Merge branch 'methylation' into main #58

	# Github action that runs all jupyter notebook after pull request
	# Jupyter notebooks will be run in the container/jupyter.Dockerfile

	name: render-jupyter-notebook

	on:
	pull_request:
	types:
	- opened
	- reopened
	- edited
	push:

	jobs:
	run_notebooks:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Build and push Docker image
	uses: docker/build-push-action@v5
	with:
	file: container/jupyter.Dockerfile
	context: .
	push: false # Set to true if you want to push the image to a registry
	tags: notebook-runner


	- name: Run Docker container to compile JupyterNotebook
	uses: addnab/docker-run-action@v3
	with:
	image: notebook-runner
	options: -v ${{ github.workspace }}:/workspace --rm -u root
	run: \|
	notebooks=$(find /workspace -name "*.ipynb")
	if [ -n "$notebooks" ]; then
	find /workspace -name "*.ipynb" -exec jupyter nbconvert --to notebook --execute {} \;
	else
	echo "No Jupyter notebooks found. Skipping execution."
	fi

	- uses: stefanzweifel/git-auto-commit-action@v5

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