Extra rocker builds #227
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| name: Extra rocker builds | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| rver: | |
| default: "devel" | |
| biocver: | |
| default: "3.19" | |
| schedule: | |
| - cron: '0 18 * * *' | |
| jobs: | |
| 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 || '3.19' }}) >> $GITHUB_OUTPUT | |
| echo registryuser=$(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: 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 || '3.19' }}) >> $GITHUB_OUTPUT | |
| echo registryuser=$(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: 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 || '3.19' }}) >> $GITHUB_OUTPUT | |
| echo registryuser=$(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: 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 || '3.19' }}) >> $GITHUB_OUTPUT | |
| echo registryuser=$(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: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Prep rocker rocker files | |
| run: | | |
| ## git clone rocker | |
| git clone --depth 1 https://github.com/rocker-org/rocker-versioned2 | |
| sed -i 's#rocker/cuda:${{ 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_${{ steps.defs.outputs.rver }}.Dockerfile | |
| BIOC_MINOR=$(echo "${{ steps.defs.outputs.biocver }}" | awk -F'.' '{print $NF}') | |
| echo "Bioconductor Version: ${{ steps.defs.outputs.biocver }}" | |
| if [ "${{ steps.defs.outputs.rver }}" = "devel" ]; then | |
| 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=${{ steps.defs.outputs.rver }}#R_VERSION=patched#g' rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile | |
| fi | |
| fi | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v2 | |
| with: | |
| platforms: linux/${{ matrix.arch }} | |
| - name: Build and load cuda | |
| uses: docker/build-push-action@v3 | |
| with: | |
| file: rocker-versioned2/dockerfiles/cuda_${{ 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 }} |