TEST: Use matches or comments to make clear expected warnings

Author: effigies

nibabel/freesurfer/tests/test_io.py

@@ -86,16 +86,15 @@ def test_geometry():
 
         # now write an incomplete file
         write_geometry(surf_path, coords, faces)
-        with pytest.warns(Warning) as w:
-            warnings.filterwarnings('always', category=DeprecationWarning)
+        with pytest.warns(UserWarning) as w:
             read_geometry(surf_path, read_metadata=True)
-
         assert any('volume information contained' in str(ww.message) for ww in w)
         assert any('extension code' in str(ww.message) for ww in w)
+
         volume_info['head'] = [1, 2]
-        with pytest.warns(Warning) as w:
+        with pytest.warns(UserWarning, match="Unknown extension"):
             write_geometry(surf_path, coords, faces, create_stamp, volume_info)
-        assert any('Unknown extension' in str(ww.message) for ww in w)
+
         volume_info['a'] = 0
         with pytest.raises(ValueError):
             write_geometry(surf_path, coords, faces, create_stamp, volume_info)
@@ -266,10 +265,9 @@ def test_write_annot_fill_ctab():
         # values back.
         badannot = (10 * np.arange(nlabels, dtype=np.int32)).reshape(-1, 1)
         rgbal = np.hstack((rgba, badannot))
-        with pytest.warns(Warning) as w:
+        with pytest.warns(UserWarning,
+                          match=f'Annotation values in {annot_path} will be incorrect'):
             write_annot(annot_path, labels, rgbal, names, fill_ctab=False)
-        assert any(f'Annotation values in {annot_path} will be incorrect' == str(ww.message)
-                   for ww in w)
         labels2, rgbal2, names2 = read_annot(annot_path, orig_ids=True)
         names2 = [n.decode('ascii') for n in names2]
         assert np.all(np.isclose(rgbal2[:, :4], rgba))

nibabel/freesurfer/tests/test_mghformat.py

@@ -345,13 +345,13 @@ def test_deprecated_fields():
 
     # mrparams is the only deprecated field at the moment
     # Accessing hdr_data is equivalent to accessing hdr, so double all checks
-    with pytest.deprecated_call():
+    with pytest.deprecated_call(match="from version: 2.3"):
         assert_array_equal(hdr['mrparams'], 0)
     assert_array_equal(hdr_data['mrparams'], 0)
 
-    with pytest.deprecated_call():
+    with pytest.deprecated_call(match="from version: 2.3"):
         hdr['mrparams'] = [1, 2, 3, 4]
-    with pytest.deprecated_call():
+    with pytest.deprecated_call(match="from version: 2.3"):
         assert_array_almost_equal(hdr['mrparams'], [1, 2, 3, 4])
     assert hdr['tr'] == 1
     assert hdr['flip_angle'] == 2
@@ -369,15 +369,15 @@ def test_deprecated_fields():
     hdr['flip_angle'] = 6
     hdr['te'] = 7
     hdr['ti'] = 8
-    with pytest.deprecated_call():
+    with pytest.deprecated_call(match="from version: 2.3"):
         assert_array_almost_equal(hdr['mrparams'], [5, 6, 7, 8])
     assert_array_almost_equal(hdr_data['mrparams'], [5, 6, 7, 8])
 
     hdr_data['tr'] = 9
     hdr_data['flip_angle'] = 10
     hdr_data['te'] = 11
     hdr_data['ti'] = 12
-    with pytest.deprecated_call():
+    with pytest.deprecated_call(match="from version: 2.3"):
         assert_array_almost_equal(hdr['mrparams'], [9, 10, 11, 12])
     assert_array_almost_equal(hdr_data['mrparams'], [9, 10, 11, 12])
 

nibabel/nicom/tests/test_dicomwrappers.py

@@ -660,14 +660,14 @@ def test_data_derived_shape(self):
         # Test 4D diffusion data with an additional trace volume included
         # Excludes the trace volume and generates the correct shape
         dw = didw.wrapper_from_file(DATA_FILE_4D_DERIVED)
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Derived images found and removed"):
             assert dw.image_shape == (96, 96, 60, 33)
 
