STY: Manually review style issues

Author: effigies

smriprep/cli/run.py

@@ -595,6 +595,8 @@ def build_workflow(opts, retval):
         smriprep_dir = str(output_dir / 'smriprep')
         warnings.warn(
             f'Received DEPRECATED --fast-track flag. Adding {smriprep_dir} to --derivatives list.'
+            f'Received DEPRECATED --fast-track flag. Adding {smriprep_dir} to --derivatives list.',
+            stacklevel=1,
         )
         derivatives.append(smriprep_dir)
 

smriprep/interfaces/cifti.py

@@ -1,5 +1,4 @@
 import json
-import typing as ty
 from pathlib import Path
 
 import nibabel as nb
@@ -135,7 +134,7 @@ def _create_cifti_image(
     scalar_surfs: tuple[str, str],
     surface_labels: tuple[str, str],
     scalar_name: str,
-    metadata: ty.Optional[dict] = None,
+    metadata: dict | None = None,
 ):
     """
     Generate CIFTI image in target space.

smriprep/interfaces/surf.py

@@ -23,7 +23,6 @@
 """Handling surfaces."""
 import os
 from pathlib import Path
-from typing import Optional
 
 import nibabel as nb
 import nitransforms as nt
@@ -183,9 +182,7 @@ def _run_interface(self, runtime):
         return runtime
 
 
-def normalize_surfs(
-    in_file: str, transform_file: str | None, newpath: Optional[str] = None
-) -> str:
+def normalize_surfs(in_file: str, transform_file: str | None, newpath: str | None = None) -> str:
     """
     Update GIFTI metadata and apply rigid coordinate correction.
 
@@ -242,7 +239,7 @@ def normalize_surfs(
     return out_file
 
 
-def fix_gifti_metadata(in_file: str, newpath: Optional[str] = None) -> str:
+def fix_gifti_metadata(in_file: str, newpath: str | None = None) -> str:
     """Fix known incompatible metadata in GIFTI files.
 
     Currently resolves:
@@ -269,15 +266,15 @@ def fix_gifti_metadata(in_file: str, newpath: Optional[str] = None) -> str:
 def make_ribbon(
     white_distvols: list[str],
     pial_distvols: list[str],
-    newpath: Optional[str] = None,
+    newpath: str | None = None,
 ) -> str:
     base_img = nb.load(white_distvols[0])
     header = base_img.header
     header.set_data_dtype('uint8')
 
     ribbons = [
         (np.array(nb.load(white).dataobj) > 0) & (np.array(nb.load(pial).dataobj) < 0)
-        for white, pial in zip(white_distvols, pial_distvols)
+        for white, pial in zip(white_distvols, pial_distvols, strict=True)
     ]
 
     if newpath is None:

smriprep/workflows/anatomical.py

@@ -1541,7 +1541,7 @@ def _set_threads(in_list, maximum):
 
 
 def _pop(inlist):
-    if isinstance(inlist, (list, tuple)):
+    if isinstance(inlist, list | tuple):
         return inlist[0]
     return inlist
 

smriprep/workflows/fit/registration.py

@@ -115,8 +115,7 @@ def init_register_template_wf(
 and accessed with *TemplateFlow* [{tf_ver}, @templateflow]:
 """.format(
             ants_ver=ANTsInfo.version() or '(version unknown)',
-            targets='%s standard space%s'
-            % (
+            targets='{} standard space{}'.format(
                 defaultdict('several'.format, {1: 'one', 2: 'two', 3: 'three', 4: 'four'})[ntpls],
                 's' * (ntpls != 1),
             ),

smriprep/workflows/outputs.py

@@ -1199,7 +1199,7 @@ def init_template_iterator_wf(*, spaces, name='template_iterator_wf'):
 def _bids_relative(in_files, bids_root):
     from pathlib import Path
 
-    if not isinstance(in_files, (list, tuple)):
+    if not isinstance(in_files, list | tuple):
         in_files = [in_files]
     ret = []
     for file in in_files:

smriprep/workflows/surfaces.py

@@ -697,10 +697,10 @@ def init_fsLR_reg_wf(*, name='fsLR_reg_wf'):
 
     # Via
     # ${CARET7DIR}/wb_command -surface-sphere-project-unproject
-    #   "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii
-    #   "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
-    #   "$AtlasSpaceFolder"/fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
-    #   "$AtlasSpaceFolder"/"$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
+    #   "$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.native.surf.gii
+    #   fsaverage/"$Subject"."$Hemisphere".sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
+    #   fsaverage/"$Subject"."$Hemisphere".def_sphere."$HighResMesh"k_fs_"$Hemisphere".surf.gii
+    #   "$NativeFolder"/"$Subject"."$Hemisphere".sphere.reg.reg_LR.native.surf.gii
     project_unproject = pe.MapNode(
         SurfaceSphereProjectUnproject(),
         iterfield=['sphere_in', 'sphere_project_to', 'sphere_unproject_from'],
@@ -820,7 +820,7 @@ def init_msm_sulc_wf(*, sloppy: bool = False, name: str = 'msm_sulc_wf'):
 
 def init_gifti_surfaces_wf(
     *,
-    surfaces: list[str] = ['pial', 'midthickness', 'inflated', 'white'],
+    surfaces: list[str] = ('pial', 'midthickness', 'inflated', 'white'),
     to_scanner: bool = True,
     name: str = 'gifti_surface_wf',
 ):
@@ -917,7 +917,7 @@ def init_gifti_surfaces_wf(
 
 def init_gifti_morphometrics_wf(
     *,
-    morphometrics: list[str] = ['thickness', 'curv', 'sulc'],
+    morphometrics: list[str] = ('thickness', 'curv', 'sulc'),
     name: str = 'gifti_morphometrics_wf',
 ):
     r"""