Merge pull request #37 from fhdsl/repo-sync/AnVIL_Template/default

🔄 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
@@ -39,16 +38,19 @@ 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 }}"
@@ -62,8 +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
@@ -73,8 +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
@@ -84,8 +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:
@@ -103,15 +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:
@@ -153,8 +178,15 @@ jobs:
       # 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
@@ -171,22 +203,24 @@ jobs:
           rm -r tmp1
           git add student-guide/*
           git commit -m 'Create student guide' || echo "No changes to commit"
-          
-      # 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()"
 
       # 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
@@ -217,12 +251,10 @@ 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-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
-          student_guide=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/Student_Guide.docx")          
+          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" >> $GITHUB_OUTPUT
           echo "student_guide=$student_guide" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT

.github/workflows/render-all.yml

@@ -1,5 +1,5 @@
-
-# Candace Savonen Apr 2021
+# Candace Savonen 2021
+# Updated May 2024
 
 name: Render all output courses
 
@@ -8,7 +8,8 @@ on:
   push:
     branches: [ main, staging ]
     paths:
-      - '**.Rmd'
+      - '*.qmd'
+      - '*.Rmd'
       - assets/*
       - quizzes/*
 
@@ -27,21 +28,20 @@ jobs:
         with:
             files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
     outputs:
-      toggle_bookdown: "${{ env.RENDER_BOOKDOWN }}"
+      toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_coursera: "${{ env.RENDER_COURSERA }}"
       toggle_leanpub: "${{ env.RENDER_LEANPUB }}"
       toggle_feedback_link: "${{ env.FEEDBACK_LINK }}"
       toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
 
-  render-bookdown:
-    name: Render bookdown
+  render-course:
+    name: Render course preview
     needs: yaml-check
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
-    if: ${{needs.yaml-check.outputs.toggle_bookdown == 'yes'}}
 
     steps:
       - name: checkout
@@ -58,7 +58,10 @@ jobs:
 
       # We want a fresh run of the renders each time
       - name: Delete old docs/*
-        run: rm -rf docs/*
+        run: |
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
 
       # Make sure the link for AnVIL feedback is prepopulated for the specific course
       - name: Set up feedback link
@@ -68,12 +71,19 @@ jobs:
           git add _output.yml
           git commit -m 'Set up feedback link' || echo "No changes to commit"
 
-      # Run bookdown rendering
+      # Run Rmd rendering
       - name: Run bookdown render
         id: bookdown
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
+          rm -rf docs/*
           Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all');
           file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
+
+      - 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 
@@ -94,27 +104,35 @@ jobs:
 
       # 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 step
-        if: steps.bookdown.outcome != 'success'
+      - name: Check on Rmd render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
           echo Bookdown status ${{steps.bookdown.outcome}}
-          exit 1
+          if [${{steps.bookdown.outcome}} != 'success']; then
+            exit 1
+          fi
 
-      # Commit the rendered bookdown files
-      - name: Commit rendered bookdown files
+      - 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
+
+      # Commit the rendered course files
+      - name: Commit rendered course files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git fetch origin
           git add --force docs/*
-          git commit -m 'Render bookdown' || echo "No changes to commit"
-          git pull --allow-unrelated-histories --strategy-option=ours
-          git push -u origin main  || echo "No changes to push"
+          git commit -m 'Render course' || echo "No changes to commit"
+          git status docs/*
+          git push --force -u origin main  || echo "No changes to push"
 
   render-tocless:
     name: Render TOC-less version for Leanpub or Coursera
-    needs: [yaml-check, render-bookdown]
+    needs: [yaml-check, render-course]
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
@@ -132,31 +150,40 @@ jobs:
           git config --global --add safe.directory $GITHUB_WORKSPACE
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
 
       # 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
+      - name: Run TOC-less version of render -- Rmd version
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
+        id: tocless_rmd
         run: Rscript -e "ottrpal::render_without_toc()"
 
