🔄 Synced file(s) with jhudsl/OTTR_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
@@ -39,15 +38,18 @@ 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: "${{ env.CHECK_QUIZZES }}"
+      toggle_md_linter: "${{ env.MARKDOWN_LINTER }}"
+      toggle_readability: "${{ env.READABILITY_REPORT }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
 
@@ -60,8 +62,9 @@ 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
@@ -71,8 +74,9 @@ 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
@@ -82,8 +86,9 @@ 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:
@@ -101,15 +106,35 @@ 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:
@@ -139,46 +164,35 @@ jobs:
           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
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         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.
-      # This job creates a shared scaffold for both.
-      - name: Run TOC-less version of render
-        id: tocless
-        run: Rscript -e "ottrpal::render_without_toc()"
+      # Run quarto rendering
+      - name: Render quarto version
+        id: quarto
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: Rscript -e "quarto::quarto_render('.')"
 
       # 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
@@ -207,14 +221,13 @@ 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")          zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+          docx_link=$(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}}