STY: Enable more ruff rules

niworkflows/func/tests/test_util.py

@@ -156,9 +156,7 @@ def test_masking(input_fname, expected_fname):
 
     res = wf.run(plugin='MultiProc')
 
-    combine_masks = [node for node in res.nodes if node.name.endswith('combine_masks')][
-        0
-    ]
+    combine_masks = next(node for node in res.nodes if node.name.endswith('combine_masks'))
     overlap = symmetric_overlap(expected_fname, combine_masks.result.outputs.out_file)
 
     mask_dir = reports_dir / 'fmriprep_bold_mask' / dsname

niworkflows/interfaces/bids.py

@@ -673,7 +673,7 @@ def _run_interface(self, runtime):
                         data_dtype = nb.load(self.inputs.source_file[0]).get_data_dtype()
                     except Exception:  # noqa: BLE001
                         LOGGER.warning(
-                            f'Could not get data type of file {self.inputs.source_file[0]}'
+                            'Could not get data type of file %s', self.inputs.source_file[0]
                         )
                         data_dtype = None
 
@@ -682,8 +682,10 @@ def _run_interface(self, runtime):
                     orig_dtype = nii.get_data_dtype()
                     if orig_dtype != data_dtype:
                         LOGGER.warning(
-                            f'Changing {Path(dest_file).name} dtype '
-                            f'from {orig_dtype} to {data_dtype}'
+                            'Changing %s dtype from %s to %s',
+                            Path(dest_file).name,
+                            orig_dtype,
+                            data_dtype,
                         )
                         # coerce dataobj to new data dtype
                         if np.issubdtype(data_dtype, np.integer):
@@ -1186,7 +1188,7 @@ def _run_interface(self, runtime):
                         data_dtype = nb.load(self.inputs.source_file[0]).get_data_dtype()
                     except Exception:  # noqa: BLE001
                         LOGGER.warning(
-                            f'Could not get data type of file {self.inputs.source_file[0]}'
+                            'Could not get data type of file %s', self.inputs.source_file[0]
                         )
                         data_dtype = None
 
@@ -1195,7 +1197,7 @@ def _run_interface(self, runtime):
                     orig_dtype = nii.get_data_dtype()
                     if orig_dtype != data_dtype:
                         LOGGER.warning(
-                            f'Changing {out_file} dtype from {orig_dtype} to {data_dtype}'
+                            'Changing %s dtype from %s to %s', out_file, orig_dtype, orig_dtype
                         )
                         # coerce dataobj to new data dtype
                         if np.issubdtype(data_dtype, np.integer):

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(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)
+    model_formula = model_formula.replace('wm', wm)
+    model_formula = model_formula.replace('gsr', gsr)
+    model_formula = model_formula.replace('rps', rps)
+    model_formula = model_formula.replace('fd', fd)
+    model_formula = model_formula.replace('acc', acc)
+    model_formula = model_formula.replace('tcc', tcc)
+    model_formula = model_formula.replace('dv', dv)
+    model_formula = model_formula.replace('dvall', dvall)
+    model_formula = model_formula.replace('nss', nss)
+    model_formula = model_formula.replace('spikes', spikes)
 
     formula_variables = _get_variables_from_formula(model_formula)
     others = ' + '.join(set(variables) - set(formula_variables))
-    model_formula = re.sub(r'others', others, model_formula)
+    model_formula = model_formula.replace('others', others)
     return model_formula
 
 

niworkflows/interfaces/tests/test_bids.py

@@ -571,7 +571,7 @@ def make_empty_nii_with_dtype(fname, dtype):
         for s in source_file:
             make_empty_nii_with_dtype(s, source_dtype)
 
