render-qmd.yml

name: Rintro2HTML
run-name: ${{ github.actor }} is testing

on:
  push:
    branches: ["thomas"] 

permissions:
  contents: read
  pages: write
  id-token: write

defaults:
  run:
    shell: bash -l {0}

jobs:
  
  build:
    name: Build Pages
    runs-on: ubuntu-latest
#    container: node:latest

    steps:
      - name: Checkout repo
        uses: actions/checkout@v4

      - name: Install Conda environment with Micromamba
        uses: mamba-org/setup-micromamba@main
        with:
          environment-file: configs/conda.yml
          cache-environment: true
          cache-downloads: true
          environment-name: Rintro

      - name: Activate Environment
        run: micromamba activate Rintro

      - name: Check Installation
        run: |
          echo "after conda activate Rintro: PATH=$PATH;"
          which R || true
          R --version || true
          which micromamba || true 
          micromamba --version || true
          which quarto || true 
          quarto --version || true

      - name: Installation non-conda packages 
        run: |
          Rscript -e 'install.packages(c("KernSmooth"), repos="https://cloud.r-project.org")'
          Rscript -e '.libPaths()' || true

      - name: Render quarto
        #continue-on-error: true # only for error tracking
        run: |
          quarto render .

      - name: Show all files in docs
        run: ls -Ral docs

      - name: Show file contents
        run: |
          cat docs/index.html

      - name: Upload
        uses: actions/upload-pages-artifact@v3
        with:
          path: ./docs

#      - name: Deploy to GitHub Pages
#        uses: peaceiris/actions-gh-pages@v3
#        if: ${{ !env.ACT }}
#        with:
#          github_token: ${{ secrets.GITHUB_TOKEN }}
#          publish_dir: |
#            ./docs

  deploy:
    needs: build
    environment:
      name: github-pages
      url: ${{ steps.deployment.outputs.page_url }}
    runs-on: ubuntu-latest
    steps:
      - name: Deploy to GitHub Pages
        id: deployment
        uses: actions/deploy-pages@v4

# the following does not work; micromamba env and installs seem not to be recognized
# see also: https://github.com/quarto-dev/quarto-actions/issues/47
#      - name: Set up Quarto
#        uses: quarto-dev/quarto-actions/setup@v2
#      - name: Render and Publish
#        uses: quarto-dev/quarto-actions/publish@v2
#        with:
#          target: gh-pages
#        env:
#          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}