chore: Update ruff, address complaints

.git-blame-ignore-revs

@@ -1,3 +1,7 @@
+# Sun Jan 12 12:22:13 2025 -0500 - [email protected] - sty: ruff format [git-blame-ignore-rev]
+40e41208a0f04063b3c4e373a65da1a2a6a275b5
+# Sun Jan 12 11:51:49 2025 -0500 - [email protected] - STY: ruff format [git-blame-ignore-rev]
+7e5d584910c67851dcfcd074ff307122689b61f5
 # Sun Jan 1 12:38:02 2023 -0500 - [email protected] - STY: Run pre-commit config on all files
 d14c1cf282a9c3b19189f490f10c35f5739e24d1
 # Thu Dec 29 22:53:17 2022 -0500 - [email protected] - STY: Reduce array().astype() and similar constructs

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 exclude: ".*/data/.*"
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,7 +13,7 @@ repos:
       - id: check-merge-conflict
       - id: check-vcs-permalinks
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.4
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [ --fix ]
@@ -24,7 +24,7 @@ repos:
         args: [ --select, ISC001, --fix ]
         exclude: = ["doc", "tools"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.14.1
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

bin/parrec2nii

@@ -1,6 +1,5 @@
 #!python
-"""PAR/REC to NIfTI converter
-"""
+"""PAR/REC to NIfTI converter"""
 
 from nibabel.cmdline.parrec2nii import main
 

nibabel/benchmarks/bench_array_to_file.py

@@ -29,24 +29,25 @@ def bench_array_to_file():
     sys.stdout.flush()
     print_git_title('\nArray to file')
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save float64 to float32', mtime))
+    fmt = '{:30s} {:6.2f}'.format
+    print(fmt('Save float64 to float32', mtime))
     mtime = measure('array_to_file(arr, BytesIO(), np.int16)', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16', mtime))
+    print(fmt('Save float64 to int16', mtime))
     # Set a lot of NaNs to check timing
     arr[:, :, :, 1] = np.nan
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save float64 to float32, NaNs', mtime))
+    print(fmt('Save float64 to float32, NaNs', mtime))
     mtime = measure('array_to_file(arr, BytesIO(), np.int16)', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16, NaNs', mtime))
+    print(fmt('Save float64 to int16, NaNs', mtime))
     # Set a lot of infs to check timing
     arr[:, :, :, 1] = np.inf
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save float64 to float32, infs', mtime))
+    print(fmt('Save float64 to float32, infs', mtime))
     mtime = measure('array_to_file(arr, BytesIO(), np.int16)', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16, infs', mtime))
+    print(fmt('Save float64 to int16, infs', mtime))
     # Int16 input, float output
     arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
     mtime = measure('array_to_file(arr, BytesIO(), np.float32)', repeat)
-    print('%30s %6.2f' % ('Save Int16 to float32', mtime))
+    print(fmt('Save Int16 to float32', mtime))
     sys.stdout.flush()

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -96,7 +96,7 @@ def fmt_sliceobj(sliceobj):
                 slcstr.append(s)
             else:
                 slcstr.append(str(int(s * SHAPE[i])))
-        return f"[{', '.join(slcstr)}]"
+        return f'[{", ".join(slcstr)}]'
 
     with InTemporaryDirectory():
         print(f'Generating test data... ({int(round(np.prod(SHAPE) * 4 / 1048576.0))} MB)')

nibabel/benchmarks/bench_finite_range.py

@@ -28,16 +28,17 @@ def bench_finite_range():
     sys.stdout.flush()
     print_git_title('\nFinite range')
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('float64 all finite', mtime))
+    fmt = '{:30s} {:6.2f}'.format
+    print(fmt('float64 all finite', mtime))
     arr[:, :, :, 1] = np.nan
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('float64 many NaNs', mtime))
+    print(fmt('float64 many NaNs', mtime))
     arr[:, :, :, 1] = np.inf
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('float64 many infs', mtime))
+    print(fmt('float64 many infs', mtime))
     # Int16 input, float output
     arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
     mtime = measure('finite_range(arr)', repeat)
-    print('%30s %6.2f' % ('int16', mtime))
+    print(fmt('int16', mtime))
     sys.stdout.flush()

