Extra rocker builds #607
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| 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 }} | |