scheduled #1114
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| name: Deploy image to GHCR 🪂 | |
| env: | |
| REGISTRY: ghcr.io | |
| # PLATFORMs is a comma-separted list of architectures to build for. | |
| # We disable linux/arm64 due to runner mem saturation. | |
| PLATFORMS: linux/amd64 | |
| on: | |
| repository_dispatch: | |
| types: | |
| - scheduled | |
| workflow_dispatch: | |
| inputs: | |
| origin: | |
| description: DockerHub org or username where the base image is located | |
| required: true | |
| type: choice | |
| default: rocker | |
| options: | |
| - rocker | |
| - rhub | |
| distribution: | |
| description: Rocker/RHub Distro Name. | |
| required: true | |
| type: choice | |
| default: rstudio | |
| options: | |
| - rstudio | |
| - rstudio-local | |
| - gcc13 | |
| - gcc14 | |
| - atlas | |
| - valgrind | |
| - intel | |
| - nosuggests | |
| - mkl | |
| r_version: | |
| description: | | |
| R version (also used as the tag to pull the origin image). | |
| required: true | |
| type: choice | |
| default: "4.4.1" | |
| options: | |
| - "4.1.0" | |
| - "4.1.1" | |
| - "4.1.2" | |
| - "4.1.3" | |
| - "4.2.0" | |
| - "4.2.1" | |
| - "4.2.2" | |
| - "4.3.0" | |
| - "4.3.1" | |
| - "4.3.2" | |
| - "4.3.3" | |
| - "4.4.0" | |
| - "4.4.1" | |
| - "latest" | |
| latest_r_version: | |
| description: | | |
| R Version to be aliased as the 'latest' tag". | |
| (Only relevant for rocker images). | |
| required: false | |
| type: string | |
| default: "4.4.1" | |
| bioc_version: | |
| description: BioConductor Release | |
| required: true | |
| type: choice | |
| default: "3.19" | |
| options: | |
| - "3.13" | |
| - "3.14" | |
| - "3.15" | |
| - "3.16" | |
| - "3.17" | |
| - "3.18" | |
| - "3.19" | |
| - "devel" | |
| latest_bioc_version: | |
| description: | | |
| BioC Version to be aliased as the 'latest' tag". | |
| (Only relevant for rocker images). | |
| required: false | |
| type: string | |
| default: "3.19" | |
| tag: | |
| description: | | |
| Custom Image Tag/Version. Defaults to current date in the `YYYY.MM.DD` format if unspecified. | |
| required: false | |
| default: "" | |
| tag_latest: | |
| description: Tag image as `latest` | |
| default: false | |
| type: boolean | |
| release_tag: | |
| description: | | |
| Release tag to which SBOM generated for image should be attached. | |
| Release tags follow the `YYYY.MM.DD` format. | |
| This must be specified if you want to upload artifacts to the release. | |
| required: false | |
| default: "" | |
| jobs: | |
| normalize-inputs: | |
| name: Normalize inputs 🧹 | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Normalize 🧽 | |
| id: normalizer | |
| run: | | |
| function normalize() { | |
| local var=$1 | |
| if [ "$var" == "" ] | |
| then { | |
| var=$2 | |
| } | |
| fi | |
| echo ${var} | |
| } | |
| ORIGIN=$(normalize ${{ github.event.inputs.origin }} ${{ github.event.client_payload.origin }}) | |
| DISTRIBUTION=$(normalize ${{ github.event.inputs.distribution }} ${{ github.event.client_payload.distribution }}) | |
