publish.yml

on:
  pull_request:
  push:
    branches: main

name: Publish

jobs:
  build-deploy:
    runs-on: ubuntu-latest

    permissions:
      contents: write

    steps:
      - name: Check out repository
        uses: actions/checkout@v4

      - name: Set up specific version of Python
        uses: actions/setup-python@v5
        with:
          python-version: '3.12'

      - name: Install R
        uses: r-lib/actions/setup-r@v2

      - name: Set up Quarto
        uses: quarto-dev/quarto-actions/setup@v2
        
      - name: Make sure data is available
        run: |
          AWS_EC2_METADATA_DISABLED=true \
            aws s3 cp \
            --no-sign-request \
            s3://openproblems-bio/public/neurips-2023-competition/sc_counts_reannotated_with_counts.h5ad \
            book/usecase/data/sc_counts_reannotated_with_counts.h5ad

      # attempt with renv
      - name: Set up renv
        uses: r-lib/actions/setup-renv@v2

      - name: Cache certain directories to speed up build
        uses: actions/cache@v2
        with:
          path: |
            book/usecase/data
          key: quarto_cache_${{ github.ref_name }}
          restore-keys: |
            quarto_cache_main
      
      - name: Render book
        run: |
          Rscript -e "renv::restore()"
          source renv/python/virtualenvs/renv-python-3.12/bin/activate
          quarto render

      - name: Deploy 🚀
        if: github.event_name != 'pull_request'
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: _book
          branch: gh-pages
          force: false
          clean-exclude: pr-preview/

      - name: Deploy preview
        if: github.event_name == 'pull_request'
        uses: rossjrw/pr-preview-action@v1
        with:
          source-dir: _book
          preview-branch: gh-pages
          umbrella-dir: pr-preview
          action: auto