.github/workflows/publish.yml

name: Render Quarto Files and Deploy to GitHub Pages

on:
  push:
    branches:
      - main
  pull_request:
    branches:
      - main
  workflow_dispatch: # Manual trigger

jobs:
  render_quarto:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@v3

    - name: Build Docker image
      run: |
        docker build -t demo-quarto-image .

    - name: Create gallery directory on the host
      run: |
        echo 'Creating gallery directory...'
        mkdir -p gallery && chmod -R 777 gallery
        echo 'gallery directory created.'

    - name: Run Quarto in Docker container
      run: |
        docker run --rm -v ${{ github.workspace }}:/workspace -w /workspace demo-quarto-image bash -c "
        
          source /opt/venv/bin/activate
          echo 'activated virtualenv.'
          
          chmod +x /workspace/r/install_quarto_extensions.expect
          /workspace/r/install_quarto_extensions.expect
          quarto list extensions
          echo 'Check Quarto status:'
          quarto check
          echo 'Check R script path:'
          which Rscript
        
          FOLDERS=(python r)
          echo 'Folders to process: \${FOLDERS[@]}'

          for FOLDER in \"\${FOLDERS[@]}\"; do
            echo \"Searching for .qmd and .ipynb files in /workspace/\$FOLDER...\"
            find \"/workspace/\$FOLDER\" \( -name '*.qmd' -o -name '*.ipynb' \) | while read -r file; do
              
              echo \"Processing file: \$file\"
              # Remove the /workspace prefix from the file path
              relative_dir=\$(dirname \"\${file#'/workspace/'}\")
              target_dir=\"/workspace/gallery/\$relative_dir\"
              echo \"Creating target directory: \$target_dir\"
              mkdir -p \"\$target_dir\" && echo \"Directory \$target_dir created.\"

              echo \"Attempting to render \$file with execution...\"
              if quarto render \"\$file\" --to html --output-dir \"\$target_dir\"; then
                echo \"Successfully rendered \$file with execution.\"
              else
                echo \"Failed to render \$file with execution. Rendering without execution...\"
                if quarto render \"\$file\" --to html --no-execute --output-dir \"\$target_dir\"; then
                  echo \"Successfully rendered \$file without execution.\"
                else
                  echo \"Rendering failed for \$file, even without execution.\"
                fi
              fi

            done
          done"


    - name: Generate Index HTML
      run: |
        ls -laR gallery
        echo "<html><body><h1>Gallery Index</h1><ul>" > gallery/index.html
        find gallery -name "*.html" | while read -r file; do
          # Remove the 'gallery/' prefix from the file path
          relative_path="${file#gallery/}"
          file_name=$(basename "$file")
          echo "<li><a href=\"./$relative_path\">$file_name</a></li>" >> gallery/index.html
        done
        echo "</ul></body></html>" >> gallery/index.html

    - name: Upload HTML output
      uses: actions/upload-artifact@v4
      with:
        name: gallery
        path: gallery/

    - name: Set up Git user
      run: |
        git config --global user.name 'github-actions[bot]'
        git config --global user.email 'github-actions[bot]@users.noreply.github.com'

    - name: Deploy to GitHub Pages
      uses: peaceiris/actions-gh-pages@v4
      with:
        github_token: ${{ secrets.GITHUB_TOKEN }}
        publish_dir: ./gallery  # Path to the folder that you want to publish (the gallery folder)
        publish_branch: docs  # The branch used for GitHub Pages