cicd: add basic precommit hooks #1274
Workflow file for this run
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| name: Python CQA | |
| on: [push, pull_request] | |
| # TODO: separate lint and test jobs; lint first, test "needs" lint | |
| # https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobs | |
| jobs: | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| env: | |
| SEQREPO_ROOT_DIR: ./tests/data/seqrepo/latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-test-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Update pip and setuptools | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| - name: Install dependencies | |
| run: | | |
| pip install -e .[dev,extras] | |
| - name: Test with pytest | |
| run: | | |
| python -m pytest | |
| precommit_hooks: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| hook: | |
| - cmd: "end-of-file-fixer" | |
| - cmd: "trailing-whitespace" | |
| - cmd: "mixed-line-ending" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-precommit-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.12 | |
| - name: Update pip and setuptools | |
| run: | | |
| python -m pip install --upgrade pip setuptools | |
| - name: Install dependencies | |
| run: | | |
| pip install -e .[dev] | |
| - name: Run pre-commit ${{ matrix.hook.cmd }} command | |
| run: pre-commit run ${{ matrix.hook.cmd }} --all-files |