[MAINT] apply pre-commit autofixes

nibabel/_typing.py

@@ -1,11 +1,7 @@
 """Helpers for typing compatibility across Python versions"""
 
 import sys
-
-if sys.version_info < (3, 10):
-    from typing_extensions import ParamSpec
-else:
-    from typing import ParamSpec
+from typing import ParamSpec
 
 if sys.version_info < (3, 11):
     from typing_extensions import Self

nibabel/cifti2/cifti2_axes.py

@@ -910,7 +910,7 @@ def to_mapping(self, dim):
             mim.volume = cifti2.Cifti2Volume(self.volume_shape, affine)
         for name, nvertex in self.nvertices.items():
             mim.append(cifti2.Cifti2Surface(name, nvertex))
-        for name, voxels, vertices in zip(self.name, self.voxels, self.vertices):
+        for name, voxels, vertices in zip(self.name, self.voxels, self.vertices, strict=False):
             cifti_voxels = cifti2.Cifti2VoxelIndicesIJK(voxels)
             element = cifti2.Cifti2Parcel(name, cifti_voxels)
             for name_vertex, idx_vertices in vertices.items():
@@ -963,7 +963,10 @@ def __eq__(self, other):
             or len(self) != len(other)
             or not np.array_equal(self.name, other.name)
             or self.nvertices != other.nvertices
-            or any(not np.array_equal(vox1, vox2) for vox1, vox2 in zip(self.voxels, other.voxels))
+            or any(
+                not np.array_equal(vox1, vox2)
+                for vox1, vox2 in zip(self.voxels, other.voxels, strict=False)
+            )
         ):
             return False
         if self.affine is not None:
@@ -975,7 +978,7 @@ def __eq__(self, other):
                 return False
         elif other.affine is not None:
             return False
-        for vert1, vert2 in zip(self.vertices, other.vertices):
+        for vert1, vert2 in zip(self.vertices, other.vertices, strict=False):
             if len(vert1) != len(vert2):
                 return False
             for name in vert1.keys():
@@ -1130,7 +1133,7 @@ def to_mapping(self, dim):
         :class:`.cifti2.Cifti2MatrixIndicesMap`
         """
         mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_SCALARS')
-        for name, meta in zip(self.name, self.meta):
+        for name, meta in zip(self.name, self.meta, strict=False):
             named_map = cifti2.Cifti2NamedMap(name, cifti2.Cifti2MetaData(meta))
             mim.append(named_map)
         return mim
@@ -1268,7 +1271,7 @@ def to_mapping(self, dim):
         :class:`.cifti2.Cifti2MatrixIndicesMap`
         """
         mim = cifti2.Cifti2MatrixIndicesMap([dim], 'CIFTI_INDEX_TYPE_LABELS')
-        for name, label, meta in zip(self.name, self.label, self.meta):
+        for name, label, meta in zip(self.name, self.label, self.meta, strict=False):
             label_table = cifti2.Cifti2LabelTable()
             for key, value in label.items():
                 label_table[key] = (value[0],) + tuple(value[1])

nibabel/cifti2/tests/test_axes.py

@@ -131,6 +131,7 @@ def test_brain_models():
         bml,
         ['ThalamusRight', 'Other', 'cortex_left', 'Other'],
         (False, False, True, True),
+        strict=False,
     ):
         assert np.all(bm.surface_mask == ~bm.volume_mask)
         structures = list(bm.iter_structures())
@@ -148,7 +149,7 @@ def test_brain_models():
     assert len(bmt) == 10
     structures = list(bmt.iter_structures())
     assert len(structures) == 3
-    for bm, (name, _, bm_split) in zip(bml[:3], structures):
+    for bm, (name, _, bm_split) in zip(bml[:3], structures, strict=False):
         assert bm == bm_split
         assert (bm_split.name == name).all()
         assert bm == bmt[bmt.name == bm.name[0]]
@@ -725,7 +726,7 @@ def test_common_interface():
     """
     Tests the common interface for all custom created CIFTI-2 axes
     """
-    for axis1, axis2 in zip(get_axes(), get_axes()):
+    for axis1, axis2 in zip(get_axes(), get_axes(), strict=False):
         assert axis1 == axis2
         concatenated = axis1 + axis2
         assert axis1 != concatenated

