Fix issues in deploy action #54

	name: Build and Deploy Docs

	on:
	push:
	branches:
	- main
	- dev
	tags:
	- '*'

	jobs:
	build-and-deploy:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout Code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: '3.11'

	- name: Setup Graphviz
	uses: ts-graphviz/setup-graphviz@v2

	- name: Install Dependencies
	run: \|
	pip install poetry
	poetry install

	- name: Build Docs with sphinx-multiversion
	run: \|
	# Create a temporary directory
	TEMP_DIR=$(mktemp -d)
	chmod 777 $TEMP_DIR
	echo "TEMP_DIR=$TEMP_DIR" >> $GITHUB_ENV
	echo "Temporary directory is $TEMP_DIR"
	poetry run sphinx-multiversion docs $TEMP_DIR
	touch $TEMP_DIR/.nojekyll
	echo '<meta http-equiv="refresh" content="0; URL='https://saezlab.github.io/corneto/main'" />' > $TEMP_DIR/index.html

	- name: Deploy to GitHub Pages
	run: \|
	git config --local user.email "action@github.com"
	git config --local user.name "GitHub Action"

	# Now checkout to gh-pages
	git fetch origin gh-pages
	git checkout gh-pages \|\| git checkout --orphan gh-pages

	# Clean existing files for the branch and copy new ones
	echo "Removing current folder content: $BRANCH_NAME"
	rm -rf "./$BRANCH_NAME"
	cp -r "$TEMP_DIR/$BRANCH_NAME" "$BRANCH_NAME"

	# Adding changes to git
	git add .
	git commit -m "Update docs for branch $BRANCH_NAME" --allow-empty
	git push -u origin gh-pages

	# Optionally, remove the temporary directory (not necessary on CI environments)
	# rm -rf "$TEMP_DIR"
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	BRANCH_NAME: ${{ github.head_ref \|\| github.ref_name }}

Provide feedback