Merge pull request #1406 from DimitriPapadopoulos/ruff_0.9.1

chore: Updates after pre-commit autoupdate

.pre-commit-config.yaml

@@ -20,9 +20,6 @@ repos:
         exclude: = ["doc", "tools"]
       - id: ruff-format
         exclude: = ["doc", "tools"]
-      - id: ruff
-        args: [ --select, ISC001, --fix ]
-        exclude: = ["doc", "tools"]
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.14.1
     hooks:

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -99,7 +99,7 @@ def fmt_sliceobj(sliceobj):
         return f'[{", ".join(slcstr)}]'
 
     with InTemporaryDirectory():
-        print(f'Generating test data... ({int(round(np.prod(SHAPE) * 4 / 1048576.0))} MB)')
+        print(f'Generating test data... ({round(np.prod(SHAPE) * 4 / 1048576.0)} MB)')
 
         data = np.array(np.random.random(SHAPE), dtype=np.float32)
 

nibabel/cmdline/diff.py

@@ -309,11 +309,11 @@ def display_diff(files, diff):
                 item_str = str(item)
             # Value might start/end with some invisible spacing characters so we
             # would "condition" it on both ends a bit
-            item_str = re.sub('^[ \t]+', '<', item_str)
-            item_str = re.sub('[ \t]+$', '>', item_str)
+            item_str = re.sub(r'^[ \t]+', '<', item_str)
+            item_str = re.sub(r'[ \t]+$', '>', item_str)
             # and also replace some other invisible symbols with a question
             # mark
-            item_str = re.sub('[\x00]', '?', item_str)
+            item_str = re.sub(r'[\x00]', '?', item_str)
             output += value_width.format(item_str)
 
         output += '\n'

nibabel/cmdline/utils.py

@@ -53,7 +53,7 @@ def table2string(table, out=None):
         table[i] += [''] * (nelements_max - len(table_))
 
     # eat whole entry while computing width for @w (for wide)
-    markup_strip = re.compile('^@([lrc]|w.*)')
+    markup_strip = re.compile(r'^@([lrc]|w.*)')
     col_width = [max(len(markup_strip.sub('', x)) for x in column) for column in zip(*table)]
     trans = str.maketrans('lrcw', '<>^^')
     lines = []

nibabel/nicom/dicomwrappers.py

@@ -153,11 +153,11 @@ def vendor(self):
         # Look at manufacturer tag first
         mfgr = self.get('Manufacturer')
         if mfgr:
-            if re.search('Siemens', mfgr, re.IGNORECASE):
+            if re.search(r'Siemens', mfgr, re.IGNORECASE):
                 return Vendor.SIEMENS
-            if re.search('Philips', mfgr, re.IGNORECASE):
+            if re.search(r'Philips', mfgr, re.IGNORECASE):
                 return Vendor.PHILIPS
-            if re.search('GE Medical', mfgr, re.IGNORECASE):
+            if re.search(r'GE Medical', mfgr, re.IGNORECASE):
                 return Vendor.GE
         # Next look at UID prefixes
         for uid_src in ('StudyInstanceUID', 'SeriesInstanceUID', 'SOPInstanceUID'):

nibabel/nicom/tests/test_utils.py

@@ -15,7 +15,7 @@ def test_find_private_section_real():
     # On real data first
     assert fps(DATA, 0x29, 'SIEMENS CSA HEADER') == 0x1000
     assert fps(DATA, 0x29, b'SIEMENS CSA HEADER') == 0x1000
-    assert fps(DATA, 0x29, re.compile('SIEMENS CSA HEADER')) == 0x1000
+    assert fps(DATA, 0x29, re.compile(r'SIEMENS CSA HEADER')) == 0x1000
     assert fps(DATA, 0x29, 'NOT A HEADER') is None
     assert fps(DATA, 0x29, 'SIEMENS MEDCOM HEADER2') == 0x1100
     assert fps(DATA_PHILIPS, 0x29, 'SIEMENS CSA HEADER') == None
@@ -55,7 +55,7 @@ def test_find_private_section_fake():
     ds.add_new((0x11, 0x15), 'LO', b'far section')
     assert fps(ds, 0x11, 'far section') == 0x1500
     # More than one match - find the first.
-    assert fps(ds, 0x11, re.compile('(another|third) section')) == 0x1100
+    assert fps(ds, 0x11, re.compile(r'(another|third) section')) == 0x1100
     # The signalling element number must be <= 0xFF
     ds = pydicom.dataset.Dataset({})
     ds.add_new((0x11, 0xFF), 'LO', b'some section')

