Merge branch 'main' of https://github.com/theislab/ehrapy #1785

	name: Run Notebooks

	on:
	- push
	- pull_request_target

	jobs:
	run:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	notebook: [
	"docs/tutorials/notebooks/ehrapy_introduction.ipynb",
	"docs/tutorials/notebooks/mimic_2_introduction.ipynb",
	"docs/tutorials/notebooks/mimic_2_survival_analysis.ipynb",
	"docs/tutorials/notebooks/mimic_3_demo.ipynb",
	# "docs/tutorials/notebooks/medcat.ipynb",
	]
	steps:
	- uses: actions/checkout@v3
	with:
	submodules: "true"
	token: "${{ secrets.CT_SYNC_TOKEN }}"
	- name: Set up Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.10"

	- name: Install ehrapy
	run: pip install .

	- name: Install additional dependencies
	run: pip install medcat cellrank

	- name: Install nbconvert ipykernel
	run: pip install nbconvert ipykernel

	- name: Run ${{ matrix.notebook }} Notebook
	run: jupyter nbconvert --to notebook --execute ${{ matrix.notebook }}

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