Upgrade to ruff 0.9.1

.maint/update_authors.py

@@ -132,7 +132,7 @@ def get_git_lines(fname='line-contributors.txt'):
 def _namelast(inlist):
     retval = []
     for i in inlist:
-        i['name'] = (f"{i.pop('name', '')} {i.pop('lastname', '')}").strip()
+        i['name'] = (f'{i.pop("name", "")} {i.pop("lastname", "")}').strip()
         retval.append(i)
     return retval
 
@@ -187,7 +187,7 @@ def zenodo(
     misses = set(miss_creators).intersection(miss_contributors)
     if misses:
         print(
-            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
+            f'Some people made commits, but are missing in .maint/ files: {", ".join(misses)}',
             file=sys.stderr,
         )
 
@@ -268,7 +268,7 @@ def _aslist(value):
 
     if misses:
         print(
-            f"Some people made commits, but are missing in .maint/ files: {', '.join(misses)}",
+            f'Some people made commits, but are missing in .maint/ files: {", ".join(misses)}',
             file=sys.stderr,
         )
 

.maint/update_zenodo.py

@@ -73,7 +73,7 @@ def get_git_lines(fname='line-contributors.txt'):
     if cmd == [None]:
         cmd = [shutil.which('git-summary'), '--line']
     if not lines and cmd[0]:
-        print(f"Running {' '.join(cmd)!r} on repo")
+        print(f'Running {" ".join(cmd)!r} on repo')
         lines = sp.check_output(cmd).decode().splitlines()
         lines = [line for line in lines if 'Not Committed Yet' not in line]
         contrib_file.write_text('\n'.join(lines))

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
       - id: check-toml
       - id: check-added-large-files
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.2
+    rev: v0.9.1
     hooks:
       - id: ruff
         args: [ --fix ]

fmriprep/_warnings.py

@@ -35,7 +35,7 @@ def _warn(message, category=None, stacklevel=1, source=None):
         category = type(category).__name__
         category = category.replace('type', 'WARNING')
 
-    logging.getLogger('py.warnings').warning(f"{category or 'WARNING'}: {message}")
+    logging.getLogger('py.warnings').warning(f'{category or "WARNING"}: {message}')
 
 
 def _showwarning(message, category, filename, lineno, file=None, line=None):

fmriprep/cli/parser.py

@@ -54,8 +54,8 @@ class DeprecatedAction(Action):
         def __call__(self, parser, namespace, values, option_string=None):
             new_opt, rem_vers = deprecations.get(self.dest, (None, None))
             msg = (
-                f"{self.option_strings} has been deprecated and will be removed in "
-                f"{rem_vers or 'a later version'}."
+                f'{self.option_strings} has been deprecated and will be removed in '
+                f'{rem_vers or "a later version"}.'
             )
             if new_opt:
                 msg += f' Please use `{new_opt}` instead.'
@@ -557,8 +557,7 @@ def _slice_time_ref(value, parser):
         action='store',
         default=0.5,
         type=float,
-        help='Threshold for flagging a frame as an outlier on the basis of framewise '
-        'displacement',
+        help='Threshold for flagging a frame as an outlier on the basis of framewise displacement',
     )
     g_confounds.add_argument(
         '--dvars-spike-threshold',
@@ -900,8 +899,7 @@ def parse_args(args=None, namespace=None):
         from ..utils.bids import validate_input_dir
 
         build_log.info(
-            'Making sure the input data is BIDS compliant (warnings can be ignored in most '
-            'cases).'
+            'Making sure the input data is BIDS compliant (warnings can be ignored in most cases).'
         )
         validate_input_dir(
             config.environment.exec_env,

fmriprep/cli/workflow.py

@@ -58,11 +58,11 @@
     notice_path = data.load.readable('NOTICE')
     if notice_path.exists():
         banner[0] += '\n'
-        banner += [f"License NOTICE {'#' * 50}"]
+        banner += [f'License NOTICE {"#" * 50}']
         banner += [f'fMRIPrep {version}']
         banner += notice_path.read_text().splitlines(keepends=False)[1:]
         banner += ['#' * len(banner[1])]
-    build_log.log(25, f"\n{' ' * 9}".join(banner))
+    build_log.log(25, f'\n{" " * 9}'.join(banner))
 
     # warn if older results exist: check for dataset_description.json in output folder
     msg = check_pipeline_version('fMRIPrep', version, fmriprep_dir / 'dataset_description.json')
@@ -121,7 +121,7 @@
     if config.execution.fs_subjects_dir:
         init_msg += [f"Pre-run FreeSurfer's SUBJECTS_DIR: {config.execution.fs_subjects_dir}."]
 
