Improve survival analysis interface #3003

	name: Run Notebooks

	on:
	- push
	- pull_request

	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_2_fate.ipynb", # https://github.com/theislab/cellrank/issues/1235
	"docs/tutorials/notebooks/mimic_2_causal_inference.ipynb",
	# "docs/tutorials/notebooks/mimic_3_demo.ipynb",
	# "docs/tutorials/notebooks/medcat.ipynb",
	]
	steps:
	- uses: actions/checkout@v4
	with:
	submodules: "true"
	token: "${{ secrets.CT_SYNC_TOKEN }}"
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"

	- name: Install UV
	run: pip install uv

	- name: Install ehrapy and additional dependencies
	run: uv pip install --system . cellrank nbconvert ipykernel graphviz

	- name: Install scvelo from Github
	run: uv pip install --system git+https://github.com/theislab/scvelo.git

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

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