render-qmd.yml

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

on:
  push:
    branches: ["2024.04"] 


jobs:
  
  build:
    name: Conda Tests
    runs-on: ubuntu-latest
    defaults:
       run:
         shell: bash -l {0}
    container: node:latest

    steps:
      - name: Print shell information
        run: |
          echo "Shell: $SHELL"
          echo "Shell version: $($SHELL --version)"
          uname -a || true

      - uses: actions/checkout@v2
      - name: Check yaml
        run: |
          cat configs/conda.yml || true

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

      - name: List Available Environment
        shell: bash -l {0}
        run: micromamba list

      - name: Activate Environment
        run: micromamba activate Rintro

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

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

      - name: Inspect dslabs ext_data
        run: |
          Rscript -e '.libPaths()'
          Rscript -e 'find.package("dslabs")'
          Rscript -e 'list.files(system.file(package="dslabs"))'
          Rscript -e 'list.files(system.file("extdata", package="dslabs"))'           

      - name: Render quarto
        continue-on-error: true # only for error tracking
        run: |
          ls -Rl /github/home/micromamba/envs/Rintro/lib/R/library/dslabs
          quarto render qmd

      - name: Show all files
        run: ls -Ral

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