pull_request.yml

# Candace Savonen 2021
# Updated May 2025

name: Pull Request

on:
  pull_request:
    branches: [ main, staging ]

jobs:

  yaml-check:
    name: Load user automation choices
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          fetch-depth: 0

        # Use the yaml-env-action action.
      - name: Load environment from YAML
        uses: doughepi/yaml-env-action@v1.0.0
        with:
            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.

      # Delete the branch if this has been run before
      - name: Delete branch locally and remotely
        run: git push origin --delete preview-${{ github.event.pull_request.number }} || 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'

          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 branch exists remotely
        shell: bash


    outputs:
      toggle_website: "${{ env.RENDER_WEBSITE }}"
      toggle_spell_check: "${{ env.SPELL_CHECK }}"
      spell_error_min: "${{ env.SPELL_ERROR_MIN }}"
      toggle_style_code: "${{ env.STYLE_CODE }}"
      toggle_url_check: "${{ env.URL_CHECKER }}"
      url_error_min: "${{ env.URL_ERROR_MIN }}"
      toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
      quiz_error_min: "${{ env.QUIZ_ERROR_MIN }}"
      toggle_md_linter: "${{ env.MARKDOWN_LINTER }}"
      toggle_readability: "${{ env.READABILITY_REPORT }}"
      toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
      toggle_dictionary_sort: "${{ env.DICTIONARY_SORT }}"
      rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
      toggle_feedback_link: "${{ env.FEEDBACK_LINK }}"
      toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"

########################## Make the error reports ##############################
  ottr-reports:
    name: Run Reports
    needs: yaml-check
    if: ${{needs.yaml-check.outputs.toggle_spell_check == 'true' || needs.yaml-check.outputs.toggle_url_check == 'true' || needs.yaml-check.outputs.toggle_quiz_check == 'true'}}
    runs-on: ubuntu-latest
    permissions:
      pull-requests: write

    steps:
    - name: Checkout Actions Repository
      uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Run Reports
      id: run-reports
      uses: ottrproject/ottr-reports@main
      with:
        check_spelling: ${{needs.yaml-check.outputs.toggle_spell_check}}
        spelling_error_min: ${{needs.yaml-check.outputs.spell_error_min}}
        check_urls: ${{needs.yaml-check.outputs.toggle_url_check}}
        url_error_min: ${{needs.yaml-check.outputs.url_error_min}}
        check_quiz_form: ${{needs.yaml-check.outputs.toggle_quiz_check}}
        quiz_error_min: ${{needs.yaml-check.outputs.quiz_error_min}}
        sort_dictionary: ${{needs.yaml-check.outputs.toggle_dictionary_sort}}

############################# Style the code ###################################
  style-code:
    name: Style code
    needs: yaml-check
    runs-on: ubuntu-latest
    if: ${{needs.yaml-check.outputs.toggle_style_code == 'true'}}
    container:
      image: jhudsl/base_ottr:main

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

      - name: Run styler
        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 \*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 == 'true'}}

    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'

############################# AnVIL Feedback Link ##############################
  # Do not remove this section with OTTR syncs!
  anvil-feedback:
    name: Make AnVIL Feedback Link
    needs: [yaml-check]
    runs-on: ubuntu-latest
    container:
      image: ${{needs.yaml-check.outputs.rendering_docker_image}}

    steps:
      - name: Checkout files
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
      
      # Set up git checkout
      - name: Set up git checkout
        run: |
          git config --global --add safe.directory $GITHUB_WORKSPACE
          git config --global user.name 'github-actions[bot]'
          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
          branch_name='${{ github.head_ref }}'
          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 == 'true'}}
        run: |
          bash .github/AnVIL_Feedback_Script.sh
          git add _output.yml
          git commit -m 'Set up feedback link' || echo "No changes to commit"
          git push origin || echo "No changes to commit"
          
############################# Render Preview ###################################
  render-preview:
    name: Render preview
    needs: [yaml-check, anvil-feedback]
    runs-on: ubuntu-latest
    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'true'}}
    permissions:
      pull-requests: write
      contents: write

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

    - name: Run render
      uses: ottrproject/ottr-preview@main
      with:
        toggle_website: ${{needs.yaml-check.outputs.toggle_website}}
        docker_image: ${{needs.yaml-check.outputs.rendering_docker_image}}
        
############################# Render Student Guide #############################
  # Do not remove this section with OTTR syncs!
  render-anvil-special:
    name: Render AnVIL Special
    needs: [yaml-check, render-preview]
    runs-on: ubuntu-latest
    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'true'}}
    container:
      image: ${{needs.yaml-check.outputs.rendering_docker_image}}

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

      # Set up git checkout
      - name: Set up git checkout
        run: |
          git config --global --add safe.directory $GITHUB_WORKSPACE
          git config --global user.name 'github-actions[bot]'
          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
          branch_name='preview-${{ 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

      # 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 == 'true'}}
        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"
          
      # Commit the rendered bookdown files
      - name: Commit rendered bookdown files to preview branch
        id: commit
        run: |
          branch_name='preview-${{ github.event.pull_request.number }}'
          git diff origin/main -- docs >/dev/null && changes=true || changes=false
          echo "changes=$changes" >> $GITHUB_OUTPUT
          git add . --force
          git commit -m 'Render AnVIL Special' || echo "No changes to commit"
          git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
          git push --force || echo "No changes to commit"
        shell: bash