🔄 Synced file(s) with jhudsl/AnVIL_Template

.github/workflows/check-url.yml

@@ -78,6 +78,16 @@ jobs:
       run: |
         echo ${{ steps.check-report.outputs.error_url }}
         echo ${{ steps.check-report.outputs.error_num }}
+
+      # Commit file
+    - name: Commit tocless bookdown files
+      if: ${{ steps.check-report.outputs.error_num >= 1 }}
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        git add --force check_reports/url_checks.tsv
+        git commit -m 'Add spell check file' || echo "No changes to commit"
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
 
     - name: Find issues
       id: find-issue

.github/workflows/pull_request.yml

@@ -1,5 +1,5 @@
 # Candace Savonen 2021
-# Updated Jan 2023
+# Updated May 2024
 
 name: Pull Request
 
@@ -17,7 +17,6 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
-          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -39,28 +38,22 @@ jobs:
           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 || echo echo branch exists remotely
+          git push --set-upstream origin $branch_name || echo branch exists remotely
         shell: bash
 
 
     outputs:
+      toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
+      toggle_feedback_link: "${{ env.FEEDBACK_LINK }}"
+      toggle_md_linter: "${{ env.MARKDOWN_LINTER }}"
+      toggle_readability: "${{ env.READABILITY_REPORT }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+      toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-      render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
-
-  build-portal-events:
-    name: Gather Portal Events
-    needs: yaml-check
-    uses: ./.github/workflows/gather-portal-events.yml
-    with:
-      render-type: 'preview'
-      repository: $GITHUB_REPOSITORY
-    secrets:
-      gh_pat: ${{ secrets.GH_PAT }}
 
 ########################## Make the error reports ##############################
   spell-check:
@@ -71,8 +64,9 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      gh_pat: secrets.GH_PAT
       branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   url-check:
     name: Check URLs
@@ -82,8 +76,9 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: secrets.GH_PAT
       branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   quiz-check:
     name: Check quiz formatting
@@ -93,8 +88,9 @@ jobs:
     with:
       check_type: quiz_format
       error_min: 0
-      gh_pat: secrets.GH_PAT
       branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
 ############################# Style the code ###################################
   style-code:
@@ -112,15 +108,35 @@ jobs:
           fetch-depth: 0
 
       - name: Run styler
-        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+        run: Rscript -e "styler::style_file(list.files(pattern = '(R|q)md$', recursive = FALSE, full.names = TRUE));warnings()"
 
       - name: Commit styled files
         run: |
           git config --system --add safe.directory "$GITHUB_WORKSPACE"
-          git add \*.Rmd
-          git commit -m 'Style Rmds' || echo "No changes to commit"
+          git add \*md
+          git commit -m 'Style *mds' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
 
+############################# Readability Report ###################################
+
+  readability-report:
+    name: Readability report
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    if: ${{needs.yaml-check.outputs.toggle_readability == 'yes'}}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Readability report
+        uses: Rebilly/lexi@v2
+        with:
+          github-token: ${{ secrets.GH_PAT }}
+          glob: '**/*.md'
+
 ############################# Render Preview ###################################
 
   render-preview:
@@ -153,18 +169,29 @@ jobs:
       # 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
+        if: ${{needs.yaml-check.outputs.toggle_feedback_link == 'yes'}}
+        run: |
+          bash scripts/AnVIL_Feedback_Script.sh
+          git add _output.yml
+          git commit -m 'Set up feedback link' || echo "No changes to commit"
 
       # Run bookdown rendering
       - name: Run bookdown render
         id: bookdown
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
 
+      # Run quarto rendering
+      - name: Render quarto version
+        id: quarto
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: Rscript -e "quarto::quarto_render('.')"
+
       # 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'}}
+        if: ${{needs.yaml-check.outputs.toggle_student_guide == 'yes'}}
         id: student_guide
         run: |
           mkdir tmp1
@@ -174,22 +201,26 @@ jobs:
           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.
-      # This job creates a shared scaffold for both.
-      - name: Run TOC-less version of render
-        id: tocless
-        run: Rscript -e "ottrpal::render_without_toc()"
+          git add student-guide/*
+          git commit -m 'Create student guide' || echo "No changes to commit"
 
       # This checks on the steps before it and makes sure that they completed.
       # If the renders didn't complete we don't want to commit the file changes
-      - name: Check on render steps
-        if: steps.bookdown.outcome != 'success' || steps.tocless.outcome != 'success'
+      - name: Check on Rmd render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
           echo Bookdown status ${{steps.bookdown.outcome}}
-          echo Toc-less status ${{steps.tocless.outcome}}
-          exit 1
+          if [${{steps.bookdown.outcome}} != 'success']; then
+            exit 1
+          fi
+
+      - name: Check on quarto render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: |
+          echo Quarto status ${{steps.quarto.outcome}}
+          if [${{steps.quarto.outcome}} != 'success']; then
+            exit 1
+          fi
 
       - name: Website preview for download
         run: zip website-preview.zip docs/* -r
@@ -220,12 +251,11 @@ jobs:
         run: |
           course_name=$(head -n 1 student-guide/_bookdown.yml | cut -d'"' -f 2| tr " " "-")
           bookdown_link=$(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/$course_name.docx")          zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+          student_guide=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/Student_Guide.docx")
+          zip_link=$(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" >> $GITHUB_OUTPUT
+          echo "student_guide=$student_guide" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
@@ -240,7 +270,7 @@ jobs:
             Re-rendered previews from the latest commit:
             - :eyes: Quick [preview of course website here](${{ 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 }})
+            - Download the Student Guide [.docx file](${{ steps.build-components.outputs.student_guide }})
 
             \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.