| ORIGIN_DISTRIBUTION=${DISTRIBUTION//"-local"} | |
| R_VERSION=$(normalize ${{ github.event.inputs.r_version }} ${{ github.event.client_payload.r_version }}) | |
| BIOC_VERSION=$(normalize ${{ github.event.inputs.bioc_version }} ${{ github.event.client_payload.bioc_version }}) | |
| LATEST_R_VERSION=$(normalize ${{ github.event.inputs.latest_r_version }} ${{ github.event.client_payload.latest_r_version }}) | |
| LATEST_BIOC_VERSION=$(normalize ${{ github.event.inputs.latest_bioc_version }} ${{ github.event.client_payload.latest_bioc_version }}) | |
| TAG=$(normalize ${{ github.event.inputs.tag }} ${{ github.event.client_payload.tag }}) | |
| TAG_LATEST=$(normalize ${{ github.event.inputs.tag_latest }} ${{ github.event.client_payload.tag_latest }}) | |
| RELEASE_TAG=$(normalize ${{ github.event.inputs.release_tag }} ${{ github.event.client_payload.release_tag }}) | |
| RELEASE_TAG=$(normalize ${RELEASE_TAG} $(date +%Y%m%d)) | |
| echo "ORIGIN=$ORIGIN" >> $GITHUB_OUTPUT | |
| echo "ORIGIN_DISTRIBUTION=$ORIGIN_DISTRIBUTION" >> $GITHUB_OUTPUT | |
| echo "DISTRIBUTION=$DISTRIBUTION" >> $GITHUB_OUTPUT | |
| echo "R_VERSION=$R_VERSION" >> $GITHUB_OUTPUT | |
| echo "BIOC_VERSION=$BIOC_VERSION" >> $GITHUB_OUTPUT | |
| echo "LATEST_R_VERSION=$LATEST_R_VERSION" >> $GITHUB_OUTPUT | |
| echo "LATEST_BIOC_VERSION=$LATEST_BIOC_VERSION" >> $GITHUB_OUTPUT | |
| echo "TAG=$TAG" >> $GITHUB_OUTPUT | |
| echo "TAG_LATEST=$TAG_LATEST" >> $GITHUB_OUTPUT | |
| echo "RELEASE_TAG=$RELEASE_TAG" >> $GITHUB_OUTPUT | |
| shell: bash | |
| outputs: | |
| origin: ${{ steps.normalizer.outputs.ORIGIN }} | |
| origin_distribution: ${{ steps.normalizer.outputs.ORIGIN_DISTRIBUTION }} | |
| distribution: ${{ steps.normalizer.outputs.DISTRIBUTION }} | |
| r_version: ${{ steps.normalizer.outputs.R_VERSION }} | |
| bioc_version: ${{ steps.normalizer.outputs.BIOC_VERSION }} | |
| latest_r_version: ${{ steps.normalizer.outputs.LATEST_R_VERSION }} | |
| latest_bioc_version: ${{ steps.normalizer.outputs.LATEST_BIOC_VERSION }} | |
| tag: ${{ steps.normalizer.outputs.TAG }} | |
| tag_latest: ${{ steps.normalizer.outputs.TAG_LATEST }} | |
| release_tag: ${{ steps.normalizer.outputs.RELEASE_TAG }} | |
| build: | |
| runs-on: ubuntu-latest | |
| needs: normalize-inputs | |
| name: Build & Deploy 🚀 ${{ needs.normalize-inputs.outputs.distribution }} - ${{ needs.normalize-inputs.outputs.r_version }} | BioC - ${{ needs.normalize-inputs.outputs.bioc_version }} | |
| # Token permissions | |
| permissions: | |
| contents: read | |
| packages: write | |
| # Build steps | |
| steps: | |
| - name: Reclaim Disk Space 🚮 | |
| uses: insightsengineering/disk-space-reclaimer@v1 | |
| with: | |
| tools-cache: false | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| swap-storage: false | |
| docker-images: true | |
| - name: Checkout repository 💳 | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| id: buildx | |
| with: | |
| install: true | |
| - name: Set up QEMU | |
| id: qemu | |
| uses: docker/setup-qemu-action@v3 | |
| with: | |
| platforms: ${{ env.PLATFORMS }} | |
| - name: Cache Docker layers ♻️ | |
