Deploy Docker Image #37
Workflow file for this run
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| --- | |
| name: Deploy Docker Image | |
| on: | |
| push: | |
| branches: | |
| - main | |
| paths: | |
| - 'renv/profiles/**/renv.lock' | |
| workflow_dispatch: # give possibility to run it manually | |
| permissions: write-all | |
| env: | |
| REGISTRY: ghcr.io | |
| concurrency: | |
| group: deploy-docker-image-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| get_renv_list: | |
| runs-on: ubuntu-latest | |
| outputs: | |
| matrix: ${{ steps.matrix.outputs.renv }} | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 2 # "2" -> To retrieve the preceding commit. | |
| - name: Get changed files in renv/profiles | |
| id: changed-files | |
| uses: tj-actions/changed-files@v35 | |
| with: | |
| files: renv/profiles/**/renv.lock | |
| # TODO: what to do with renv_legacy ? | |
| - name: Get Updated renv # note: for case schedules job, we update every docker images, and for renv.lock files updates we only update modified renv.lock versions | |
| id: matrix | |
| run: | | |
| if [[ "${{github.event_name}}" == "schedule" || "${{github.event_name}}" == "workflow_dispatch" ]] | |
| then | |
| renv_list=$(find renv/profiles | grep renv.lock ) | |
| else | |
| renv_list="${{ steps.changed-files.outputs.all_changed_files }}" | |
| fi | |
| renv_list=$(echo $renv_list | sed 's/ /", "/g') | |
| echo "renv=[\"$renv_list\"]" >> $GITHUB_OUTPUT | |
| deploy-image: | |
| needs: [ get_renv_list ] | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false # if one of the job "deploy-image" fails, the other parallel jobs will just continue | |
| matrix: | |
| value: ${{ fromJson(needs.get_renv_list.outputs.matrix) }} | |
| # 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 renv ${{ matrix.value }}" | |
| - name: Set image specs | |
| id: image_specs | |
| run: | | |
| package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}') | |
| r_version=$(basename $(dirname ${{ matrix.value }})) # TODO: check here if legacy renv (if yes, delete _legacy suffix and add _legacy suffix to docker im?) | |
| renv=$(echo "${{ matrix.value }}" | tr -d '"') | |
| echo "renv_lock_path=$renv" >> $GITHUB_OUTPUT | |
| echo "r_version=$r_version" >> $GITHUB_OUTPUT | |
| echo "image_name=$package_name-$r_version" >> $GITHUB_OUTPUT | |
| - name: Call deploy docker image action for every renv | |
| uses: insightsengineering/r-image-creator@feature/create_image_from_description | |
| with: | |
| image-name: "${{ steps.image_specs.outputs.image_name }}" | |
| tag-latest: true | |
| base-image: "rocker/rstudio:${{ steps.image_specs.outputs.r_version }}" | |
| sysdeps: qpdf,libxt-dev,curl,npm,libicu-dev,libcurl4-openssl-dev,libssl-dev,make,zlib1g-dev,libfontconfig1-dev,libfreetype6-dev,libfribidi-dev,libharfbuzz-dev,libjpeg-dev,libpng-dev,libtiff-dev,pandoc,libxml2-dev,libgit2-dev,libgit2-dev,jq | |
| renv-lock-file: "${{ steps.image_specs.outputs.renv_lock_path }}" | |
| repository-owner: ${{ github.repository_owner }} | |
| repo-user: ${{ github.actor }} # pharmaverse-bot | |
| repo-token: "${{ secrets.GITHUB_TOKEN }}" # ${{ secrets.PHARMAVERSE_BOT }} | |
| deploy-image-devel: | |
| runs-on: ubuntu-latest | |
| # Token permissions | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - name: Checkout repo | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Set image specs | |
| id: image_specs | |
| run: | | |
| package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}') | |
| echo "image_name=$package_name-devel" >> $GITHUB_OUTPUT | |
| - name: Call deploy docker image action devel | |
| uses: insightsengineering/r-image-creator@feature/create_image_from_description | |
| with: | |
| image-name: "${{ steps.image_specs.outputs.image_name }}" | |
| tag-latest: true | |
| base-image: "rocker/rstudio:devel" | |
| 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: "./DESCRIPTION" | |
| repository-owner: ${{ github.repository_owner }} | |
| repo-user: ${{ github.actor }} # pharmaverse-bot | |
| repo-token: "${{ secrets.GITHUB_TOKEN }}" # ${{ secrets.PHARMAVERSE_BOT }} | |
| # 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 |