deploy-jupyter-book.yml

name: Deploy Jupyter Book

on:
  push:
    branches:
    - main
  pull_request:
  workflow_dispatch:

# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
permissions:
  contents: read
  pages: write
  id-token: write

concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

jobs:

  build-book:
    runs-on: ubuntu-latest
    container: atlasamglab/stats-base:root6.28.04

    steps:
    - uses: actions/checkout@v3

    - name: Install Python dependencies
      run: |
        python -m pip install --upgrade pip setuptools wheel
        python -m pip install --no-deps --require-hashes --requirement book/requirements.lock

    - name: List installed Python packages
      run: |
        python -m pip list

    - name: Build the book
      run: |
        jupyter-book build book/

    - name: Upload jupyter book
      uses: actions/upload-artifact@v3
      with:
        name: jupyterbook
        path: 'book/_build/html/'

  build-pyodide:
    runs-on: ubuntu-latest

    steps:
    - uses: actions/checkout@v3

    - name: Set up Python
      uses: actions/setup-python@v4
      with:
        python-version: "3.x"

    - name: Install pyodide
      run: |
        python -m pip install --upgrade pip setuptools wheel
        python -m pip install --upgrade \
          "jupyterlite[lab]" \
          "jupytext>=1.14.0"

    - name: List installed Python packages
      run: |
        python -m pip list

    - name: Convert .py to notebook
      run: |
        jupytext --to notebook lite/jupyterlite.py
        cp lite/*.ipynb  book/

    - name: Build the Pyodide output
      run: |
        jupyter lite --help
        jupyter lite init
        jupyter lite build --contents=book
        jupyter lite check

    - name: Upload Pyodide build
      uses: actions/upload-artifact@v3
      with:
        name: jupyterlite
        path: _output/

  deploy:
    environment:
      name: github-pages
      url: ${{ steps.deployment.outputs.page_url }}
    runs-on: ubuntu-latest
    needs: [build-book, build-pyodide]
    if: github.event_name != 'pull_request' && github.ref == 'refs/heads/main'

    steps:

    - name: Setup Pages
      uses: actions/configure-pages@v2

    - uses: actions/download-artifact@v3
      with:
        name: jupyterbook
        path: 'public'

    - uses: actions/download-artifact@v3
      with:
        name: jupyterlite
        path: 'public/live'

    - name: Fix permissions
      run: |
        chmod -c -R +rX "public/" | while read line; do
          echo "::warning title=Invalid file permissions automatically fixed::$line"
        done

    - name: Upload artifact
      uses: actions/upload-pages-artifact@v2
      with:
        path: 'public'

    - name: Deploy to GitHub Pages
      id: deployment
      uses: actions/deploy-pages@v1