updated readme #33
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ "main", "release" ] | |
| pull_request: | |
| branches: [ "main", "release" ] | |
| jobs: | |
| lint: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: "3.10" | |
| - name: Set up pre-commit | |
| run: python -m pip install pre-commit && pre-commit install | |
| - name: Run pre-commit | |
| run: pre-commit run --all-files | |
| test: | |
| runs-on: ubuntu-latest | |
| needs: lint | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.9", "3.10", "3.11"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install ".[test]" | |
| - name: Test with pytest | |
| run: | | |
| pytest | |
| - name: Codecov | |
| # You may pin to the exact commit or the version. | |
| # uses: codecov/codecov-action@eaaf4bedf32dbdc6b720b63067d99c4d77d6047d | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| uses: codecov/[email protected] | |
| with: | |
| # Specify whether the Codecov output should be verbose | |
| verbose: true # optional | |
| docker_test: | |
| runs-on: ubuntu-latest | |
| needs: [lint] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install ".[build]" | |
| - name: build wheel | |
| run: python -m build | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| # Docker Setup | |
| - name: Build Docker image | |
| id: dockerbuild | |
| run: | | |
| docker build -t ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") . | |
| # Quick test on the docker image | |
| - name: Test Docker image | |
| run: | | |
| docker run --rm -v ${PWD}:/data/ \ | |
| ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") \ | |
| flimsay fill_blib /data/tests/unit_tests/data/test.blib /data/out.blib | |
| publish: | |
| runs-on: ubuntu-latest | |
| if: startsWith(github.event_name, 'push') && startsWith(github.ref, 'refs/heads/release') | |
| needs: [lint, test, docker_test] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install ".[build]" | |
| - name: Set up quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - name: Render README | |
| run: quarto render README.qmd | |
| - name: build wheel | |
| run: python -m build | |
| - name: pypi-publish | |
| uses: pypa/[email protected] | |
| with: | |
| # Password for your PyPI user or an access token | |
| password: ${{ secrets.PYPI_TOKEN }} # optional | |
| # The target directory for distribution | |
| packages-dir: dist # optional | |
| # Show verbose output. | |
| verbose: true # optional, default is false | |
| skip-existing: true | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Login to the GitHub Container Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| # Docker Setup | |
| - name: Build Docker image | |
| id: dockerbuild | |
| run: | | |
| docker build -t ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") . | |
| # Quick test on the docker image | |
| - name: Test Docker image | |
| run: | | |
| docker run --rm -v ${PWD}:/data/ ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") \ | |
| flimsay fill_blib /data/tests/unit_tests/data/test.blib /data/out.blib | |
| # Publish Docker | |
| - name: Push the Docker image to the GHCR | |
| id: ghcr_push | |
| run: | | |
| docker push ghcr.io/talusbio/flimsay:v$(python -c "import flimsay ; print(flimsay.__version__)") |