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Merge pull request #101 from jhudsl/repo-sync/AnVIL_Template/default
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@avahoffman
avahoffman authored Jan 17, 2025
2 parents fca864d + 5327cde commit bf07e2a
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117 changes: 117 additions & 0 deletions .github/workflows/check-url.yml
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@@ -0,0 +1,117 @@
name: Periodic URL Check

on:
workflow_dispatch:
schedule:
- cron: '0 0 1 * *'

jobs:
set-up:
name: Load user automation choices
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
with:
fetch-depth: 0

# Use the yaml-env-action action.
- name: Load environment from YAML
uses: doughepi/[email protected]
with:
files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
outputs:
toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"

url-check:
name: Check URLs
needs: set-up
if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
runs-on: ubuntu-latest
container:
image: jhudsl/base_ottr:main

steps:
- name: Checkout
uses: actions/checkout@v3
with:
fetch-depth: 0

# Delete the branch if this has been run before
- name: Delete branch locally and remotely
run: git push origin --delete preview-spell-error || echo "No branch to delete"

# Make the branch fresh
- name: Make the branch fresh
run: |
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'
echo branch doesnt exist
git checkout -b preview-spell-error || echo branch exists
git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
shell: bash

- name: Run the check
uses: jhudsl/ottr-reports@main
id: check_results
continue-on-error: true
with:
check_type: urls
error_min: 1

- name: Declare file path and time
id: check-report
run: |
error_num=$(cat check_reports/url_checks.tsv | wc -l)
error_num="$((error_num-1))"
echo "error_num=$error_num" >> $GITHUB_OUTPUT
echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
shell: bash

- name: Stop if failure
if: steps.check_results.outcome == 'failure'
run: exit 1

- name: Print out error variables
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
env:
GH_PAT: ${{ secrets.GH_PAT }}
run: |
echo "$GITHUB_REPOSITORY"
curl -o find_issue.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/find_issue.R
issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
echo URL issue exists: $issue_exists
echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
- name: If too many URL errors, then make an issue
if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
uses: JasonEtco/create-an-issue@v2
with:
filename: .github/ISSUE_TEMPLATE/url-error.md
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
FILE_URL: ${{ steps.check-report.outputs.error_url }}
ERROR_NUM: ${{ steps.check-report.outputs.error_num }}

- name: If no URL errors than delete the branch we made
if: ${{ steps.check-report.outputs.error_num < 1 }}
run: |
git config --system --add safe.directory "$GITHUB_WORKSPACE"
git push origin --delete preview-spell-error || echo "No branch to delete"
2 changes: 1 addition & 1 deletion .github/workflows/delete-preview.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:

# Check out current repository
- name: checkout
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 0

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135 changes: 96 additions & 39 deletions .github/workflows/pull_request.yml
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@@ -1,5 +1,5 @@
# Candace Savonen 2021
# Updated Jan 2023
# Updated May 2024

name: Pull Request

Expand All @@ -14,7 +14,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 0

Expand All @@ -31,23 +31,29 @@ jobs:
# Make the branch fresh
- name: Make the branch fresh
run: |
git config --local user.email "[email protected]"
git config --local user.name "jhudsl-robot"
git config --global --add safe.directory $GITHUB_WORKSPACE
git config --global user.name 'github-actions[bot]'
git config --global user.email 'github-actions[bot]@users.noreply.github.com'
branch_name='preview-${{ github.event.pull_request.number }}'
echo branch doesnt exist
git checkout -b $branch_name || echo branch exists
git push --set-upstream origin $branch_name
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: "${{ env.RENDERING_DOCKER_IMAGE }}"
render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"

########################## Make the error reports ##############################
spell-check:
Expand All @@ -58,7 +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
Expand All @@ -68,7 +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
Expand All @@ -78,7 +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:
Expand All @@ -91,20 +103,40 @@ jobs:

steps:
- name: Checkout files
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
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:
Expand All @@ -117,33 +149,49 @@ jobs:

steps:
- name: Checkout files
uses: actions/checkout@v3
uses: actions/checkout@v4
with:
fetch-depth: 0

# Set up git checkout
- name: Set up git checkout
run: |
git config --system --add safe.directory "$GITHUB_WORKSPACE"
git config --local user.email "[email protected]"
git config --local user.name "jhudsl-robot"
git config --global --add safe.directory $GITHUB_WORKSPACE
git config --global user.name 'github-actions[bot]'
git config --global user.email 'github-actions[bot]@users.noreply.github.com'
branch_name='preview-${{ github.event.pull_request.number }}'
git fetch --all
git checkout $branch_name
git merge -s recursive --strategy-option=theirs origin/${{ 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')"


# 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
- name: Run student guide render
if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
if: ${{needs.yaml-check.outputs.toggle_student_guide == 'yes'}}
id: student_guide
run: |
mkdir tmp1
Expand All @@ -153,22 +201,29 @@ jobs:
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()"
git add student-guide/*
git commit -m 'Create student guide' || echo "No changes to commit"
# 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

# Commit the rendered bookdown files
- name: Commit rendered bookdown files to preview branch
Expand All @@ -179,7 +234,7 @@ 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 @@ -196,11 +251,11 @@ 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-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx")
student_guide=$(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" >> $GITHUB_OUTPUT
echo "student_docx_link=$student_docx_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
echo ${{steps.commit.outputs.changes}}
Expand All @@ -213,11 +268,13 @@ jobs:
issue-number: ${{ github.event.pull_request.number }}
body: |
Re-rendered previews from the latest commit:
- See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
- See [preview of Coursera/Leanpub version here](${{ steps.build-components.outputs.tocless_link }})
- Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.student_docx_link }})
- :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 }})
_Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
\* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.
_Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ steps.build-components.outputs.commit_id }}_
edit-mode: replace

- name: Comment if no changes
Expand Down
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