Fix readthedocs build. #11

	name: Documentation

	on:
	push:
	branches: [ master, main, dev-master, dev-refactored ]
	paths:
	- 'docs/**'
	- 'OrthoEvol/**'
	- 'setup.py'
	- '.readthedocs.yml'
	pull_request:
	branches: [ master, main, dev-master, dev-refactored ]
	paths:
	- 'docs/**'
	- 'OrthoEvol/**'
	- 'setup.py'
	- '.readthedocs.yml'
	workflow_dispatch:

	jobs:
	build-docs:
	runs-on: ubuntu-latest
	timeout-minutes: 15

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.9'

	- name: Cache pip
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-docs-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-docs-

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	pip install sphinx pypandoc
	pip install -r requirements.txt
	pip install -e .

	- name: Update and build documentation
	run: \|
	python docs/update_docs.py

	- name: Check for documentation errors
	run: \|
	if [ -d "docs/docs/_build" ] && [ -f "docs/docs/_build/index.html" ]; then
	echo "✓ Documentation built successfully"
	echo "Found HTML files:"
	find docs/docs/_build -maxdepth 1 -name "*.html" \| head -5
	echo "Build directory structure:"
	ls -la docs/docs/_build/ \| head -10
	else
	echo "✗ Documentation build failed"
	echo "Checking build directory:"
	ls -la docs/docs/_build/ 2>&1 \|\| echo "Build directory does not exist"
	exit 1
	fi

	- name: Upload documentation artifacts
	if: success()
	uses: actions/upload-artifact@v4
	with:
	name: documentation
	path: docs/docs/_build
	retention-days: 7

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