Potential fix for code scanning alert no. 3: Workflow does not contain permissions #159
Workflow file for this run
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| name: Tests | |
| on: | |
| push: | |
| branches: [ master, main, develop ] | |
| pull_request: | |
| branches: [ master, main, develop ] | |
| schedule: | |
| # Run tests daily at 2 AM UTC to catch any dependency issues | |
| - cron: '0 2 * * *' | |
| permissions: | |
| contents: read | |
| jobs: | |
| test: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| python-version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13'] | |
| exclude: | |
| - os: windows-latest | |
| python-version: '3.8' | |
| - os: windows-latest | |
| python-version: '3.9' | |
| - os: windows-latest | |
| python-version: '3.10' | |
| - os: windows-latest | |
| python-version: '3.11' | |
| - os: windows-latest | |
| python-version: '3.13' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip setuptools wheel | |
| pip install numpy scipy | |
| pip install -e ".[dev]" | |
| - name: Cache pip wheels | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.cache/pip | |
| key: pip-${{ runner.os }}-${{ matrix.python-version }}-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: | | |
| pip-${{ runner.os }}-${{ matrix.python-version }}- | |
| - name: Install OpenBabel | |
| run: pip install openbabel-wheel | |
| continue-on-error: true | |
| - name: Run tests with pytest | |
| run: | | |
| if [[ "${{ matrix.os }}" == "ubuntu-latest" && "${{ matrix.python-version }}" == "3.12" ]]; then | |
| pytest -v --cov=chempy --cov-report=xml | |
| else | |
| pytest -q | |
| fi | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' | |
| with: | |
| files: ./coverage.xml | |
| flags: unittests | |
| name: codecov-umbrella | |
| fail_ci_if_error: false | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| quality: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| python-version: ['3.12', '3.13'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: 'pip' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -e ".[dev]" | |
| - name: Check formatting with black | |
| run: black --check chempy unittest | |
| continue-on-error: true | |
| - name: Check import sorting with isort | |
| run: isort --check-only chempy unittest | |
| continue-on-error: true | |
| - name: Lint with flake8 | |
| run: | | |
| flake8 chempy unittest --max-line-length=100 --extend-ignore=E203,W503,E501 | |
| continue-on-error: true | |
| - name: Type check with mypy | |
| run: mypy chempy --ignore-missing-imports | |
| continue-on-error: true |