Merge pull request #988 from effigies/mnt/pyupgrade

chore: Drop Python 3.9 support

Author: effigies

.github/workflows/tox.yml

@@ -94,17 +94,17 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
         dependencies: [latest, pre]
         include:
-          - python-version: "3.9"
+          - python-version: "3.10"
             dependencies: min
         exclude:
           # Do not test pre-releases for versions out of SPEC0
-          - python-version: "3.9"
-            dependencies: pre
           - python-version: "3.10"
             dependencies: pre
+          - python-version: "3.11"
+            dependencies: pre
 
     env:
       DEPENDS: ${{ matrix.dependencies }}

niworkflows/func/tests/test_util.py

@@ -74,7 +74,7 @@
 
     bold_datasets = [[str((datapath / p).absolute()) for p in ds] for ds in bold_datasets]
 
-    parameters = zip(bold_datasets, exp_masks)
+    parameters = zip(bold_datasets, exp_masks, strict=False)
 
     if not bold_datasets:
         raise RuntimeError(

niworkflows/interfaces/bids.py

@@ -25,7 +25,6 @@
 import os
 import re
 import shutil
-import sys
 from collections import defaultdict
 from contextlib import suppress
 from json import dumps, loads
@@ -66,15 +65,6 @@
 LOGGER = logging.getLogger('nipype.interface')
 
 
-if sys.version_info < (3, 10):  # PY39
-    builtin_zip = zip
-
-    def zip(*args, strict=False):  # noqa: A001
-        if strict and any(len(args[0]) != len(arg) for arg in args):
-            raise ValueError('strict_zip() requires all arguments to have the same length')
-        return builtin_zip(*args)
-
-
 def _none():
     return None
 
@@ -629,7 +619,7 @@ def _run_interface(self, runtime):
         self._results['out_path'] = dest_files
         self._results['out_meta'] = metadata
 
-        for i, (orig_file, dest_file) in enumerate(zip(in_file, dest_files)):
+        for i, (orig_file, dest_file) in enumerate(zip(in_file, dest_files, strict=False)):
             # Set data and header iff changes need to be made. If these are
             # still None when it's time to write, just copy.
             new_data, new_header = None, None
@@ -1132,7 +1122,7 @@ def _run_interface(self, runtime):
                 f'by interpolated patterns ({len(dest_files)}).'
             )
 
-        for i, (orig_file, dest_file) in enumerate(zip(in_file, dest_files)):
+        for i, (orig_file, dest_file) in enumerate(zip(in_file, dest_files, strict=False)):
             out_file = out_path / dest_file
             out_file.parent.mkdir(exist_ok=True, parents=True)
             self._results['out_file'].append(str(out_file))

niworkflows/interfaces/confounds.py

@@ -303,7 +303,7 @@ def spike_regressors(
         post_final = data.shape[0] + 1
         epoch_length = np.diff(sorted(mask | {-1, post_final})) - 1
         epoch_end = sorted(mask | {post_final})
-        for end, length in zip(epoch_end, epoch_length):
+        for end, length in zip(epoch_end, epoch_length, strict=False):
             if length < minimum_contiguous:
                 mask = mask | set(range(end - length, end))
         mask = mask.intersection(indices)

niworkflows/interfaces/images.py

@@ -284,7 +284,9 @@ def _run_interface(self, runtime):
         self._results['out_file'] = fname(suffix='_average')
         self._results['out_volumes'] = fname(suffix='_sliced')
 
-        sliced = nb.concat_images(i for i, t in zip(nb.four_to_three(img), t_mask) if t)
+        sliced = nb.concat_images(
+            i for i, t in zip(nb.four_to_three(img), t_mask, strict=False) if t
+        )
 
         data = sliced.get_fdata(dtype='float32')
         # Data can come with outliers showing very high numbers - preemptively prune

niworkflows/interfaces/itk.py

@@ -141,7 +141,7 @@ def _run_interface(self, runtime):
         if num_threads == 1:
             out_files = [
                 _applytfms((in_file, in_xfm, ifargs, i, runtime.cwd))
-                for i, (in_file, in_xfm) in enumerate(zip(in_files, xfms_list))
+                for i, (in_file, in_xfm) in enumerate(zip(in_files, xfms_list, strict=False))
             ]
         else:
             from concurrent.futures import ThreadPoolExecutor
@@ -152,7 +152,9 @@ def _run_interface(self, runtime):
                         _applytfms,
                         [
                             (in_file, in_xfm, ifargs, i, runtime.cwd)
-                            for i, (in_file, in_xfm) in enumerate(zip(in_files, xfms_list))
+                            for i, (in_file, in_xfm) in enumerate(
+                                zip(in_files, xfms_list, strict=False)
+                            )
                         ],
                     )
                 )
@@ -264,4 +266,4 @@ def _arrange_xfms(transforms, num_files, tmp_folder):
         xfms_T.append(split_xfms)
 
     # Transpose back (only Python 3)
-    return list(map(list, zip(*xfms_T)))
+    return list(map(list, zip(*xfms_T, strict=False)))

niworkflows/interfaces/surf.py

@@ -743,6 +743,7 @@ def ply2gii(in_file, metadata, out_file=None):
         zip(
             ('SurfaceCenterX', 'SurfaceCenterY', 'SurfaceCenterZ'),
             [f'{c:.4f}' for c in surf.centroid],
+            strict=False,
         )
     )
 

niworkflows/interfaces/tests/test_bids.py

@@ -361,10 +361,10 @@ def test_DerivativesDataSink_build_path(
             ]
 
     base = (out_path_base or 'niworkflows') if interface == bintfs.DerivativesDataSink else ''
-    for out, exp in zip(output, expectation):
+    for out, exp in zip(output, expectation, strict=False):
         assert Path(out).relative_to(base_directory) == Path(base) / exp
 
-    for out, exp in zip(output, expectation):
+    for out, exp in zip(output, expectation, strict=False):
         assert Path(out).relative_to(base_directory) == Path(base) / exp
         # Regression - some images were given nan scale factors
         if out.endswith(('.nii', '.nii.gz')):
@@ -374,7 +374,7 @@ def test_DerivativesDataSink_build_path(
                     hdr = img.header.from_fileobj(fobj)
                 assert not np.isnan(hdr['scl_slope'])
                 assert not np.isnan(hdr['scl_inter'])
-    for out, chksum in zip(output, checksum):
+    for out, chksum in zip(output, checksum, strict=False):
         if chksum == '335f1394ce90b58bbf27026b6eeec4d2124c11da':
             if Version(nb.__version__) < Version('5.3'):
                 # Nibabel 5.3 avoids unnecessary roundtrips for Cifti2Headers

niworkflows/interfaces/tests/test_images.py

@@ -195,7 +195,7 @@ def test_TemplateDimensions(tmp_path):
         (0.9, 0.9, 0.9),
     ]
 
-    for i, (shape, zoom) in enumerate(zip(shapes, zooms)):
+    for i, (shape, zoom) in enumerate(zip(shapes, zooms, strict=False)):
         img = nb.Nifti1Image(np.ones(shape, dtype='float32'), np.eye(4))
         img.header.set_zooms(zoom)
         img.to_filename(tmp_path / f'test{i}.nii')

niworkflows/interfaces/utility.py

@@ -371,7 +371,7 @@ def _run_interface(self, runtime):
             raise ValueError('Number of columns in datasets do not match')
 
         merged = []
-        for d, j in zip(data, join):
+        for d, j in zip(data, join, strict=False):
             line = '%s\t%s' % ((j, d) if self.inputs.side == 'left' else (d, j))
             merged.append(line)