close quotes properly #74
Workflow file for this run
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| # When a new release is published, | |
| # upload image to Dockerhub. | |
| # | |
| # Requires the following repository secrets: | |
| # - DOCKER_IMAGE - Configured as a secret so it can be configured per fork. | |
| # - DOCKER_HUB_USERNAME | |
| # - DOCKER_HUB_ACCESS_TOKEN | |
| # - GITHUBPAT - The github account to use for downloading CRAN dependencies. | |
| # Needed to avoid "API rate limit exceeded" from github. | |
| name: release docker | |
| on: | |
| push: | |
| tags: | |
| - 'v*' | |
| workflow_dispatch: | |
| env: | |
| DOCKER_IMAGE: 'ohdsi/deep_plp' | |
| jobs: | |
| build: | |
| name: "${{ matrix.config.arch }}" | |
| runs-on: ${{ matrix.config.runs_on}} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { runs_on: "ubuntu-latest", arch: "amd64"} | |
| - { runs_on: "ubuntu-latest", arch: "arm64"} | |
| steps: | |
| - name: Delete huge unnecessary tools folder | |
| run: rm -rf /opt/hostedtoolcache | |
| - name: Prepare | |
| run: | | |
| platform=${{ matrix.config.arch }} | |
| echo "PLATFORM_PAIR=${platform//\//-}" >> $GITHUB_ENV | |
| # Add Docker labels and tags | |
| - name: Docker meta | |
| id: docker_meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.DOCKER_IMAGE }} | |
| tags: | | |
| type=semver,pattern={{version}} | |
| # Setup docker build environment | |
| - name: Set up QEMU | |
| if: matrix.config.arch == 'arm64' | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | |
| - name: Set build parameters | |
| id: build_params | |
| run: | | |
| echo "SHA8=${GITHUB_SHA::8}" >> $GITHUB_ENV | |
| - name: Build and push by digest | |
| id: build | |
| uses: docker/build-push-action@v6 | |
| with: | |
| cache-from: type=gha | |
| cache-to: type=gha, mode=max | |
| platforms: "linux/${{ matrix.config.arch }}" | |
| secrets: | | |
| build_github_pat=${{ secrets.GH_TOKEN }} | |
| build-args: | | |
| GIT_BRANCH=${{ steps.docker_meta.outputs.version }} | |
| GIT_COMMIT_ID_ABBREV=${{ env.SHA8 }} | |
| ARCH=${{ matrix.config.arch }} | |
| # Use runtime labels from docker_meta as well as fixed labels | |
| labels: | | |
| ${{ steps.docker_meta.outputs.labels }} | |
| maintainer=Egill A. Fridgeirsson <[email protected]> | |
| org.opencontainers.image.authors=Egill A. Fridgeirsson <[email protected]>, Henrik John <[email protected]> | |
| org.opencontainers.image.vendor=OHDSI | |
| org.opencontainers.image.licenses=Apache-2.0 | |
| outputs: type=image, name=${{ env.DOCKER_IMAGE}}, push-by-digest=true, name-canonical=true, push=true | |
| - name: Export digest | |
| run: | | |
| mkdir -p /tmp/digests | |
| digest="${{ steps.build.outputs.digest }}" | |
| touch "/tmp/digests/${digest#sha256:}" | |
| - name: Upload digest | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: digests-${{ env.PLATFORM_PAIR }} | |
| path: /tmp/digests/* | |
| if-no-files-found: error | |
| retention-days: 1 | |
| test: | |
| name: "test-${{ matrix.config.arch }}-docker" | |
| runs-on: ${{ matrix.config.runs_on}} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { runs_on: "ubuntu-latest", arch: "amd64"} | |
| - { runs_on: "ubuntu-latest", arch: "arm64"} | |
| needs: build | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Download digests | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: /tmp/digests | |
| pattern: "digests-${{ matrix.config.arch }}*" | |
| merge-multiple: true | |
| - name: Run R CMD check | |
| run: | | |
| digest=$(ls /tmp/digests) | |
| # Run package checks | |
| docker run --rm \ | |
| --platform "linux/${{ matrix.config.arch }}" \ | |
| -e _R_CHECK_FORCE_SUGGESTS_=false \ | |
| -e _R_CHECK_CRAN_INCOMING_=false \ | |
| -v $(pwd):/workspace -w /workspace \ | |
| ${{ env.DOCKER_IMAGE }}@sha256:$digest Rscript -e \ | |
| "install.packages('rcmdcheck');rcmdcheck::rcmdcheck('.', args=c('--no-manual', '--as-cran'), build_args = '--no-manual', error_on = 'warning')" | |
| merge: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build | |
| - test | |
| steps: | |
| - name: Download digests | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: /tmp/digests | |
| pattern: digests-* | |
| merge-multiple: true | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Docker meta | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.DOCKER_IMAGE }} | |
| tags: | | |
| type=semver,pattern={{version}} | |
| - name: Login to DockerHub | |
| uses: docker/login-action@v3 | |
| with: | |
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | |
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | |
| - name: Create manifest list and push | |
| working-directory: /tmp/digests | |
| run: | | |
| docker buildx imagetools create $(jq -cr '.tags | map("-t " + .) | join(" ")' <<< "$DOCKER_METADATA_OUTPUT_JSON") \ | |
| $(printf '${{ env.DOCKER_IMAGE }}@sha256:%s ' *) | |
| - name: Inspect image | |
| run: | | |
| docker buildx imagetools inspect ${{ env.DOCKER_IMAGE }}:${{ steps.meta.outputs.version }} |