bioconductor-training/.github/workflows/quarto-publish.yml at ccb857f5427a4380928485f4e5ae2c1eac531336 · Bioconductor/bioconductor-training · GitHub

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# NOTE: We render the site in GitHub Actions because some pages (e.g., instructors.qmd)
# require R execution to pull dynamic data from CSV files. Netlify's build environment
# does not include R, so we cannot rely on the Quarto Netlify plugin for rendering.
# Instead, CI installs R + Quarto, renders the site, and deploys the pre-rendered HTML
# to Netlify for both PR previews and production.

name: CI/CD

on:
  pull_request:
    branches: [devel]
  push:
    branches: [devel]
  schedule:
    - cron: '0 1 * * 0'  # every Sunday at 01:00 UTC

env:
  cache-version: v1

jobs:
  # Build & preview deploy for PRs
  build-preview:
    if: github.event_name == 'pull_request'
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev

      - name: Cache R packages
        uses: actions/cache@v3
        with:
          path: ~/.R
          key: ${{ env.cache-version }}-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION', '**/renv.lock') }}
          restore-keys: |
            ${{ env.cache-version }}-${{ runner.os }}-

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install R dependencies
        run: |
          Rscript -e 'install.packages("remotes", repos = "https://cloud.r-project.org")'
          Rscript -e 'remotes::install_deps(dependencies = TRUE)'

      - name: Render Quarto Project
        run: quarto render

      - name: Deploy Preview to Netlify
        run: |
          npm install -g netlify-cli
          netlify deploy \
            --auth "$NETLIFY_AUTH_TOKEN" \
            --site "$NETLIFY_SITE_ID" \
            --dir docs \
            --message "PR #${{ github.event.number }} - ${{ github.sha }}" \
            --alias "pr-${{ github.event.number }}"
        env:
          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}

  # Production deploy on push/schedule to devel
  deploy-prod:
    if: github.ref == 'refs/heads/devel' && (github.event_name == 'push' || github.event_name == 'schedule')
    runs-on: ubuntu-latest
    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev

      - name: Cache R packages
        uses: actions/cache@v3
        with:
          path: ~/.R
          key: ${{ env.cache-version }}-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION', '**/renv.lock') }}
          restore-keys: |
            ${{ env.cache-version }}-${{ runner.os }}-

      - name: Set up R
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - name: Install R dependencies
        run: |
          Rscript -e 'install.packages("remotes", repos = "https://cloud.r-project.org")'
          Rscript -e 'remotes::install_deps(dependencies = TRUE)'

      - name: Render Quarto Project
        run: quarto render

      # If you still want GitHub Pages in addition to Netlify, keep this step.
      # Otherwise you can remove it and use Netlify as your sole host.
      - name: Add CNAME for GitHub Pages custom domain
        run: echo "training.bioconductor.org" > docs/CNAME

      - name: Publish to GitHub Pages (optional)
        uses: quarto-dev/quarto-actions/publish@v2
        with:
          target: gh-pages
        env:
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

      - name: Deploy Production to Netlify
        run: |
          npm install -g netlify-cli
          netlify deploy \
            --auth "$NETLIFY_AUTH_TOKEN" \
            --site "$NETLIFY_SITE_ID" \
            --dir docs \
            --prod \
            --message "devel @ ${{ github.sha }}"
        env:
          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}