(func_doc)
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func(1) == None
+        with pytest.deprecated_call() as w:
+            assert func(1) is None
             assert len(w) == 1
         assert func.__doc__ == 'A docstring\n\nfoo\n'
         func = dec('foo')(func_doc_long)
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func(1, 2) == None
+        with pytest.deprecated_call() as w:
+            assert func(1, 2) is None
             assert len(w) == 1
         assert func.__doc__ == 'A docstring\n   \n   foo\n   \n   Some text\n'
 
         # Try some since and until versions
         func = dec('foo', '1.1')(func_no_doc)
         assert func.__doc__ == 'foo\n\n* deprecated from version: 1.1\n'
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func() == None
+        with pytest.deprecated_call() as w:
+            assert func() is None
             assert len(w) == 1
         func = dec('foo', until='99.4')(func_no_doc)
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func() == None
+        with pytest.deprecated_call() as w:
+            assert func() is None
             assert len(w) == 1
         assert (func.__doc__ ==
                     'foo\n\n* Will raise {} as of version: 99.4\n'
@@ -107,39 +100,36 @@ def test_dep_func(self):
         with pytest.raises(ExpiredDeprecationError):
             func()
         assert (func.__doc__ ==
-                    'foo\n\n* Raises {} as of version: 1.8\n'
-                    .format(ExpiredDeprecationError))
+                'foo\n\n* Raises {} as of version: 1.8\n'
+                .format(ExpiredDeprecationError))
         func = dec('foo', '1.2', '1.8')(func_no_doc)
         with pytest.raises(ExpiredDeprecationError):
             func()
         assert (func.__doc__ ==
-                    'foo\n\n* deprecated from version: 1.2\n'
-                    '* Raises {} as of version: 1.8\n'
-                    .format(ExpiredDeprecationError))
+                'foo\n\n* deprecated from version: 1.2\n'
+                '* Raises {} as of version: 1.8\n'
+                .format(ExpiredDeprecationError))
         func = dec('foo', '1.2', '1.8')(func_doc_long)
         assert (func.__doc__ ==
-                    'A docstring\n   \n   foo\n   \n'
-                    '   * deprecated from version: 1.2\n'
-                    '   * Raises {} as of version: 1.8\n   \n'
-                    '   Some text\n'
-                    .format(ExpiredDeprecationError))
+                'A docstring\n   \n   foo\n   \n'
+                '   * deprecated from version: 1.2\n'
+                '   * Raises {} as of version: 1.8\n   \n'
+                '   Some text\n'
+                .format(ExpiredDeprecationError))
         with pytest.raises(ExpiredDeprecationError):
             func()
 
         # Check different warnings and errors
         func = dec('foo', warn_class=UserWarning)(func_no_doc)
         with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
             warnings.simplefilter('always')
-            assert func() == None
+            assert func() is None
             assert len(w) == 1
             assert w[0].category is UserWarning
 
         func = dec('foo', error_class=CustomError)(func_no_doc)
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func() == None
-            assert len(w) == 1
-            assert w[0].category is DeprecationWarning
+        with pytest.deprecated_call():
+            assert func() is None
 
         func = dec('foo', until='1.8', error_class=CustomError)(func_no_doc)
         with pytest.raises(CustomError):
@@ -154,19 +144,15 @@ class TestDeprecatorMaker(object):
     def test_deprecator_maker(self):
         dec = self.dep_maker(warn_class=UserWarning)
         func = dec('foo')(func_no_doc)
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func() == None
+        with pytest.warns(UserWarning) as w:
+            # warnings.simplefilter('always')
+            assert func() is None
             assert len(w) == 1
-            assert w[0].category is UserWarning
 
         dec = self.dep_maker(error_class=CustomError)
         func = dec('foo')(func_no_doc)
-        with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
-            warnings.simplefilter('always')
-            assert func() == None
-            assert len(w) == 1
-            assert w[0].category is DeprecationWarning
+        with pytest.deprecated_call():
+            assert func() is None
 
         func = dec('foo', until='1.8')(func_no_doc)
         with pytest.raises(CustomError):

nibabel/tests/test_ecat.py

@@ -21,7 +21,7 @@
 
 from numpy.testing import assert_array_equal, assert_array_almost_equal
 
-from ..testing_pytest import data_path, suppress_warnings, clear_and_catch_warnings
+from ..testing_pytest import data_path, suppress_warnings
 from ..tmpdirs import InTemporaryDirectory
 