nibabel/benchmarks/bench_load_save.py

@@ -34,20 +34,21 @@ def bench_load_save():
     print_git_title('Image load save')
     hdr.set_data_dtype(np.float32)
     mtime = measure('sio.truncate(0); img.to_file_map()', repeat)
-    print('%30s %6.2f' % ('Save float64 to float32', mtime))
+    fmt = '{:30s} {:6.2f}'.format
+    print(fmt('Save float64 to float32', mtime))
     mtime = measure('img.from_file_map(img.file_map)', repeat)
-    print('%30s %6.2f' % ('Load from float32', mtime))
+    print(fmt('Load from float32', mtime))
     hdr.set_data_dtype(np.int16)
     mtime = measure('sio.truncate(0); img.to_file_map()', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16', mtime))
+    print(fmt('Save float64 to int16', mtime))
     mtime = measure('img.from_file_map(img.file_map)', repeat)
-    print('%30s %6.2f' % ('Load from int16', mtime))
+    print(fmt('Load from int16', mtime))
     # Set a lot of NaNs to check timing
     arr[:, :, :20] = np.nan
     mtime = measure('sio.truncate(0); img.to_file_map()', repeat)
-    print('%30s %6.2f' % ('Save float64 to int16, NaNs', mtime))
+    print(fmt('Save float64 to int16, NaNs', mtime))
     mtime = measure('img.from_file_map(img.file_map)', repeat)
-    print('%30s %6.2f' % ('Load from int16, NaNs', mtime))
+    print(fmt('Load from int16, NaNs', mtime))
     # Int16 input, float output
     arr = np.random.random_integers(low=-1000, high=1000, size=img_shape)
     arr = arr.astype(np.int16)
@@ -57,5 +58,5 @@ def bench_load_save():
     hdr = img.header
     hdr.set_data_dtype(np.float32)
     mtime = measure('sio.truncate(0); img.to_file_map()', repeat)
-    print('%30s %6.2f' % ('Save Int16 to float32', mtime))
+    print(fmt('Save Int16 to float32', mtime))
     sys.stdout.flush()

nibabel/benchmarks/butils.py

@@ -5,6 +5,6 @@
 
 def print_git_title(title):
     """Prints title string with git hash if possible, and underline"""
-    title = f"{title} for git revision {get_info()['commit_hash']}"
+    title = f'{title} for git revision {get_info()["commit_hash"]}'
     print(title)
     print('-' * len(title))

nibabel/brikhead.py

@@ -555,7 +555,7 @@ def filespec_to_file_map(klass, filespec):
             fname = fholder.filename
             if key == 'header' and not os.path.exists(fname):
                 for ext in klass._compressed_suffixes:
-                    fname = fname[: -len(ext)] if fname.endswith(ext) else fname
+                    fname = fname.removesuffix(ext)
             elif key == 'image' and not os.path.exists(fname):
                 for ext in klass._compressed_suffixes:
                     if os.path.exists(fname + ext):

nibabel/cifti2/cifti2.py

@@ -294,8 +294,7 @@ def __setitem__(self, key, value):
             self._labels[key] = Cifti2Label(*([key] + list(value)))
         except ValueError:
             raise ValueError(
-                'Key should be int, value should be sequence '
-                'of str and 4 floats between 0 and 1'
+                'Key should be int, value should be sequence of str and 4 floats between 0 and 1'
             )
 
     def __delitem__(self, key):

nibabel/cifti2/cifti2_axes.py

@@ -634,8 +634,10 @@ def __eq__(self, other):
         return (
             (
                 self.affine is None
-                or np.allclose(self.affine, other.affine)
-                and self.volume_shape == other.volume_shape
+                or (
+                    np.allclose(self.affine, other.affine)
+                    and self.volume_shape == other.volume_shape
+                )
             )
             and self.nvertices == other.nvertices
             and np.array_equal(self.name, other.name)

nibabel/cifti2/parse_cifti2.py

@@ -384,8 +384,7 @@ def StartElementHandler(self, name, attrs):
             model = self.struct_state[-1]
             if not isinstance(model, Cifti2BrainModel):
                 raise Cifti2HeaderError(
-                    'VertexIndices element can only be a child '
-                    'of the CIFTI-2 BrainModel element'
+                    'VertexIndices element can only be a child of the CIFTI-2 BrainModel element'
                 )
             self.fsm_state.append('VertexIndices')
             model.vertex_indices = index

nibabel/cmdline/dicomfs.py

@@ -231,7 +231,7 @@
 
     if opts.verbose:
         logger.addHandler(logging.StreamHandler(sys.stdout))
-        logger.setLevel(opts.verbose > 1 and logging.DEBUG or logging.INFO)
+        logger.setLevel(logging.DEBUG if opts.verbose > 1 else logging.INFO)
 
     if len(files) != 2:
         sys.stderr.write(f'Please provide two arguments:\n{parser.usage}\n')

nibabel/cmdline/ls.py

@@ -103,8 +103,8 @@ def proc_file(f, opts):
 
     row += [
         str(safe_get(h, 'data_dtype')),
-        f"@l[{ap(safe_get(h, 'data_shape'), '%3g')}]",
-        f"@l{ap(safe_get(h, 'zooms'), '%.2f', 'x')}",
+        f'@l[{ap(safe_get(h, "data_shape"), "%3g")}]',
+        f'@l{ap(safe_get(h, "zooms"), "%.2f", "x")}',
     ]
     # Slope
     if (

