STY: Enforce more ruff rules (#3437)

Author: effigies

.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: v0.12.2
+    rev: v0.13.0
     hooks:
       - id: ruff-check
         args: [ --fix ]

docs/conf.py

@@ -22,7 +22,7 @@
 sys.path.append(os.path.abspath('sphinxext'))
 sys.path.insert(0, os.path.abspath('../wrapper'))
 
-from github_link import make_linkcode_resolve  # noqa: E402
+from github_link import make_linkcode_resolve
 
 # -- General configuration ------------------------------------------------
 

fmriprep/cli/tests/test_parser.py

@@ -254,7 +254,7 @@ def test_derivatives(tmp_path):
     # Providing --derivatives with names should use them
     temp_args = args + [
         '--derivatives',
-        f'anat={str(bids_path / "derivatives/smriprep")}',
+        f'anat={bids_path / "derivatives/smriprep"}',
     ]
     opts = parser.parse_args(temp_args)
     assert opts.derivatives == {'anat': bids_path / 'derivatives/smriprep'}

fmriprep/cli/version.py

@@ -72,7 +72,7 @@ def check_latest():
             versions = [Version(rel) for rel in response.json()['releases'].keys()]
             versions = [rel for rel in versions if not rel.is_prerelease]
             if versions:
-                latest = sorted(versions)[-1]
+                latest = max(versions)
         else:
             latest = None
 

fmriprep/config.py

@@ -540,8 +540,7 @@ def _process_value(value):
             'raw': cls.bids_dir,
             'templateflow': Path(TF_LAYOUT.root),
         }
-        for deriv_name, deriv_path in cls.derivatives.items():
-            dataset_links[deriv_name] = deriv_path
+        dataset_links.update(cls.derivatives)
         cls.dataset_links = dataset_links
 
         if 'all' in cls.debug:
@@ -794,9 +793,7 @@ def get(flat=False):
         return settings
 
     return {
-        '.'.join((section, k)): v
-        for section, configs in settings.items()
-        for k, v in configs.items()
+        f'{section}.{k}': v for section, configs in settings.items() for k, v in configs.items()
     }
 
 

fmriprep/interfaces/confounds.py

@@ -429,8 +429,8 @@ def less_breakable(a_string):
     # Taken from https://stackoverflow.com/questions/1175208/
     # If we end up using it more than just here, probably worth pulling in a well-tested package
     def camel_to_snake(name):
-        s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
-        return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower()
+        s1 = re.sub(r'(.)([A-Z][a-z]+)', r'\1_\2', name)
+        return re.sub(r'([a-z0-9])([A-Z])', r'\1_\2', s1).lower()
 
     def _adjust_indices(left_df, right_df):
         # This forces missing values to appear at the beginning of the DataFrame

fmriprep/interfaces/conftest.py

@@ -10,7 +10,7 @@
     import os
     from contextlib import contextmanager
 
-    @contextmanager  # type: ignore
+    @contextmanager
     def _chdir(path):
         cwd = os.getcwd()
         os.chdir(path)

fmriprep/interfaces/reports.py

@@ -131,12 +131,12 @@ def _run_interface(self, runtime):
     def _generate_segment(self):
         BIDS_NAME = re.compile(
             r'^(.*\/)?'
-            '(?P<subject_id>sub-[a-zA-Z0-9]+)'
-            '(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
-            '(_(?P<task_id>task-[a-zA-Z0-9]+))?'
-            '(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
-            '(_(?P<rec_id>rec-[a-zA-Z0-9]+))?'
-            '(_(?P<run_id>run-[a-zA-Z0-9]+))?'
+            r'(?P<subject_id>sub-[a-zA-Z0-9]+)'
+            r'(_(?P<session_id>ses-[a-zA-Z0-9]+))?'
+            r'(_(?P<task_id>task-[a-zA-Z0-9]+))?'
+            r'(_(?P<acq_id>acq-[a-zA-Z0-9]+))?'
+            r'(_(?P<rec_id>rec-[a-zA-Z0-9]+))?'
+            r'(_(?P<run_id>run-[a-zA-Z0-9]+))?'
         )
 
         if not isdefined(self.inputs.subjects_dir):

fmriprep/interfaces/workbench.py

@@ -292,7 +292,7 @@ def _format_arg(self, opt, spec, val):
         if opt == 'valid_roi_out' and val:
             # generate a filename and add it to argstr
             roi_out = self._gen_filename(self.inputs.in_file, suffix='_roi')
-            iflogger.info('Setting roi output file as', roi_out)
+            iflogger.info('Setting roi output file as %s', roi_out)
             spec.argstr += ' ' + roi_out
         return super()._format_arg(opt, spec, val)
 

fmriprep/utils/telemetry.py

@@ -156,7 +156,7 @@ def before_send(event, hints):
             return None
         if msg.startswith('Saving crash info to '):
             return None
-        if re.match('Node .+ failed to run on host .+', msg):
+        if re.match(r'Node .+ failed to run on host .+', msg):
             return None
 
     if 'breadcrumbs' in event and isinstance(event['breadcrumbs'], list):