Run ruff format.

.circleci/get_data.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Download test data."""
+
 import sys
 
 from aslprep.tests.utils import download_test_data

aslprep/__about__.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Base module variables."""
+
 try:
     from aslprep._version import __version__
 except ImportError:

aslprep/cli/aggregate_qc.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Aggregate QC measures across all subjects in dataset."""
+
 import os
 from pathlib import Path
 

aslprep/cli/parser.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Parser."""
+
 import sys
 
 from aslprep import config
@@ -252,7 +253,7 @@ def _bids_filter(value, parser):
         default=False,
         help=(
             "only generate reports, don't run workflows. This will only rerun report "
-            "aggregation, not reportlet generation for specific nodes."
+            'aggregation, not reportlet generation for specific nodes.'
         ),
     )
 
@@ -473,7 +474,7 @@ def _bids_filter(value, parser):
         help=(
             "determiner for T1-weighted skull stripping ('force' ensures skull "
             "stripping, 'skip' ignores skull stripping, and 'auto' applies brain extraction "
-            "based on the outcome of a heuristic to check whether the brain is already masked)."
+            'based on the outcome of a heuristic to check whether the brain is already masked).'
         ),
     )
 

aslprep/cli/run.py

@@ -22,6 +22,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """ASL preprocessing workflow."""
+
 from aslprep import config
 
 

aslprep/config.py

@@ -87,6 +87,7 @@
     :py:class:`~bids.layout.BIDSLayout`, etc.)
 
 """
+
 import os
 from multiprocessing import set_start_method
 

aslprep/interfaces/__init__.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Nipype interfaces for aslprep."""
+
 from aslprep.interfaces import (
     ants,
     bids,

aslprep/interfaces/cbf.py

@@ -843,7 +843,7 @@ class _BASILCBFInputSpec(FSLCommandInputSpec):
     )
     alpha = traits.Float(
         desc=(
-            "Inversion efficiency - [default: 0.98 (pASL); 0.85 (cASL)]. "
+            'Inversion efficiency - [default: 0.98 (pASL); 0.85 (cASL)]. '
             "This is equivalent to the BIDS metadata field 'LabelingEfficiency'."
         ),
         argstr='--alpha %.2f',

aslprep/interfaces/confounds.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Interfaces for calculating and collecting confounds."""
+
 import json
 import os
 
@@ -337,8 +338,8 @@ def _run_interface(self, runtime):
             'rmsd': {
                 'LongName': 'Mean Relative Root Mean Squared',
                 'Description': (
-                    "Average relative root mean squared calculated from motion parameters, "
-                    "after removal of dummy volumes and high-motion outliers. "
+                    'Average relative root mean squared calculated from motion parameters, '
+                    'after removal of dummy volumes and high-motion outliers. '
                     "Relative in this case means 'relative to the previous scan'."
                 ),
                 'Units': 'arbitrary',

aslprep/interfaces/parcellation.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Handling functional connectvity."""
+
 import nibabel as nb
 import numpy as np
 import pandas as pd
@@ -117,16 +118,16 @@ def _run_interface(self, runtime):
 
         if n_poor_parcels:
             LOGGER.warning(
-                f"{n_poor_parcels}/{n_nodes} of parcels have <50% coverage. "
+                f'{n_poor_parcels}/{n_nodes} of parcels have <50% coverage. '
                 "These parcels' time series will be replaced with zeros."
             )
 
         if n_partial_parcels:
             LOGGER.warning(
-                f"{n_partial_parcels}/{n_nodes} of parcels have at least one uncovered "
-                "voxel, but have enough good voxels to be usable. "
+                f'{n_partial_parcels}/{n_nodes} of parcels have at least one uncovered '
+                'voxel, but have enough good voxels to be usable. '
                 "The bad voxels will be ignored and the parcels' time series will be "
-                "calculated from the remaining voxels."
+                'calculated from the remaining voxels.'
             )
 
         masker = NiftiLabelsMasker(

aslprep/interfaces/reports.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Interfaces to generate reportlets."""
+
 import os
 import re
 import time

aslprep/interfaces/utility.py

@@ -44,7 +44,7 @@ def _run_interface(self, runtime):
         if asl_img.shape[3] != aslcontext.shape[0]:
             raise ValueError(
                 f"Number of volumes in {self.inputs.asl_file} ({asl_img.shape[3]}) doesn't equal "
-                f"number of rows in {self.inputs.aslcontext} ({aslcontext.shape[0]})."
+                f'number of rows in {self.inputs.aslcontext} ({aslcontext.shape[0]}).'
             )
 
