sty: ruff check --fix --unsafe-fixes, reviewed and curated

Follow up with ruff format and ruff check --select ISC001 --fix

Author: effigies

niworkflows/__init__.py

@@ -27,9 +27,9 @@
 NIWORKFLOWS_LOG.setLevel(logging.INFO)
 
 try:
-    import matplotlib
+    import matplotlib as mpl
 
-    matplotlib.use('Agg')
+    mpl.use('Agg')
 except ImportError:
     pass
 

niworkflows/engine/plugin.py

@@ -54,7 +54,7 @@ def run_node(node, updatehash, taskid):
 
     """
     # Init variables
-    result = dict(result=None, traceback=None, taskid=taskid)
+    result = {'result': None, 'traceback': None, 'taskid': taskid}
 
     # Try and execute the node via node.run()
     try:
@@ -188,7 +188,8 @@ def run(self, graph, config, updatehash=False):
                             self._remove_node_dirs()
                         self._clear_task(taskid)
                     else:
-                        assert self.proc_done[jobid] and self.proc_pending[jobid]
+                        assert self.proc_done[jobid]
+                        assert self.proc_pending[jobid]
                         toappend.insert(0, (taskid, jobid))
 
             if toappend:
@@ -354,12 +355,12 @@ def _remove_node_deps(self, jobid, crashfile, graph):
             dfs_preorder = nx.dfs_preorder
         except AttributeError:
             dfs_preorder = nx.dfs_preorder_nodes
-        subnodes = [s for s in dfs_preorder(graph, self.procs[jobid])]
+        subnodes = list(dfs_preorder(graph, self.procs[jobid]))
         for node in subnodes:
             idx = self.procs.index(node)
             self.proc_done[idx] = True
             self.proc_pending[idx] = False
-        return dict(node=self.procs[jobid], dependents=subnodes, crashfile=crashfile)
+        return {'node': self.procs[jobid], 'dependents': subnodes, 'crashfile': crashfile}
 
     def _remove_node_dirs(self):
         """Remove directories whose outputs have already been used up."""

niworkflows/engine/tests/test_plugin.py

@@ -94,4 +94,5 @@ def test_plugin_app_config(tmp_path, workflow, caplog):
     caplog.set_level(logging.INFO, logger='nipype.workflow')
     workflow.run(plugin=MultiProcPlugin(plugin_args={'n_procs': 2, 'app_config': app_config}))
 
-    assert init_flag.exists() and init_flag.read_text() == 'flag'
+    assert init_flag.exists()
+    assert init_flag.read_text() == 'flag'

niworkflows/func/tests/test_util.py

@@ -45,7 +45,7 @@
 
     for ds in datapath.glob('ds*/'):
         paths = [p for p in ds.glob('*_bold.nii.gz') if p.exists()]
-        subjects = set([p.name.replace('sub-', '').split('_')[0] for p in paths])
+        subjects = {p.name.replace('sub-', '').split('_')[0] for p in paths}
 
         for sub in subjects:
             subject_data = [p for p in paths if p.name.startswith(f'sub-{sub}')]
@@ -100,7 +100,7 @@ def symmetric_overlap(img1, img2):
     reason='FMRIPREP_REGRESSION_SOURCE env var not set, or no data is available',
 )
 @pytest.mark.skipif(not which('antsAI'), reason='antsAI executable not found')
-@pytest.mark.parametrize('input_fname,expected_fname', parameters)
+@pytest.mark.parametrize(('input_fname', 'expected_fname'), parameters)
 def test_masking(input_fname, expected_fname):
     """Check for regressions in masking."""
     from nipype import config as ncfg

niworkflows/interfaces/bids.py

@@ -1339,7 +1339,7 @@ def _run_interface(self, runtime):
         for fname in self._fields:
             if not self._undef_fields and fname not in metadata:
                 raise KeyError(
-                    'Metadata field "%s" not found for file %s' % (fname, self.inputs.in_file)
+                    f'Metadata field "{fname}" not found for file {self.inputs.in_file}'
                 )
             self._results[fname] = metadata.get(fname, Undefined)
         return runtime
@@ -1423,7 +1423,7 @@ def _run_interface(self, runtime):
                 if dest.exists():
                     continue
                 else:
-                    raise FileNotFoundError("Expected to find '%s' to copy" % source)
+                    raise FileNotFoundError(f"Expected to find '{source}' to copy")
 
             if (
                 space == 'fsaverage'

niworkflows/interfaces/cifti.py

@@ -164,7 +164,7 @@ def _run_interface(self, runtime):
         return runtime
 
 
-def _prepare_cifti(grayordinates: str) -> typing.Tuple[list, str, dict]:
+def _prepare_cifti(grayordinates: str) -> tuple[list, str, dict]:
     """
     Fetch the required templates needed for CIFTI-2 generation, based on input surface density.
 
