Improved Benchmark (#166) #177
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| name: Container Builds | |
| on: | |
| push: | |
| branches: | |
| - 'main' | |
| jobs: | |
| build-docker: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v2 | |
| with: | |
| username: ${{ secrets.DOCKERHUB_USERNAME }} | |
| password: ${{ secrets.DOCKERHUB_TOKEN }} | |
| - name: Build and push container | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: . | |
| file: Dockerfile | |
| push: true | |
| tags: | | |
| jeffquinnmsk/nuc2seg:latest | |
| jeffquinnmsk/nuc2seg:${{ github.sha }} | |
| cache-from: type=registry,ref=jeffquinnmsk/nuc2seg:latest | |
| cache-to: type=inline | |
| - name: Build and push container | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: containers/spatialdata | |
| file: containers/spatialdata/Dockerfile | |
| push: true | |
| tags: | | |
| jeffquinnmsk/spatialdata:latest | |
| jeffquinnmsk/spatialdata:${{ github.sha }} | |
| cache-from: type=registry,ref=jeffquinnmsk/spatialdata:latest | |
| - name: Build and push container | |
| uses: docker/build-push-action@v3 | |
| with: | |
| context: containers/sopa | |
| file: containers/sopa/Dockerfile | |
| push: true | |
| tags: | | |
| jeffquinnmsk/sopa:latest | |
| jeffquinnmsk/sopa:${{ github.sha }} | |
| cache-from: type=registry,ref=jeffquinnmsk/sopa:latest | |
| nextflow-integration: | |
| runs-on: ubuntu-20.04 | |
| name: pytest | |
| needs: build-docker | |
| env: | |
| NXF_ANSI_LOG: false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.x" | |
| - uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('pyproject.toml') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pytest-workflow cryptography | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Run pytest-workflow | |
| working-directory: ./nextflow | |
| run: TMPDIR=~ PROFILE=docker pytest --symlink --kwdof --git-aware --color=yes |