| uses: actions/cache@v4 | |
| with: | |
| path: /tmp/.buildx-cache | |
| key: ${{ runner.os }}-buildx-${{ needs.normalize-inputs.outputs.distribution }}-${{ needs.normalize-inputs.outputs.r_version }}-${{ needs.normalize-inputs.outputs.bioc_version }} | |
| restore-keys: | | |
| ${{ runner.os }}-buildx-${{ needs.normalize-inputs.outputs.distribution }}-${{ needs.normalize-inputs.outputs.r_version }}-${{ needs.normalize-inputs.outputs.bioc_version }} | |
| ${{ runner.os }}-buildx-${{ needs.normalize-inputs.outputs.distribution }}-${{ needs.normalize-inputs.outputs.r_version }}- | |
| ${{ runner.os }}-buildx-${{ needs.normalize-inputs.outputs.distribution }}- | |
| ${{ runner.os }}-buildx- | |
| - name: Log in to the Container registry 🗝 | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Set build variables 📐 | |
| id: build_vars | |
| run: | | |
| # Set Image name | |
| image_name="${{ needs.normalize-inputs.outputs.distribution }}_${{ needs.normalize-inputs.outputs.r_version }}_bioc_${{ needs.normalize-inputs.outputs.bioc_version }}" | |
| # For Fedora-based rhub images. | |
| if [[ "${{ needs.normalize-inputs.outputs.distribution }}" =~ ^gcc.*|^atlas$|^valgrind$|^intel$|^nosuggests$|^mkl$ ]] | |
| then { | |
| image_name="${{ needs.normalize-inputs.outputs.distribution }}" | |
| } | |
| fi | |
| # Set default tag as 'YYYY.MM.DD' date if it isn't set | |
| tag="${{ needs.normalize-inputs.outputs.tag }}" | |
| if [ "${tag}" == "" ] | |
| then { | |
| tag=$(date +%Y.%m.%d) | |
| } | |
| fi | |
| tag_latest="${{ needs.normalize-inputs.outputs.tag_latest }}" | |
| # Set full image name | |
| full_names="${{ env.REGISTRY }}/${{ github.repository_owner }}/${image_name}:${tag}" | |
| echo "OUTPUT_IMAGE_NAME=${full_names}" >> $GITHUB_OUTPUT | |
| if [ "${tag_latest}" == "true" ] | |
| then | |
| full_names="$full_names,${{ env.REGISTRY }}/${{ github.repository_owner }}/${image_name}:latest" | |
| fi | |
| if [ "${image_name}" == "rstudio-local_${{ needs.normalize-inputs.outputs.latest_r_version }}_bioc_${{ needs.normalize-inputs.outputs.latest_bioc_version }}" ] \ | |
| || [ "${image_name}" == "rstudio_${{ needs.normalize-inputs.outputs.latest_r_version }}_bioc_${{ needs.normalize-inputs.outputs.latest_bioc_version }}" ] | |
| then | |
| full_names="$full_names,${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ needs.normalize-inputs.outputs.distribution }}:latest" | |
| full_names="$full_names,${{ env.REGISTRY }}/${{ github.repository_owner }}/${{ needs.normalize-inputs.outputs.distribution }}:${tag}" | |
| fi | |
| echo "FULL_NAMES=${full_names}" >> $GITHUB_OUTPUT | |
| echo "github.ref = ${{ github.ref }}" | |
| # Set push if branch is main | |
| if [ "${{ github.ref }}" == 'refs/heads/main' ]; then | |
| echo "DOCKER_PUSH=true" >> $GITHUB_OUTPUT | |
| echo "DOCKER_PUSH = true" | |
| else | |
| echo "DOCKER_PUSH=false" >> $GITHUB_OUTPUT | |
| echo "DOCKER_PUSH = false" | |
| fi | |
| echo "SBOM_OUTPUT_FILENAME=$GITHUB_WORKSPACE/sbom.json" >> $GITHUB_OUTPUT | |