 from .test_wrapstruct import _TestWrapStructBase
@@ -164,7 +164,7 @@ def test_subheader(self):
         assert self.subhdr.get_nframes() == 1
         assert (self.subhdr.get_nframes() ==
                      len(self.subhdr.subheaders))
-        assert self.subhdr._check_affines() == True
+        assert self.subhdr._check_affines() is True
         assert_array_almost_equal(np.diag(self.subhdr.get_frame_affine()),
                                   np.array([2.20241979, 2.20241979, 3.125, 1.]))
         assert self.subhdr.get_zooms()[0] == 2.20241978764534
@@ -271,8 +271,7 @@ def test_mlist_regression(self):
 
 def test_from_filespec_deprecation():
     # Check from_filespec raises Deprecation
-    with clear_and_catch_warnings() as w:
-        warnings.simplefilter('always', DeprecationWarning)
+    with pytest.deprecated_call() as w:
         # No warning for standard load
         img_loaded = EcatImage.load(ecat_file)
         assert len(w) == 0

nibabel/tests/test_environment.py

@@ -60,4 +60,4 @@ def test_sys_dir():
     elif os.name == 'posix':
         assert sys_dir == r'/etc/nipy'
     else:
-        assert sys_dir == None
+        assert sys_dir is None

nibabel/tests/test_files_interface.py

@@ -29,8 +29,8 @@ def test_files_spatialimages():
     for klass in klasses:
         file_map = klass.make_file_map()
         for key, value in file_map.items():
-            assert value.filename == None
-            assert value.fileobj == None
+            assert value.filename is None
+            assert value.fileobj is None
             assert value.pos == 0
         # If we can't create new images in memory without loading, bail here
         if not klass.makeable:
@@ -42,8 +42,8 @@ def test_files_spatialimages():
         else:
             img = klass(arr, aff)
         for key, value in img.file_map.items():
-            assert value.filename == None
-            assert value.fileobj == None
+            assert value.filename is None
+            assert value.fileobj is None
             assert value.pos == 0
 
 

nibabel/tests/test_fileslice.py

@@ -47,7 +47,7 @@ def test_is_fancy():
     assert not is_fancy((None, 1))
     assert not is_fancy((1, None))
     # Chack that actual False returned (rather than falsey)
-    assert is_fancy(1) == False
+    assert is_fancy(1) is False
 
 
 def test_canonical_slicers():
@@ -243,9 +243,9 @@ def test_threshold_heuristic():
     # Test for default skip / read heuristic
     # int
     assert threshold_heuristic(1, 9, 1, skip_thresh=8) == 'full'
-    assert threshold_heuristic(1, 9, 1, skip_thresh=7) == None
+    assert threshold_heuristic(1, 9, 1, skip_thresh=7) is None
     assert threshold_heuristic(1, 9, 2, skip_thresh=16) == 'full'
-    assert threshold_heuristic(1, 9, 2, skip_thresh=15) == None
+    assert threshold_heuristic(1, 9, 2, skip_thresh=15) is None
     # full slice, smallest step size
     assert (threshold_heuristic(
         slice(0, 9, 1), 9, 2, skip_thresh=2) ==

nibabel/tests/test_funcs.py

@@ -138,7 +138,7 @@ def test_closest_canonical():
     # And a case where the Analyze image has to be flipped
     img = AnalyzeImage(arr, np.diag([-1, 1, 1, 1]))
     xyz_img = as_closest_canonical(img)
-    assert not img is xyz_img
+    assert img is not xyz_img
     out_arr = xyz_img.get_fdata()
     assert_array_equal(out_arr, np.flipud(arr))
 
@@ -156,7 +156,7 @@ def test_closest_canonical():
     img = Nifti1Image(arr, np.diag([-1, 1, 1, 1]))
     img.header.set_dim_info(0, 1, 2)
     xyz_img = as_closest_canonical(img)
-    assert not img is xyz_img
+    assert img is not xyz_img
     assert img.header.get_dim_info() == xyz_img.header.get_dim_info()
     out_arr = xyz_img.get_fdata()
     assert_array_equal(out_arr, np.flipud(arr))
@@ -181,7 +181,7 @@ def test_closest_canonical():
     img.header.set_dim_info(0, 1, 2)
 
     xyz_img = as_closest_canonical(img)
-    assert not img is xyz_img
+    assert img is not xyz_img
     # Check both the original and new objects
     assert img.header.get_dim_info() == (0, 1, 2)
     assert xyz_img.header.get_dim_info() == (0, 2, 1)