build: add pkgdown GHA

.github/workflows/pkgdown.yaml

@@ -0,0 +1,93 @@
+# This workflow is used to update static webpage with documentation for the given GitHub repository.
+# It's triggered by the push of the default branch. 
+# More details: https://docs.google.com/document/d/1WGW4_lOOZ73lEfVZwIWMivbyCgDTJAajxP5N8767DZY
+
+name: pkgdown
+
+on:
+  push:
+    branches: [main, master, test_ci_pkgdown]
+  release:
+    types: [published]
+  workflow_call:
+    inputs:
+      USERNAME:
+        required: true
+        type: string
+      PACKAGE_NAME:
+        required: true
+        type: string
+      BRANCH_NAME:
+        required: true
+        type: string
+      IS_SUBDIR:
+        description: "Is the R package stored as the subdirectory of the repository?"
+        required: false
+        type: string
+        default: 'false'
+    secrets:
+      PRIVATE_ACCESS_TOKEN:
+        required: true
+
+permissions:
+  contents: write
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.PRIVATE_ACCESS_TOKEN }}
+      TEST_TAG: user/app:latest-${{ github.sha }}
+      USERNAME: ${{ github.actor }}
+      PACKAGE_NAME: ${{ github.event.repository.name }}
+      BRANCH_NAME: ${{ github.head_ref }}
+      BASE_IMAGE: marcinkam/gdrshiny:1.0
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Build
+        uses: docker/build-push-action@v5
+        with:
+          context: .
+          fetch-depth: 0
+          ref: ${{ env.BRANCH_NAME }}
+          tags: ${{ env.TEST_TAG }}
+          build-args: |
+            GITHUB_TOKEN=${{ secrets.PRIVATE_ACCESS_TOKEN }}
+            BASE_IMAGE=${{ env.BASE_IMAGE }}
+
+      - name: Run pkgdown
+        if: ${{ inputs.IS_SUBDIR  != 'true' }}
+        run: |
+          docker run -v `pwd`:/mnt/vol ${{ env.TEST_TAG }} Rscript -e 'pkgdown::build_site_github_pages("/mnt/vol", new_process = FALSE, install = FALSE)'
+      
+      # currently, internal packages are stored as subdirectories in the repository
+      # eventually, this loop becomes obsolete (subdirectory structure is not allowed in Bioconductor))
+      - name: Run pkgdown (R package as subdirectory)
+        if: ${{ inputs.IS_SUBDIR  == 'true' }}
+        run: |
+          docker run -v $GITHUB_WORKSPACE:/mnt/vol ${{ env.TEST_TAG }} bash  -c "find /mnt/vol/${{ env.PACKAGE_NAME }}"
+          docker run -v `pwd`:/mnt/vol ${{ env.TEST_TAG }} Rscript -e 'pkgdown::build_site_github_pages("/mnt/vol/${{ env.PACKAGE_NAME }}", new_process = FALSE, install = FALSE)'
+
+      - name: Deploy to GitHub pages 🚀
+        if: ${{ inputs.IS_SUBDIR  != 'true' }}
+        uses: JamesIves/[email protected]
+        with:
+          clean: true
+          branch: pages
+          folder: docs
+          target-folder: docs
+
+      - name: Deploy to GitHub pages 🚀 (R package as subdirectory)
+        if: ${{ inputs.IS_SUBDIR  == 'true' }}
+        uses: JamesIves/[email protected]
+        with:
+          clean: true
+          branch: pages
+          folder: ${{ env.PACKAGE_NAME }}/docs
+          target-folder: docs