Build Container Image for Naive BBS #212
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| name: Build Container Image for Naive BBS | |
| on: | |
| workflow_dispatch: | |
| push: | |
| paths: | |
| - "**/Dockerfile" | |
| schedule: | |
| - cron: '0 0 */2 * *' | |
| # Avoids Github UI bugs https://github.com/orgs/community/discussions/45969 | |
| env: | |
| BUILDX_NO_DEFAULT_ATTESTATIONS: 1 | |
| BUILDKIT_STEP_LOG_MAX_SIZE: 50000000 | |
| jobs: | |
| ghcrbuild: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| ubuntu: [jammy] | |
| platform: [linux/amd64] | |
| branch: [devel, release] | |
| name: Build container images for GHCR | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Free root space | |
| uses: almahmoud/free-root-space@main | |
| with: | |
| verbose: true | |
| - uses: actions/checkout@v3 | |
| - name: Extract metadata for container image | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: ghcr.io/${{ github.repository }} | |
| tags: | | |
| type=raw,value=${{ matrix.ubuntu }} | |
| - name: Extract container name without tag | |
| id: vars | |
| run: | | |
| echo container=$(echo '${{ steps.meta.outputs.tags }}' | awk -F':' '{print $1}') >> $GITHUB_OUTPUT | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v2 | |
| with: | |
| platforms: arm64 | |
| if: contains(steps.versions.outputs.platform, 'arm64') | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| with: | |
| platforms: ${{matrix.platform}} | |
| - name: Login to GHCR | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Build and push container image to ghcr | |
| id: build | |
| uses: docker/build-push-action@v4 | |
| with: | |
| build-args: CYCLE=${{matrix.branch}} | |
| labels: ${{ steps.meta.outputs.labels }} | |
| outputs: type=image,name=${{ steps.vars.outputs.container }},push-by-digest=true,name-canonical=true,push=true | |
| platforms: ${{matrix.platform}} | |
| provenance: false | |
| - name: Prepare Dockerfile to extract R version with emulator | |
| run: | | |
| mkdir -p ${{matrix.ubuntu}}-${{matrix.platform}} | |
| cat << "EOF" > ${{matrix.ubuntu}}-${{matrix.platform}}-r.Dockerfile | |
| FROM ${{ steps.vars.outputs.container }}@${{ steps.build.outputs.digest }} as extract | |
| USER root | |
| RUN mkdir /bioctmp && /bbs_r_start -e 'BiocManager::version()' | grep '\[1\]' | awk -F"'" '{print $2}' > /bioctmp/biocver && /bbs_r_start --slave -e 'cat(paste(version$major, version$minor, sep = "."))' > /bioctmp/rver && cat /etc/os-release > /bioctmp/os-release | |
| FROM scratch as export | |
| COPY --from=extract /bioctmp/* / | |
| EOF | |
| - name: Build and push container image to ghcr | |
| uses: docker/build-push-action@v4 | |
| with: | |
| file: ${{matrix.ubuntu}}-${{matrix.platform}}-r.Dockerfile | |
| context: . | |
| push: false | |
| load: false | |
| provenance: false | |
| outputs: type=tar,dest=${{matrix.ubuntu}}-${{matrix.platform}}/r.tar | |
| tags: ${{ steps.meta.outputs.tags }}-r | |
| platforms: ${{ matrix.platform }} | |
| - name: Extract rversion | |
| id: versions | |
| run: | | |
| cd ${{matrix.ubuntu}}-${{matrix.platform}} | |
| tar -xvf r.tar | |
| echo rver=$(cat rver) >> $GITHUB_OUTPUT | |
| echo biocver=$(cat biocver) >> $GITHUB_OUTPUT | |
| echo osver=$(awk -F= '/VERSION_ID/ {gsub("\"", "", $2); print $2}' os-release) >> $GITHUB_OUTPUT | |
| BASEPREFIX="" | |
| if [ '${{matrix.branch}}' == 'devel' ]; then BASEPREFIX="devel-"; fi | |
| echo baseprefix=$BASEPREFIX >> $GITHUB_OUTPUT | |
| - name: Export digest by ubuntu and r versions | |
| run: | | |
| R_VER_EXPECTED=$(curl https://bioconductor.org/config.yaml | yq e '.r_ver_for_bioc_ver."${{steps.versions.outputs.biocver}}"') | |
| R_VER_FOUND="${{steps.versions.outputs.rver}}" | |
| R_FOUND_MAJOR_MINOR=${R_VER_FOUND%.*} | |
| if [ "$R_FOUND_MAJOR_MINOR" != "$R_VER_EXPECTED" ]; then | |
| echo "Mismatched versions found '$R_VER_FOUND' and expected '$R_VER_EXPECTED'" | |
| exit 1 | |
| fi | |
| digest="${{ steps.build.outputs.digest }}" | |
| mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}} | |
| touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}/${digest#sha256:}" | |
| mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}} | |
| touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}" | |
| mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}} | |
| touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}" | |
| mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}} | |
| touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}/${digest#sha256:}" | |
| mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}} | |
| touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}" | |
| mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}} | |
| touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}" | |
| - name: Upload digests | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: r2udigests-${{ github.run_id }} | |
| path: /tmp/digests/** | |
| if-no-files-found: error | |
| retention-days: 1 | |
| merge: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - ghcrbuild | |
| if: always() | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| ubuntu: [jammy] | |
| steps: | |
| - name: Download digests | |
| uses: actions/download-artifact@v3 | |
| with: | |
| name: r2udigests-${{ github.run_id }} | |
| path: /tmp/digests | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| with: | |
| platforms: ${{matrix.platform}} | |
| - name: Login to GHCR | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Extract metadata for container image | |
| id: meta | |
| uses: docker/metadata-action@v4 | |
| with: | |
| images: ghcr.io/${{ github.repository }} | |
| tags: | | |
| type=raw,value=${{ matrix.ubuntu }} | |
| - name: Extract container name without tag | |
| id: vars | |
| run: | | |
| echo container=$(echo '${{ steps.meta.outputs.tags }}' | awk -F':' '{print $1}') >> $GITHUB_OUTPUT | |
| - name: Create manifest list and push | |
| run: | | |
| cd /tmp/digests | |
| ls --hide=digestdirs > digestdirs | |
| cat digestdirs | xargs -i bash -c 'docker buildx imagetools create -t ${{steps.vars.outputs.container}}:{} $(for f in {}/*; do basename "$f"; done | xargs printf "${{steps.vars.outputs.container}}@sha256:%s ")' |