From 6572d1ed92a3d008d983b77ebda139105201b962 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos Orfanos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Fri, 1 Mar 2024 01:30:21 +0100
Subject: [PATCH] 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 +
 .maint/update_authors.py                | 1 +
 .maint/update_zenodo.py                 | 1 +
 docs/sphinxext/github_link.py           | 1 +
 fmriprep/_warnings.py                   | 1 +
 fmriprep/cli/parser.py                  | 1 +
 fmriprep/cli/run.py                     | 1 +
 fmriprep/cli/tests/test_parser.py       | 1 +
 fmriprep/cli/tests/test_version.py      | 1 +
 fmriprep/config.py                      | 1 +
 fmriprep/interfaces/confounds.py        | 1 +
 fmriprep/interfaces/gifti.py            | 1 +
 fmriprep/interfaces/multiecho.py        | 1 +
 fmriprep/interfaces/workbench.py        | 1 +
 fmriprep/tests/test_config.py           | 1 +
 fmriprep/utils/bids.py                  | 1 +
 fmriprep/utils/misc.py                  | 1 +
 fmriprep/utils/telemetry.py             | 1 +
 fmriprep/workflows/bold/confounds.py    | 1 +
 fmriprep/workflows/bold/outputs.py      | 1 +
 fmriprep/workflows/bold/registration.py | 1 +
 fmriprep/workflows/bold/resampling.py   | 1 +
 fmriprep/workflows/bold/stc.py          | 1 +
 fmriprep/workflows/bold/t2s.py          | 1 +
 fmriprep/workflows/tests/__init__.py    | 1 +
 wrapper/src/fmriprep_docker/__main__.py | 1 +
 26 files changed, 26 insertions(+)

diff --git a/.maint/paper_author_list.py b/.maint/paper_author_list.py
index 579b61ca0..a6300c635 100755
--- a/.maint/paper_author_list.py
+++ b/.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
diff --git a/.maint/update_authors.py b/.maint/update_authors.py
index d2b1b639a..263f88631 100755
--- a/.maint/update_authors.py
+++ b/.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
diff --git a/.maint/update_zenodo.py b/.maint/update_zenodo.py
index b1d35ef2c..5b30707b8 100755
--- a/.maint/update_zenodo.py
+++ b/.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
diff --git a/docs/sphinxext/github_link.py b/docs/sphinxext/github_link.py
index 2fe41b66b..fabba0ab5 100644
--- a/docs/sphinxext/github_link.py
+++ b/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
diff --git a/fmriprep/_warnings.py b/fmriprep/_warnings.py
index 70a32cc7e..e4563750b 100644
--- a/fmriprep/_warnings.py
+++ b/fmriprep/_warnings.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Manipulate Python warnings."""
+
 import logging
 import warnings
 
diff --git a/fmriprep/cli/parser.py b/fmriprep/cli/parser.py
index 822815ffb..f7c8581ed 100644
--- a/fmriprep/cli/parser.py
+++ b/fmriprep/cli/parser.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Parser."""
+
 import sys
 
 from .. import config
diff --git a/fmriprep/cli/run.py b/fmriprep/cli/run.py
index d095440fe..1ebd14841 100644
--- a/fmriprep/cli/run.py
+++ b/fmriprep/cli/run.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """fMRI preprocessing workflow."""
+
 from .. import config
 
 
diff --git a/fmriprep/cli/tests/test_parser.py b/fmriprep/cli/tests/test_parser.py
index f27d4e14b..0fbca9eee 100644
--- a/fmriprep/cli/tests/test_parser.py
+++ b/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
 
diff --git a/fmriprep/cli/tests/test_version.py b/fmriprep/cli/tests/test_version.py
index 753dd9ea8..c4eb2d5b6 100644
--- a/fmriprep/cli/tests/test_version.py
+++ b/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
diff --git a/fmriprep/config.py b/fmriprep/config.py
index 96deb1046..337b463ca 100644
--- a/fmriprep/config.py
+++ b/fmriprep/config.py
@@ -87,6 +87,7 @@
     :py:class:`~bids.layout.BIDSLayout`, etc.)
 
