daily-rocker-builds.yaml

name: Extra rocker builds

on:
  workflow_dispatch:
    inputs:
      rver:
        default: "devel"
      biocver:
        default: "3.21"
      check-rocker-image:
        default: "rocker/rstudio"
  schedule:
    - cron: '0 18 * * *'

jobs:
  check_versions:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v4
    - name: Set defaults for schedule
      id: defs
      run: |
        echo rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
        BIOCVER=$(echo ${{ github.event.inputs.biocver || '3.21' }})
        echo "develbiocver=$BIOCVER" >> $GITHUB_OUTPUT
        echo check-rocker-image=$(echo ${{ github.event.inputs.check-rocker-image || 'rocker/rstudio' }}) >> $GITHUB_OUTPUT
        RELEASE_BIOC_VER=$(echo "${BIOCVER%.*}.$((${BIOCVER##*.}-1))")
        echo "releasebiocver=$RELEASE_BIOC_VER" >> $GITHUB_OUTPUT
        echo release-tag=$(echo "RELEASE_${RELEASE_BIOC_VER}" | sed 's/\./_/g')  >> $GITHUB_OUTPUT

    - name: Bump R version
      id: rbump
      run: |
        curl https://hub.docker.com/v2/repositories/${{steps.defs.outputs.check-rocker-image}}/tags | jq '.results[].name' | tr -d '"' > /tmp/taglist
        curl https://raw.githubusercontent.com/${{ github.repository }}/${{steps.defs.outputs.release-tag}}/.github/workflows/build_containers.yaml | grep 'amdtag' | awk -F"'" '/amdtag:/ {print $4}' | uniq > /tmp/currtag
        RELEASE_R_VER=$(curl https://bioconductor.org/config.yaml | yq e '.r_ver_for_bioc_ver."${{steps.defs.outputs.releasebiocver}}"')
        LATEST_TAG=$(cat /tmp/taglist | grep "$RELEASE_R_VER" | sort -n | tail -n 1)
        CURR_TAG=$(cat /tmp/currtag | sort -n | tail -n 1)
        echo latest-tag=$LATEST_TAG >> $GITHUB_OUTPUT
        if [ "$LATEST_TAG" == "$CURR_TAG" ]; then
          echo "Detected '$LATEST_TAG' == '$CURR_TAG' as latest available tag"
          echo verdict="no"  >> $GITHUB_OUTPUT
        else 
          echo "Detected mismatching versions latest '$LATEST_TAG' != '$CURR_TAG' current tag"
          mkdir -p ${{github.workspace}}/tmp/${{github.repository}}
          git clone https://github.com/${{github.repository}} -b ${{steps.defs.outputs.release-tag}} ${{github.workspace}}/tmp/${{github.repository}}
          cd ${{github.workspace}}/tmp/${{github.repository}}
          AUTO_BRANCH="auto-bump-${{steps.defs.outputs.releasebiocver}}-for-${LATEST_TAG}"
          sed -i "s/$CURR_TAG/$LATEST_TAG/g" .github/workflows/build_containers.yaml
          sed -r -i 's/(^ARG BIOCONDUCTOR_PATCH=)([0-9]+)$/echo "\1$((\2+1))"/ge' Dockerfile
          echo verdict="yes" >> $GITHUB_OUTPUT
        fi

    - name: Open pull request
      id: cpr
      uses: peter-evans/create-pull-request@v6
      if: steps.rbump.outputs.verdict == 'yes'
      with:
          token: ${{secrets.PAT}}
          commit-message: Auto-bump ${{steps.rbump.outputs.latest-tag}}
          committer: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
          author: ${{ github.actor }} <${{ github.actor_id }}+${{ github.actor }}@users.noreply.github.com>
          base: ${{steps.defs.outputs.release-tag}}
          path: ${{github.workspace}}/tmp/${{github.repository}}
          branch: auto-bump-bioc-${{steps.defs.outputs.release-tag}}-r-${{steps.rbump.outputs.latest-tag}}
          title: '[Auto] Bumping ${{steps.defs.outputs.release-tag}} branch to R ${{steps.rbump.outputs.latest-tag}}'
          body: |
            Bumping R version.
            Note that the Bioconductor automatic PR bot is experimental, please make sure to check the changes manually before merging.
          labels: |
            auto-bump

  buildrver:
    strategy:
      matrix:
        arch: [amd64, arm64]
    runs-on: ubuntu-latest
    steps:
    - 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 rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
        echo biocver=$(echo ${{ github.event.inputs.biocver || '3.21' }}) >> $GITHUB_OUTPUT
        echo registryuser=$(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: Prep rocker rocker files
      run: bash .github/scripts/rocker_prep.sh ${{ steps.defs.outputs.rver }} ${{ steps.defs.outputs.biocver }} ${{ steps.defs.outputs.rockerintermediateprefix }} ${{ matrix.arch }}

