fix: errors from tests #424
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| name: CI-CD | |
| # only run on pushes to main or pull requests | |
| on: | |
| push: | |
| # push to any branch * | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main , development ] | |
| jobs: | |
| Unit-Tests: | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 15 # Consider increasing timeout | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, macos-14] | |
| python-version: ["3.12", "3.11", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install dependencies | |
| run: poetry install | |
| - name: Test with pytest | |
| run: | | |
| # Github action runners now have 4 cores | |
| poetry run pytest -s -v -n 4 --cov --cov-report xml:coverage-report/coverage.xml | |
| - name: Upload coverage report artifact to be used by Codecov | |
| # only upload if matrix.os is ubuntu-latest and matrix.python-version is 3.12 | |
| if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.12' | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: coverage-report | |
| path: coverage-report | |
| Code-Coverage: | |
| needs: Unit-Tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Download coverage.xml artifact | |
| uses: actions/download-artifact@v2 | |
| with: | |
| name: coverage-report | |
| path: coverage-report | |
| - name: Use Codecov to track coverage | |
| uses: codecov/codecov-action@v3 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage-report/coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| name: codecov-umbrella | |
| Build-Documentation: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.10.4 | |
| - name: Install poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install dependencies | |
| run: poetry install | |
| - name: Build documentation | |
| run: | | |
| pip install -r docs/requirements.txt | |
| pip install . | |
| make html --directory=docs | |
| Continuous-Deployment: | |
| permissions: | |
| contents: write | |
| packages: write | |
| issues: write | |
| pull-requests: write | |
| needs: [Unit-Tests] | |
| # if pulling to main, deploy to PyPI | |
| if: github.ref == 'refs/heads/main' | |
| # Set up operating system | |
| runs-on: ubuntu-latest | |
| outputs: | |
| released: ${{ steps.release.outputs.released }} | |
| version: ${{ steps.release.outputs.version }} | |
| tag: ${{ steps.release.outputs.tag }} | |
| # Define job steps | |
| steps: | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.12 | |
| - name: Check-out repository | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Python Semantic Release | |
| id: release | |
| uses: python-semantic-release/python-semantic-release@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| Publish-To-PyPi: | |
| needs: Continuous-Deployment | |
| if: needs.Continuous-Deployment.outputs.released == 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout the code with tag ${{ needs.Continuous-Deployment.outputs.tag }} | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ needs.Continuous-Deployment.outputs.tag }} | |
| - name: Set up Python 3.12 | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: 3.12 | |
| - name: Install Package-Building Tool | |
| run: | |
| python3 -m pip install build twine | |
| - name: Build package | |
| run: | |
| python3 -m build --sdist --wheel --outdir dist/ | |
| - name: Publish to PyPI | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| verbose: true | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| Build-Docker-Images: | |
| needs: Continuous-Deployment | |
| if: needs.Continuous-Deployment.outputs.released == 'true' | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ needs.Continuous-Deployment.outputs.tag }} | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Login to the GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata (tags, labels) for Docker | |
| id: meta | |
| uses: docker/metadata-action@v3 | |
| with: | |
| images: | | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} | |
| ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} | |
| - name: Build and push Docker images | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| platforms: linux/amd64,linux/arm64 | |
| file: ./Dockerfile | |
| push: true | |
| tags: | | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} | |
| ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:latest | |
| ghcr.io/${{ github.repository }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} | |
| ghcr.io/${{ github.repository }}/nbiatoolkit:latest | |
| labels: ${{ steps.meta.outputs.labels }} | |
| Test-PyPi-Install: | |
| needs: Publish-To-PyPi | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest, macos-14] | |
| python-version: ["3.12", "3.11", "3.10"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install using PyPi | |
| run: | | |
| pip install nbiatoolkit==${{ needs.Continuous-Deployment.outputs.version }} | |
| NBIAToolkit | |
| Test-Docker-Image: | |
| needs: Build-Docker-Images | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| steps: | |
| - name: Setup Docker to pull images | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Install using Docker | |
| run: | | |
| docker pull ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }}; | |
| docker run --rm ${{ secrets.DOCKERHUB_USERNAME }}/nbiatoolkit:${{ needs.Continuous-Deployment.outputs.tag }} NBIAToolkit |