Add devel image (#165)

* add checks for devel * fix branch name * update push job * re-test * fix checks * fix typo * fix * fix * fix * install rcmdcheck for devel im * templates: retrieve temp folder * add checks on existing branches - templates * debug traces * fix cp cmd * fix * debug traces * add other debug traces * update * add other debug traces * test other folder * fix condition branch * fix checks * test checks on maintenance versions * fix * trigger checks * try ignore note * retry * try another regexp * retry * rework rcmdcheck * fix * fix * fix * fix * fix * cleanup * change r-im-creator tag * Update check-templates.yml remove @devel * add cron job --------- Co-authored-by: pharmaverse-bot <[email protected]>
pharmaverse · Nov 8, 2023 · 19bfb1d · 19bfb1d
1 parent b7c8e96
commit 19bfb1d
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Showing 5 changed files with 76 additions and 9 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -27,4 +27,4 @@
 ^admiralci.*\.tgz$
 ^staged_dependencies.yaml$
 ^README.Rmd$
-^.devcontainer
+^.devcontainer
diff --git a/.github/workflows/check-templates.yml b/.github/workflows/check-templates.yml
@@ -365,13 +365,18 @@ jobs:
         id: branch
         run: |
           repo_name=$(basename "${{ github.repository }}")
-          echo "source-branch=${{ env.source-branch }}_${repo_name}@devel" >> $GITHUB_OUTPUT
+          source_br="${{ env.source-branch }}_${repo_name}"
+          source_grep=$(git branch -a | grep $source_br)
+          if [ -z $source_grep ]; then branch_exists=false; else branch_exists=true; fi
+          echo "source-branch=$source_br" >> $GITHUB_OUTPUT
+          echo "branch-exists=$branch_exists" >> $GITHUB_OUTPUT
+          warn_msg="WARNING:: the branch $source_br already exists in pharmaverseadam, please merge it and delete it, and re-execute this job"
+          if [ '${{ steps.changes.outputs.diff }}' == 'true' ] && [ '$branch_exists' == 'true' ]; then echo "$warn_msg"; fi
         shell: bash {0}
 
-
       # if diff detected, push changes
       - name: Commit and push changes in {{ env.repo }}
-        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }}
+        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' && steps.branch.outputs.branch-exists == 'false' }}
         uses: stefanzweifel/git-auto-commit-action@v4
         with:
           commit_message: templates data updates from ${{ github.repository }}
@@ -382,7 +387,7 @@ jobs:
           create_branch: true
 
       - name: Create Pull Request
-        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' }}
+        if: ${{ inputs.push-templates-data && steps.changes.outputs.diff == 'true' && steps.branch.outputs.branch-exists == 'false' }}
         uses: actions/github-script@v6
         with:
           github-token: ${{ secrets.PHARMAVERSE_BOT }}

diff --git a/.github/workflows/propagate.yml b/.github/workflows/propagate.yml
@@ -13,6 +13,7 @@ on:
       - renv/**
       - .Rprofile
       - .devcontainer/*
+  workflow_dispatch: # give possibility to run it manually
 
 jobs:
   integrity:

diff --git a/.github/workflows/push-docker-image.yml b/.github/workflows/push-docker-image.yml
@@ -8,6 +8,8 @@ on:
     paths:
       - 'renv/profiles/**/renv.lock'
   workflow_dispatch: # give possibility to run it manually
+  schedule:
+    - cron: '0 0 * * *' # Run every day at midnight UTC
 
 permissions: write-all
 env:
@@ -50,6 +52,7 @@ jobs:
           echo "renv=[\"$renv_list\"]" >> $GITHUB_OUTPUT
 
   deploy-image:
+    if: github.event_name != 'schedule'
     needs: [ get_renv_list ]
     runs-on: ubuntu-latest
     strategy:
@@ -77,10 +80,10 @@ jobs:
         run: |
           package_name=$(grep "Package:" DESCRIPTION | awk '{print $NF}')
           r_version=$(basename $(dirname ${{ matrix.value }})) # TODO: check here if legacy renv (if yes, delete _legacy suffix and add _legacy suffix to docker im?)
-          echo "r_version=$r_version" >> $GITHUB_OUTPUT
-          echo "image_name=$package_name-$r_version" >> $GITHUB_OUTPUT
           renv=$(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@v1
@@ -94,5 +97,40 @@ jobs:
           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" >> $GITHUB_OUTPUT
+    
+      - name: Call deploy docker image action devel
+        uses: insightsengineering/r-image-creator@v1
+        with:
+          image-name: "${{ 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
diff --git a/.github/workflows/r-cmd-check.yml b/.github/workflows/r-cmd-check.yml
@@ -37,6 +37,7 @@ jobs:
           - {r: '4.1', repos: 'https://packagemanager.posit.co/cran/2021-05-03/'}
           - {r: '4.2', repos: 'https://packagemanager.posit.co/cran/2022-01-03/'}
           - {r: '4.3', repos: 'https://packagemanager.posit.co/cran/__linux__/focal/latest'}
+          - {r: 'devel', repos: 'https://packagemanager.posit.co/cran/__linux__/focal/latest'} # not needed for devel ?
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -81,11 +82,33 @@ jobs:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       #####################c#####################
 
+      - name: Check Version
+        id: check_version
+        run: |
+          maintenance_version="F"
+          description_dat <- readLines("DESCRIPTION")
+          for (i in seq_along(description_dat)) {
+            if (grepl("^Version:", description_dat[i])) {
+              current_version <- sub("^Version: ", "", description_dat[i])
+              version_parts <- strsplit(current_version, "\\.")[[1]]
+              # check if maintenance version - if yes, temp update the DESCRIPTION for rcmdchecks
+              if (length(version_parts) == 4) {
+                print("Maintenance version detected (format X.Y.Z.M with M >= 9000)")
+                maintenance_version="T"
+              }
+            }
+          }
+          cat(sprintf("maintenance_version=%s", maintenance_version), file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+        shell: Rscript {0}
+
       - name: Check
         env:
           _R_CHECK_CRAN_INCOMING_REMOTE_: false
           _R_CHECK_FORCE_SUGGESTS_: false
         run: |
+          if ("${{steps.check_version.outputs.maintenance_version}}" == "T"){
+            Sys.setenv("_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_" = TRUE)
+          }
           if (!requireNamespace("rcmdcheck", quietly = TRUE)) install.packages("rcmdcheck")
           options(crayon.enabled = TRUE)
           check_error_on <- "${{ inputs.error-on }}"
@@ -103,5 +126,5 @@ jobs:
         if: failure()
         uses: actions/upload-artifact@main
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          name: r${{ matrix.config.r }}-results
+          path: check