 """
+
 import os
 from multiprocessing import set_start_method
 
diff --git a/fmriprep/interfaces/confounds.py b/fmriprep/interfaces/confounds.py
index 299a99286..410b46194 100644
--- a/fmriprep/interfaces/confounds.py
+++ b/fmriprep/interfaces/confounds.py
@@ -29,6 +29,7 @@
     >>> import pandas as pd
 
 """
+
 import os
 import re
 
diff --git a/fmriprep/interfaces/gifti.py b/fmriprep/interfaces/gifti.py
index 54a537acd..517e5c375 100644
--- a/fmriprep/interfaces/gifti.py
+++ b/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
diff --git a/fmriprep/interfaces/multiecho.py b/fmriprep/interfaces/multiecho.py
index ab03ffe25..51ad6a8f0 100644
--- a/fmriprep/interfaces/multiecho.py
+++ b/fmriprep/interfaces/multiecho.py
@@ -27,6 +27,7 @@
 For using multi-echo EPI data.
 
 """
+
 import os
 
 from nipype import logging
diff --git a/fmriprep/interfaces/workbench.py b/fmriprep/interfaces/workbench.py
index 5c20dee51..6c3330a61 100644
--- a/fmriprep/interfaces/workbench.py
+++ b/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
diff --git a/fmriprep/tests/test_config.py b/fmriprep/tests/test_config.py
index 2a6b8dadd..c4222280c 100644
--- a/fmriprep/tests/test_config.py
+++ b/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
 
diff --git a/fmriprep/utils/bids.py b/fmriprep/utils/bids.py
index 700f30def..57bc29269 100644
--- a/fmriprep/utils/bids.py
+++ b/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
diff --git a/fmriprep/utils/misc.py b/fmriprep/utils/misc.py
index 6f7973913..5183f9397 100644
--- a/fmriprep/utils/misc.py
+++ b/fmriprep/utils/misc.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Miscellaneous utilities."""
+
 from functools import cache
 
 
diff --git a/fmriprep/utils/telemetry.py b/fmriprep/utils/telemetry.py
index c95067a68..35b05b91f 100644
--- a/fmriprep/utils/telemetry.py
+++ b/fmriprep/utils/telemetry.py
@@ -21,6 +21,7 @@
 #     https://www.nipreps.org/community/licensing/
 #
 """Stripped out routines for telemetry"""
+
 import os
 import re
 
diff --git a/fmriprep/workflows/bold/confounds.py b/fmriprep/workflows/bold/confounds.py
index f16904633..bdd7c1990 100644
--- a/fmriprep/workflows/bold/confounds.py
+++ b/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
diff --git a/fmriprep/workflows/bold/outputs.py b/fmriprep/workflows/bold/outputs.py
index 094484156..798e42b69 100644
--- a/fmriprep/workflows/bold/outputs.py
+++ b/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
diff --git a/fmriprep/workflows/bold/registration.py b/fmriprep/workflows/bold/registration.py
index c08a4fa94..6824fc526 100644
--- a/fmriprep/workflows/bold/registration.py
+++ b/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
diff --git a/fmriprep/workflows/bold/resampling.py b/fmriprep/workflows/bold/resampling.py
index b5f13ee0b..e632b7577 100644
--- a/fmriprep/workflows/bold/resampling.py
+++ b/fmriprep/workflows/bold/resampling.py
@@ -30,6 +30,7 @@
 .. autofunction:: init_goodvoxels_bold_mask_wf
 
 """
+
 from __future__ import annotations
 
 import typing as ty
diff --git a/fmriprep/workflows/bold/stc.py b/fmriprep/workflows/bold/stc.py
index 0a820c184..5f5ef7329 100644
--- a/fmriprep/workflows/bold/stc.py
+++ b/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
diff --git a/fmriprep/workflows/bold/t2s.py b/fmriprep/workflows/bold/t2s.py
index 313593a79..e7a347414 100644
--- a/fmriprep/workflows/bold/t2s.py
+++ b/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
diff --git a/fmriprep/workflows/tests/__init__.py b/fmriprep/workflows/tests/__init__.py
index e6c33399e..53c1c521f 100644
--- a/fmriprep/workflows/tests/__init__.py
+++ b/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
diff --git a/wrapper/src/fmriprep_docker/__main__.py b/wrapper/src/fmriprep_docker/__main__.py
index 44d6e1a3b..622f35926 100755
--- a/wrapper/src/fmriprep_docker/__main__.py
+++ b/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