-    build_log.log(25, f"\n{' ' * 11}* ".join(init_msg))
+    build_log.log(25, f'\n{" " * 11}* '.join(init_msg))
 
     retval['workflow'] = init_fmriprep_wf()
 

fmriprep/config.py

@@ -432,7 +432,7 @@ class execution(_Config):
     the command line) as spatial references for outputs."""
     reports_only = False
     """Only build the reports, based on the reportlets found in a cached working directory."""
-    run_uuid = f"{strftime('%Y%m%d-%H%M%S')}_{uuid4()}"
+    run_uuid = f'{strftime("%Y%m%d-%H%M%S")}_{uuid4()}'
     """Unique identifier of this particular run."""
     participant_label = None
     """List of participant identifiers that are to be preprocessed."""

fmriprep/interfaces/workbench.py

@@ -114,8 +114,7 @@ class MetricDilateInputSpec(OpenMPTraitedSpec):
         argstr='-exponent %f ',
         position=9,
         default=6.0,
-        desc='exponent n to use in (area / (distance ^ n)) as the '
-        'weighting function (default 6)',
+        desc='exponent n to use in (area / (distance ^ n)) as the weighting function (default 6)',
     )
 
     corrected_areas = File(

fmriprep/reports/tests/test_reports.py

@@ -101,11 +101,11 @@ def mock_session_list(*args, **kwargs):
 
     html_content = Path.read_text(tmp_path / expected_files[0])
     if boilerplate:
-        assert (
-            'The boilerplate text was automatically generated' in html_content
-        ), f'The file {expected_files[0]} did not contain the reported error.'
+        assert 'The boilerplate text was automatically generated' in html_content, (
+            f'The file {expected_files[0]} did not contain the reported error.'
+        )
 
     if error:
-        assert (
-            'One or more execution steps failed' in html_content
-        ), f'The file {expected_files[0]} did not contain the reported error.'
+        assert 'One or more execution steps failed' in html_content, (
+            f'The file {expected_files[0]} did not contain the reported error.'
+        )

fmriprep/utils/bids.py

@@ -131,7 +131,7 @@ def write_derivative_description(bids_dir, deriv_dir, dataset_links=None):
     if 'FMRIPREP_DOCKER_TAG' in os.environ:
         desc['GeneratedBy'][0]['Container'] = {
             'Type': 'docker',
-            'Tag': f"nipreps/fmriprep:{os.environ['FMRIPREP_DOCKER_TAG']}",
+            'Tag': f'nipreps/fmriprep:{os.environ["FMRIPREP_DOCKER_TAG"]}',
         }
     if 'FMRIPREP_SINGULARITY_URL' in os.environ:
         desc['GeneratedBy'][0]['Container'] = {

fmriprep/workflows/base.py

@@ -232,9 +232,9 @@ def init_single_subject_wf(subject_id: str):
 
     if subject_data['roi']:
         warnings.warn(
-            f"Lesion mask {subject_data['roi']} found. "
-            "Future versions of fMRIPrep will use alternative conventions. "
-            "Please refer to the documentation before upgrading.",
+            f'Lesion mask {subject_data["roi"]} found. '
+            'Future versions of fMRIPrep will use alternative conventions. '
+            'Please refer to the documentation before upgrading.',
             FutureWarning,
             stacklevel=1,
         )
@@ -828,7 +828,7 @@ def map_fieldmap_estimation(
     for bold_file, estimator_key in all_estimators.items():
         if len(estimator_key) > 1:
             config.loggers.workflow.warning(
-                f"Several fieldmaps <{', '.join(estimator_key)}> are "
+                f'Several fieldmaps <{", ".join(estimator_key)}> are '
                 f"'IntendedFor' <{bold_file}>, using {estimator_key[0]}"
             )
             estimator_key[1:] = []

fmriprep/workflows/bold/stc.py

@@ -121,7 +121,7 @@ def init_bold_stc_wf(
     slice_timing_correction = pe.Node(
         TShift(
             outputtype='NIFTI_GZ',
-            tr=f"{metadata['RepetitionTime']}s",
+            tr=f'{metadata["RepetitionTime"]}s',
             slice_timing=metadata['SliceTiming'],
             slice_encoding_direction=metadata.get('SliceEncodingDirection', 'k'),
             tzero=tzero,

pyproject.toml

@@ -178,7 +178,6 @@ extend-select = [
 ]
 ignore = [
   "S311",  # We are not using random for cryptographic purposes
-  "ISC001",
   "S603",
 ]
 

wrapper/pyproject.toml

@@ -94,7 +94,6 @@ extend-select = [
 ]
 ignore = [
   "S311",  # We are not using random for cryptographic purposes
-  "ISC001",
 ]
 
 [tool.ruff.lint.flake8-quotes]