chore/sty: Replace black+flake8 with ruff, add pre-commit (#904)

* sty: Disable black, configure ruff

* sty: ruff format [ignore-rev]

Follow-up with ruff check --select ISC001 --fix

* sty: ruff check --fix [ignore-rev]

* rf: Remove unused sphinxext modules

* sty: ruff check --fix --unsafe-fixes, reviewed and curated

Follow up with ruff format and ruff check --select ISC001 --fix

* sty: Manual fixes for remaining checks

* Add pre-commit configuration

* sty: Apply pre-commit hooks

* chore: Remove flake8 config

* chore(pre-commit): Improve names for ruff hooks

* chore: Move codespell config to pyproject.toml

* ci: Run tox checks

* ci: Rename workflow to tox.yml

.github/workflows/pythonpackage.yml → .github/workflows/tox.yml

@@ -158,13 +158,20 @@ jobs:
           token: ${{ secrets.CODECOV_TOKEN }}
         if: ${{ always() }}
 
-  flake8:
-    if: github.event_name != 'schedule'
-    runs-on: ubuntu-latest
+  checks:
+    runs-on: 'ubuntu-latest'
+    continue-on-error: true
+    strategy:
+      matrix:
+        check: ['style', 'spellcheck']
+
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python 3
-      uses: actions/setup-python@v5
-      with:
-        python-version: 3
-    - run: pipx run flake8 niworkflows/
+      - uses: actions/checkout@v4
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v3
+      - name: Show tox config
+        run: uvx tox c
+      - name: Show tox config (this call)
+        run: uvx tox c -e ${{ matrix.check }}
+      - name: Run check
+        run: uvx tox -e ${{ matrix.check }}

.pre-commit-config.yaml

@@ -0,0 +1,24 @@
+exclude: ".*/data/.*"
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+        exclude: 'examples'
+      - id: end-of-file-fixer
+        exclude: 'examples|docs/_static/.*\.(css|js)'
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.7.4
+    hooks:
+      - name: ruff check --fix
+        id: ruff
+        args: [ --fix ]
+      - name: ruff format
+        id: ruff-format
+      - name: fix implicit string concatenation
+        id: ruff
+        args: [ --select, ISC001, --fix ]

LICENSE

@@ -199,4 +199,3 @@
    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
    See the License for the specific language governing permissions and
    limitations under the License.
-

docker/fetch_templates.py

@@ -19,11 +19,11 @@ def fetch_MNI2009():
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg.nii.gz
     """
-    template = "MNI152NLin2009cAsym"
+    template = 'MNI152NLin2009cAsym'
 
-    tf.get(template, resolution=2, desc="brain", suffix="mask")
-    tf.get(template, resolution=2, desc="fMRIPrep", suffix="boldref")
-    tf.get(template, resolution=1, label="brain", suffix="probseg")
+    tf.get(template, resolution=2, desc='brain', suffix='mask')
+    tf.get(template, resolution=2, desc='fMRIPrep', suffix='boldref')
+    tf.get(template, resolution=1, label='brain', suffix='probseg')
 
 
 def fetch_MNI152Lin():
@@ -33,10 +33,10 @@ def fetch_MNI152Lin():
     tpl-MNI152Lin/tpl-MNI152Lin_res-02_T1w.nii.gz
     tpl-MNI152Lin/tpl-MNI152Lin_res-02_desc-brain_mask.nii.gz
     """
-    template = "MNI152Lin"
+    template = 'MNI152Lin'
 
-    tf.get(template, resolution=2, desc=None, suffix="T1w")
-    tf.get(template, resolution=2, desc="brain", suffix="mask")
+    tf.get(template, resolution=2, desc=None, suffix='T1w')
+    tf.get(template, resolution=2, desc='brain', suffix='mask')
 
 
 def fetch_OASIS():
@@ -50,13 +50,13 @@ def fetch_OASIS():
     tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-brain_mask.nii.gz
     tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
     """
-    template = "OASIS30ANTs"
+    template = 'OASIS30ANTs'
 
-    tf.get(template, resolution=1, desc="4", suffix="dseg")
-    tf.get(template, resolution=1, desc=None, suffix="T1w")
-    tf.get(template, resolution=1, label="brain", suffix="mask")
-    tf.get(template, resolution=1, desc="BrainCerebellumExtraction", suffix="mask")
-    tf.get(template, resolution=1, label="brain", suffix="probseg")
+    tf.get(template, resolution=1, desc='4', suffix='dseg')
+    tf.get(template, resolution=1, desc=None, suffix='T1w')
+    tf.get(template, resolution=1, label='brain', suffix='mask')
+    tf.get(template, resolution=1, desc='BrainCerebellumExtraction', suffix='mask')
+    tf.get(template, resolution=1, label='brain', suffix='probseg')
 
 
 def fetch_fsaverage():
@@ -70,10 +70,10 @@ def fetch_fsaverage():
     tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_midthickness.surf.gii
     tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_midthickness.surf.gii
     """
-    template = "fsaverage"
+    template = 'fsaverage'
 
-    tf.get(template, density="164k", desc="std", suffix="sphere")
-    tf.get(template, density="164k", suffix="midthickness")
+    tf.get(template, density='164k', desc='std', suffix='sphere')
+    tf.get(template, density='164k', suffix='midthickness')
 
 
 def fetch_fsLR():
@@ -89,7 +89,7 @@ def fetch_fsLR():
     tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-L_den-32k_sphere.surf.gii
     tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-R_den-32k_sphere.surf.gii
     """
-    tf.get("fsLR", density="32k")
+    tf.get('fsLR', density='32k')
 
 
 def fetch_all():
@@ -100,21 +100,21 @@ def fetch_all():
     fetch_fsLR()
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     parser = argparse.ArgumentParser(
-        description="Helper script for pre-caching required templates to run fMRIPrep",
+        description='Helper script for pre-caching required templates to run fMRIPrep',
     )
     parser.add_argument(
-        "--tf-dir",
+        '--tf-dir',
         type=os.path.abspath,
-        help="Directory to save templates in. If not provided, templates will be saved to"
-        " `${HOME}/.cache/templateflow`.",
+        help='Directory to save templates in. If not provided, templates will be saved to'
+        ' `${HOME}/.cache/templateflow`.',
     )
     opts = parser.parse_args()
 
     # set envvar (if necessary) prior to templateflow import
     if opts.tf_dir is not None:
-        os.environ["TEMPLATEFLOW_HOME"] = opts.tf_dir
+        os.environ['TEMPLATEFLOW_HOME'] = opts.tf_dir
 
     import templateflow.api as tf