nibabel/cifti2/tests/test_cifti2io_axes.py

@@ -69,7 +69,7 @@ def check_hcp_grayordinates(brain_model):
     assert len(structures) == len(hcp_labels)
     idx_start = 0
     for idx, (name, _, bm), label, nel in zip(
-        range(len(structures)), structures, hcp_labels, hcp_n_elements
+        range(len(structures)), structures, hcp_labels, hcp_n_elements, strict=False
     ):
         if idx < 2:
             assert name in bm.nvertices.keys()

nibabel/cifti2/tests/test_cifti2io_header.py

@@ -86,11 +86,11 @@ def test_readwritedata():
             img2 = ci.load('test.nii')
             assert len(img.header.matrix) == len(img2.header.matrix)
             # Order should be preserved in load/save
-            for mim1, mim2 in zip(img.header.matrix, img2.header.matrix):
+            for mim1, mim2 in zip(img.header.matrix, img2.header.matrix, strict=False):
                 named_maps1 = [m_ for m_ in mim1 if isinstance(m_, ci.Cifti2NamedMap)]
                 named_maps2 = [m_ for m_ in mim2 if isinstance(m_, ci.Cifti2NamedMap)]
                 assert len(named_maps1) == len(named_maps2)
-                for map1, map2 in zip(named_maps1, named_maps2):
+                for map1, map2 in zip(named_maps1, named_maps2, strict=False):
                     assert map1.map_name == map2.map_name
                     if map1.label_table is None:
                         assert map2.label_table is None
@@ -109,11 +109,11 @@ def test_nibabel_readwritedata():
             img2 = nib.load('test.nii')
             assert len(img.header.matrix) == len(img2.header.matrix)
             # Order should be preserved in load/save
-            for mim1, mim2 in zip(img.header.matrix, img2.header.matrix):
+            for mim1, mim2 in zip(img.header.matrix, img2.header.matrix, strict=False):
                 named_maps1 = [m_ for m_ in mim1 if isinstance(m_, ci.Cifti2NamedMap)]
                 named_maps2 = [m_ for m_ in mim2 if isinstance(m_, ci.Cifti2NamedMap)]
                 assert len(named_maps1) == len(named_maps2)
-                for map1, map2 in zip(named_maps1, named_maps2):
+                for map1, map2 in zip(named_maps1, named_maps2, strict=False):
                     assert map1.map_name == map2.map_name
                     if map1.label_table is None:
                         assert map2.label_table is None
@@ -228,7 +228,7 @@ def test_read_geometry():
         ('CIFTI_STRUCTURE_THALAMUS_RIGHT', 1248, [32, 47, 34], [38, 55, 46]),
     ]
     current_index = 0
-    for from_file, expected in zip(geometry_mapping.brain_models, expected_geometry):
+    for from_file, expected in zip(geometry_mapping.brain_models, expected_geometry, strict=False):
         assert from_file.model_type in ('CIFTI_MODEL_TYPE_SURFACE', 'CIFTI_MODEL_TYPE_VOXELS')
         assert from_file.brain_structure == expected[0]
         assert from_file.index_offset == current_index
@@ -328,11 +328,13 @@ def test_read_parcels():
     assert img.shape[1] == len(expected_parcels)
     assert len(list(parcel_mapping.parcels)) == len(expected_parcels)
 