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

    - name: Build and push 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 }}

  buildrstudio:
    strategy:
      matrix:
        arch: [amd64, arm64]
    needs: buildrver
    runs-on: ubuntu-latest
    steps:
    - 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 rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
        echo biocver=$(echo ${{ github.event.inputs.biocver || '3.21' }}) >> $GITHUB_OUTPUT
        echo registryuser=$(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: Prep rocker rocker files
      run: |
        bash .github/scripts/rocker_prep.sh ${{ steps.defs.outputs.rver }} ${{ steps.defs.outputs.biocver }} ${{ steps.defs.outputs.rockerintermediateprefix }} ${{ matrix.arch }}
        

    - name: Move some tidyverse builds to docker for arm64 to avoid timeout
      run: |
        head -n44 rocker-versioned2/scripts/install_tidyverse.sh >> rocker-versioned2/scripts/install_rstudio.sh
        sed -i "\|RUN /rocker_scripts/install_rstudio.sh|i COPY scripts /rocker_scripts" rocker-versioned2/dockerfiles/rstudio_${{ steps.defs.outputs.rver }}.Dockerfile
      if: matrix.arch == 'arm64'

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

    - name: Build and push 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 }}

  buildtidyverse:
    strategy:
      matrix:
        arch: [amd64, arm64]
    runs-on: ubuntu-latest
    needs: buildrstudio
    steps:
    - 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 rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
        echo biocver=$(echo ${{ github.event.inputs.biocver || '3.21' }}) >> $GITHUB_OUTPUT
        echo registryuser=$(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: Prep rocker rocker files
      run: bash .github/scripts/rocker_prep.sh ${{ steps.defs.outputs.rver }} ${{ steps.defs.outputs.biocver }} ${{ steps.defs.outputs.rockerintermediateprefix }} ${{ matrix.arch }}

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

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

  mlbuild:
    strategy:
      matrix:
        arch: [amd64]
    runs-on: ubuntu-latest
    steps:
    - 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 rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
        echo biocver=$(echo ${{ github.event.inputs.biocver || '3.21' }}) >> $GITHUB_OUTPUT
        echo registryuser=$(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: Prep rocker rocker files
      run: |
        ## git clone rocker
        git clone --depth 1 https://github.com/rocker-org/rocker-versioned2
        sed -i 's#11.8.0-cudnn8-devel-ubuntu22.04#12.6.2-cudnn-devel-ubuntu24.04#g' rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile
        sed -i 's#11.8.0-cudnn8-devel-ubuntu22.04#12.6.2-cudnn-devel-ubuntu24.04#g' rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile
        sed -i 's#11.8.0-cudnn8-devel-ubuntu22.04#12.6.2-cudnn-devel-ubuntu24.04#g' rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile

        # Package archived from CRAN
        sed -i '/rmdshower/d' rocker-versioned2/scripts/install_verse.sh

        sed -i 's#rocker/cuda:${{ steps.defs.outputs.rver }}#${{ steps.defs.outputs.rockerintermediateprefix }}-cuda:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}#g' rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile
        sed -i 's#rocker/ml:${{ steps.defs.outputs.rver }}#${{ steps.defs.outputs.rockerintermediateprefix }}-ml:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}#g' rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile

        echo "Bioconductor Version: ${{ steps.defs.outputs.biocver }}"
        if [ "${{ steps.defs.outputs.rver }}" == "devel" ]; then
          bash .github/scripts/devel_or_patched_rversion.sh "${{ steps.defs.outputs.biocver }}" "rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile"
          bash .github/scripts/devel_or_patched_rversion.sh "${{ steps.defs.outputs.biocver }}" "rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile"
          bash .github/scripts/devel_or_patched_rversion.sh "${{ steps.defs.outputs.biocver }}" "rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile"
        fi

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

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

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

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