Merge pull request #919 from DimitriPapadopoulos/RUF

STY: Apply ruff rules (RUF)

Author: effigies

niworkflows/__init__.py

@@ -15,11 +15,11 @@
 
 
 __all__ = [
-    '__version__',
-    '__packagename__',
+    'NIWORKFLOWS_LOG',
     '__copyright__',
     '__credits__',
-    'NIWORKFLOWS_LOG',
+    '__packagename__',
+    '__version__',
     'load_resource',
 ]
 

niworkflows/engine/plugin.py

@@ -303,7 +303,7 @@ def _local_hash_check(self, jobid, graph):
         overwrite = self.procs[jobid].overwrite
         always_run = self.procs[jobid].interface.always_run
 
-        if cached and updated and (overwrite is False or overwrite is None and not always_run):
+        if cached and updated and (overwrite is False or (overwrite is None and not always_run)):
             try:
                 self._task_finished_cb(jobid, cached=True)
                 self._remove_node_dirs()

niworkflows/interfaces/bids.py

@@ -1469,7 +1469,7 @@ def _get_tf_resolution(space: str, resolution: str) -> str:
     res_meta = None
 
     # Due to inconsistencies, resolution keys may or may not be zero-padded
-    padded_res = f'{str(resolution):0>2}'
+    padded_res = f'{resolution:0>2}'
     for r in (resolution, padded_res):
         if r in resolutions:
             res_meta = resolutions[r]

niworkflows/interfaces/cifti.py

@@ -202,7 +202,7 @@ def _prepare_cifti(grayordinates: str) -> tuple[list, str, dict]:
         '170k': {'surface-den': '59k', 'tf-res': '06', 'grayords': '170,494', 'res-mm': '1.6mm'},
     }
     if grayordinates not in grayord_key:
-        raise NotImplementedError('Grayordinates {grayordinates} is not supported.')
+        raise NotImplementedError(f'Grayordinates {grayordinates} is not supported.')
 
     tf_vol_res = grayord_key[grayordinates]['tf-res']
     total_grayords = grayord_key[grayordinates]['grayords']

niworkflows/interfaces/confounds.py

@@ -534,20 +534,20 @@ def _expand_shorthand(model_formula, variables):
     nss = _get_matches_from_data('non_steady_state_outlier[0-9]+', variables)
     spikes = _get_matches_from_data('motion_outlier[0-9]+', variables)
 
-    model_formula = re.sub('wm', wm, model_formula)
-    model_formula = re.sub('gsr', gsr, model_formula)
-    model_formula = re.sub('rps', rps, model_formula)
-    model_formula = re.sub('fd', fd, model_formula)
-    model_formula = re.sub('acc', acc, model_formula)
-    model_formula = re.sub('tcc', tcc, model_formula)
-    model_formula = re.sub('dv', dv, model_formula)
-    model_formula = re.sub('dvall', dvall, model_formula)
-    model_formula = re.sub('nss', nss, model_formula)
-    model_formula = re.sub('spikes', spikes, model_formula)
+    model_formula = re.sub(r'wm', wm, model_formula)
+    model_formula = re.sub(r'gsr', gsr, model_formula)
+    model_formula = re.sub(r'rps', rps, model_formula)
+    model_formula = re.sub(r'fd', fd, model_formula)
+    model_formula = re.sub(r'acc', acc, model_formula)
+    model_formula = re.sub(r'tcc', tcc, model_formula)
+    model_formula = re.sub(r'dv', dv, model_formula)
+    model_formula = re.sub(r'dvall', dvall, model_formula)
+    model_formula = re.sub(r'nss', nss, model_formula)
+    model_formula = re.sub(r'spikes', spikes, model_formula)
 
     formula_variables = _get_variables_from_formula(model_formula)
     others = ' + '.join(set(variables) - set(formula_variables))
-    model_formula = re.sub('others', others, model_formula)
+    model_formula = re.sub(r'others', others, model_formula)
     return model_formula
 
 

niworkflows/interfaces/nibabel.py

@@ -22,6 +22,8 @@
 #
 """Nibabel-based interfaces."""
 
+from __future__ import annotations
+
 from pathlib import Path
 from warnings import warn
 
@@ -520,9 +522,9 @@ def _run_interface(self, runtime):
 def reorient_file(
     in_file: str,
     *,
-    target_file: str = None,
-    target_ornt: str = None,
-    newpath: str = None,
+    target_file: str | None = None,
+    target_ornt: str | None = None,
+    newpath: str | None = None,
 ) -> str:
     """
     Reorient an image.

niworkflows/interfaces/nilearn.py

@@ -47,7 +47,7 @@
     NILEARN_VERSION = 'unknown'
 
 LOGGER = logging.getLogger('nipype.interface')
-__all__ = ['NILEARN_VERSION', 'MaskEPI', 'Merge', 'ComputeEPIMask']
+__all__ = ['NILEARN_VERSION', 'ComputeEPIMask', 'MaskEPI', 'Merge']
 
 
 class _MaskEPIInputSpec(BaseInterfaceInputSpec):

niworkflows/interfaces/tests/test_nibabel.py

@@ -49,7 +49,7 @@ def create_roi(tmp_path):
     def _create_roi(affine, img_data, roi_index):
         img_data[tuple(roi_index)] = 1
         nii = nb.Nifti1Image(img_data, affine)
-        filename = tmp_path / f'{str(uuid.uuid4())}.nii.gz'
+        filename = tmp_path / f'{uuid.uuid4()}.nii.gz'
         files.append(filename)
         nii.to_filename(filename)
         return filename

niworkflows/reports/core.py

@@ -384,7 +384,7 @@ def generate_report(self):
 
         if (logs_path / 'CITATION.html').exists():
             text = (
-                re.compile('<body>(.*?)</body>', re.DOTALL | re.IGNORECASE)
+                re.compile(r'<body>(.*?)</body>', re.DOTALL | re.IGNORECASE)
                 .findall((logs_path / 'CITATION.html').read_text())[0]
                 .strip()
             )

niworkflows/utils/bids.py

@@ -388,7 +388,7 @@ def group_multiecho(bold_sess):
     def _grp_echos(x):
         if '_echo-' not in x:
             return x
-        echo = re.search('_echo-\\d*', x).group(0)
+        echo = re.search(r'_echo-\d*', x).group(0)
         return x.replace(echo, '_echo-?')
 
     ses_uids = []