applying suggestions from 865

Author: djarecka

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_deprecator.py

@@ -69,11 +69,8 @@ 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')
+        with pytest.deprecated_call():
             assert func() == None
-            assert len(w) == 1
-            assert w[0].category is DeprecationWarning
         assert func.__doc__ == 'foo\n'
         func = dec('foo')(func_doc)
         with clear_and_catch_warnings(modules=[_OWN_MODULE]) as w:
@@ -135,11 +132,8 @@ def test_dep_func(self):
             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')
+        with pytest.deprecated_call():
             assert func() == None
-            assert len(w) == 1
-            assert w[0].category is DeprecationWarning
 
         func = dec('foo', until='1.8', error_class=CustomError)(func_no_doc)
         with pytest.raises(CustomError):
@@ -162,11 +156,8 @@ def test_deprecator_maker(self):
 
         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')
+        with pytest.deprecated_call():
             assert func() == None
-            assert len(w) == 1
-            assert w[0].category is DeprecationWarning
 
         func = dec('foo', until='1.8')(func_no_doc)
         with pytest.raises(CustomError):

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():

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)

nibabel/tests/test_image_api.py

@@ -113,10 +113,8 @@ def validate_header(self, imaker, params):
     def validate_header_deprecated(self, imaker, params):
         # Check deprecated header API
         img = imaker()
-        with clear_and_catch_warnings() as w:
-            warnings.simplefilter('always', DeprecationWarning)
+        with pytest.deprecated_call():
             hdr = img.get_header()
-            assert len(w) == 1
             assert hdr is img.header
 
     def validate_filenames(self, imaker, params):
@@ -171,7 +169,7 @@ def validate_no_slicing(self, imaker, params):
     def validate_get_data_deprecated(self, imaker, params):
         # Check deprecated header API
         img = imaker()
-        with assert_warns(DeprecationWarning):
+        with pytest.deprecated_call():
             data = img.get_data()
         assert_array_equal(np.asanyarray(img.dataobj), data)
 
@@ -395,10 +393,8 @@ def _check_array_caching(self, imaker, meth_name, caching):
     def validate_data_deprecated(self, imaker, params):
         # Check _data property still exists, but raises warning
         img = imaker()
-        with warnings.catch_warnings(record=True) as warns:
-            warnings.simplefilter("always")
+        with pytest.deprecated_call():
             assert_data_similar(img._data, params)
-            assert warns.pop(0).category == DeprecationWarning
         # Check setting _data raises error
         fake_data = np.zeros(img.shape).astype(img.get_data_dtype())
         with pytest.raises(AttributeError):
@@ -502,10 +498,8 @@ def validate_affine(self, imaker, params):
     def validate_affine_deprecated(self, imaker, params):
         # Check deprecated affine API
         img = imaker()
-        with clear_and_catch_warnings() as w:
-            warnings.simplefilter('always', DeprecationWarning)
+        with pytest.deprecated_call():
             assert_almost_equal(img.get_affine(), params['affine'], 6)
-            assert len(w) == 1
             assert img.get_affine().dtype == np.float64
             aff = img.get_affine()
             aff[0, 0] = 1.5

nibabel/tests/test_orientations.py

@@ -380,9 +380,6 @@ def test_inv_ornt_aff():
 
 def test_orientation_affine_deprecation():
     aff1 = inv_ornt_aff([[0, 1], [1, -1], [2, 1]], (3, 4, 5))
-    with warnings.catch_warnings(record=True) as warns:
-        warnings.simplefilter('always')
+    with pytest.deprecated_call():
         aff2 = orientation_affine([[0, 1], [1, -1], [2, 1]], (3, 4, 5))
-        assert len(warns) == 1
-        assert warns[0].category == DeprecationWarning
     assert_array_equal(aff1, aff2)

nibabel/tests/test_parrec.py

@@ -263,10 +263,8 @@ def test_affine_regression():
 
 def test_get_voxel_size_deprecated():
     hdr = PARRECHeader(HDR_INFO, HDR_DEFS)
-    with clear_and_catch_warnings(modules=[parrec], record=True) as wlist:
-        simplefilter('always')
+    with pytest.deprecated_call():
         hdr.get_voxel_size()
-    assert wlist[0].category == DeprecationWarning
 
 
 def test_get_sorted_slice_indices():
@@ -304,9 +302,9 @@ def test_sorting_dual_echo_T1():
     sorted_echos = t1_hdr.image_defs['echo number'][sorted_indices]
     n_half = len(t1_hdr.image_defs) // 2
     # first half (volume 1) should all correspond to echo 1
-    assert np.all(sorted_echos[:n_half] == 1) == True
+    assert np.all(sorted_echos[:n_half] == 1)
     # second half (volume 2) should all correspond to echo 2
-    assert np.all(sorted_echos[n_half:] == 2) == True
+    assert np.all(sorted_echos[n_half:] == 2)
 
     # check volume labels
     vol_labels = t1_hdr.get_volume_labels()
@@ -350,10 +348,10 @@ def test_sorting_multiple_echos_and_contrasts():
         assert (np.all(sorted_echos[istart:iend] == current_echo) ==
                      True)
     # outermost sort index is image_type_mr
-    assert np.all(sorted_types[:ntotal//4] == 0) == True
-    assert np.all(sorted_types[ntotal//4:ntotal//2] == 1) == True
-    assert np.all(sorted_types[ntotal//2:3*ntotal//4] == 2) == True
-    assert np.all(sorted_types[3*ntotal//4:ntotal] == 3) == True
+    assert np.all(sorted_types[:ntotal//4] == 0)
+    assert np.all(sorted_types[ntotal//4:ntotal//2] == 1)
+    assert np.all(sorted_types[ntotal//2:3*ntotal//4] == 2)
+    assert np.all(sorted_types[3*ntotal//4:ntotal] == 3)
 