     @dicom_test
     @needs_nibabel_data('nitest-dicom')
     def test_data_unreadable_private_headers(self):
         # Test CT image with unreadable CSA tags
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Error while attempting to read CSA header"):
             dw = didw.wrapper_from_file(DATA_FILE_CT)
         assert dw.image_shape == (512, 571)
 

nibabel/streamlines/tests/test_array_sequence.py

@@ -94,14 +94,18 @@ def test_creating_arraysequence_from_list(self):
         check_arr_seq(ArraySequence(iter(SEQ_DATA['data']), buffer_size),
                       SEQ_DATA['data'])
 
+    def test_deprecated_data_attribute(self):
+        seq = ArraySequence(SEQ_DATA['data'])
+        with pytest.deprecated_call(match="from version: 3.0"):
+            seq.data
+
     def test_creating_arraysequence_from_generator(self):
         gen_1, gen_2 = itertools.tee((e for e in SEQ_DATA['data']))
         seq = ArraySequence(gen_1)
         seq_with_buffer = ArraySequence(gen_2, buffer_size=256)
 
         # Check buffer size effect
-        with pytest.warns(Warning):
-            assert seq_with_buffer.data.shape == seq.data.shape
+        assert seq_with_buffer.get_data().shape == seq.get_data().shape
         assert seq_with_buffer._buffer_size > seq._buffer_size
 
         # Check generator result

nibabel/streamlines/tests/test_streamlines.py

@@ -201,14 +201,11 @@ def test_save_tractogram_file(self):
             nib.streamlines.save(trk_file, "dummy.trk", header={})
 
         # Wrong extension.
-        with pytest.warns(ExtensionWarning) as w:
+        with pytest.warns(ExtensionWarning, match="extension"):
             trk_file = trk.TrkFile(tractogram)
             with self.assertRaises(ValueError):
                 nib.streamlines.save(trk_file, "dummy.tck", header={})
 
-        assert len(w) == 1
-        assert "extension" in str(w[0].message)
-
         with InTemporaryDirectory():
             nib.streamlines.save(trk_file, "dummy.trk")
             tfile = nib.streamlines.load("dummy.trk", lazy_load=False)
@@ -243,19 +240,16 @@ def test_save_complex_file(self):
             with InTemporaryDirectory():
                 filename = 'streamlines' + ext
 
-                with pytest.warns(None) as w:
-                    nib.streamlines.save(complex_tractogram, filename)
-
                 # If streamlines format does not support saving data
                 # per point or data per streamline, warning messages
                 # should be issued.
                 nb_expected_warnings = \
                     ((not cls.SUPPORTS_DATA_PER_POINT) +
                      (not cls.SUPPORTS_DATA_PER_STREAMLINE))
 
+                with pytest.warns(Warning if nb_expected_warnings else None) as w:
+                    nib.streamlines.save(complex_tractogram, filename)
                 assert len(w) == nb_expected_warnings
-                for i in range(nb_expected_warnings):
-                    assert issubclass(w[i].category, Warning)
 
                 tractogram = Tractogram(DATA['streamlines'],
                                         affine_to_rasmm=np.eye(4))

nibabel/streamlines/tests/test_tck.py

@@ -113,18 +113,14 @@ def test_load_file_with_wrong_information(self):
         new_tck_file = tck_file.replace(b"datatype: Float32LE\n", b"")
         # Need to adjust data offset.
         new_tck_file = new_tck_file.replace(b"file: . 67\n", b"file: . 47\n")
-        with pytest.warns(HeaderWarning) as w:
+        with pytest.warns(HeaderWarning, match="Missing 'datatype'"):
             tck = TckFile.load(BytesIO(new_tck_file))
-        assert len(w) == 1
-        assert "Missing 'datatype'" in str(w[0].message)
         assert_array_equal(tck.header['datatype'], "Float32LE")
 