nibabel/cmdline/tests/test_conform.py

@@ -47,8 +47,8 @@ def test_nondefault(tmpdir):
     voxel_size = (1, 2, 4)
     orientation = 'LAS'
     args = (
-        f"{infile} {outfile} --out-shape {' '.join(map(str, out_shape))} "
-        f"--voxel-size {' '.join(map(str, voxel_size))} --orientation {orientation}"
+        f'{infile} {outfile} --out-shape {" ".join(map(str, out_shape))} '
+        f'--voxel-size {" ".join(map(str, voxel_size))} --orientation {orientation}'
     )
     main(args.split())
     assert outfile.isfile()

nibabel/cmdline/utils.py

@@ -55,7 +55,7 @@ def table2string(table, out=None):
     # eat whole entry while computing width for @w (for wide)
     markup_strip = re.compile('^@([lrc]|w.*)')
     col_width = [max(len(markup_strip.sub('', x)) for x in column) for column in zip(*table)]
-    trans = str.maketrans("lrcw", "<>^^")
+    trans = str.maketrans('lrcw', '<>^^')
     lines = []
     for row in table:
         line = []

nibabel/data.py

@@ -290,7 +290,7 @@ def make_datasource(pkg_def, **kwargs):
         pkg_hint = pkg_def.get('install hint', DEFAULT_INSTALL_HINT)
         msg = f'{e}; Is it possible you have not installed a data package?'
         if 'name' in pkg_def:
-            msg += f"\n\nYou may need the package \"{pkg_def['name']}\""
+            msg += f'\n\nYou may need the package "{pkg_def["name"]}"'
         if pkg_hint is not None:
             msg += f'\n\n{pkg_hint}'
         raise DataError(msg)

nibabel/deprecator.py

@@ -212,7 +212,7 @@ def __call__(
             messages.append('* deprecated from version: ' + since)
         if until:
             messages.append(
-                f"* {'Raises' if self.is_bad_version(until) else 'Will raise'} "
+                f'* {"Raises" if self.is_bad_version(until) else "Will raise"} '
                 f'{exception} as of version: {until}'
             )
         message = '\n'.join(messages)

nibabel/filename_parser.py

@@ -111,8 +111,7 @@ def types_filenames(
     template_fname = _stringify_path(template_fname)
     if not isinstance(template_fname, str):
         raise TypesFilenamesError('Need file name as input to set_filenames')
-    if template_fname.endswith('.'):
-        template_fname = template_fname[:-1]
+    template_fname = template_fname.removesuffix('.')
     filename, found_ext, ignored, guessed_name = parse_filename(
         template_fname, types_exts, trailing_suffixes, match_case
     )

nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -177,9 +177,9 @@ def assert_default_types(loaded):
             continue
         with suppress_warnings():
             loadedtype = type(getattr(loaded, attr))
-        assert (
-            loadedtype == defaulttype
-        ), f'Type mismatch for attribute: {attr} ({loadedtype} != {defaulttype})'
+        assert loadedtype == defaulttype, (
+            f'Type mismatch for attribute: {attr} ({loadedtype} != {defaulttype})'
+        )
 
 
 def test_default_types():

nibabel/nifti1.py

@@ -1804,7 +1804,7 @@ def set_slice_times(self, slice_times):
             raise HeaderDataError(f'slice ordering of {st_order} fits with no known scheme')
         if len(matching_labels) > 1:
             warnings.warn(
-                f"Multiple slice orders satisfy: {', '.join(matching_labels)}. "
+                f'Multiple slice orders satisfy: {", ".join(matching_labels)}. '
                 'Choosing the first one'
             )
         label = matching_labels[0]

nibabel/parrec.py

@@ -782,10 +782,10 @@ def as_analyze_map(self):
         # Here we set the parameters we can to simplify PAR/REC
         # to NIfTI conversion.
         descr = (
-            f"{self.general_info['exam_name']};"
-            f"{self.general_info['patient_name']};"
-            f"{self.general_info['exam_date'].replace(' ', '')};"
-            f"{self.general_info['protocol_name']}"
+            f'{self.general_info["exam_name"]};'
+            f'{self.general_info["patient_name"]};'
+            f'{self.general_info["exam_date"].replace(" ", "")};'
+            f'{self.general_info["protocol_name"]}'
         )[:80]
         is_fmri = self.general_info['max_dynamics'] > 1
         # PAR/REC uses msec, but in _calc_zooms we convert to sec

nibabel/pointset.py

@@ -178,7 +178,7 @@ def to_mask(self, shape=None) -> SpatialImage:
 class GridIndices:
     """Class for generating indices just-in-time"""
 
