Fixes small mistakes in manuals #150

	name: Generate documentation

	on:
	push:
	branches:
	- master
	- sphinx-testing

	jobs:
	build:

	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v3
	- name: Install Conda environment from environment-sphinx.yml
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: environment-sphinx.yml
	# Run Sphinx build
	- name: Run Sphinx build
	shell: bash -l {0}
	run: \|
	sphinx-apidoc -o manuals/ organoid_tracker --separate --force -d 1 --no-toc
	sphinx-build -b html manuals/ manuals_build/html
	# Create an artifact of the html output.
	- uses: actions/upload-artifact@v4
	with:
	name: DocumentationHTML
	path: manuals_build/html/
	# Publish built docs to gh-pages branch.
	# ===============================
	- name: Commit documentation changes
	run: \|
	git clone https://github.com/jvzonlab/OrganoidTracker.git --branch gh-pages --single-branch gh-pages
	cp -r manuals_build/html/* gh-pages/
	cd gh-pages
	touch .nojekyll
	git config --local user.email "[email protected]"
	git config --local user.name "GitHub Action"
	git add .
	git commit -m "Update documentation" -a \|\| true
	# The above command will fail if no changes were present, so we ignore
	# that.
	- name: Push changes
	uses: ad-m/github-push-action@master
	with:
	branch: gh-pages
	directory: gh-pages
	github_token: ${{ secrets.GITHUB_TOKEN }}
	# ===============================

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