Make GHA yml's compatible with quarto (#746)

* Update render-all.yml * add if statement * Update config_automation.yml * Add quarto rendering * Update pull request.yml * Add fhdsl/ottr to sync.yml * Update with the changes on fhdsl/ottr * Fix styler part 3 * Updates to git handling * Some rebases and some rearrangements of git stuffs
jhudsl · Jul 16, 2024 · beb1e0d · beb1e0d
1 parent d45fa8b
commit beb1e0d
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diff --git a/.github/sync.yml b/.github/sync.yml
@@ -68,6 +68,7 @@ group:
  fhdsl/Intermediate-Git-GitHub
  fhdsl/GitHub_Automation_for_Scientists
  williamtmillsiv/introduction_to_bioinformatics
+ fhdsl/OTTR_Quarto
  fhdsl/bench_to_bytes
  fhdsl/Intermediate_R
  fhdsl/DataViz_Practice
@@ -148,7 +149,7 @@ group:
  deleteOrphaned: true
  repos: |
  C-MOOR/C-MOOR_Template
- 
+
  - files:
  - source: config_automation.yml
  dest: config_automation.yml

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -1,5 +1,5 @@
 # Candace Savonen 2021
-# Updated Jan 2023
+# Updated May 2024
 
 name: Pull Request
 
@@ -39,11 +39,12 @@ 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 }}"
@@ -101,13 +102,13 @@ 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"
 
 ############################# Render Preview ###################################
@@ -142,23 +143,32 @@ 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 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
@@ -189,12 +199,10 @@ jobs:
  run: |
  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-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
  docx_link=$(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" >> $GITHUB_OUTPUT
  echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
  echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
  echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT

diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml
@@ -12,7 +12,7 @@ jobs:
  runs-on: ubuntu-latest
  steps:
 
- - uses: mshick/add-pr-comment@v1
+ - uses: mshick/add-pr-comment@v2
  if: ${{ github.head_ref == 'repo-sync/OTTR_Template/default' }}
  with:
  message: |

diff --git a/.github/workflows/render-all.yml b/.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 +8,7 @@ on:
  push:
  branches: [ main, staging ]
  paths:
- - '**.Rmd'
+ - '**md$'
  - assets/*
  - quizzes/*
 
@@ -27,20 +27,19 @@ 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 }}"
  make_book_txt: "${{ env.MAKE_BOOK_TXT }}"
  rendering_docker_image: "${{ 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
@@ -57,38 +56,56 @@ 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
 
- # 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('.')"
+
  # 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 --rebase --allow-unrelated-histories --strategy-option=ours
+ git commit -m 'Render course' || echo "No changes to commit"
+ git status docs/*
  git push -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}}
@@ -106,31 +123,40 @@ 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 --rebase --allow-unrelated-histories --strategy-option=ours
+ git status docs/no_toc*
  git push -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:
@@ -145,6 +171,10 @@ 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
@@ -165,20 +195,19 @@ jobs:
  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 --rebase --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
@@ -187,7 +216,7 @@ 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
@@ -199,7 +228,8 @@ jobs:
  git add --force resources/*
  git add --force docs/*
  git commit -m 'Render Leanpub' || echo "No changes to commit"
- git pull --rebase --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:
@@ -222,27 +252,28 @@ 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 status
  git push -u origin main || echo "No changes to push"
diff --git a/config_automation.yml b/config_automation.yml
@@ -17,7 +17,7 @@ url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
-render-bookdown: yes
+render-website: rmd
 render-leanpub: yes
 render-coursera: no