STY: Enforce more ruff rules

.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: v0.12.7
     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

@@ -530,8 +530,7 @@ 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:
@@ -780,9 +779,7 @@ 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):
@@ -261,20 +261,15 @@ def _generate_segment(self):
 
         pedir = get_world_pedir(self.inputs.orientation, self.inputs.pe_direction)
 
-        dummy_scan_tmp = '{n_dum}'
         if self.inputs.dummy_scans == self.inputs.algo_dummy_scans:
-            dummy_scan_msg = ' '.join(
-                [dummy_scan_tmp, '(Confirmed: {n_alg} automatically detected)']
-            ).format(n_dum=self.inputs.dummy_scans, n_alg=self.inputs.algo_dummy_scans)
+            dummy_scan_msg = f'{self.inputs.dummy_scans} (Confirmed: {self.inputs.algo_dummy_scans} automatically detected)'
         # the number of dummy scans was specified by the user and
         # it is not equal to the number detected by the algorithm
         elif self.inputs.dummy_scans is not None:
-            dummy_scan_msg = ' '.join(
-                [dummy_scan_tmp, '(Warning: {n_alg} automatically detected)']
-            ).format(n_dum=self.inputs.dummy_scans, n_alg=self.inputs.algo_dummy_scans)
+            dummy_scan_msg = f'{self.inputs.dummy_scans} (Warning: {self.inputs.algo_dummy_scans} automatically detected)'
         # the number of dummy scans was not specified by the user
         else:
-            dummy_scan_msg = dummy_scan_tmp.format(n_dum=self.inputs.algo_dummy_scans)
+            dummy_scan_msg = f'{self.inputs.algo_dummy_scans}'
 
         multiecho = 'Single-echo EPI sequence.'
         n_echos = len(self.inputs.echo_idx)

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):

fmriprep/workflows/base.py

@@ -876,8 +876,8 @@ def map_fieldmap_estimation(
     fmap_estimators = find_estimators(
         layout=layout,
         subject=subject_id,
-        fmapless=bool(use_syn) or ignore_fieldmaps and force_syn,
-        force_fmapless=force_syn or ignore_fieldmaps and use_syn,
+        fmapless=bool(use_syn) or (ignore_fieldmaps and force_syn),
+        force_fmapless=force_syn or (ignore_fieldmaps and use_syn),
         bids_filters=filters,
     )
 

fmriprep/workflows/bold/base.py

@@ -55,7 +55,7 @@
 def init_bold_wf(
     *,
     bold_series: list[str],
-    precomputed: dict = None,
+    precomputed: dict | None = None,
     fieldmap_id: str | None = None,
     jacobian: bool = False,
 ) -> pe.Workflow:

fmriprep/workflows/bold/fit.py

@@ -95,7 +95,7 @@ def get_sbrefs(
 def init_bold_fit_wf(
     *,
     bold_series: list[str],
-    precomputed: dict = None,
+    precomputed: dict | None = None,
     fieldmap_id: str | None = None,
     jacobian: bool = False,
     omp_nthreads: int = 1,
@@ -231,7 +231,7 @@ def init_bold_fit_wf(
     metadata = layout.get_metadata(bold_file)
     orientation = ''.join(nb.aff2axcodes(nb.load(bold_file).affine))
 
-    bold_tlen, mem_gb = estimate_bold_mem_usage(bold_file)
+    _bold_tlen, mem_gb = estimate_bold_mem_usage(bold_file)
 
     # Boolean used to update workflow self-descriptions
     multiecho = len(bold_series) > 1
@@ -793,7 +793,7 @@ def init_bold_native_wf(
     bold_file = bold_series[0]
     metadata = all_metadata[0]
 
-    bold_tlen, mem_gb = estimate_bold_mem_usage(bold_file)
+    _bold_tlen, mem_gb = estimate_bold_mem_usage(bold_file)
 
     if multiecho:
         shapes = [nb.load(echo).shape for echo in bold_series]
@@ -841,7 +841,7 @@ def init_bold_native_wf(
                 # Multiecho outputs
                 'bold_echos',  # Individual corrected echos
                 't2star_map',  # T2* map
-            ],  # fmt:skip
+            ],
         ),
         name='outputnode',
     )

fmriprep/workflows/tests/test_base.py

@@ -115,9 +115,9 @@ def _make_params(
     skull_strip_t1w: str = 'auto',
     use_syn_sdc: str | bool = False,
     freesurfer: bool = True,
-    ignore: list[str] = None,
-    force: list[str] = None,
-    bids_filters: dict = None,
+    ignore: list[str] | None = None,
+    force: list[str] | None = None,
+    bids_filters: dict | None = None,
 ):
     if ignore is None:
         ignore = []

pyproject.toml

@@ -154,31 +154,49 @@ line-length = 99
 
 [tool.ruff.lint]
 extend-select = [
-  "F",
-  "E",
-  "W",
   "I",
   "UP",
   "YTT",
   "S",
   "BLE",
   "B",
   "A",
-  # "CPY",
   "C4",
+  # "CPY",
   "DTZ",
   "T10",
   # "EM",
   "EXE",
   "FA",
   "ISC",
   "ICN",
+  "LOG",
+  "PIE",
+  "PYI",
   "PT",
   "Q",
+  # "SIM",
+  # "TID",
+  "FLY",
+  # "PD",
+  "PERF",
+  "W",
+  "PGH",
+  "PLC",
+  "PLE",
+  "PLW",
+  "FURB",
+  "RUF",
 ]
 ignore = [
   "S311",  # We are not using random for cryptographic purposes
   "S603",
+  "PIE790",
+  "PERF203",
+  "PLC0415",
+  "PLW2901",
+  "RUF005",
+  "RUF012",
 ]
 
 [tool.ruff.lint.flake8-quotes]

tox.ini

@@ -73,7 +73,6 @@ skip_install = true
 commands =
   ruff check --fix
   ruff format
-  ruff check --select ISC001
 
 [testenv:spellcheck]
 description = Check spelling