Merge pull request #7 from fhdsl/copying-Ava-fixes-to-ottr

copying ava fixes for ottr

.github/workflows/pull_request.yml

@@ -14,9 +14,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -31,23 +32,24 @@ jobs:
       # Make the branch fresh
       - name: Make the branch fresh
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
-          git push --set-upstream origin $branch_name
+          git push --set-upstream origin $branch_name || echo echo branch exists remotely
         shell: bash
 
+
     outputs:
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-      render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
 
 ########################## Make the error reports ##############################
   spell-check:
@@ -59,6 +61,7 @@ jobs:
       check_type: spelling
       error_min: 3
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   url-check:
     name: Check URLs
@@ -69,6 +72,7 @@ jobs:
       check_type: urls
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   quiz-check:
     name: Check quiz formatting
@@ -79,6 +83,7 @@ jobs:
       check_type: quiz_format
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
 ############################# Style the code ###################################
   style-code:
@@ -91,7 +96,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -117,47 +122,27 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       # Set up git checkout
       - name: Set up git checkout
         run: |
-          git config --system --add safe.directory "$GITHUB_WORKSPACE"
-          git config --local user.email "[email protected]"
-          git config --local user.name "jhudsl-robot"
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           git fetch --all
           git checkout $branch_name
           git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
         shell: bash
-
-      # Make sure the link for AnVIL feedback is prepopulated for the specific course
-      - name: Set up feedback link
-        id: feedback
-        run: bash scripts/AnVIL_Feedback_Script.sh
-
+
       # Run bookdown rendering
       - name: Run bookdown render
         id: bookdown
         run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-
-      # Render a student guide if specified. This is a bit clunky because
-      # Bookdown does not work well if the files aren't named as such in the
-      # root directory
-      - name: Run student guide render
-        if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
-        id: student_guide
-        run: |
-          mkdir tmp1
-          mv _bookdown.yml _output.yml tmp1
-          mv student-guide/_bookdown.yml student-guide/_output.yml .
-          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
-          mv _bookdown.yml _output.yml student-guide
-          mv tmp1/_bookdown.yml tmp1/_output.yml .
-          rm -r tmp1
 
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
@@ -175,6 +160,9 @@ jobs:
           echo Toc-less status ${{steps.tocless.outcome}}
           exit 1
 
+      - name: Website preview for download
+        run: zip website-preview.zip docs/* -r
+
       # Commit the rendered bookdown files
       - name: Commit rendered bookdown files to preview branch
         id: commit
@@ -184,7 +172,7 @@ jobs:
           echo "changes=$changes" >> $GITHUB_OUTPUT
           git add . --force
           git commit -m 'Render preview' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+          git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push --force || echo "No changes to commit"
         shell: bash
 
@@ -199,13 +187,15 @@ jobs:
       - name: Build components of the comment
         id: build-components
         run: |
-          course_name=$(head -n 1 student-guide/_bookdown.yml | cut -d'"' -f 2| tr " " "-")
+          course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
           bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
           tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
-          student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx")
+          docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
+          zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+          echo "zip_link=$zip_link" >> $GITHUB_OUTPUT
           echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
           echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT
-          echo "student_docx_link=$student_docx_link" >> $GITHUB_OUTPUT
+          echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
@@ -218,11 +208,13 @@ jobs:
           issue-number: ${{ github.event.pull_request.number }}
           body: |
             Re-rendered previews from the latest commit:
-            - See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
-            - See [preview of Coursera/Leanpub version here](${{ steps.build-components.outputs.tocless_link }})
-            - Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.student_docx_link }})
+            - :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \*
+            - :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }})
+            - Download the [.docx file](${{ steps.build-components.outputs.docx_link }})
 
-            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+            \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.
+
+            _Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace
 
       - name: Comment if no changes