render_book_on_pr.yml

name: Render Book on PR to Main

on:
  workflow_dispatch:  # Allows the workflow to be triggered manually
  pull_request_target:
    types: [closed]
    branches:
      - deploy-preview

jobs:
  render-and-commit:
    if: github.event.pull_request.merged == true && github.event.pull_request.base.ref == 'deploy-preview' && startsWith(github.event.pull_request.head.ref, 'handbook_v')
    runs-on: ubuntu-latest
    continue-on-error: true
    env:
      RENV_PATHS_ROOT: ~/.cache/R/renv
      R_LIBS_USER: ~/.cache/R/renv/Library
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      
    steps:
      - name: Check out repository
        uses: actions/checkout@v4
        with:
          ref: deploy-preview

      - name: Fetch latest changes
        run: |
          git fetch origin
          git reset --hard origin/deploy-preview

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          r-version: '4.3.2'

      - name: Setup pandoc
        uses: r-lib/actions/setup-pandoc@v2

      - name: Install system dependencies and R packages
        run: |
          sudo apt-get update
          sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libglpk-dev r-cran-rjava r-base-dev openjdk-11-jdk gdal-bin libgdal-dev libxslt1-dev libgit2-dev libgeos-dev libproj-dev libudunits2-dev libcairo2-dev libxt-dev libmagick++-dev libpoppler-cpp-dev libpq-dev libmysqlclient-dev libsqlite3-dev libssh2-1-dev libgmp3-dev libmpfr-dev libprotobuf-dev protobuf-compiler libgl1-mesa-dev libglu1-mesa-dev libpoppler-glib-dev libtbb-dev libsodium-dev libv8-dev libnetcdf-dev netcdf-bin libjq-dev libharfbuzz-dev libfribidi-dev libnode-dev jq
          sudo R CMD javareconf
          
      - name: Set up renv
        uses: r-lib/actions/setup-renv@v2
        with:
          cache-version: 2

      # - name: Install Bioconductor packages
      #   run: |
      #     Rscript -e 'install.packages("babelquarto", repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))'   
      #     Rscript -e 'install.packages("babeldown", repos = c("https://ropensci.r-universe.dev", "https://cloud.r-project.org"))'   
      #     Rscript -e 'renv::snapshot()'                

      - name: Install quarto
        uses: quarto-dev/quarto-actions/setup@v2
        with:
          version: 1.4.550

      # - name: Print packages
      #   run: Rscript -e 'names(installed.packages()[,3])'
      - name: Fix locale
        run: |
          export LANG=en_US.UTF-8
          export LC_CTYPE=en_US.UTF-8
          export LC_ALL=en_US.UTF-8      

      - name: Render the book
        # uses: quarto-dev/quarto-actions/render@v2
        run: Rscript -e 'source("quarto_runfile.R")'
        continue-on-error: true
      
      # - name: Render the book
      #   run: Rscript -e 'library(babelquarto); babelquarto::render_book()'
        
  # render-and-publish:
  #   needs: setup-environment-packages
  #   runs-on: ubuntu-latest
  #   if: success()  
  #   steps:
  #     - name: Check out repository
  #       uses: actions/checkout@v4
        
      - name: Commit results to main branch
        run: |
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          git add .
          git commit -m "CI added changes `date +'%Y-%m-%d %H:%M:%S'`" || echo "No changes to commit"
          git push origin deploy-preview || echo "No changes to commit"

      # - name: Push changes
      #   uses: ad-m/github-push-action@master
      #   with:
      #     branch: main
      #     github_token: ${{ secrets.GITHUB_TOKEN }}
      #     force: true

      # - name: Publish to Netlify
      #   uses: quarto-dev/quarto-actions/publish@v2
      #   with:
      #     target: netlify
      #     NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}