test: ignore existing NCBI_API_KEY env var #125
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Python package | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| cqa: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --use-deprecated=legacy-resolver -e .[dev] | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Format check with isort | |
| run: | | |
| isort --check src | |
| - name: Format check with Ruff | |
| run: | | |
| ruff format --check src | |
| # Disable bandit until issues are resolved | |
| # - name: Security check with bandit | |
| # run: | | |
| # bandit -ll -r src | |
| test: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install --use-deprecated=legacy-resolver -e .[test] | |
| - name: Test with pytest | |
| run: | | |
| make test | |
| deploy: | |
| needs: | |
| - cqa | |
| - test | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: hello world | |
| run: | | |
| echo "::group::Environment info" | |
| echo github.event_name = ${{ github.event_name }} | |
| echo refs = ${{ github.ref }} | |
| echo tags = ${{ startsWith(github.ref, 'refs/tags') }} | |
| echo "::endgroup::" | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| cache: pip | |
| cache-dependency-path: '**/setup.cfg' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install build | |
| - name: Build package | |
| run: python -m build --wheel | |
| - name: Publish package | |
| if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags') | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| password: ${{ secrets.PYPI_API_TOKEN }} |