Merge branch 'master' into PGH

Author: effigies

nibabel/batteryrunners.py

@@ -252,7 +252,7 @@ def __str__(self):
     def message(self):
         """formatted message string, including fix message if present"""
         if self.fix_msg:
-            return '; '.join((self.problem_msg, self.fix_msg))
+            return f'{self.problem_msg}; {self.fix_msg}'
         return self.problem_msg
 
     def log_raise(self, logger, error_level=40):

nibabel/cmdline/tests/test_convert.py

@@ -71,7 +71,7 @@ def test_convert_dtype(tmp_path, data_dtype):
 
 
 @pytest.mark.parametrize(
-    'ext,img_class',
+    ('ext', 'img_class'),
     [
         ('mgh', nib.MGHImage),
         ('img', nib.Nifti1Pair),
@@ -94,7 +94,7 @@ def test_convert_by_extension(tmp_path, ext, img_class):
 
 
 @pytest.mark.parametrize(
-    'ext,img_class',
+    ('ext', 'img_class'),
     [
         ('mgh', nib.MGHImage),
         ('img', nib.Nifti1Pair),
@@ -141,7 +141,7 @@ def test_convert_nifti_int_fail(tmp_path):
 
 
 @pytest.mark.parametrize(
-    'orig_dtype,alias,expected_dtype',
+    ('orig_dtype', 'alias', 'expected_dtype'),
     [
         ('int64', 'mask', 'uint8'),
         ('int64', 'compat', 'int32'),

nibabel/cmdline/tests/test_roi.py

@@ -119,7 +119,7 @@ def test_nib_roi(tmp_path, inplace):
 
 
 @pytest.mark.parametrize(
-    'args, errmsg',
+    ('args', 'errmsg'),
     (
         (('-i', '1:1'), 'Cannot take zero-length slice'),
         (('-j', '1::2'), 'Downsampling is not supported'),
@@ -138,12 +138,8 @@ def test_nib_roi_bad_slices(capsys, args, errmsg):
 def test_entrypoint(capsys):
     # Check that we handle missing args as expected
     with mock.patch('sys.argv', ['nib-roi', '--help']):
-        try:
+        with pytest.raises(SystemExit):
             main()
-        except SystemExit:
-            pass
-        else:
-            assert False, 'argparse exits on --help. If changing to another parser, update test.'
     captured = capsys.readouterr()
     assert captured.out.startswith('usage: nib-roi')
 

nibabel/data.py

@@ -87,8 +87,7 @@ def list_files(self, relative=True):
         for base, dirs, files in os.walk(self.base_path):
             if relative:
                 base = base[len(self.base_path) + 1 :]
-            for filename in files:
-                out_list.append(pjoin(base, filename))
+            out_list.extend(pjoin(base, filename) for filename in files)
         return out_list
 
 

nibabel/gifti/gifti.py

@@ -374,7 +374,7 @@ def _to_xml_element(self):
     def print_summary(self):
         print('Dataspace: ', xform_codes.niistring[self.dataspace])
         print('XFormSpace: ', xform_codes.niistring[self.xformspace])
-        print('Affine Transformation Matrix: \n', self.xform)
+        print('Affine Transformation Matrix:\n', self.xform)
 
 
 def _data_tag_element(dataarray, encoding, dtype, ordering):

nibabel/gifti/tests/test_gifti.py

@@ -423,13 +423,14 @@ def test_gifti_coord(capsys):
     gcs.xform = None
     gcs.print_summary()
     captured = capsys.readouterr()
-    assert captured.out == '\n'.join(
-        [
-            'Dataspace:  NIFTI_XFORM_UNKNOWN',
-            'XFormSpace:  NIFTI_XFORM_UNKNOWN',
-            'Affine Transformation Matrix: ',
-            ' None\n',
-        ]
+    assert (
+        captured.out
+        == """\
+Dataspace:  NIFTI_XFORM_UNKNOWN
+XFormSpace:  NIFTI_XFORM_UNKNOWN
+Affine Transformation Matrix:
+ None
+"""
     )
     gcs.to_xml()
 

