full-rstudio-build.yml

# This is a basic workflow to help you get started with Actions
name: Full rocker & bioc build

# Controls when the action will run. Triggers the workflow on push or pull request
# events but only for the master branch
on:
  workflow_dispatch:
    inputs:
      rver:
        default: "devel"
      biocver:
        default: "3.19"
      outname:
        default: "bioconductor_docker"
  schedule:
    - cron: '0 18 * * 5'

jobs:
  bump:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Push patch bump
        uses: nick-fields/retry@v2
        with:
          timeout_minutes: 10
          max_attempts: 50
          shell: bash
          command: |
            set -x
            git config --global --add safe.directory "$GITHUB_WORKSPACE"
            git config user.name github-actions
            git config user.email github-actions@github.com
            git pull origin main || git reset --hard origin/main
            sed -r -i 's/(^ARG BIOCONDUCTOR_PATCH=)([0-9]+)$/echo "\1$((\2+1))"/ge' Dockerfile
            git add Dockerfile
            git commit -m "Bump BIOCONDUCTOR_PATCH"
            git push
            
  build:
    outputs:
      registryuser: ${{ steps.defs.outputs.registryuser }}
      outname: ${{ steps.defs.outputs.outname }}
      rver: ${{ steps.defs.outputs.rver }}
    strategy:
      matrix:
        arch: [amd64, arm64]
    runs-on: ubuntu-latest
    needs: bump
    steps:
    # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
    - uses: actions/checkout@v3

    - name: Free root space
      uses: almahmoud/free-root-space@main
      with:
        verbose: true

    - name: Set defaults for schedule
      id: defs
      run: |
        echo outname=$(echo ${{ github.event.inputs.outname || 'bioconductor_docker' }}) >> $GITHUB_OUTPUT
        echo rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
        echo biocver=$(echo ${{ github.event.inputs.biocver || '3.19' }}) >> $GITHUB_OUTPUT
        echo registryuser=$(echo ${{ github.repository_owner }} | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
        echo rockerintermediateprefix=$(echo "ghcr.io/${{ github.repository_owner }}/rocker" | awk '{print tolower($0)}') >> $GITHUB_OUTPUT

    - name: Set up QEMU
      uses: docker/setup-qemu-action@v2
      with:
        platforms: arm64
      if: matrix.arch == 'arm64'

    - name: Login to GHCR
      uses: docker/login-action@v2
      with:
        registry: ghcr.io
        username: ${{ github.actor }}
        password: ${{ secrets.GITHUB_TOKEN }}

    - name: Login to Dockerhub
      uses: docker/login-action@v2
      with:
        username: ${{ secrets.DOCKER_USERNAME }}
        password: ${{ secrets.DOCKER_PASSWORD }}

    - name: Extract metadata for container image
      id: meta
      uses: docker/metadata-action@v4
      with:
        images: ${{ steps.defs.outputs.registryuser }}/${{ steps.defs.outputs.outname }}
        tags: |
          type=raw,value=${{ steps.defs.outputs.rver }}-${{ matrix.arch }}

    - name: Set comma-separated list with all repository names
      id: images
      run: |
        IMG=${{ steps.meta.outputs.tags }}
        REPOLIST="docker.io/$IMG,ghcr.io/$IMG"
        echo ghcr=$(echo "ghcr.io/$IMG") >> $GITHUB_OUTPUT
        SUB="_docker"
        # Also add alternative without _docker when in name
        echo list=$(if [[ $REPOLIST == *$SUB* ]]; then echo "$REPOLIST,$(echo $REPOLIST | sed 's/_docker//g')"; else echo $REPOLIST; fi) >> $GITHUB_OUTPUT

