Use ruff for linting (#1312)

.circleci/get_data.py

@@ -1,10 +1,11 @@
 #!/usr/bin/env python3
 """Download test data."""
+
 import sys
 
 from xcp_d.tests.utils import download_test_data
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     data_dir = sys.argv[1]
     dset = sys.argv[2]
     download_test_data(dset, data_dir)

.codespellrc

@@ -1,6 +1,8 @@
 [codespell]
-skip = .git,*.pdf,*.svg,*.html,dataset_description.json
+skip = .git,*.pdf,*.svg,*.html,dataset_description.json,*.gii
 # te - TE
 # Weill - name
 # reson - Reson. abbreviation in citation
-ignore-words-list = te,weill,reson
+# DNE: acronym for does not exist
+# fo: acronym for file object
+ignore-words-list = te,weill,reson,DNE,fo

.github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Lint code
+name: Contribution checks
 
 on:
   push:
@@ -12,26 +12,27 @@ defaults:
   run:
     shell: bash
 
-jobs:
-  stable:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        os: ['ubuntu-latest']
-        python-version: ["3.10"]
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
 
+jobs:
+  style:
+    runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
-        with:
-          python-version: ${{ matrix.python-version }}
-      - name: Display Python version
-        run: python -c "import sys; print(sys.version)"
-      - name: Install flake8 and related packages
-        run: python -m pip install \
-          flake8 flake8-absolute-import flake8-black flake8-docstrings \
-          flake8-isort flake8-pyproject flake8-unused-arguments \
-          flake8-use-fstring pep8-naming
-      - name: Check xcp_d
-        run: python -m flake8 xcp_d
+      - run: pipx run ruff check .
+      - run: pipx run ruff format --diff .
+
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.pre-commit-config.yaml

@@ -1,16 +1,21 @@
+exclude: ".*/data/.*"
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
--   repo: https://github.com/psf/black
-    rev: 23.1.0
+      - id: trailing-whitespace
+        exclude: '.*\.svg'
+      - id: end-of-file-fixer
+        exclude: '.*\.svg'
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.6.2
     hooks:
-    -   id: black
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-    -   id: isort
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+      - id: ruff
+        args: [ --select, ISC001, --fix ]

CODE_OF_CONDUCT.md

@@ -6,7 +6,7 @@ experience for everyone.
 
 Although no list can hope to be all-encompassing, we explicitly honor diversity in age,
 body size, disability, ethnicity, gender identity and expression, level of experience,
-native language, education, socio-economic status, nationality, personal appearance, race, religion,
+native language, education, socioeconomic status, nationality, personal appearance, race, religion,
 or sexual identity and orientation.
 
 ## Our Standards

docs/changes.md

@@ -152,7 +152,7 @@ This is a patch release that fixes two important bugs.
 The two bugs are:
 (1) band-pass filter values were not respected in versions 0.7.1 - 0.7.3 (they were hardcoded to 0.01 - 0.1) and
 (2) when processing CIFTI files, parcellated ReHo values in TSVs were not correct, due to a problem with how we were reconstructing CIFTI ReHo files.
-The dense CIFTI files should still be useable though.
+The dense CIFTI files should still be usable though.
 
 ### 🎉 Exciting New Features