CI: Pass ruff tests (#3243)

Apply the very simple fixes suggested by ruff.

Fixes CI failures, probably related to a recent ruff upgrade.

.maint/paper_author_list.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Generate an author list for a new paper or abstract."""
+
 import json
 import sys
 from pathlib import Path

.maint/update_authors.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Update and sort the creators list of the zenodo record."""
+
 import json
 import sys
 from pathlib import Path

.maint/update_zenodo.py

@@ -1,5 +1,6 @@
 #!/usr/bin/env python3
 """Update and sort the creators list of the zenodo record."""
+
 import json
 import sys
 from pathlib import Path

docs/sphinxext/github_link.py

@@ -2,6 +2,7 @@
 This vendored script comes from scikit-learn:
 https://github.com/scikit-learn/scikit-learn/blob/master/doc/sphinxext/github_link.py
 """
+
 import inspect
 import os
 import subprocess

fmriprep/_warnings.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Manipulate Python warnings."""
+
 import logging
 import warnings
 

fmriprep/cli/parser.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Parser."""
+
 import sys
 
 from .. import config

fmriprep/cli/run.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """fMRI preprocessing workflow."""
+
 from .. import config
 
 

fmriprep/cli/tests/test_parser.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test parser."""
+
 from argparse import ArgumentError
 from contextlib import nullcontext
 

fmriprep/cli/tests/test_version.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Test version checks."""
+
 from datetime import datetime, timezone
 from os import getenv, geteuid
 from pathlib import Path

fmriprep/config.py

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

fmriprep/interfaces/confounds.py

@@ -29,6 +29,7 @@
     >>> import pandas as pd
 
 """
+
 import os
 import re
 

fmriprep/interfaces/gifti.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 manipulating GIFTI files."""
+
 import os
 
 import nibabel as nb

fmriprep/interfaces/multiecho.py

@@ -27,6 +27,7 @@
 For using multi-echo EPI data.
 
 """
+
 import os
 
 from nipype import logging

fmriprep/interfaces/workbench.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:
 """This module provides interfaces for workbench surface commands."""
+
 import os
 
 from nipype import logging

fmriprep/tests/test_config.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Check the configuration module and file."""
+
 import os
 from unittest.mock import patch
 

fmriprep/utils/bids.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Utilities to handle BIDS inputs."""
+
 from __future__ import annotations
 
 import json

fmriprep/utils/misc.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Miscellaneous utilities."""
+
 from functools import cache
 
 

fmriprep/utils/telemetry.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Stripped out routines for telemetry"""
+
 import os
 import re
 

fmriprep/workflows/bold/confounds.py

@@ -27,6 +27,7 @@
 .. autofunction:: init_bold_confs_wf
 
 """
+
 from nipype.algorithms import confounds as nac
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe

fmriprep/workflows/bold/outputs.py

@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Writing out derivative files."""
+
 from __future__ import annotations
 
 import numpy as np

fmriprep/workflows/bold/registration.py

@@ -29,6 +29,7 @@
 .. autofunction:: init_fsl_bbr_wf
 
 """
+
 import os
 import os.path as op
 import typing as ty

fmriprep/workflows/bold/resampling.py

@@ -30,6 +30,7 @@
 .. autofunction:: init_goodvoxels_bold_mask_wf
 
 """
+
 from __future__ import annotations
 
 import typing as ty

fmriprep/workflows/bold/stc.py

@@ -27,6 +27,7 @@
 .. autofunction:: init_bold_stc_wf
 
 """
+
 import nibabel as nb
 import numpy as np
 from nipype.interfaces import afni

fmriprep/workflows/bold/t2s.py

@@ -27,6 +27,7 @@
 .. autofunction:: init_bold_t2s_wf
 
 """
+
 import typing as ty
 
 from nipype.interfaces import utility as niu

fmriprep/workflows/tests/__init__.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

wrapper/src/fmriprep_docker/__main__.py

@@ -15,6 +15,7 @@
 `NiPreps documentation <https://www.nipreps.org/intro/transparency/#citation-boilerplates>`__.
 Please report any feedback to our `GitHub repository <https://github.com/nipreps/fmriprep>`__.
 """
+
 import os
 import re
 import subprocess