name: Run Notebooks

on:

    - 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: "3.13"

            - 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 }}