nibabel/nicom/tests/test_dicomwrappers.py

@@ -429,10 +429,9 @@ def fake_shape_dependents(
 
     class PrintBase:
         def __repr__(self):
-            attr_strs = []
-            for attr in dir(self):
-                if attr[0].isupper():
-                    attr_strs.append(f'{attr}={getattr(self, attr)}')
+            attr_strs = [
+                f'{attr}={getattr(self, attr)}' for attr in dir(self) if attr[0].isupper()
+            ]
             return f"{self.__class__.__name__}({', '.join(attr_strs)})"
 
     class DimIdxSeqElem(pydicom.Dataset):

nibabel/nifti1.py

@@ -325,15 +325,15 @@ class NiftiExtension(ty.Generic[T]):
     """
 
     code: int
-    encoding: ty.Optional[str] = None
+    encoding: str | None = None
     _content: bytes
-    _object: ty.Optional[T] = None
+    _object: T | None = None
 
     def __init__(
         self,
-        code: ty.Union[int, str],
+        code: int | str,
         content: bytes = b'',
-        object: ty.Optional[T] = None,
+        object: T | None = None,
     ) -> None:
         """
         Parameters
@@ -565,9 +565,9 @@ class Nifti1DicomExtension(Nifti1Extension[DicomDataset]):
 
     def __init__(
         self,
-        code: ty.Union[int, str],
-        content: ty.Union[bytes, DicomDataset, None] = None,
-        parent_hdr: ty.Optional[Nifti1Header] = None,
+        code: int | str,
+        content: bytes | DicomDataset | None = None,
+        parent_hdr: Nifti1Header | None = None,
     ) -> None:
         """
         Parameters

nibabel/streamlines/tests/test_streamlines.py

@@ -191,13 +191,13 @@ def test_save_tractogram_file(self):
         trk_file = trk.TrkFile(tractogram)
 
         # No need for keyword arguments.
-        with self.assertRaises(ValueError):
+        with pytest.raises(ValueError):
             nib.streamlines.save(trk_file, 'dummy.trk', header={})
 
         # Wrong extension.
         with pytest.warns(ExtensionWarning, match='extension'):
             trk_file = trk.TrkFile(tractogram)
-            with self.assertRaises(ValueError):
+            with pytest.raises(ValueError):
                 nib.streamlines.save(trk_file, 'dummy.tck', header={})
 
         with InTemporaryDirectory():
@@ -207,7 +207,7 @@ def test_save_tractogram_file(self):
 
     def test_save_empty_file(self):
         tractogram = Tractogram(affine_to_rasmm=np.eye(4))
-        for ext, cls in FORMATS.items():
+        for ext in FORMATS:
             with InTemporaryDirectory():
                 filename = 'streamlines' + ext
                 nib.streamlines.save(tractogram, filename)
@@ -216,7 +216,7 @@ def test_save_empty_file(self):
 
     def test_save_simple_file(self):
         tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))
-        for ext, cls in FORMATS.items():
+        for ext in FORMATS:
             with InTemporaryDirectory():
                 filename = 'streamlines' + ext
                 nib.streamlines.save(tractogram, filename)
@@ -262,7 +262,7 @@ def test_save_complex_file(self):
     def test_save_sliced_tractogram(self):
         tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))
         original_tractogram = tractogram.copy()
-        for ext, cls in FORMATS.items():
+        for ext in FORMATS:
             with InTemporaryDirectory():
                 filename = 'streamlines' + ext
                 nib.streamlines.save(tractogram[::2], filename)
@@ -272,18 +272,18 @@ def test_save_sliced_tractogram(self):
                 assert_tractogram_equal(tractogram, original_tractogram)
 
     def test_load_unknown_format(self):
-        with self.assertRaises(ValueError):
+        with pytest.raises(ValueError):
             nib.streamlines.load('')
 
     def test_save_unknown_format(self):
-        with self.assertRaises(ValueError):
+        with pytest.raises(ValueError):
             nib.streamlines.save(Tractogram(), '')
 
     def test_save_from_generator(self):
         tractogram = Tractogram(DATA['streamlines'], affine_to_rasmm=np.eye(4))
 