-    for (name, expected_surfaces), parcel in zip(expected_parcels, parcel_mapping.parcels):
+    for (name, expected_surfaces), parcel in zip(
+        expected_parcels, parcel_mapping.parcels, strict=False
+    ):
         assert parcel.name == name
         assert len(parcel.vertices) == 2
         for vertices, orientation, (length, first_element, last_element) in zip(
-            parcel.vertices, ('LEFT', 'RIGHT'), expected_surfaces
+            parcel.vertices, ('LEFT', 'RIGHT'), expected_surfaces, strict=False
         ):
             assert len(vertices) == length
             assert vertices[0] == first_element
@@ -350,7 +352,7 @@ def test_read_scalar():
     assert len(list(scalar_mapping.named_maps)) == len(expected_names)
 
     expected_meta = [('PaletteColorMapping', '<PaletteColorMapping Version="1">\n   <ScaleMo')]
-    for scalar, name in zip(scalar_mapping.named_maps, expected_names):
+    for scalar, name in zip(scalar_mapping.named_maps, expected_names, strict=False):
         assert scalar.map_name == name
 
         assert len(scalar.metadata) == len(expected_meta)
@@ -402,7 +404,7 @@ def test_read_labels():
         95: ('13b_OFP03', (1.0, 1.0, 0.0, 1.0)),
     }
 
-    for named_map, name in zip(label_mapping.named_maps, expected_names):
+    for named_map, name in zip(label_mapping.named_maps, expected_names, strict=False):
         assert named_map.map_name == name
         assert len(named_map.metadata) == 0
         assert len(named_map.label_table) == 96

nibabel/cifti2/tests/test_new_cifti2.py

@@ -180,7 +180,7 @@ def create_parcel_map(applies_to_matrix_dimension):
 def check_parcel_map(mapping):
     assert mapping.indices_map_to_data_type == 'CIFTI_INDEX_TYPE_PARCELS'
     assert len(list(mapping.parcels)) == len(parcels)
-    for (name, elements), parcel in zip(parcels, mapping.parcels):
+    for (name, elements), parcel in zip(parcels, mapping.parcels, strict=False):
         assert parcel.name == name
         idx_surface = 0
         for element in elements:
@@ -192,7 +192,7 @@ def check_parcel_map(mapping):
             else:
                 assert parcel.voxel_indices_ijk._indices == element
 
-    for surface, orientation in zip(mapping.surfaces, ('LEFT', 'RIGHT')):
+    for surface, orientation in zip(mapping.surfaces, ('LEFT', 'RIGHT'), strict=False):
         assert surface.brain_structure == f'CIFTI_STRUCTURE_CORTEX_{orientation}'
         assert surface.surface_number_of_vertices == number_of_vertices
 
@@ -214,7 +214,7 @@ def check_scalar_map(mapping):
     assert mapping.indices_map_to_data_type == 'CIFTI_INDEX_TYPE_SCALARS'
     assert len(list(mapping.named_maps)) == 2
 
-    for expected, named_map in zip(scalars, mapping.named_maps):
+    for expected, named_map in zip(scalars, mapping.named_maps, strict=False):
         assert named_map.map_name == expected[0]
         if len(expected[1]) == 0:
             assert named_map.metadata is None
@@ -258,7 +258,7 @@ def check_label_map(mapping):
     assert mapping.indices_map_to_data_type == 'CIFTI_INDEX_TYPE_LABELS'
     assert len(list(mapping.named_maps)) == 2
 
-    for expected, named_map in zip(scalars, mapping.named_maps):
+    for expected, named_map in zip(scalars, mapping.named_maps, strict=False):
         assert named_map.map_name == expected[0]
         if len(expected[1]) == 0:
             assert named_map.metadata is None

nibabel/cmdline/ls.py

@@ -175,7 +175,7 @@ def proc_file(f, opts):
                     counts = _err(f'{len(items)} uniques. Use --all-counts')
                 else:
                     freq = np.bincount(inv)
-                    counts = ' '.join(f'{i:g}:{f}' for i, f in zip(items, freq))
+                    counts = ' '.join(f'{i:g}:{f}' for i, f in zip(items, freq, strict=False))
                 row += ['@l' + counts]
         except OSError as e:
             verbose(2, f'Failed to obtain stats/counts -- {e}')

