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🔄 Synced file(s) with jhudsl/OTTR_Template #226

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a325511
🔄 Synced local '.github/workflows/' with remote '.github/workflows/'
cansavvy Sep 17, 2024
48589b1
🔄 Synced local 'config_automation.yml' with remote 'config_automation…
cansavvy Sep 17, 2024
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78 changes: 29 additions & 49 deletions .github/workflows/pull_request.yml
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
# Candace Savonen 2021
# Updated Jan 2023
# Updated May 2024

name: Pull Request

Expand Down Expand Up @@ -39,18 +39,17 @@ 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_render_preview: "${{ env.RENDER_PREVIEW }}"
toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"

########################## Make the error reports ##############################
Expand Down Expand Up @@ -103,13 +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 ###################################
Expand Down Expand Up @@ -141,52 +140,35 @@ 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
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')"

# 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.toggle_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
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()"
# 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
Expand Down Expand Up @@ -215,15 +197,13 @@ 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_guide=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/Student_Guide.docx")
docx_link=$(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" >> $GITHUB_OUTPUT
echo "student_guide=$student_guide" >> $GITHUB_OUTPUT
echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
echo ${{steps.commit.outputs.changes}}
Expand All @@ -238,7 +218,7 @@ jobs:
Re-rendered previews from the latest commit:
- :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \*
- :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }})
- Download the Student Guide [.docx file](${{ steps.build-components.outputs.student_guide }})
- Download the [.docx file](${{ steps.build-components.outputs.docx_link }})

\* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.

Expand Down
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