         # Simulate a TCK file with no `file` field.
         new_tck_file = tck_file.replace(b"\nfile: . 67", b"")
-        with pytest.warns(HeaderWarning) as w:
+        with pytest.warns(HeaderWarning, matches="Missing 'file'") as w:
             tck = TckFile.load(BytesIO(new_tck_file))
-        assert len(w) == 1
-        assert "Missing 'file'" in str(w[0].message)
         assert_array_equal(tck.header['file'], ". 56")
 
         # Simulate a TCK file with `file` field pointing to another file.

nibabel/streamlines/tests/test_tractogram.py

@@ -811,7 +811,7 @@ def test_lazy_tractogram_creation(self):
 
         # Empty `LazyTractogram`
         tractogram = LazyTractogram()
-        with pytest.warns(Warning):
+        with pytest.warns(Warning, match="Number of streamlines will be determined manually"):
             check_tractogram(tractogram)
         assert tractogram.affine_to_rasmm is None
 
@@ -833,7 +833,7 @@ def test_lazy_tractogram_creation(self):
     def test_lazy_tractogram_from_data_func(self):
         # Create an empty `LazyTractogram` yielding nothing.
         tractogram = LazyTractogram.from_data_func(lambda: iter([]))
-        with pytest.warns(Warning):
+        with pytest.warns(Warning, match="Number of streamlines will be determined manually"):
             check_tractogram(tractogram)
 
         # Create `LazyTractogram` from a generator function yielding
@@ -854,7 +854,7 @@ def _data_gen():
                                      data_for_points)
 
         tractogram = LazyTractogram.from_data_func(_data_gen)
-        with pytest.warns(Warning):
+        with pytest.warns(Warning, match="Number of streamlines will be determined manually"):
             assert_tractogram_equal(tractogram, DATA['tractogram'])
 
         # Creating a LazyTractogram from not a corouting should raise an error.
@@ -924,7 +924,7 @@ def test_lazy_tractogram_apply_affine(self):
         assert_array_equal(transformed_tractogram._affine_to_apply, affine)
         assert_array_equal(transformed_tractogram.affine_to_rasmm,
                            np.dot(np.eye(4), np.linalg.inv(affine)))
-        with pytest.warns(Warning):
+        with pytest.warns(Warning, match="Number of streamlines will be determined manually"):
             check_tractogram(transformed_tractogram,
                              streamlines=[s*scaling for s in DATA['streamlines']],
                              data_per_streamline=DATA['data_per_streamline'],
@@ -950,7 +950,7 @@ def test_lazy_tractogram_apply_affine(self):
         transformed_tractogram = tractogram.apply_affine(affine)
         assert_array_equal(transformed_tractogram._affine_to_apply, affine)
         assert transformed_tractogram.affine_to_rasmm is None
-        with pytest.warns(Warning):
+        with pytest.warns(Warning, match="Number of streamlines will be determined manually"):
             check_tractogram(transformed_tractogram,
                              streamlines=[s*scaling for s in DATA['streamlines']],
                              data_per_streamline=DATA['data_per_streamline'],
@@ -1024,5 +1024,5 @@ def test_lazy_tractogram_copy(self):
                            DATA['lazy_tractogram']._affine_to_apply)
 
         # Check the data are the equivalent.
-        with pytest.warns(Warning):
+        with pytest.warns(Warning, match="Number of streamlines will be determined manually"):
             assert_tractogram_equal(tractogram, DATA['tractogram'])

nibabel/streamlines/tests/test_trk.py

@@ -135,10 +135,8 @@ def test_load_file_with_wrong_information(self):
         # Simulate a TRK where `vox_to_ras` is not recorded (i.e. all zeros).
         trk_struct, trk_bytes = self.trk_with_bytes()
         trk_struct[Field.VOXEL_TO_RASMM] = np.zeros((4, 4))
-        with pytest.warns(HeaderWarning) as w:
+        with pytest.warns(HeaderWarning, match="identity"):
             trk = TrkFile.load(BytesIO(trk_bytes))
-        assert len(w) == 1
-        assert "identity" in str(w[0].message)
         assert_array_equal(trk.affine, np.eye(4))
 
