STY: ruff --fix smriprep [git-blame-ignore-rev]

Author: effigies

smriprep/__about__.py

@@ -38,6 +38,4 @@
 ]
 __url__ = 'https://github.com/nipreps/smriprep'
 
-DOWNLOAD_URL = 'https://github.com/nipreps/{name}/archive/{ver}.tar.gz'.format(
-    name=__package__, ver=__version__
-)
+DOWNLOAD_URL = f'https://github.com/nipreps/{__package__}/archive/{__version__}.tar.gz'

smriprep/cli/run.py

@@ -43,14 +43,15 @@ def check_deps(workflow):
 
 def get_parser():
     """Build parser object."""
+    from argparse import ArgumentParser, RawTextHelpFormatter
     from pathlib import Path
-    from argparse import ArgumentParser
-    from argparse import RawTextHelpFormatter
+
     from niworkflows.utils.spaces import (
+        OutputReferencesAction,
         Reference,
         SpatialReferences,
-        OutputReferencesAction,
     )
+
     from ..__about__ import __version__
 
     parser = ArgumentParser(
@@ -318,13 +319,14 @@ def get_parser():
 
 def build_opts(opts):
     """Trigger a new process that builds the workflow graph, based on the input options."""
-    import os
-    from pathlib import Path
+    import gc
     import logging
+    import os
     import sys
-    import gc
     import warnings
-    from multiprocessing import set_start_method, Process, Manager
+    from multiprocessing import Manager, Process, set_start_method
+    from pathlib import Path
+
     from nipype import logging as nlogging
     from niworkflows.utils.misc import check_valid_fs_license
 
@@ -409,16 +411,17 @@ def _warn_redirect(message, category, filename, lineno, file=None, line=None):
         errno = 1
     else:
         if opts.run_reconall:
-            from templateflow import api
             from niworkflows.utils.misc import _copy_any
+            from templateflow import api
 
             dseg_tsv = str(api.get('fsaverage', suffix='dseg', extension=['.tsv']))
             _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aseg_dseg.tsv'))
             _copy_any(dseg_tsv, str(Path(output_dir) / 'smriprep' / 'desc-aparcaseg_dseg.tsv'))
         logger.log(25, 'sMRIPrep finished without errors')
     finally:
         from niworkflows.reports import generate_reports
-        from ..utils.bids import write_derivative_description, write_bidsignore
+
+        from ..utils.bids import write_bidsignore, write_derivative_description
 
         logger.log(25, 'Writing reports for participants: %s', ', '.join(subject_list))
         # Generate reports phase
@@ -439,17 +442,19 @@ def build_workflow(opts, retval):
     a hard-limited memory-scope.
 
     """
-    from shutil import copyfile
-    from os import cpu_count
+    import json
     import uuid
     import warnings
+    from os import cpu_count
+    from shutil import copyfile
+    from subprocess import CalledProcessError, TimeoutExpired, check_call
     from time import strftime
-    from subprocess import check_call, CalledProcessError, TimeoutExpired
 
-    import json
     from bids import BIDSLayout
-    from nipype import logging, config as ncfg
+    from nipype import config as ncfg
+    from nipype import logging
     from niworkflows.utils.bids import collect_participants
+
     from ..__about__ import __version__
     from ..data import load_resource
     from ..workflows.base import init_smriprep_wf

smriprep/conftest.py

@@ -1,7 +1,7 @@
 import os
 
-import pytest
 import numpy
+import pytest
 
 from smriprep.data import load_resource
 

smriprep/data/__init__.py

@@ -8,9 +8,9 @@
     from functools import lru_cache as cache
 
 try:  # Prefer backport to leave consistency to dependency spec
-    from importlib_resources import files, as_file
+    from importlib_resources import as_file, files
 except ImportError:
-    from importlib.resources import files, as_file
+    from importlib.resources import as_file, files
 
 __all__ = ['load_resource']
 

smriprep/interfaces/cifti.py

@@ -1,12 +1,11 @@
 import json
-from pathlib import Path
 import typing as ty
+from pathlib import Path
 
 import nibabel as nb
 import numpy as np
-
 from nibabel import cifti2 as ci
-from nipype.interfaces.base import TraitedSpec, traits, File, SimpleInterface
+from nipype.interfaces.base import File, SimpleInterface, TraitedSpec, traits
 from templateflow import api as tf
 
 
@@ -52,7 +51,7 @@ def _run_interface(self, runtime):
         return runtime
 
 
-def _prepare_cifti(grayordinates: str) -> ty.Tuple[list, dict]:
+def _prepare_cifti(grayordinates: str) -> tuple[list, dict]:
     """
     Fetch the required templates needed for CIFTI-2 generation, based on input surface density.
 
