chore(main): release 0.2.10 #2389
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| name: LAPIS-SILO | |
| on: | |
| push: | |
| concurrency: | |
| group: ci-${{ github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| DOCKER_DEPENDENCY_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo-dependencies | |
| DOCKER_IMAGE_NAME: ghcr.io/genspectrum/lapis-silo | |
| jobs: | |
| formatting-check: | |
| name: Formatting Check | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| path: | |
| - check: 'src' | |
| - check: 'include' | |
| exclude: '(PerfEvent.hpp)' | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Run clang-format style check | |
| uses: jidicula/clang-format-action@v4.13.0 | |
| with: | |
| clang-format-version: '17' | |
| check-path: ${{ matrix.path['check'] }} | |
| exclude-regex: ${{ matrix.path['exclude'] }} | |
| dependencyImage: | |
| name: Build Docker Image Dependencies | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Generate dependency files hash | |
| id: files-hash | |
| run: | | |
| DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_dependencies') }}) | |
| echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV | |
| - name: Docker metadata | |
| id: dockerMetadata | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }} | |
| tags: | | |
| type=ref,event=branch | |
| type=raw,value=latest,enable=${{ github.ref == 'refs/heads/main' }} | |
| type=raw,value=${{ env.DIR_HASH }} | |
| type=sha,format=long,prefix=commit- | |
| - name: Login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Check if image exists | |
| id: check-image | |
| run: | | |
| EXISTS=$(docker manifest inspect ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} > /dev/null 2>&1 && echo "true" || echo "false") | |
| echo "CACHE_HIT=$EXISTS" >> $GITHUB_ENV | |
| - name: Set up Docker Buildx | |
| if: env.CACHE_HIT == 'false' | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build and push image if input files changed | |
| if: env.CACHE_HIT == 'false' | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: Dockerfile_dependencies | |
| push: true | |
| tags: ${{ steps.dockerMetadata.outputs.tags }} | |
| cache-from: type=gha,ref=builder-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile') }} | |
| cache-to: type=gha,mode=min,ref=builder-image-cache-${{ hashFiles('conanfile.py', 'Dockerfile') }} | |
| platforms: linux/amd64,linux/arm64 | |
| - name: Retag and push existing image if cache hit | |
| if: env.CACHE_HIT == 'true' | |
| run: | | |
| TAGS=(${{ steps.dockerMetadata.outputs.tags }}) | |
| for TAG in "${TAGS[@]}"; do | |
| docker buildx imagetools create --tag $TAG ${{ env.DOCKER_DEPENDENCY_IMAGE_NAME }}:${{ env.DIR_HASH }} | |
| done | |
| dockerImageUnitTests: | |
| name: Build Docker Image and Run Unit Tests | |
| runs-on: ubuntu-latest | |
| needs: dependencyImage | |
| permissions: | |
| packages: write | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Generate dependency files hash | |
| id: files-hash | |
| run: | | |
| DIR_HASH=$(echo -n ${{ hashFiles('conanfile.py', 'conanprofile.docker', '.github/workflows/ci.yml', './Dockerfile_dependencies') }}) | |
| echo "DIR_HASH=$DIR_HASH" >> $GITHUB_ENV | |
| - name: Docker metadata | |
| id: dockerMetadata | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.DOCKER_IMAGE_NAME }} | |
| tags: | | |
| type=ref,event=branch | |
| type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'main') }} | |
| type=sha,format=long,prefix=commit- | |
| - name: Login to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build unit test image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| target: builder | |
| tags: builder | |
| load: true | |
| cache-from: type=gha,ref=${{ github.ref_name }}-image-cache | |
| cache-to: type=gha,mode=min,ref=${{ github.ref_name }}-image-cache | |
| build-args: | | |
| DEPENDENCY_IMAGE=ghcr.io/genspectrum/lapis-silo-dependencies:${{ env.DIR_HASH }} | |
| - name: Run tests | |
| uses: addnab/docker-run-action@v3 | |
| with: | |
| image: builder | |
| run: ./silo_test | |
| - name: Build and push production image | |
| if: ${{ github.event_name == 'push' }} | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| push: true | |
| platforms: ${{ github.ref == 'refs/heads/main' && 'linux/amd64,linux/arm64' || 'linux/amd64' }} | |
| tags: ${{ steps.dockerMetadata.outputs.tags }} | |
| build-args: | | |
| DEPENDENCY_IMAGE=ghcr.io/genspectrum/lapis-silo-dependencies:${{ env.DIR_HASH }} | |
| endToEndTests: | |
| name: Run End To End Tests | |
| needs: dockerImageUnitTests | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| preprocessing-docker-compose: [ | |
| docker-compose-for-tests-preprocessing-from-tsv.yml, | |
| docker-compose-for-tests-preprocessing-from-ndjson.yml | |
| ] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Use Node.js ${{ matrix.node-version }} | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: 18.x | |
| - uses: actions/cache@v4 | |
| with: | |
| path: ~/.npm | |
| key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }} | |
| - name: npm install | |
| run: cd endToEndTests && npm ci | |
| - name: Check Format | |
| run: cd endToEndTests && npm run check-format | |
| - name: Docker Metadata | |
| id: dockerMetadata | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.DOCKER_IMAGE_NAME }} | |
| tags: type=ref,event=branch | |
| - name: Start Docker Container and preprocess data | |
| run: docker compose -f ${{ matrix.preprocessing-docker-compose }} up | |
| env: | |
| SILO_IMAGE: ${{ steps.dockerMetadata.outputs.tags }} | |
| - name: Start Docker Container and run api | |
| run: docker compose -f docker-compose-for-tests-api.yml up -d --wait | |
| env: | |
| SILO_IMAGE: ${{ steps.dockerMetadata.outputs.tags }} | |
| - name: Run Tests | |
| run: cd endToEndTests && SILO_URL=localhost:8080 npm run test |