Build-sphinx-doc #23

	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

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