@@ -133,8 +132,8 @@ def _prepare_cifti(grayordinates: str) -> ty.Tuple[list, dict]:
 
 
 def _create_cifti_image(
-    scalar_surfs: ty.Tuple[str, str],
-    surface_labels: ty.Tuple[str, str],
+    scalar_surfs: tuple[str, str],
+    surface_labels: tuple[str, str],
     scalar_name: str,
     metadata: ty.Optional[dict] = None,
 ):

smriprep/interfaces/freesurfer.py

@@ -22,11 +22,12 @@
 #
 """Nipype's recon-all replacement."""
 import os
+
 from looseversion import LooseVersion
 from nipype import logging
-from nipype.utils.filemanip import check_depends
-from nipype.interfaces.base import traits, InputMultiObject, isdefined, File
 from nipype.interfaces import freesurfer as fs
+from nipype.interfaces.base import File, InputMultiObject, isdefined, traits
+from nipype.utils.filemanip import check_depends
 from niworkflows.interfaces import freesurfer as nwfs
 
 iflogger = logging.getLogger('nipype.interface')

smriprep/interfaces/reports.py

@@ -22,26 +22,24 @@
 #
 """Interfaces to generate reportlets."""
 
-from pathlib import Path
 import time
+from pathlib import Path
 
+from nipype.interfaces import freesurfer as fs
 from nipype.interfaces.base import (
-    TraitedSpec,
     BaseInterfaceInputSpec,
-    File,
     Directory,
+    File,
     InputMultiObject,
+    SimpleInterface,
     Str,
+    TraitedSpec,
     isdefined,
-    SimpleInterface,
 )
-from nipype.interfaces import freesurfer as fs
 from nipype.interfaces.io import FSSourceInputSpec as _FSSourceInputSpec
 from nipype.interfaces.mixins import reporting
-
 from niworkflows.interfaces.reportlets.base import _SVGReportCapableInputSpec
 
-
 SUBJECT_TEMPLATE = """\
 \t<ul class="elem-desc">
 \t\t<li>Subject ID: {subject_id}</li>
@@ -173,12 +171,12 @@ class FSSurfaceReport(SimpleInterface):
     output_spec = _FSSurfaceReportOutputSpec
 
     def _run_interface(self, runtime):
+        from nibabel import load
         from niworkflows.viz.utils import (
-            plot_registration,
-            cuts_from_bbox,
             compose_view,
+            cuts_from_bbox,
+            plot_registration,
         )
-        from nibabel import load
 
         rootdir = Path(self.inputs.subjects_dir) / self.inputs.subject_id
         _anat_file = str(rootdir / 'mri' / 'brain.mgz')

smriprep/interfaces/surf.py

@@ -25,17 +25,16 @@
 from pathlib import Path
 from typing import Optional
 
-import numpy as np
 import nibabel as nb
 import nitransforms as nt
-
+import numpy as np
 from nipype.interfaces.base import (
     BaseInterfaceInputSpec,
-    TraitedSpec,
-    SimpleInterface,
     File,
-    isdefined,
     InputMultiObject,
+    SimpleInterface,
+    TraitedSpec,
+    isdefined,
     traits,
 )
 
@@ -140,9 +139,9 @@ class AggregateSurfaces(SimpleInterface):
     output_spec = AggregateSurfacesOutputSpec
 
     def _run_interface(self, runtime):
-        from collections import defaultdict
         import os
         import re
+        from collections import defaultdict
 
         container = defaultdict(list)
         inputs = (self.inputs.surfaces or []) + (self.inputs.morphometrics or [])

smriprep/interfaces/templateflow.py

@@ -22,16 +22,17 @@
 #
 """Interfaces to get templates from TemplateFlow."""
 import logging
-from templateflow import api as tf
+
 from nipype.interfaces.base import (
-    SimpleInterface,
     BaseInterfaceInputSpec,
+    File,
+    InputMultiObject,
+    SimpleInterface,
     TraitedSpec,
     isdefined,
     traits,
-    File,
-    InputMultiObject,
 )
+from templateflow import api as tf
 
 LOGGER = logging.getLogger('nipype.interface')
 

smriprep/interfaces/tests/test_surf.py

@@ -1,22 +1,22 @@
 import nibabel as nb
-from nipype.pipeline import engine as pe
 import numpy as np
+from nipype.pipeline import engine as pe
 
 from ...data import load_resource
 from ..surf import MakeRibbon
 
 
 def test_MakeRibbon(tmp_path):
     res_template = '{path}/sub-fsaverage_res-4_hemi-{hemi}_desc-cropped_{surf}dist.nii.gz'
-    white, pial = [
+    white, pial = (
         [
             load_resource(
                 res_template.format(path='../interfaces/tests/data', hemi=hemi, surf=surf)
             )
             for hemi in 'LR'
         ]
         for surf in ('wm', 'pial')
-    ]
+    )
 
     make_ribbon = pe.Node(
         MakeRibbon(white_distvols=white, pial_distvols=pial),