         # Just to create a generator
-        for ext, _ in FORMATS.items():
+        for ext in FORMATS:
             filtered = (s for s in tractogram.streamlines if True)
             lazy_tractogram = LazyTractogram(lambda: filtered, affine_to_rasmm=np.eye(4))
 

nibabel/testing/helpers.py

@@ -14,7 +14,7 @@
 def bytesio_filemap(klass):
     """Return bytes io filemap for this image class `klass`"""
     file_map = klass.make_file_map()
-    for name, fileholder in file_map.items():
+    for fileholder in file_map.values():
         fileholder.fileobj = BytesIO()
         fileholder.pos = 0
     return file_map

nibabel/tests/test_analyze.py

@@ -728,8 +728,8 @@ def test_data_hdr_cache(self):
         IC = self.image_class
         # save an image to a file map
         fm = IC.make_file_map()
-        for key, value in fm.items():
-            fm[key].fileobj = BytesIO()
+        for value in fm.values():
+            value.fileobj = BytesIO()
         shape = (2, 3, 4)
         data = np.arange(24, dtype=np.int8).reshape(shape)
         affine = np.eye(4)
@@ -831,7 +831,7 @@ def test_header_updating(self):
         hdr = img.header
         hdr.set_zooms((4, 5, 6))
         # Save / reload using bytes IO objects
-        for key, value in img.file_map.items():
+        for value in img.file_map.values():
             value.fileobj = BytesIO()
         img.to_file_map()
         hdr_back = img.from_file_map(img.file_map).header
@@ -842,7 +842,7 @@ def test_header_updating(self):
         assert_array_equal(hdr.get_zooms(), (2, 3, 4))
         # Modify affine in-place? Update on save.
         img.affine[0, 0] = 9
-        for key, value in img.file_map.items():
+        for value in img.file_map.values():
             value.fileobj = BytesIO()
         img.to_file_map()
         hdr_back = img.from_file_map(img.file_map).header
@@ -864,7 +864,7 @@ def test_pickle(self):
         assert_array_equal(img.get_fdata(), img2.get_fdata())
         assert img.header == img2.header
         # Save / reload using bytes IO objects
-        for key, value in img.file_map.items():
+        for value in img.file_map.values():
             value.fileobj = BytesIO()
         img.to_file_map()
         img_prox = img.from_file_map(img.file_map)

nibabel/tests/test_dft.py

@@ -58,7 +58,7 @@ def db(monkeypatch):
     and not modify the host filesystem."""
     database = dft._DB(fname=':memory:')
     monkeypatch.setattr(dft, 'DB', database)
-    yield database
+    return database
 
 
 def test_init(db):

nibabel/tests/test_euler.py

@@ -21,12 +21,8 @@
 FLOAT_EPS = np.finfo(np.float64).eps
 
 # Example rotations """
-eg_rots = []
 params = np.arange(-pi * 2, pi * 2.5, pi / 2)
-for x in params:
-    for y in params:
-        for z in params:
-            eg_rots.append((x, y, z))
+eg_rots = [(x, y, z) for x in params for y in params for z in params]
 
 
 def x_only(x):
@@ -123,7 +119,7 @@ def test_euler_mat_1():
     assert_array_equal(M, np.eye(3))
 
 
-@pytest.mark.parametrize('x, y, z', eg_rots)
+@pytest.mark.parametrize(('x', 'y', 'z'), eg_rots)
 def test_euler_mat_2(x, y, z):
     M1 = nea.euler2mat(z, y, x)
     M2 = sympy_euler(z, y, x)
@@ -176,7 +172,7 @@ def test_euler_instability():
     assert not np.allclose(M_e, M_e_back)
 