     # check volume labels
     vol_labels = t1_hdr.get_volume_labels()

nibabel/tests/test_parrec_data.py

@@ -60,8 +60,7 @@ def test_fieldmap():
     fieldmap_nii = pjoin(BALLS, 'NIFTI', 'fieldmap.nii.gz')
     load(fieldmap_par)
     top_load(fieldmap_nii)
-    # TODO dj: i believe this shouldn't be here
-    #raise pytest.skip('Fieldmap remains puzzling')
+    raise pytest.skip('Fieldmap remains puzzling')
 
 
 @needs_nibabel_data('parrec_oblique')

nibabel/tests/test_recoder.py

@@ -22,14 +22,14 @@ def test_recoder_1():
     assert rc.code[1] == 1
     assert rc.code[2] == 2
     with pytest.raises(KeyError):
-        rc.code.__getitem__(3)
+        rc.code[3]
 
 def test_recoder_2():
     # with explicit name for code
     codes = ((1,), (2,))
     rc = Recoder(codes, ['code1'])
     with pytest.raises(AttributeError):
-        rc.__getattribute__('code')
+        rc.code
     assert rc.code1[1] == 1
     assert rc.code1[2] == 2
 
@@ -41,20 +41,20 @@ def test_recoder_3():
     assert rc.code[1] == 1
     assert rc.code[2] == 2
     with pytest.raises(KeyError):
-        rc.code.__getitem__(3)
+        rc.code[3]
     assert rc.code['one'] == 1
     assert rc.code['two'] == 2
     with pytest.raises(KeyError):
-        rc.code.__getitem__('three')
+        rc.code['three']
     with pytest.raises(AttributeError):
-        rc.__getattribute__('label')
+        rc.label
 
 def test_recoder_3():
     # with explicit column names
     codes = ((1, 'one'), (2, 'two'))
     rc = Recoder(codes, ['code1', 'label'])
     with pytest.raises(AttributeError):
-        rc.__getattribute__('code')
+        rc.code
     assert rc.code1[1] == 1
     assert rc.code1['one'] == 1
     assert rc.label[1] == 'one'
@@ -119,7 +119,7 @@ def test_add_codes():
     rc = Recoder(codes)
     assert rc.code['two'] == 2
     with pytest.raises(KeyError):
-        rc.code.__getitem__('three')
+        rc.code['three']
     rc.add_codes(((3, 'three'), (1, 'number 1')))
     assert rc.code['three'] == 3
     assert rc.code['number 1'] == 1
@@ -151,7 +151,7 @@ def test_dtmapper():
     # dict-like that will lookup on dtypes, even if they don't hash properly
     d = DtypeMapper()
     with pytest.raises(KeyError):
-        d.__getitem__(1)
+        d[1]
     d[1] = 'something'
     assert d[1] == 'something'
     assert list(d.keys()) == [1]
@@ -182,7 +182,7 @@ def test_dtmapper():
     sw_dt = canonical_dt.newbyteorder(swapped_code)
     d[sw_dt] = 'spam'
     with pytest.raises(KeyError):
-        d.__getitem__(canonical_dt)
+        d[canonical_dt]
     assert d[sw_dt] == 'spam'
     sw_intp_dt = intp_dt.newbyteorder(swapped_code)
     assert d[sw_intp_dt] == 'spam'

nibabel/tests/test_scaling.py

@@ -159,35 +159,33 @@ def test_array_file_scales(in_type, out_type, err):
     # Max rounding error for integer type
     max_miss = slope / 2.
     assert np.all(np.abs(arr - arr3) <= max_miss)
-    bio.truncate(0)
-    bio.seek(0)
 
 
-@pytest.mark.parametrize("category0, category1",[
+@pytest.mark.parametrize("in_type, out_type",[
     ('int', 'int'),
     ('uint', 'int'),
 ])
-def test_scaling_in_abstract(category0, category1):
+def test_scaling_in_abstract(in_type, out_type):
     # Confirm that, for all ints and uints as input, and all possible outputs,
     # for any simple way of doing the calculation, the result is near enough
-    for in_type in np.sctypes[category0]:
-        for out_type in np.sctypes[category1]:
-            check_int_a2f(in_type, out_type)
+    for in_tp in np.sctypes[in_type]:
+        for out_tp in np.sctypes[out_type]:
+            check_int_a2f(in_tp, out_tp)
 
 
-@pytest.mark.parametrize("category0, category1", [
+@pytest.mark.parametrize("in_type, out_type", [
     ('float', 'int'),
     ('float', 'uint'),
     ('complex', 'int'),
     ('complex', 'uint'),
 ])
-def test_scaling_in_abstract_warn(category0, category1):
+def test_scaling_in_abstract_warn(in_type, out_type):
 
     # Converting floats to integer
-    for in_type in np.sctypes[category0]:
-        for out_type in np.sctypes[category1]:
+    for in_tp in np.sctypes[in_type]:
+        for out_tp in np.sctypes[out_type]:
             with suppress_warnings():  # overflow
-                check_int_a2f(in_type, out_type)
+                check_int_a2f(in_tp, out_tp)
 
 
 def check_int_a2f(in_type, out_type):