refactor: upgrade FOCA & major app rewrite #18
Workflow file for this run
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| name: cwl-WES checks | |
| on: | |
| push: | |
| branches: [dev] | |
| pull_request: | |
| branches: [dev] | |
| jobs: | |
| lint: | |
| name: Run linting | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.7" | |
| - name: Install requirements | |
| run: | | |
| pip install . | |
| pip install -r requirements_dev.txt | |
| - name: Lint with Flake8 | |
| run: flake8 cwl_wes/ setup.py | |
| - name: Lint with Pylint | |
| run: pylint cwl_wes/ setup.py | |
| test: | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Deploy app | |
| run: docker-compose up -d --build | |
| - name: Wait for app startup | |
| shell: bash | |
| run: sleep 20 | |
| - name: Run integration tests | |
| shell: bash | |
| run: bash tests/integration_tests.sh | |
| - name: Tear down app | |
| run: docker-compose down | |
| publish: | |
| name: Build and publish app image | |
| runs-on: ubuntu-latest | |
| if: ${{ github.event_name == 'push' }} | |
| needs: [lint, test] | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v3 | |
| - name: Generate tag | |
| run: | | |
| echo "TAG=$(date '+%Y%m%d')" >> $GITHUB_ENV | |
| - name: Build and publish image | |
| id: docker | |
| uses: philips-software/docker-ci-scripts@v5.0.0 | |
| with: | |
| dockerfile: . | |
| image-name: "cwl-wes" | |
| tags: "latest ${{ env.TAG }}" | |
| push-branches: "${{ github.event.repository.default_branch }}" | |
| env: | |
| REGISTRY_USERNAME: ${{ secrets.DOCKERHUB_LOGIN }} | |
| REGISTRY_TOKEN: "${{ secrets.DOCKERHUB_TOKEN }}" | |
| DOCKER_ORGANIZATION: ${{ secrets.DOCKERHUB_ORG }} | |
| GITHUB_ORGANIZATION: ${{ github.repository_owner }} | |
| - name: Verify that image was pushed | |
| run: | | |
| echo "Push indicator: ${{ steps.docker.outputs.push-indicator }}" | |
| echo "# Set to 'true' if image was pushed, empty string otherwise" | |
| test "${{ steps.docker.outputs.push-indicator }}" == "true" |