nibabel/tests/test_analyze.py

@@ -497,7 +497,7 @@ def test_str(self):
         hdr = self.header_class()
         s1 = str(hdr)
         # check the datacode recoding
-        rexp = re.compile('^datatype +: float32', re.MULTILINE)
+        rexp = re.compile(r'^datatype +: float32', re.MULTILINE)
         assert rexp.search(s1) is not None
 
     def test_from_header(self):

nibabel/tests/test_fileslice.py

@@ -489,16 +489,16 @@ def test_optimize_read_slicers():
         (slice(None),),
     )
     # Check gap threshold with 3D
-    _depends0 = partial(threshold_heuristic, skip_thresh=10 * 4 - 1)
-    _depends1 = partial(threshold_heuristic, skip_thresh=10 * 4)
+    depends0 = partial(threshold_heuristic, skip_thresh=10 * 4 - 1)
+    depends1 = partial(threshold_heuristic, skip_thresh=10 * 4)
     assert optimize_read_slicers(
-        (slice(9), slice(None), slice(None)), (10, 6, 2), 4, _depends0
+        (slice(9), slice(None), slice(None)), (10, 6, 2), 4, depends0
     ) == ((slice(None), slice(None), slice(None)), (slice(0, 9, 1), slice(None), slice(None)))
     assert optimize_read_slicers(
-        (slice(None), slice(5), slice(None)), (10, 6, 2), 4, _depends0
+        (slice(None), slice(5), slice(None)), (10, 6, 2), 4, depends0
     ) == ((slice(None), slice(0, 5, 1), slice(None)), (slice(None), slice(None), slice(None)))
     assert optimize_read_slicers(
-        (slice(None), slice(5), slice(None)), (10, 6, 2), 4, _depends1
+        (slice(None), slice(5), slice(None)), (10, 6, 2), 4, depends1
     ) == ((slice(None), slice(None), slice(None)), (slice(None), slice(0, 5, 1), slice(None)))
     # Check longs as integer slices
     sn = slice(None)

nibabel/tests/test_loadsave.py

@@ -88,7 +88,7 @@ def test_load_bad_compressed_extension(tmp_path, extension):
         pytest.skip()
     file_path = tmp_path / f'img.nii{extension}'
     file_path.write_bytes(b'bad')
-    with pytest.raises(ImageFileError, match='.*is not a .* file'):
+    with pytest.raises(ImageFileError, match=r'.*is not a .* file'):
         load(file_path)
 
 
@@ -99,7 +99,7 @@ def test_load_good_extension_with_bad_data(tmp_path, extension):
     file_path = tmp_path / f'img.nii{extension}'
     with Opener(file_path, 'wb') as fobj:
         fobj.write(b'bad')
-    with pytest.raises(ImageFileError, match='Cannot work out file type of .*'):
+    with pytest.raises(ImageFileError, match=r'Cannot work out file type of .*'):
         load(file_path)
 