@@ -249,8 +249,8 @@ def _prepare_cifti(grayordinates: str) -> typing.Tuple[list, str, dict]:
 def _create_cifti_image(
     bold_file: str,
     volume_label: str,
-    bold_surfs: typing.Tuple[str, str],
-    surface_labels: typing.Tuple[str, str],
+    bold_surfs: tuple[str, str],
+    surface_labels: tuple[str, str],
     tr: float,
     metadata: typing.Optional[dict] = None,
 ):

niworkflows/interfaces/confounds.py

@@ -297,13 +297,13 @@ def spike_regressors(
     mask = reduce(operator.or_, mask.values())
 
     for lag in lags:
-        mask = set([m + lag for m in mask]) | mask
+        mask = {m + lag for m in mask} | mask
 
     mask = mask.intersection(indices)
     if minimum_contiguous is not None:
         post_final = data.shape[0] + 1
-        epoch_length = np.diff(sorted(mask | set([-1, post_final]))) - 1
-        epoch_end = sorted(mask | set([post_final]))
+        epoch_length = np.diff(sorted(mask | {-1, post_final})) - 1
+        epoch_end = sorted(mask | {post_final})
         for end, length in zip(epoch_end, epoch_length):
             if length < minimum_contiguous:
                 mask = mask | set(range(end - length, end))
@@ -356,7 +356,7 @@ def temporal_derivatives(order, variables, data):
     if 0 in order:
         data_deriv[0] = data[variables]
         variables_deriv[0] = variables
-        order = set(order) - set([0])
+        order = set(order) - {0}
     for o in order:
         variables_deriv[o] = [f'{v}_derivative{o}' for v in variables]
         data_deriv[o] = np.tile(np.nan, data[variables].shape)
@@ -399,7 +399,7 @@ def exponential_terms(order, variables, data):
     if 1 in order:
         data_exp[1] = data[variables]
         variables_exp[1] = variables
-        order = set(order) - set([1])
+        order = set(order) - {1}
     for o in order:
         variables_exp[o] = [f'{v}_power{o}' for v in variables]
         data_exp[o] = data[variables] ** o

niworkflows/interfaces/fixes.py

@@ -69,7 +69,7 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
         _copyxform(
             self.inputs.reference_image,
             os.path.abspath(self._gen_filename('output_image')),
-            message='%s (niworkflows v%s)' % (self.__class__.__name__, __version__),
+            message=f'{self.__class__.__name__} (niworkflows v{__version__})',
         )
         return runtime
 
@@ -109,7 +109,7 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
             _copyxform(
                 self.inputs.fixed_image[0],
                 os.path.abspath(out_file),
-                message='%s (niworkflows v%s)' % (self.__class__.__name__, __version__),
+                message=f'{self.__class__.__name__} (niworkflows v{__version__})',
             )
 
         # Inverse transform
@@ -118,7 +118,7 @@ def _run_interface(self, runtime, correct_return_codes=(0,)):
             _copyxform(
                 self.inputs.moving_image[0],
                 os.path.abspath(out_file),
-                message='%s (niworkflows v%s)' % (self.__class__.__name__, __version__),
+                message=f'{self.__class__.__name__} (niworkflows v{__version__})',
             )
 
         return runtime

niworkflows/interfaces/freesurfer.py

@@ -565,7 +565,7 @@ def mri_info(fname, argument):
 
     import numpy as np
 
-    cmd_info = 'mri_info --%s %s' % (argument, fname)
+    cmd_info = f'mri_info --{argument} {fname}'
     proc = sp.Popen(cmd_info, stdout=sp.PIPE, shell=True)
     data = bytearray(proc.stdout.read())
     mstring = np.fromstring(data.decode('utf-8'), sep='\n')

niworkflows/interfaces/header.py

@@ -99,7 +99,7 @@ def _run_interface(self, runtime):
                 _copyxform(
                     self.inputs.hdr_file,
                     out_name,
-                    message='CopyXForm (niworkflows v%s)' % __version__,
+                    message=f'CopyXForm (niworkflows v{__version__})',
                 )
                 self._results[f].append(out_name)
 
@@ -306,7 +306,7 @@ def _run_interface(self, runtime):
     Analyses of this dataset MAY BE INVALID.
 </p>
 """
-        snippet = '<h3 class="elem-title">%s</h3>\n%s\n' % (warning_txt, description)
+        snippet = f'<h3 class="elem-title">{warning_txt}</h3>\n{description}\n'
         # Store new file and report
         img.to_filename(out_fname)
         with open(out_report, 'w') as fobj:
@@ -522,10 +522,7 @@ def _run_interface(self, runtime):
             img.to_filename(out_fname)
 
         if warning_txt:
-            snippet = '<h3 class="elem-title">%s</h3>\n%s\n' % (
-                warning_txt,
-                description,
-            )
+            snippet = f'<h3 class="elem-title">{warning_txt}</h3>\n{description}\n'
             with open(out_report, 'w') as fobj:
                 fobj.write(indent(snippet, '\t' * 3))