deploy-book-python-and-r.yml

name: deploy-book-python-and-r

on:
  push:
    branches:
    - main

# This job installs dependencies, builds the book, and deploys it to GitHub Pages
jobs:
  deploy-book:
    runs-on: ubuntu-latest
    permissions:
      pages: write
      id-token: write
    steps:
    - uses: actions/checkout@v4

    # Install dependencies for Python
    - name: Set up Python 3.11
      uses: actions/setup-python@v5
      with:
        python-version: 3.11
        cache: pip

    - name: Install dependencies
      run: |
        pip install -r requirements.txt
          
    # Install R and its dependencies
    - name: Set up R
      uses: r-lib/actions/setup-r@v2
    
    # Cache R packages to speed up installation
    - name: Cache R packages
      uses: actions/cache@v3
      with:
        path: ${{ env.R_LIBS_USER }}
        key: ${{ runner.os }}-r-${{ hashFiles('**/renv.lock') }}
        restore-keys: ${{ runner.os }}-r-

    # Install R packages including IRkernel - with optimizations for speed
    - name: Install R packages
      run: |
        # Use binary packages and RSPM for faster installation
        Rscript -e 'options(repos = c(RSPM = "https://packagemanager.rstudio.com/all/__linux__/focal/latest", CRAN = "https://cloud.r-project.org"))'
        Rscript -e 'options(install.packages.check.source = "no")'  # Prefer binaries
        Rscript -e 'install.packages("IRkernel", dependencies=TRUE)'
        Rscript -e 'IRkernel::installspec(name="ir", displayname="R")'
    
    # - name: Install R_requirements
    #   run: |
    #     Rscript install_dependencies.R

    # log available kernels
    - name: Print all available kernels
      run: |
        jupyter kernelspec list

    # (optional) Cache your executed notebooks between runs
    # if you have config:
    # execute:
    #   execute_notebooks: cache
    - name: cache executed notebooks
      uses: actions/cache@v3
      with:
        path: _build/.jupyter_cache
        key: jupyter-book-cache-${{ hashFiles('requirements.txt') }}

    # Build the book
    - name: Build the book
      run: |
        jupyter-book build .

    # Upload the book's HTML as an artifact
    - name: Upload artifact
      uses: actions/upload-pages-artifact@v3
      with:
        path: "_build/html"

    # Deploy the book's HTML to GitHub Pages
    - name: Deploy to GitHub Pages
      id: deployment
      uses: actions/deploy-pages@v4