doc.yml

name: Build-sphinx-doc

on:
  push:
    branches: [main]
  workflow_dispatch:

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
      - uses: actions/checkout@v4

      - name: Set up Python 3.10
        uses: actions/setup-python@v5
        with:
          python-version: "3.10"

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install -e .[doc]
          pip install ghp-import

      - name: Build HTML
        env:
          TOKEN: ${{ secrets.TOKEN }}
        run: |
          # Convert the dummy token to the real token for executing the jupyter notebook
          sed -i "s/YOUR_TOKEN/$TOKEN/" doc/source/Tutorial/onc_Library_Tutorial.ipynb
          sed -i '/nb_execution_mode = "off"/d' doc/source/conf.py # enable executing jupyter notebook
          sphinx-build -W doc/source doc/build/html

      - name: Remove ampersand encoding and token in the generated html
        env:
          TOKEN: ${{ secrets.TOKEN }}
        run: |
          # See issues about ampersand encoding at https://github.com/executablebooks/MyST-Parser/issues/760
          sed -i 's/amp;//g' doc/build/html/Tutorial/Oceans_3.0_API_Tutorial.html
          # Some cell outputs in the Jupyter notebook contain the token
          sed -i "s/$TOKEN/YOUR_TOKEN/g" doc/build/html/Tutorial/onc_Library_Tutorial.html

      - name: Run ghp-import to generate GitHub Pages
        run: |
          ghp-import -npfo doc/build/html