add new EPP for replacing flow cell output path (#455)(minor) #143
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: 'Merge-master-CI' | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| - 'main' | |
| jobs: | |
| bump-version: | |
| runs-on: ubuntu-latest | |
| name: Bump version and push tags to master | |
| steps: | |
| - name: Bump version | |
| uses: Clinical-Genomics/bump2version-ci@master | |
| env: | |
| BUMPVERSION_TOKEN: ${{ secrets.BUMPVERSION_TOKEN }} | |
| BUMPVERSION_AUTHOR: ${{ secrets.BUMPVERSION_AUTHOR }} | |
| BUMPVERSION_EMAIL: ${{ secrets.BUMPVERSION_EMAIL }} | |
| GITHUB_REPOSITORY: ${{ github.repository }} | |
| docker-image-push: | |
| runs-on: ubuntu-latest | |
| name: Push staging docker image to dockerhub | |
| steps: | |
| - name: Check out git repository | |
| uses: actions/checkout@v2 | |
| - name: Extract branch name and remove illegal chars | |
| id: get_branch_name | |
| shell: bash | |
| run: echo "##[set-output name=branch;]$(echo "$(tr "/" "-" <<<${GITHUB_REF#refs/heads/})")" | |
| - name: Login to Docker Hub | |
| uses: docker/login-action@v1 | |
| with: | |
| username: ${{ secrets.DOCKER_USERNAME }} | |
| password: ${{ secrets.DOCKER_PASSWORD }} | |
| - name: Set up Docker Buildx | |
| id: buildx | |
| uses: docker/setup-buildx-action@v1 | |
| - name: Build and push | |
| id: docker_build | |
| uses: docker/build-push-action@v2 | |
| with: | |
| context: ./ | |
| file: ./Dockerfile | |
| push: true | |
| tags: "clinicalgenomics/cg_lims-stage:${{steps.get_branch_name.outputs.branch}}, clinicalgenomics/cg_lims-stage:latest" | |
| tests-coverage: | |
| runs-on: ubuntu-latest | |
| name: Test and coveralls | |
| steps: | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Check out limsmock | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: "Clinical-Genomics/limsmock" | |
| - name: Install limsmock dependencies | |
| run: | | |
| python -m pip install --upgrade pip==21.1.2 | |
| pip install -r requirements.txt -r requirements-dev.txt . | |
| - name: Check out cg_lims | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: "Clinical-Genomics/cg_lims" | |
| - name: Install cg_lims dependencies | |
| run: | | |
| pip install -r requirements.txt -r requirements-dev.txt . | |
| - name: Install coveralls dependencies | |
| run: | | |
| pip install pytest-cov coveralls | |
| - name: Test with pytest & Coveralls | |
| run: | | |
| pytest --cov=cg_lims/ | |
| coveralls | |
| env: | |
| GITHUB: 1 | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }} |