 
-@pytest.mark.parametrize('x, y, z', eg_rots)
+@pytest.mark.parametrize(('x', 'y', 'z'), eg_rots)
 def test_quats(x, y, z):
     M1 = nea.euler2mat(z, y, x)
     quatM = nq.mat2quat(M1)

nibabel/tests/test_filehandles.py

@@ -33,8 +33,7 @@ def test_multiload():
         tmpdir = mkdtemp()
         fname = pjoin(tmpdir, 'test.img')
         save(img, fname)
-        for i in range(N):
-            imgs.append(load(fname))
+        imgs.extend(load(fname) for _ in range(N))
     finally:
         del img, imgs
         shutil.rmtree(tmpdir)

nibabel/tests/test_files_interface.py

@@ -28,7 +28,7 @@ def test_files_spatialimages():
     ]
     for klass in klasses:
         file_map = klass.make_file_map()
-        for key, value in file_map.items():
+        for value in file_map.values():
             assert value.filename is None
             assert value.fileobj is None
             assert value.pos == 0
@@ -41,7 +41,7 @@ def test_files_spatialimages():
             img = klass(arr.astype(np.float32), aff)
         else:
             img = klass(arr, aff)
-        for key, value in img.file_map.items():
+        for value in img.file_map.values():
             assert value.filename is None
             assert value.fileobj is None
             assert value.pos == 0

nibabel/tests/test_init.py

@@ -13,7 +13,7 @@
 
 
 @pytest.mark.parametrize(
-    'verbose, v_args', [(-2, ['-qq']), (-1, ['-q']), (0, []), (1, ['-v']), (2, ['-vv'])]
+    ('verbose', 'v_args'), [(-2, ['-qq']), (-1, ['-q']), (0, []), (1, ['-v']), (2, ['-vv'])]
 )
 @pytest.mark.parametrize('doctests', (True, False))
 @pytest.mark.parametrize('coverage', (True, False))

nibabel/tests/test_nifti1.py

@@ -820,7 +820,7 @@ def _qform_rt(self, img):
         hdr['qform_code'] = 3
         hdr['sform_code'] = 4
         # Save / reload using bytes IO objects
-        for key, value in img.file_map.items():
+        for value in img.file_map.values():
             value.fileobj = BytesIO()
         img.to_file_map()
         return img.from_file_map(img.file_map)
@@ -1239,7 +1239,7 @@ def test_extension_content_access():
     assert ext.text == '123'
 
     # Test that encoding errors are caught
-    ascii_ext = Nifti1Extension('comment', 'hôpital'.encode('utf-8'))
+    ascii_ext = Nifti1Extension('comment', 'hôpital'.encode())
     ascii_ext.encoding = 'ascii'
     with pytest.raises(UnicodeDecodeError):
         ascii_ext.text

nibabel/tests/test_pkg_info.py

@@ -37,7 +37,7 @@ def test_cmp_pkg_version_0():
 
 
 @pytest.mark.parametrize(
-    'test_ver, pkg_ver, exp_out',
+    ('test_ver', 'pkg_ver', 'exp_out'),
     [
         ('1.0', '1.0', 0),
         ('1.0.0', '1.0', 0),
@@ -54,8 +54,6 @@ def test_cmp_pkg_version_0():
         ('1.2.1rc1', '1.2.1', -1),
         ('1.2.1rc1', '1.2.1rc', 1),
         ('1.2.1rc', '1.2.1rc1', -1),
-        ('1.2.1rc1', '1.2.1rc', 1),
-        ('1.2.1rc', '1.2.1rc1', -1),
         ('1.2.1b', '1.2.1a', 1),
         ('1.2.1a', '1.2.1b', -1),
         ('1.2.0+1', '1.2', 1),