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44 changes: 26 additions & 18 deletions .github/workflows/pull_request.yml
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 @@ -39,11 +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 }}"
Expand Down Expand Up @@ -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 ###################################
Expand Down Expand Up @@ -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
Expand All @@ -172,7 +182,7 @@ jobs:
echo "changes=$changes" >> $GITHUB_OUTPUT
git add . --force
git commit -m 'Render preview' || echo "No changes to commit"
git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
git push --force || echo "No changes to commit"
shell: bash

Expand All @@ -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
Expand Down
105 changes: 68 additions & 37 deletions .github/workflows/render-all.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@

# Candace Savonen Apr 2021
# Candace Savonen 2021
# Updated May 2024

name: Render all output courses

Expand All @@ -8,7 +8,7 @@ on:
push:
branches: [ main, staging ]
paths:
- '**.Rmd'
- '**md$'
- assets/*
- quizzes/*

Expand All @@ -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
Expand All @@ -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 --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]
needs: [yaml-check, render-course]
runs-on: ubuntu-latest
container:
image: ${{needs.yaml-check.outputs.rendering_docker_image}}
Expand All @@ -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 --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:
Expand All @@ -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
Expand All @@ -165,29 +195,28 @@ 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 --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'
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
if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
run: |
Rscript -e "ottrpal::bookdown_to_embed_leanpub(
render = FALSE, \
chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
make_book_txt = as.logical('${{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
Expand All @@ -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 --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:
Expand All @@ -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 --allow-unrelated-histories --strategy-option=ours
git status
git push -u origin main || echo "No changes to push"
16 changes: 10 additions & 6 deletions config_automation.yml
Original file line number Diff line number Diff line change
Expand Up @@ -12,15 +12,19 @@ spell-check: yes
style-code: yes
# Test build the docker image if any docker-relevant files have been changed
docker-test: no
# Should the book_txt be generated?
make_book_txt: yes
# 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: yes
render-coursera: yes
render-coursera: no

## Automate the creation of Book.txt file? yes/no
## This is only relevant if render-leanpub is yes, otherwise it will be ignored
make-book-txt: yes

# What docker image should be used for rendering?
# The default is jhudsl/course_template:main
rendering-docker-image: 'jhudsl/course_template:main'
# The default is jhudsl/base_ottr:main
rendering-docker-image: 'jhudsl/base_ottr:main'
3 changes: 2 additions & 1 deletion style-sets/data-trail/_output.yml
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,8 @@ bookdown::gitbook:
before: |
<a href="https://www.datatrail.org/"><img src="assets/DataTrail_logo.jpg" style="padding-left: 0px; padding-top: 8px;"</a>
after: |
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
<p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
<a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</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>
Expand Down
3 changes: 2 additions & 1 deletion style-sets/fhdasl/_output.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ bookdown::gitbook:
before: |
<a href="https://hutchdatascience.org/" target="_blank"><img src="assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
after: |
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
<p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
<p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
<p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
<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://forms.gle/W6Mg4rzuMK6Yk3Am8"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
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