-    __slots__ = ('gridshape', 'dtype', 'shape')
+    __slots__ = ('dtype', 'gridshape', 'shape')
     ndim = 2
 
     def __init__(self, shape, dtype=None):

nibabel/rstutils.py

@@ -52,7 +52,7 @@ def rst_table(
     cross = format_chars.pop('cross', '+')
     title_heading = format_chars.pop('title_heading', '*')
     if len(format_chars) != 0:
-        raise ValueError(f"Unexpected ``format_char`` keys {', '.join(format_chars)}")
+        raise ValueError(f'Unexpected ``format_char`` keys {", ".join(format_chars)}')
     down_joiner = ' ' + down + ' '
     down_starter = down + ' '
     down_ender = ' ' + down

nibabel/streamlines/__init__.py

@@ -125,8 +125,7 @@ def save(tractogram, filename, **kwargs):
         tractogram_file = tractogram
         if tractogram_file_class is None or not isinstance(tractogram_file, tractogram_file_class):
             msg = (
-                'The extension you specified is unusual for the provided'
-                " 'TractogramFile' object."
+                "The extension you specified is unusual for the provided 'TractogramFile' object."
             )
             warnings.warn(msg, ExtensionWarning)
 

nibabel/streamlines/array_sequence.py

@@ -87,7 +87,7 @@ def fn_binary_op(self, value):
         '__xor__',
     ):
         _wrap(cls, op=op, inplace=False)
-        _wrap(cls, op=f"__i{op.strip('_')}__", inplace=True)
+        _wrap(cls, op=f'__i{op.strip("_")}__', inplace=True)
 
     for op in ('__eq__', '__ne__', '__lt__', '__le__', '__gt__', '__ge__'):
         _wrap(cls, op)

nibabel/streamlines/tests/test_array_sequence.py

@@ -397,7 +397,7 @@ def _test_binary(op, arrseq, scalars, seqs, inplace=False):
             if op in CMP_OPS:
                 continue
 
-            op = f"__i{op.strip('_')}__"
+            op = f'__i{op.strip("_")}__'
             _test_binary(op, seq, SCALARS, ARRSEQS, inplace=True)
 
             if op == '__itruediv__':

nibabel/streamlines/trk.py

@@ -579,7 +579,7 @@ def _read_header(fileobj):
                 header_rec = header_rec.view(header_rec.dtype.newbyteorder())
                 if header_rec['hdr_size'] != TrkFile.HEADER_SIZE:
                     msg = (
-                        f"Invalid hdr_size: {header_rec['hdr_size']} "
+                        f'Invalid hdr_size: {header_rec["hdr_size"]} '
                         f'instead of {TrkFile.HEADER_SIZE}'
                     )
                     raise HeaderError(msg)

nibabel/tests/data/check_parrec_reslice.py

@@ -60,7 +60,7 @@ def gmean_norm(data):
     normal_data = normal_img.get_fdata()
     normal_normed = gmean_norm(normal_data)
 
-    print(f'RMS of standard image {normal_fname:<44}: {np.sqrt(np.sum(normal_normed ** 2))}')
+    print(f'RMS of standard image {normal_fname:<44}: {np.sqrt(np.sum(normal_normed**2))}')
 
     for parfile in glob.glob('*.PAR'):
         if parfile == normal_fname:
@@ -69,4 +69,4 @@ def gmean_norm(data):
         fixed_img = resample_img2img(normal_img, funny_img)
         fixed_data = fixed_img.get_fdata()
         difference_data = normal_normed - gmean_norm(fixed_data)
-        print(f'RMS resliced {parfile:<52} : {np.sqrt(np.sum(difference_data ** 2))}')
+        print(f'RMS resliced {parfile:<52} : {np.sqrt(np.sum(difference_data**2))}')

nibabel/tests/test_funcs.py

@@ -101,9 +101,9 @@ def test_concat():
                             except ValueError as ve:
                                 assert expect_error, str(ve)
                             else:
-                                assert (
-                                    not expect_error
-                                ), 'Expected a concatenation error, but got none.'
+                                assert not expect_error, (
+                                    'Expected a concatenation error, but got none.'
+                                )
                                 assert_array_equal(all_imgs.get_fdata(), all_data)
                                 assert_array_equal(all_imgs.affine, affine)
 
@@ -117,9 +117,9 @@ def test_concat():
                             except ValueError as ve:
                                 assert expect_error, str(ve)
                             else:
-                                assert (
-                                    not expect_error
-                                ), 'Expected a concatenation error, but got none.'
+                                assert not expect_error, (
+                                    'Expected a concatenation error, but got none.'
+                                )
                                 assert_array_equal(all_imgs.get_fdata(), all_data)
                                 assert_array_equal(all_imgs.affine, affine)