Deploy Docker Image #139
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| --- | |
| name: Deploy Docker Image | |
| on: | |
| workflow_dispatch: # give possibility to run it manually | |
| schedule: | |
| - cron: '0 0 * * Wed,Sun' # Run every day at midnight UTC | |
| permissions: write-all | |
| env: | |
| REGISTRY: ghcr.io | |
| R_REPOS: "https://cran.r-project.org" | |
| OLD_RELEASE: "4.3" | |
| concurrency: | |
| group: deploy-docker-image-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| get_old_release: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| oldrel: ${{ steps.oldrelease.outputs.oldrelease }} | |
| steps: | |
| - name: get old release | |
| id: oldrelease | |
| run: | |
| echo "oldrelease=${{ env.OLD_RELEASE }}" >> $GITHUB_OUTPUT | |
| deploy-image: | |
| runs-on: ubuntu-latest | |
| needs: [ "get_old_release" ] | |
| strategy: | |
| fail-fast: false # if one of the job "deploy-image" fails, the other parallel jobs will just continue | |
| matrix: | |
| tags: ["devel", "latest", "${{ needs.get_old_release.outputs.oldrel }}"] | |
| # Token permissions | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Print message | |
| run: | | |
| echo "updating docker image for R version ${{ matrix.tags }}" | |
| - name: Set image specs | |
| id: image_specs | |
| run: | | |
| package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}') | |
| if [ "${{ matrix.tags }}" == "latest" ]; then image_name="$package_name-release"; else image_name="$package_name-${{ matrix.tags }}"; fi | |
| if [ "${{ matrix.tags }}" == "devel" ]; then R_REPOS="https://packagemanager.posit.co/cran/__linux__/focal/latest"; fi | |
| echo "r_repos=$R_REPOS" >> $GITHUB_OUTPUT | |
| r_version="${{ matrix.tags }}" | |
| if [ "$r_version" == "${{ env.OLD_RELEASE }}" ]; then image_name="$package_name-oldrel"; fi # TODO: del temporary -test suffix for testing | |
| echo "image_name=$image_name" >> $GITHUB_OUTPUT | |
| - name: Call deploy docker image action ${{ matrix.tags }} | |
| uses: insightsengineering/r-image-creator@install_suggests_deps | |
| with: | |
| image-name: "${{ steps.image_specs.outputs.image_name }}" | |
| tag-latest: true | |
| base-image: "rocker/rstudio:${{ matrix.tags }}" | |
| sysdeps: qpdf,libxt-dev,curl,npm,libicu-dev,libcurl4-openssl-dev,libssl-dev,make,zlib1g-dev,libfontconfig1-dev,libfreetype6-dev,libfribidi-dev,libharfbuzz-dev,libjpeg-dev,libpng-dev,libtiff-dev,pandoc,libxml2-dev,libgit2-dev,libgit2-dev,jq | |
| description-file: "https://raw.githubusercontent.com/pharmaverse/admiral/main/DESCRIPTION" | |
| repository-owner: ${{ github.repository_owner }} | |
| repo-user: ${{ github.actor }} | |
| repo-token: "${{ secrets.GITHUB_TOKEN }}" | |
| repos: ${{ steps.image_specs.outputs.r_repos }} | |
| packages: "DT,R.cache,R.methodsS3,R.oo,R.utils,backports,cellranger,collections,covr,crosstalk,cyclocomp,diffdf,git2r,hunspell,languageserver,lazyeval,lintr,progress,readxl,rematch,renv,rex,spelling,staged.dependencies,styler,xmlparsedata" | |
| store_deps: | |
| name: Store Deps | |
| runs-on: ubuntu-latest | |
| needs: [ "get_old_release", "deploy-image" ] | |
| container: | |
| image: "ghcr.io/pharmaverse/admiralci-${{ matrix.tags }}:latest" | |
| strategy: | |
| fail-fast: false # if one of the job "deploy-image" fails, the other parallel jobs will just continue | |
| matrix: | |
| tags: ["devel", "latest", "${{ needs.get_old_release.outputs.oldrel }}"] | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Store deps into csv file - image ${{ matrix.tags }} | |
| id: store_deps | |
| run: | | |
| installed_packages <- as.data.frame(installed.packages()) | |
| r_version <- "${{ matrix.tags }}" | |
| if (r_version == "${{ needs.get_old_release.outputs.oldrel }}"){ | |
| r_version <- "oldrelease" | |
| } | |
| content <- sprintf("r_version=%s\n", r_version) | |
| output_file <- Sys.getenv("GITHUB_OUTPUT") | |
| write(content, file = output_file, append = TRUE) | |
| write.csv(installed_packages, sprintf("/workspace/deps-%s.csv", r_version), row.names = FALSE) | |
| shell: Rscript {0} | |
| - name: Upload deps.csv artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: deps | |
| path: "/workspace/deps-${{ steps.store_deps.outputs.r_version }}.csv" | |
| - name: Delete current release existing artifacts | |
| uses: mknejp/delete-release-assets@v1 | |
| with: | |
| token: ${{ github.token }} | |
| tag: "latest" | |
| fail-if-no-assets: false | |
| assets: | | |
| Dependencies.list.of.docker.image.admiralci-${{ steps.store_deps.outputs.r_version }}.csv | |
| - name: Upload SBOM to release 🔼 | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: "${{ secrets.GITHUB_TOKEN }}" | |
| file: "/workspace/deps-${{ steps.store_deps.outputs.r_version }}.csv" | |
| asset_name: "Dependencies list of docker image admiralci-${{ steps.store_deps.outputs.r_version }}.csv" | |
| tag: "latest" | |
| overwrite: true | |
| # refacto todo: image-name, sysdeps on get-renv-list job | |
| # note: in case of 403 error when pushing to ghcr : link current repo to the given package registry - https://github.com/docker/build-push-action/issues/687 | |
| # (got to https://github.com/<user name>?tab=packages to go to packages settings) and there https://github.com/users/<user name>/packages/container/admiralci-4.0/settings |