Update ehrdata to adjust for anndata v0.12.13 #240

	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/getting_started.ipynb",
	"docs/tutorials/real_dataset_example_physionet2019.ipynb",
	"docs/tutorials/omop_intro.ipynb",
	"docs/tutorials/omop_ml.ipynb",
	"docs/tutorials/interactive_visualization.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 UV
	run: pip install uv

	- name: Install ehrdata and additional dependencies
	run: uv pip install --system . nbconvert ipykernel graphviz torch ehrapy "vitessce[all]" bottleneck ome_zarr negspy

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

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