Add self-controlled cohort study design for drug screening #4176

	name: Run Notebooks

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

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	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",
	"docs/tutorials/notebooks/cohort_tracking.ipynb",
	"docs/tutorials/notebooks/longitudinal_with_ehrapy.ipynb",
	"docs/tutorials/notebooks/bias.ipynb",
	# "docs/tutorials/notebooks/mimic_2_causal_inference.ipynb",
	]
	steps:
	- uses: actions/checkout@v5
	with:
	submodules: "true"

	- name: Set up Python
	uses: actions/setup-python@v6
	with:
	python-version: "3.14"

	- name: Install OpenBLAS
	run: sudo apt-get install -y libopenblas-dev

	- name: Install UV
	run: pip install uv

	- name: Install ehrapy and additional dependencies
	run: uv pip install --system . 'cellrank[scvelo]' nbconvert ipykernel graphviz pypots fairlearn

	- name: Install ehrdata from submodule
	run: uv pip install --system --reinstall --no-deps -e submodules/ehrdata

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

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