| - name: Build and push image 🏗 | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: ./ | |
| file: Dockerfile | |
| push: ${{ steps.build_vars.outputs.DOCKER_PUSH }} | |
| tags: ${{ steps.build_vars.outputs.FULL_NAMES }} | |
| cache-from: type=local,src=/tmp/.buildx-cache | |
| cache-to: type=local,dest=/tmp/.buildx-cache-new | |
| build-args: | | |
| ORIGIN=${{ needs.normalize-inputs.outputs.origin }} | |
| ORIGIN_DISTRIBUTION=${{ needs.normalize-inputs.outputs.origin_distribution }} | |
| DISTRIBUTION=${{ needs.normalize-inputs.outputs.distribution }} | |
| R_VERSION=${{ needs.normalize-inputs.outputs.r_version }} | |
| BIOC_VERSION=${{ needs.normalize-inputs.outputs.bioc_version }} | |
| platforms: ${{ env.PLATFORMS }} | |
| - name: Generate image manifest and R package list 🐳 | |
| run: | | |
| docker manifest inspect ${{ steps.build_vars.outputs.OUTPUT_IMAGE_NAME }} > manifest.json | |
| docker run -v ${PWD}:/app ${{ steps.build_vars.outputs.OUTPUT_IMAGE_NAME }} \ | |
| R -e 'write.csv(installed.packages(), file="/app/package_list.csv")' | |
| - name: Reclaim Disk Space for SBOM Generation 🚮 | |
| uses: insightsengineering/disk-space-reclaimer@v1 | |
| with: | |
| tools-cache: false | |
| android: true | |
| dotnet: true | |
| haskell: true | |
| large-packages: true | |
| swap-storage: false | |
| docker-images: true | |
| - name: Generate SBOM 📃 | |
| uses: anchore/sbom-action@v0 | |
| with: | |
| image: "${{ steps.build_vars.outputs.OUTPUT_IMAGE_NAME }}" | |
| output-file: "${{ steps.build_vars.outputs.SBOM_OUTPUT_FILENAME }}" | |
| artifact-name: "sbom.spdx" | |
| - name: Upload image manifest to release 🔼 | |
| uses: svenstaro/upload-release-action@v2 | |
| if: "${{ needs.normalize-inputs.outputs.release_tag }} != ''" | |
| with: | |
| repo_token: ${{ secrets.REPO_GITHUB_TOKEN }} | |
| file: "manifest.json" | |
| asset_name: "image.manifest.${{ steps.build_vars.outputs.OUTPUT_IMAGE_NAME }}.json" | |
| tag: "${{ needs.normalize-inputs.outputs.release_tag }}" | |
| overwrite: true | |
| - name: Upload R package list to release 🔼 | |
| uses: svenstaro/upload-release-action@v2 | |
| if: "${{ needs.normalize-inputs.outputs.release_tag }} != ''" | |
| with: | |
| repo_token: ${{ secrets.REPO_GITHUB_TOKEN }} | |
| file: "package_list.csv" | |
| asset_name: "package.list.${{ steps.build_vars.outputs.OUTPUT_IMAGE_NAME }}.csv" | |
| tag: "${{ needs.normalize-inputs.outputs.release_tag }}" | |
| overwrite: true | |
| - name: Upload SBOM to release 🔼 | |
| uses: svenstaro/upload-release-action@v2 | |
| if: "${{ needs.normalize-inputs.outputs.release_tag }} != ''" | |
| with: | |
| repo_token: ${{ secrets.REPO_GITHUB_TOKEN }} | |
| file: "${{ steps.build_vars.outputs.SBOM_OUTPUT_FILENAME }}" | |
| asset_name: "SBOM for ${{ steps.build_vars.outputs.OUTPUT_IMAGE_NAME }}.spdx.json" | |
| tag: "${{ needs.normalize-inputs.outputs.release_tag }}" | |
| overwrite: true | |
| - name: Move cache ♻️ | |
| run: | | |
| rm -rf /tmp/.buildx-cache | |
| if [ -f /tmp/.buildx-cache-new ] | |
| then { | |
| mv /tmp/.buildx-cache-new /tmp/.buildx-cache | |
| } | |
| fi |