From 537cbd2cf965ddcc6ab89ad4bc4018690fd0edba Mon Sep 17 00:00:00 2001
From: Franciszek Walkowiak <franciszek.walkowiak@roche.com>
Date: Wed, 26 Jun 2024 10:37:25 +0200
Subject: [PATCH] Update

---
 .github/workflows/build-check-install.yaml | 17 ++++++---
 .github/workflows/pkgdown.yaml             | 41 ++++++++++++++++++++--
 2 files changed, 51 insertions(+), 7 deletions(-)

diff --git a/.github/workflows/build-check-install.yaml b/.github/workflows/build-check-install.yaml
index 5fc2fe5c2..788ac8e87 100644
--- a/.github/workflows/build-check-install.yaml
+++ b/.github/workflows/build-check-install.yaml
@@ -186,6 +186,15 @@ on:
         required: false
         type: boolean
         default: false
+      unit-test-report-directory:
+        description: |
+          Directory name on gh-pages branch where the unit test report should be uploaded.
+          For any additional unit test report directories to be retained by the pkgdown workflow
+          in the gh-pages branch, they have to be added to the additional-unit-test-report-directories
+          pkgdown workflow input.
+        required: false
+        type: string
+        default: "unit-test-report"
 
 concurrency:
   group: r-cmd-${{ inputs.concurrency-group }}-${{ github.event.pull_request.number || github.ref }}
@@ -832,7 +841,7 @@ jobs:
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
-          destination_dir: ${{ needs.build-install-check.outputs.current-branch-or-tag }}/unit-test-report
+          destination_dir: ${{ needs.build-install-check.outputs.current-branch-or-tag }}/${{ inputs.unit-test-report-directory }}
 
       - name: Upload JUnit HTML report to GitHub pages (latest-tag) 🏷️
         if: >
@@ -842,7 +851,7 @@ jobs:
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
-          destination_dir: ${{ inputs.latest-tag-alt-name }}/unit-test-report
+          destination_dir: ${{ inputs.latest-tag-alt-name }}/${{ inputs.unit-test-report-directory }}
 
       - name: Upload JUnit HTML report to GitHub pages (release-candidate) 🏷️
         if: >
@@ -852,7 +861,7 @@ jobs:
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
-          destination_dir: ${{ inputs.release-candidate-alt-name }}/unit-test-report
+          destination_dir: ${{ inputs.release-candidate-alt-name }}/${{ inputs.unit-test-report-directory }}
 
       - name: Upload JUnit HTML report to GitHub pages (non-multiversion) 🗞️
         if: needs.build-install-check.outputs.multiversion-docs == 'false'
@@ -860,7 +869,7 @@ jobs:
         with:
           github_token: ${{ steps.github-token.outputs.token }}
           publish_dir: ./unit-test-report
-          destination_dir: unit-test-report
+          destination_dir: ${{ inputs.unit-test-report-directory }}
 
   upload-release-assets:
     name: Upload build tar.gz
diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index d2a0142de..c11ce3b41 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -111,6 +111,16 @@ on:
         required: false
         type: string
         default: "."
+      additional-unit-test-report-directories:
+        description: |
+          If there are any additional unit test reports directories generated, they should be listed
+          as comma-separated directory list. If this input is empty, only coverage-report and
+          unit-test-report directories will be retained in the generated documentation directory.
+          Example:
+          unit-test-report-as-cran,unit-test-report-not-cran
+        required: false
+        type: string
+        default: ""
 
 concurrency:
   group: docs-${{ github.event.pull_request.number || github.ref }}
@@ -255,9 +265,34 @@ jobs:
           GH_PAGES_DIR="gh-pages/${{ steps.current-branch-or-tag.outputs.ref-name }}"
           mkdir -p $GH_PAGES_DIR
           ls -l $GH_PAGES_DIR
-          # Remove contents except coverage-report and unit-test-report directories.
-          find $GH_PAGES_DIR -mindepth 1 -maxdepth 1 \
-            ! -name coverage-report ! -name unit-test-report -exec rm -rf {} +
+          # Remove any existing documentation for the git tag, but retain
+          # coverage report and unit test report which might have already been generated
+          # by the coverage and build-check-install workflows respectively.
+          if [[ "${{ inputs.additional-unit-test-report-directories }}" != "" ]]; then
+            directories_to_retain="coverage-report,unit-test-report,${{ inputs.additional-unit-test-report-directories }}"
+          else
+            directories_to_retain="coverage-report,unit-test-report"
+          fi
+          IFS=',' read -ra DIRECTORIES_TO_RETAIN <<< "$directories_to_retain"
+          echo "The following directories will be retained:"
+          for dir in "${DIRECTORIES_TO_RETAIN[@]}"; do
+            echo "$dir"
+          done
+          # Remove all files from GH_PAGES_DIR, except any DIRECTORIES_TO_RETAIN.
+          find $GH_PAGES_DIR -mindepth 1 -maxdepth 1 -print0 | while IFS= read -r -d '' file; do
+            file_to_be_removed="true"
+            # Check if the file/directory matches any directory to be retained.
+            for dir in "${DIRECTORIES_TO_RETAIN[@]}"; do
+              if [[ "$GH_PAGES_DIR/$dir" == "$file" ]]; then
+                echo "Not removing $file."
+                file_to_be_removed="false"
+              fi
+            done
+            if [[ "$file_to_be_removed" == "true" ]]; then
+              echo "Removing $file."
+              rm -rf "$file"
+            fi
+          done
           ls -l $GH_PAGES_DIR
           # Copy generated pkgdown documentation to gh-pages branch.
           cp -a ${{ github.event.repository.name }}/${{ inputs.package-subdirectory }}/docs/. $GH_PAGES_DIR