website.yml

name: Website
on:
  push:
    branches:
      - gh-pages
      - main
  pull_request: []
jobs:
  build-website:
    if: ${{ !endsWith(github.repository, '/styles') }}
    runs-on: ubuntu-22.04
    env:
      RSPM: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
    defaults:
      run:
        shell: bash
    steps:
      - name: Set up Ruby
        uses: ruby/setup-ruby@v1
        with:
          ruby-version: '2.7'
          bundler-cache: true

      - name: Set up Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.x'

      - name: Install GitHub Pages, Bundler, and kramdown gems
        run: |
          gem install nokogiri -v 1.15.5
          gem install bundler -v 2.4.22
          gem install faraday-net_http -v 3.0.2
          gem install faraday -v 2.8.1
          gem install github-pages kramdown kramdown-parser-gfm

      - name: Install Python modules
        run: |
          python3 -m pip install --upgrade pip setuptools wheel pyyaml==5.3.1 requests

      - name: Checkout the lesson
        uses: actions/checkout@master
        with:
          fetch-depth: 0
          ref: ${{ github.event.pull_request.head.sha }}

      - name: Look for R-markdown files
        id: check-rmd
        run: |
          echo "count=$(shopt -s nullglob; files=($(find . -iname '*.Rmd')); echo ${#files[@]})" >> $GITHUB_OUTPUT

      - name: Set up R
        if: steps.check-rmd.outputs.count != 0
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true
          install-r: false

      - name: Restore R Cache
        if: steps.check-rmd.outputs.count != 0
        uses: actions/cache@v2
        with:
          path: ${{ env.R_LIBS_USER }}
          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-

      - name: Install needed packages
        if: steps.check-rmd.outputs.count != 0
        run: |
          source('bin/dependencies.R')
          install_required_packages()
        shell: Rscript {0}

      - name: Query dependencies
        if: steps.check-rmd.outputs.count != 0
        run: |
          source('bin/dependencies.R')
          deps <- identify_dependencies()
          create_description(deps)
          use_bioc_repos()
          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
        shell: Rscript {0}


      - name: Install system dependencies for R packages
        if: steps.check-rmd.outputs.count != 0
        run: |
          while read -r cmd
          do
            eval sudo $cmd || echo "Nothing to update"
          done < <(Rscript -e 'cat(remotes::system_requirements("ubuntu", "20.04"), sep = "\n")')

      - name: Render the markdown and confirm that the site can be built
        run: make site

      - name: Checkout github pages
        if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
        uses: actions/checkout@master
        with:
          ref: gh-pages
          path: gh-pages

      - name: Commit and Push
        if: ${{ github.event_name == 'push' && steps.check-rmd.outputs.count != 0 && github.ref != 'refs/heads/gh-pages'}}
        run: |
          # clean up gh-pages
          cd gh-pages
          git rm -rf .           # remove all previous files
          git restore --staged . # remove things from the stage
          cd ..
          # copy everything into gh-pages site
          cp -r `ls -A | grep -v 'gh-pages' | grep -v '.git' | grep -v '.bundle/' | grep -v '_site'` gh-pages
          # move into gh-pages, add, commit, and push
          cd gh-pages
          # setup git
          git config --local user.email "actions@github.com"
          git config --local user.name "GitHub Actions"
          git add -A .
          git commit --allow-empty -m "[Github Actions] render website (via ${{ github.sha }})"
          git push origin gh-pages
          # return
          cd ..

      - run: make lesson-check-all
        if: always()

      - name: Build slides
        uses: docker://pandoc/core:latest
        with:
          args: --to=revealjs --standalone -o slideshow/index.html --css=mywhite.css  slideshow/slides.md

      - name: Deploy slides
        uses: JamesIves/github-pages-deploy-action@v4.6.0
        with:
          folder: .