nibabel/cmdline/parrec2nii.py

@@ -383,7 +383,7 @@ def proc_file(infile, opts):
             with open(basefilename + '.ordering.csv', 'w', newline='') as csvfile:
                 csvwriter = csv.writer(csvfile, delimiter=',')
                 csvwriter.writerow(vol_keys)
-                for vals in zip(*[labels[k] for k in vol_keys]):
+                for vals in zip(*[labels[k] for k in vol_keys], strict=False):
                     csvwriter.writerow(vals)
 
     # write out dwell time if requested

nibabel/cmdline/utils.py

@@ -54,12 +54,14 @@ def table2string(table, out=None):
 
     # eat whole entry while computing width for @w (for wide)
     markup_strip = re.compile(r'^@([lrc]|w.*)')
-    col_width = [max(len(markup_strip.sub('', x)) for x in column) for column in zip(*table)]
+    col_width = [
+        max(len(markup_strip.sub('', x)) for x in column) for column in zip(*table, strict=False)
+    ]
     trans = str.maketrans('lrcw', '<>^^')
     lines = []
     for row in table:
         line = []
-        for item, width in zip(row, col_width):
+        for item, width in zip(row, col_width, strict=False):
             item = str(item)
             if item.startswith('@'):
                 align = item[1]

nibabel/dft.py

@@ -75,7 +75,7 @@ def __getattribute__(self, name):
                 c.execute('SELECT * FROM series WHERE study = ?', (self.uid,))
                 cols = [el[0] for el in c.description]
                 for row in c:
-                    d = dict(zip(cols, row))
+                    d = dict(zip(cols, row, strict=False))
                     val.append(_Series(d))
             self.series = val
         return val
@@ -110,7 +110,7 @@ def __getattribute__(self, name):
                 c.execute(query, (self.uid,))
                 cols = [el[0] for el in c.description]
                 for row in c:
-                    d = dict(zip(cols, row))
+                    d = dict(zip(cols, row, strict=False))
                     val.append(_StorageInstance(d))
             self.storage_instances = val
         return val
@@ -289,7 +289,7 @@ def get_studies(base_dir=None, followlinks=False):
             studies = []
             cols = [el[0] for el in c.description]
             for row in c:
-                d = dict(zip(cols, row))
+                d = dict(zip(cols, row, strict=False))
                 studies.append(_Study(d))
         return studies
     query = """SELECT study
@@ -309,7 +309,7 @@ def get_studies(base_dir=None, followlinks=False):
         for uid in study_uids:
             c.execute('SELECT * FROM study WHERE uid = ?', (uid,))
             cols = [el[0] for el in c.description]
-            d = dict(zip(cols, c.fetchone()))
+            d = dict(zip(cols, c.fetchone(), strict=False))
             studies.append(_Study(d))
     return studies
 

nibabel/freesurfer/io.py

@@ -559,7 +559,7 @@ def write_string(s):
         # num_entries
         write(ctab.shape[0])
 
-        for ind, (clu, name) in enumerate(zip(ctab, names)):
+        for ind, (clu, name) in enumerate(zip(ctab, names, strict=False)):
             write(ind)
             write_string(name)
             for val in clu[:-1]:

nibabel/gifti/tests/test_gifti.py

@@ -375,7 +375,7 @@ def test_metadata_list_interface():
 
 def test_gifti_label_rgba():
     rgba = rng.random(4)
-    kwargs = dict(zip(['red', 'green', 'blue', 'alpha'], rgba))
+    kwargs = dict(zip(['red', 'green', 'blue', 'alpha'], rgba, strict=False))
 
     gl1 = GiftiLabel(**kwargs)
     assert_array_equal(rgba, gl1.rgba)

