Merge pull request #222 from scverse/add_bsize_psbulk #10

	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 }}

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