+      - name: Run TOC-less version of render -- quarto version
+        id: tocless_quarto
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: |
+          Rscript -e "quarto::quarto_render('.', metadata = list(sidebar = F, toc = F),
+          quarto_args = c('--output-dir', 'docs/no_toc/'))"
+
       # Commit the TOC-less version files
       - name: Commit tocless bookdown files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git fetch origin
           git add --force docs/no_toc*
           git commit -m 'Render toc-less' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
-          git push -u origin main  || echo "No changes to push"
+          git status docs/no_toc*
+          git push --force -u origin main  || echo "No changes to push"
 
   render-leanpub:
     name: Finish Leanpub prep
     needs: [yaml-check, render-tocless]
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/ottrpal:main
+      image: jhudsl/ottrpal
     if: ${{needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
 
     steps:
@@ -171,6 +198,10 @@ jobs:
           git config --global --add safe.directory $GITHUB_WORKSPACE
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
+          ls docs/no_toc
 
       # Create screenshots
       - name: Run the screenshot creation
@@ -184,27 +215,27 @@ jobs:
             --git_pat ${{ secrets.GH_PAT }} \
             --repo $GITHUB_REPOSITORY \
             --output_dir resources/chapt_screen_images)
+          rm make_screenshots.R
 
       # We want a fresh run of the renders each time
       - name: Delete manuscript/
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
           rm -rf manuscript/
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git fetch origin
           git add .
           git commit -m 'Delete manuscript folder' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
         if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
         run: |
+          echo needs.yaml-check.outputs.toggle_make_book_txt == 'yes'
+          echo needs.yaml-check.outputs.toggle_make_book_txt
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'), \
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'yes'}}'), \
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
@@ -213,7 +244,7 @@ jobs:
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'))"
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'yes'}}'))"
 
       # Commit the rendered Leanpub files
       - name: Commit rendered Leanpub files
@@ -225,7 +256,8 @@ jobs:
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Leanpub' || echo "No changes to commit"
-          git pull --allow-unrelated-histories --strategy-option=ours
+          git status docs/*
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours --autostash
           git push --force --set-upstream origin main || echo "No changes to push"
 
   render-coursera:
@@ -248,27 +280,28 @@ jobs:
           git config --global --add safe.directory $GITHUB_WORKSPACE
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
 
       # Run Coursera version
       - name: Convert Leanpub quizzes to Coursera
         if: needs.yaml-check.outputs.toggle_leanpub == 'yes' && needs.yaml-check.outputs.toggle_quiz_check == 'yes'
         id: coursera
         run: Rscript -e "ottrpal::convert_coursera_quizzes()"
 
-      # Commit the rendered bookdown files
+      # Commit the rendered files
       # Only commit coursera quizzes if the directory is present
       - name: Commit rendered Coursera files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git fetch origin
           if [ -d 'coursera_quizzes' ]; then
             git add --force coursera_quizzes/*
           fi
           git add --force manuscript/*
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Coursera quizzes' || echo "No changes to commit"
-          git pull --rebase --allow-unrelated-histories --strategy-option=ours
-          git push -u origin main  || echo "No changes to push"
+          git status
+          git push --force -u origin main  || echo "No changes to push"

config_automation.yml

@@ -10,12 +10,18 @@ render-preview: yes
 spell-check: yes
 # Style any R code
 style-code: yes
+# Would you like your markdown files to be checked for formatting
+markdown-linter: yes
+# Would you like a readability report on your markdowns?
+readability-report: yes
 # Test build the docker image if any docker-relevant files have been changed
 docker-test: no
+# Should URLs be tested periodically?
+url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
-render-bookdown: yes
+render-website: rmd
 render-leanpub: no
 render-coursera: no
 
@@ -26,5 +32,5 @@ render-student-guide: yes
 feedback-link: yes
 
 # What docker image should be used for rendering?
-# The default is jhudsl/course_template:main
+# The default is jhudsl/base_ottr:main
 rendering-docker-image: 'jhudsl/base_ottr:main'

style-sets/AnVIL/_output.yml

@@ -16,6 +16,6 @@ bookdown::gitbook:
        <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
        <a href="https://hutchdatascience.org/" target="_blank"><img src="https://raw.githubusercontent.com/jhudsl/OTTR_Template/main/style-sets/fhdasl/copy_to_assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
-       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=your+course"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
+       <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span><a href="https://docs.google.com/forms/d/e/1FAIpQLScrDVb_utm55pmb_SHx-RgELTEbCCWdLea0T3IzS0Oj00GE4w/viewform?usp=pp_url&entry.1565230805=AnVIL+Book+Name"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
        
-# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows.
+# Note: Do not edit the feedback link in this file. This is automatically edited through the render-preview and render-bookdown workflows. You can deactivate this behavior in config_automation.yml.