Test

[pre-commit.ci] pre-commit autoupdate #675

	name: Test

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]
	schedule:
	- cron: "0 5 1,15 * *"

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

	jobs:
	test:
	runs-on: ${{ matrix.os }}
	defaults:
	run:
	shell: bash -e {0} # -e to fail on error

	strategy:
	fail-fast: false
	matrix:
	include:
	- os: ubuntu-latest
	python: "3.11"
	- os: ubuntu-latest
	python: "3.12"
	- os: ubuntu-latest
	python: "3.13"
	- os: macos-latest
	python: "3.12"

	name: ${{ matrix.name }} Python ${{ matrix.python }}

	env:
	OS: ${{ matrix.os }}
	PYTHON: ${{ matrix.python }}

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python ${{ matrix.python }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python }}
	cache: "pip"
	cache-dependency-path: "**/pyproject.toml"

	- name: Install test dependencies
	run: \|
	python -m pip install --upgrade pip wheel
	- name: Install dependencies
	run: \|
	pip install tox
	pip install ${{ matrix.pip-flags }} ".[optional-dependencies.dev,optional-dependencies.test,optional-dependencies.external,optional-dependencies.docs,optional-dependencies.embedding]"
	pip install wandb omegaconf
	- name: Test
	run: \|
	tox -e py-${{ matrix.python }} -- -m "not slow"
	env:
	PYTEST_ADDOPTS: -vv -n 2

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	slug: theislab/cellflow

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