nibabel/nicom/dicomwrappers.py

@@ -691,7 +691,7 @@ def __init__(self, dcm_data, frame_filters=None):
             frame_slc_pos = [np.inner(ipp, self.slice_normal) for ipp in frame_ipps]
             rnd_slc_pos = np.round(frame_slc_pos, 4)
             uniq_slc_pos = np.unique(rnd_slc_pos)
-            pos_ord_map = dict(zip(uniq_slc_pos, np.argsort(uniq_slc_pos)))
+            pos_ord_map = dict(zip(uniq_slc_pos, np.argsort(uniq_slc_pos), strict=False))
             self._frame_slc_ord = [pos_ord_map[pos] for pos in rnd_slc_pos]
             if len(self._frame_slc_ord) > 1:
                 self._slice_spacing = (

nibabel/nicom/tests/test_dicomwrappers.py

@@ -386,7 +386,7 @@ def fake_frames(seq_name, field_name, value_seq, frame_seq=None):
     """
     if frame_seq is None:
         frame_seq = [pydicom.Dataset() for _ in range(len(value_seq))]
-    for value, fake_frame in zip(value_seq, frame_seq):
+    for value, fake_frame in zip(value_seq, frame_seq, strict=False):
         if value is None:
             continue
         if hasattr(fake_frame, seq_name):
@@ -496,7 +496,7 @@ def __init__(self, div, sid, ipp, iop):
     # create the PerFrameFunctionalGroupsSequence
     frames = [
         PerFrmFuncGrpSeqElem(div, sid, ipp, iop)
-        for div, sid, ipp, iop in zip(div_seq, sid_seq, ipp_seq, iop_seq)
+        for div, sid, ipp, iop in zip(div_seq, sid_seq, ipp_seq, iop_seq, strict=False)
     ]
     return {
         'NumberOfFrames': num_of_frames,

nibabel/openers.py

@@ -88,7 +88,7 @@ def __init__(self, fileish: str | io.IOBase, *args, **kwargs):
             return
         opener, arg_names = self._get_opener_argnames(fileish)
         # Get full arguments to check for optional parameters
-        full_kwargs = {**kwargs, **dict(zip(arg_names, args))}
+        full_kwargs = {**kwargs, **dict(zip(arg_names, args, strict=False))}
         # Set default mode
         if 'mode' not in full_kwargs:
             mode = 'rb'

nibabel/orientations.py

@@ -279,7 +279,7 @@ def ornt2axcodes(ornt, labels=None):
     ('F', 'L', 'U')
     """
     if labels is None:
-        labels = list(zip('LPI', 'RAS'))
+        labels = list(zip('LPI', 'RAS', strict=False))
     axcodes = []
     for axno, direction in np.asarray(ornt):
         if np.isnan(axno):
@@ -324,7 +324,7 @@ def axcodes2ornt(axcodes, labels=None):
            [ 0., -1.],
            [ 2.,  1.]])
     """
-    labels = list(zip('LPI', 'RAS')) if labels is None else labels
+    labels = list(zip('LPI', 'RAS', strict=False)) if labels is None else labels
     allowed_labels = sum(map(list, labels), [None])
     if len(allowed_labels) != len(set(allowed_labels)):
         raise ValueError(f'Duplicate labels in {allowed_labels}')

nibabel/spaces.py

@@ -83,7 +83,7 @@ def vox2out_vox(mapped_voxels, voxel_sizes=None):
         if not np.all(np.array(voxel_sizes) > 0):
             raise ValueError('voxel sizes should all be positive')
         out_vox[:n_axes] = voxel_sizes
-    in_mn_mx = zip([0, 0, 0], np.array(in_shape) - 1)
+    in_mn_mx = zip([0, 0, 0], np.array(in_shape) - 1, strict=False)
     in_corners = list(product(*in_mn_mx))
     out_corners = apply_affine(in_affine, in_corners)
     out_mn = out_corners.min(axis=0)