Run notebooks in CI #1

	name: Notebooks

	on:
	push:
	branches: [ develop ]
	pull_request:
	branches: [ main, develop ]

	jobs:
	build:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	- name: Initialize Python
	uses: actions/[email protected]
	with:
	python-version: '3.11'
	- name: Setup Python
	run: \|
	python -m pip install --upgrade pip jupyter
	python -m pip install .
	python -m ipykernel install --user --name run-notebook --display-name "Run notebook"
	- name: Run notebooks
	run: \|
	# The functional annotation of RPGRIP1, STXBP1, and KBG takes too long.
	# However, we can add them later, if we will really want that.
	cohorts=(MAPK8IP3 PPP2R1A SUOX)
	for cohort in ${cohorts[@]}; do
	nb="notebooks/${cohort}/${cohort}.ipynb"
	printf "Processing notebook at %s\n" ${nb}
	jupyter execute --kernel_name run-notebook ${nb}
	done

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