-    prep, save = make_prep_and_save(
+    prep, _save = make_prep_and_save(
         interface,
         base_directory=str(tmp_path),
         data_dtype='source',

niworkflows/interfaces/tests/test_itk.py

@@ -50,7 +50,7 @@ def test_applytfms(tmpdir, ext, copy_dtype, in_dtype):
 
     ifargs = {'copy_dtype': copy_dtype, 'reference_image': in_file}
     args = (in_file, in_xform, ifargs, 0, str(tmpdir))
-    out_file, cmdline = _applytfms(args)
+    out_file, _cmdline = _applytfms(args)
 
     assert out_file == str(tmpdir / (f'src_xform-00000{ext}'))
 

niworkflows/interfaces/tests/test_plotting.py

@@ -34,7 +34,7 @@
 
 def test_cifti_carpetplot():
     """Exercise extraction of timeseries from CIFTI2."""
-    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
+    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
 
     cifti_file = load_test_data(
         'sub-01_task-mixedgamblestask_run-02_space-fsLR_den-91k_bold.dtseries.nii'
@@ -54,7 +54,7 @@ def test_cifti_carpetplot():
 
 def test_nifti_carpetplot():
     """Exercise extraction of timeseries from CIFTI2."""
-    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
+    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
 
     nifti_file = load_test_data('sub-ds205s03_task-functionallocalizer_run-01_bold_volreg.nii.gz')
     seg_file = load_test_data('sub-ds205s03_task-functionallocalizer_run-01_bold_parc.nii.gz')

niworkflows/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)
 

niworkflows/reports/core.py

@@ -462,9 +462,7 @@ def _process_orderings(orderings, layout):
             {value[idx] for value in all_value_combos} for idx in range(len(orderings))
         ]
         # if all values are None for an entity, we do not want to keep that entity
-        keep_idx = [
-            not (len(val_set) == 1 and None in val_set or not val_set) for val_set in unique_values
-        ]
+        keep_idx = [val_set not in (set(), {None}) for val_set in unique_values]
         # the "kept" entities
         entities = list(compress(orderings, keep_idx))
         # the "kept" value combinations

niworkflows/tests/test_confounds.py

@@ -37,7 +37,7 @@
 def _smoke_test_report(report_interface, artifact_name):
     out_report = report_interface.run().outputs.out_file
 
-    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
+    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
     if save_artifacts:
         copy(out_report, os.path.join(save_artifacts, artifact_name))
     assert os.path.isfile(out_report), f'Report "{out_report}" does not exist'

niworkflows/tests/test_registration.py

@@ -47,7 +47,7 @@ def _smoke_test_report(report_interface, artifact_name):
         res = pe.Node(report_interface, name='smoke_test', base_dir=tmpdir).run()
         out_report = res.outputs.out_report
 
-        save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
+        save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
         if save_artifacts:
             copy(out_report, os.path.join(save_artifacts, artifact_name))
         assert os.path.isfile(out_report), 'Report does not exist'

niworkflows/tests/test_segmentation.py

@@ -46,7 +46,7 @@ def _smoke_test_report(report_interface, artifact_name):
         res = pe.Node(report_interface, name='smoke_test', base_dir=tmpdir).run()
         out_report = res.outputs.out_report
 
-        save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
+        save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
         if save_artifacts:
             copy(out_report, os.path.join(save_artifacts, artifact_name))
         assert os.path.isfile(out_report), f'Report "{out_report}" does not exist'

niworkflows/tests/test_viz.py

@@ -43,7 +43,7 @@
 @pytest.mark.parametrize('sorting', [None, 'ward', 'linkage'])
 def test_carpetplot(tr, sorting):
     """Write a carpetplot"""
-    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
+    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
 
     rng = np.random.default_rng(2010)
 
@@ -137,7 +137,7 @@ def test_carpetplot(tr, sorting):
 )
 def test_fmriplot(input_files):
     """Exercise the fMRIPlot class."""
-    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS', False)
+    save_artifacts = os.getenv('SAVE_CIRCLE_ARTIFACTS')
     rng = np.random.default_rng(2010)
 
     in_file = os.path.join(datadir, input_files[0])

pyproject.toml

@@ -118,32 +118,49 @@ 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",
+  "G",
+  "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
-  "ISC001",
+  "S404",
   "S603",
+  "PLW1510",
+  "PLW2901",
+  "RUF005",
+  "RUF012",
 ]
 
 [tool.ruff.lint.flake8-quotes]