         # Simulate a TRK where `vox_to_ras` is invalid.
@@ -151,17 +149,14 @@ def test_load_file_with_wrong_information(self):
         # Simulate a TRK file where `voxel_order` was not provided.
         trk_struct, trk_bytes = self.trk_with_bytes()
         trk_struct[Field.VOXEL_ORDER] = b''
-        with pytest.warns(HeaderWarning) as w:
+        with pytest.warns(HeaderWarning, match="LPS"):
             TrkFile.load(BytesIO(trk_bytes))
-        assert len(w) == 1
-        assert "LPS" in str(w[0].message)
 
         # Simulate a TRK file with an unsupported version.
         trk_struct, trk_bytes = self.trk_with_bytes()
         trk_struct['version'] = 123
         with pytest.raises(HeaderError):
             TrkFile.load(BytesIO(trk_bytes))
-        
 
         # Simulate a TRK file with a wrong hdr_size.
         trk_struct, trk_bytes = self.trk_with_bytes()
@@ -190,10 +185,8 @@ def test_load_trk_version_1(self):
         assert_array_equal(trk.affine, np.diag([2, 3, 4, 1]))
         # Next check that affine assumed identity if version 1.
         trk_struct['version'] = 1
-        with pytest.warns(HeaderWarning) as w:
+        with pytest.warns(HeaderWarning, match="identity"):
             trk = TrkFile.load(BytesIO(trk_bytes))
-        assert len(w) == 1
-        assert "identity" in str(w[0].message)
         assert_array_equal(trk.affine, np.eye(4))
         assert_array_equal(trk.header['version'], 1)
 

nibabel/tests/test_analyze.py

@@ -734,10 +734,10 @@ def test_data_hdr_cache(self):
         assert_array_equal(np.asanyarray(img2.dataobj), data)
         # now check read_img_data function - here we do see the changed
         # header
-        with pytest.deprecated_call():
+        with pytest.deprecated_call(match="from version: 3.2"):
             sc_data = read_img_data(img2)
         assert sc_data.shape == (3, 2, 2)
-        with pytest.deprecated_call():
+        with pytest.deprecated_call(match="from version: 3.2"):
             us_data = read_img_data(img2, prefer='unscaled')
         assert us_data.shape == (3, 2, 2)
 

nibabel/tests/test_ecat.py

@@ -240,7 +240,7 @@ def test_isolation(self):
         assert not np.all(img.affine == aff)
 
     def test_get_affine_deprecated(self):
-        with pytest.deprecated_call():
+        with pytest.deprecated_call(match="from version: 2.1"):
             aff = self.img.get_affine()
         assert np.array_equal(aff, self.img.affine)
 

nibabel/tests/test_parrec.py

@@ -671,11 +671,11 @@ def assert_copy_ok(hdr1, hdr2):
             PARRECHeader.from_fileobj(fobj)
     with open(TRUNC_PAR, 'rt') as fobj:
         # Parse but warn on inconsistent header
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Header inconsistency"):
             trunc_hdr = PARRECHeader.from_fileobj(fobj, True)
     assert trunc_hdr.permit_truncated
     # Warn on inconsistent header when copying
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning, match="Header inconsistency"):
         trunc_hdr2 = trunc_hdr.copy()
     assert_copy_ok(trunc_hdr, trunc_hdr2)
 
