notebooks.yaml

name: Test notebooks

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

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

jobs:
    test:
        runs-on: ubuntu-latest
        defaults:
            run:
              # to fail on error in multiline statements (-e), in pipes (-o pipefail), and on unset variables (-u).
              shell: bash -euo pipefail {0}

        env:
            NOTEBOOK_PATH: docs/notebooks

        strategy:
            fail-fast: false
            matrix:
                notebook: [
                        "example.ipynb",
                        "bench/rna.ipynb",
                        "bulk/rna.ipynb",
                        "omnipath/licenses.ipynb",
                        "omnipath/orthologs.ipynb",
                        "scell/rna_psbk.ipynb",
                        "scell/rna_pstime.ipynb",
                        "scell/rna_sc.ipynb",
                        "spatial/rna_visium.ipynb",
                    ]

        steps:
            - uses: actions/checkout@v4
              with:
                filter: blob:none
                fetch-depth: 0
                submodules: "true"
            - name: Set up Python
              uses: actions/setup-python@v5
              with:
                  python-version: "3.13"
            - name: Install uv
              uses: astral-sh/setup-uv@v6
              with:
                enable-cache: true
                cache-dependency-glob: pyproject.toml
            - name: Install dependencies
              run: |
                  uv pip install --system ${{ matrix.pip-flags }} ".[dev,test]"
                  uv pip install --system nbconvert ipykernel
            - name: Run ${{ matrix.notebook }} Notebook
              run: jupyter nbconvert --to notebook --execute ${{ env.NOTEBOOK_PATH }}/${{ matrix.notebook }}