 

nibabel/tests/test_nifti1.py

@@ -538,11 +538,11 @@ def test_slice_times(self):
         hdr.set_slice_duration(0.1)
         # We need a function to print out the Nones and floating point
         # values in a predictable way, for the tests below.
-        _stringer = lambda val: f'{val:2.1f}' if val is not None else None
-        _print_me = lambda s: list(map(_stringer, s))
+        stringer = lambda val: f'{val:2.1f}' if val is not None else None
+        print_me = lambda s: list(map(stringer, s))
         # The following examples are from the nifti1.h documentation.
         hdr['slice_code'] = slice_order_codes['sequential increasing']
-        assert _print_me(hdr.get_slice_times()) == [
+        assert print_me(hdr.get_slice_times()) == [
             '0.0',
             '0.1',
             '0.2',
@@ -553,17 +553,17 @@ def test_slice_times(self):
         ]
         hdr['slice_start'] = 1
         hdr['slice_end'] = 5
-        assert _print_me(hdr.get_slice_times()) == [None, '0.0', '0.1', '0.2', '0.3', '0.4', None]
+        assert print_me(hdr.get_slice_times()) == [None, '0.0', '0.1', '0.2', '0.3', '0.4', None]
         hdr['slice_code'] = slice_order_codes['sequential decreasing']
-        assert _print_me(hdr.get_slice_times()) == [None, '0.4', '0.3', '0.2', '0.1', '0.0', None]
+        assert print_me(hdr.get_slice_times()) == [None, '0.4', '0.3', '0.2', '0.1', '0.0', None]
         hdr['slice_code'] = slice_order_codes['alternating increasing']
-        assert _print_me(hdr.get_slice_times()) == [None, '0.0', '0.3', '0.1', '0.4', '0.2', None]
+        assert print_me(hdr.get_slice_times()) == [None, '0.0', '0.3', '0.1', '0.4', '0.2', None]
         hdr['slice_code'] = slice_order_codes['alternating decreasing']
-        assert _print_me(hdr.get_slice_times()) == [None, '0.2', '0.4', '0.1', '0.3', '0.0', None]
+        assert print_me(hdr.get_slice_times()) == [None, '0.2', '0.4', '0.1', '0.3', '0.0', None]
         hdr['slice_code'] = slice_order_codes['alternating increasing 2']
-        assert _print_me(hdr.get_slice_times()) == [None, '0.2', '0.0', '0.3', '0.1', '0.4', None]
+        assert print_me(hdr.get_slice_times()) == [None, '0.2', '0.0', '0.3', '0.1', '0.4', None]
         hdr['slice_code'] = slice_order_codes['alternating decreasing 2']
-        assert _print_me(hdr.get_slice_times()) == [None, '0.4', '0.1', '0.3', '0.0', '0.2', None]
+        assert print_me(hdr.get_slice_times()) == [None, '0.4', '0.1', '0.3', '0.0', '0.2', None]
         # test set
         hdr = self.header_class()
         hdr.set_dim_info(slice=2)

nibabel/viewers.py

@@ -373,11 +373,11 @@ def set_volume_idx(self, v):
 
     def _set_volume_index(self, v, update_slices=True):
         """Set the plot data using a volume index"""
-        v = self._data_idx[3] if v is None else int(round(v))
+        v = self._data_idx[3] if v is None else round(v)
         if v == self._data_idx[3]:
             return
         max_ = np.prod(self._volume_dims)
-        self._data_idx[3] = max(min(int(round(v)), max_ - 1), 0)
+        self._data_idx[3] = max(min(round(v), max_ - 1), 0)
         idx = (slice(None), slice(None), slice(None))
         if self._data.ndim > 3:
             idx = idx + tuple(np.unravel_index(self._data_idx[3], self._volume_dims))
@@ -401,7 +401,7 @@ def _set_position(self, x, y, z, notify=True):
         idxs = np.dot(self._inv_affine, self._position)[:3]
         idxs_new_order = idxs[self._order]
         for ii, (size, idx) in enumerate(zip(self._sizes, idxs_new_order)):
-            self._data_idx[ii] = max(min(int(round(idx)), size - 1), 0)
+            self._data_idx[ii] = max(min(round(idx), size - 1), 0)
         for ii in range(3):
             # sagittal: get to S/A
             # coronal: get to S/L