@@ -716,13 +716,13 @@ def test_image_creation():
             func(trunc_param)
         with pytest.raises(PARRECError):
             func(trunc_param, permit_truncated=False)
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Header inconsistency"):
             img = func(trunc_param, permit_truncated=True)
         assert_array_equal(img.dataobj, arr_prox_dv)
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Header inconsistency"):
             img = func(trunc_param, permit_truncated=True, scaling='dv')
         assert_array_equal(img.dataobj, arr_prox_dv)
-        with pytest.warns(UserWarning):
+        with pytest.warns(UserWarning, match="Header inconsistency"):
             img = func(trunc_param, permit_truncated=True, scaling='fp')
         assert_array_equal(img.dataobj, arr_prox_fp)
 

nibabel/tests/test_processing.py

@@ -148,7 +148,7 @@ def test_resample_from_to(caplog):
     exp_out[1:, :, :] = data[1, :, :]
     assert_almost_equal(out.dataobj, exp_out)
     out = resample_from_to(img, trans_p_25_img)
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning):  # Suppress scipy warning
         exp_out = spnd.affine_transform(data, [1, 1, 1], [-0.25, 0, 0], order=3)
     assert_almost_equal(out.dataobj, exp_out)
     # Test cval
@@ -161,7 +161,7 @@ def test_resample_from_to(caplog):
     assert out.__class__ == Nifti1Image
     # By default, type of from_img makes no difference
     n1_img = Nifti2Image(data, affine)
-    with caplog.at_level(logging.CRITICAL):
+    with caplog.at_level(logging.CRITICAL):  # Here and below, suppress logs when changing classes
         out = resample_from_to(n1_img, trans_img)
     assert out.__class__ == Nifti1Image
     # Passed as keyword arg
@@ -254,7 +254,7 @@ def test_resample_to_output(caplog):
     assert_array_equal(out_img.dataobj, np.flipud(data))
     # Subsample voxels
     out_img = resample_to_output(Nifti1Image(data, np.diag([4, 5, 6, 1])))
-    with pytest.warns(UserWarning):
+    with pytest.warns(UserWarning):  # Suppress scipy warning
         exp_out = spnd.affine_transform(data,
                                         [1/4, 1/5, 1/6],
                                         output_shape = (5, 11, 19))
@@ -293,7 +293,7 @@ def test_resample_to_output(caplog):
     img_ni1 = Nifti2Image(data, np.eye(4))
     img_ni2 = Nifti2Image(data, np.eye(4))
     # Default is Nifti1Image
-    with caplog.at_level(logging.CRITICAL):
+    with caplog.at_level(logging.CRITICAL):  # Here and below, suppress logs when changing classes
         assert resample_to_output(img_ni2).__class__ == Nifti1Image
     # Can be overriden
     with caplog.at_level(logging.CRITICAL):
@@ -349,7 +349,7 @@ def test_smooth_image(caplog):
     img_ni1 = Nifti1Image(data, np.eye(4))
     img_ni2 = Nifti2Image(data, np.eye(4))
     # Default is Nifti1Image
-    with caplog.at_level(logging.CRITICAL):
+    with caplog.at_level(logging.CRITICAL):  # Here and below, suppress logs when changing classes
         assert smooth_image(img_ni2, 0).__class__ == Nifti1Image
     # Can be overriden
     with caplog.at_level(logging.CRITICAL):
@@ -362,7 +362,7 @@ def test_smooth_image(caplog):
 def test_spatial_axes_check(caplog):
     for fname in MINC_3DS + OTHER_IMGS:
         img = nib.load(pjoin(DATA_DIR, fname))
-        with caplog.at_level(logging.CRITICAL):
+        with caplog.at_level(logging.CRITICAL):  # Suppress logs when changing classes
             s_img = smooth_image(img, 0)
         assert_array_equal(img.dataobj, s_img.dataobj)
         with caplog.at_level(logging.CRITICAL):
@@ -447,7 +447,7 @@ def test_conform(caplog):
     assert isinstance(c, Nifti1Image)
 
     # Test with non-default arguments.
-    with caplog.at_level(logging.CRITICAL):
+    with caplog.at_level(logging.CRITICAL):  # Suppress logs when changing classes
         c = conform(anat, out_shape=(100, 100, 200), voxel_size=(2, 2, 1.5),
                     orientation="LPI", out_class=Nifti2Image)
     assert c.shape == (100, 100, 200)