        ## git clone rocker
        git clone --depth 1 https://github.com/rocker-org/rocker-versioned2
        sed -i 's#rocker/r-ver:${{ steps.defs.outputs.rver }}#${{ steps.defs.outputs.rockerintermediateprefix }}-r-ver:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}#g' rocker-versioned2/dockerfiles/rstudio_${{ steps.defs.outputs.rver }}.Dockerfile
        sed -i 's#install_quarto.sh#install_quarto.sh || true#g' rocker-versioned2/dockerfiles/rstudio_${{ steps.defs.outputs.rver }}.Dockerfile
        echo "Bioconductor Version: ${{ steps.defs.outputs.biocver }}"
        if [ "${{ steps.defs.outputs.rver }}" = "devel" ]; then
            echo "Using devel pre-release R since Bioc devel version is odd";
            DEVEL_R_VER=$(curl https://bioconductor.org/config.yaml | grep '"${{ steps.defs.outputs.rver }}":' | awk '{print $2}' | sed 's/"//g')
            REL_VER=$(curl https://cran.r-project.org/src/base/VERSION-INFO.dcf | grep "$DEVEL_R_VER" | awk -F':' '{print $1}')
            # if the matching version is under release rather than devel, use patched pre-release rather than devel pre-release
            if [ "$REL_VER" == "Release" ]; then 
                sed -i 's#R_VERSION=${{ steps.defs.outputs.rver }}#R_VERSION=patched#g' rocker-versioned2/dockerfiles/r-ver_${{ steps.defs.outputs.rver }}.Dockerfile
            fi
        fi


    - name: Set up Docker Buildx
      uses: docker/setup-buildx-action@v2
      with:
        platforms: linux/${{ matrix.arch }}

    - name: Build and load r-ver
      uses: docker/build-push-action@v3
      with:
        file: rocker-versioned2/dockerfiles/r-ver_${{ steps.defs.outputs.rver }}.Dockerfile
        context: rocker-versioned2
        push: true
        tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-r-ver:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
        platforms: linux/${{ matrix.arch }}

    - name: Build and load rstudio
      uses: docker/build-push-action@v3
      with:
        file: rocker-versioned2/dockerfiles/rstudio_${{ steps.defs.outputs.rver }}.Dockerfile
        context: rocker-versioned2
        push: true
        tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-rstudio:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
        platforms: linux/${{ matrix.arch }}

    - name: Build and push container image to all repos both arm64 and amd64
      uses: docker/build-push-action@v3
      with:
        build-args: |
          BASE_IMAGE=${{ steps.defs.outputs.rockerintermediateprefix }}-rstudio
          arm64_tag=${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
          amd64_tag=${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
          BIOCONDUCTOR_VERSION=${{ steps.defs.outputs.biocver }}
        file: Dockerfile
        context: .
        push: true
        tags: ${{ steps.images.outputs.list }}
        labels: ${{ steps.meta.outputs.labels }}
        platforms: linux/${{ matrix.arch }}

  test-built-containers:
    strategy:
      matrix:
        arch: [arm64, amd64]
    # The type of runner that the job will run on
    runs-on: ubuntu-latest
    needs: build
    steps:
      - name: Get image name
        id: image
        run: |
          IMG=$(echo "${{needs.build.outputs.registryuser}}/${{ needs.build.outputs.outname }}:${{ needs.build.outputs.rver }}-${{ matrix.arch }}")
          echo name=$IMG >> $GITHUB_OUTPUT
          cat << EOF > test.Dockerfile
          FROM $IMG as test
          USER root
          RUN mkdir -p /tmp/bioc_test && \
              apt list --installed | tee /tmp/bioc_test/aptlist && \
              Rscript -e "BiocManager::install(c('SummarizedExperiment','usethis','data.table','igraph','GEOquery'))" 2>&1 | tee /tmp/bioc_test/packages_install && \
              Rscript -e "BiocManager::install('gert'); require('gert')" 2>&1 | tee /tmp/bioc_test/gert_install
          FROM scratch as export
          COPY --from=test /tmp/bioc_test /tmp
          EOF

      - name: Set up QEMU
        uses: docker/setup-qemu-action@v2
        with:
          platforms: arm64
        if: matrix.arch == 'arm64'

      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v2
        with:
          platforms: linux/${{ matrix.arch }}

      - name: Login to GHCR
        uses: docker/login-action@v2
        with:
          registry: ghcr.io
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}

      - name: Test via build
        id: dockerbuild
        uses: docker/build-push-action@v4
        with:
          file: test.Dockerfile
          context: .
          push: false
          load: false
          outputs: type=tar,dest=/tmp/image.tar
          tags: ${{ steps.image.outputs.name }}
      
      - run: |
          mkdir -p /tmp/contents
          cd /tmp/contents
          tar -xvf /tmp/image.tar
          sudo ls tmp/* | xargs -i bash -c "echo 'cat {}' && cat {}"