         if self.inputs.processing_target == 'control':
@@ -227,13 +227,9 @@ def _run_interface(self, runtime):
         out_mat_files = [None] * aslcontext.shape[0]
 
         if len(self.inputs.volume_types) != len(self.inputs.mat_files):
-            raise ValueError(
-                'Number of volume types and number of mat files must be the same.'
-            )
+            raise ValueError('Number of volume types and number of mat files must be the same.')
         if len(self.inputs.volume_types) != len(self.inputs.par_files):
-            raise ValueError(
-                'Number of volume types and number of par files must be the same.'
-            )
+            raise ValueError('Number of volume types and number of par files must be the same.')
 
         for i_type, volume_type in enumerate(self.inputs.volume_types):
             type_mat_files = self.inputs.mat_files[i_type]

aslprep/tests/conftest.py

@@ -9,6 +9,7 @@
 def pytest_addoption(parser):
     """Collect pytest parameters for running tests."""
     import tempfile
+
     parser.addoption('--working_dir', action='store', default=tempfile.mkdtemp())
     parser.addoption('--data_dir', action='store')
     parser.addoption('--output_dir', action='store')

aslprep/tests/run_local_tests.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Run tests locally by calling Docker."""
+
 import argparse
 import os
 import subprocess

aslprep/tests/tests.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Utilities and mocks for testing and documentation building."""
+
 import os
 import shutil
 from contextlib import contextmanager

aslprep/utils/asl.py

@@ -17,7 +17,7 @@ def pcasl_or_pasl(metadata):
         is_casl = False
     else:
         raise ValueError(
-            "Labeling type cannot be classified as (P)CASL or PASL based on "
+            'Labeling type cannot be classified as (P)CASL or PASL based on '
             f"ArterialSpinLabelingType: '{aslt}'."
         )
 
@@ -185,7 +185,7 @@ def reduce_metadata_lists(metadata, n_volumes, keep_idx):
         if isinstance(value, list):
             if len(value) != n_volumes:
                 raise ValueError(
-                    f"Number of elements in list-type metadata field {field} ({len(value)}) "
+                    f'Number of elements in list-type metadata field {field} ({len(value)}) '
                     f"doesn't equal the number of volumes in the ASL file ({n_volumes})."
                 )
             # Reduce to only the selected volumes

aslprep/utils/bids.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Utilities to handle BIDS inputs."""
+
 from __future__ import annotations
 
 import json

aslprep/utils/misc.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Miscellaneous utilities."""
+
 from __future__ import annotations
 
 import os

aslprep/utils/sentry.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Stripped out routines for Sentry."""
+
 import os
 import re
 

aslprep/workflows/asl/__init__.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Workflows for the ASL processing portions of ASLPrep."""
+
 from aslprep.workflows.asl import (
     apply,
     base,

aslprep/workflows/asl/cbf.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Workflows for calculating CBF."""
+
 import numpy as np
 from nipype.interfaces import utility as niu
 from nipype.interfaces.fsl import Info

aslprep/workflows/asl/confounds.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Workflows for calculating confounds for ASL data."""
+
 from fmriprep.workflows.bold.confounds import _carpet_parcellation
 from nipype.algorithms import confounds as nac
 from nipype.interfaces import utility as niu

aslprep/workflows/asl/fit.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Fit workflows for ASLPrep."""
+
 import os
 import typing as ty
 

aslprep/workflows/asl/hmc.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Workflows for estimating and correcting head motion in ASL images."""
+
 from nipype.interfaces import fsl
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe

aslprep/workflows/asl/plotting.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Workflows for plotting ASLPrep derivatives."""
+
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow

aslprep/workflows/asl/reference.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Workflows for generating reference images."""
+
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow

aslprep/workflows/asl/resampling.py

@@ -24,6 +24,7 @@
 
 TODO: Remove once fMRIPrep releases 23.2.0.
 """
+
 from __future__ import annotations
 
 import typing as ty

aslprep/workflows/base.py

@@ -1,6 +1,7 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """ASLprep base processing workflows."""
+
 import os
 import sys
 import warnings

docs/conf.py

@@ -295,8 +295,7 @@
 linkcode_resolve = make_linkcode_resolve(
     'aslprep',
     (
-        'https://github.com/pennlinc/aslprep/blob/'
-        '{revision}/{package}/{path}#L{lineno}'  # noqa: FS003
+        'https://github.com/pennlinc/aslprep/blob/' '{revision}/{package}/{path}#L{lineno}'  # noqa: FS003
     ),
 )