Test Package #140

	name: Test Package

	on:
	workflow_dispatch:
	schedule:
	# run every Tuesday at 17:00 UTC
	- cron: "0 17 * * 2"
	push:
	branches: [main, dev]
	pull_request:
	branches: [main]

	jobs:
	build:
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: true
	matrix:
	include:
	- os: ubuntu-latest
	python: "3.11"
	- os: ubuntu-latest
	python: "3.12"
	- os: ubuntu-latest
	python: "3.13"

	name: Python ${{ matrix.python }}

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

	steps:
	- uses: actions/checkout@v5
	- name: Install the latest version of uv and setup Python
	uses: astral-sh/setup-uv@v6
	with:
	version: "latest"
	python-version: ${{ matrix.python-version }}
	enable-cache: true
	- name: Install dependencies
	uses: nick-fields/retry@v3
	with:
	timeout_minutes: 5
	max_attempts: 3 # The nvidia index is unreliable
	command: uv sync --extra cellpose --dev
	- name: Lint with ruff
	run: \|
	uv run ruff check --fix --exit-non-zero-on-fix spatiomic
	- name: Format with ruff
	run: \|
	uv run ruff format --check spatiomic
	- name: Type check with mypy
	run: \|
	uv run mypy -p spatiomic
	- name: Check security with bandit
	run: \|
	uv run bandit --verbose --ini .bandit.ini -ll --recursive spatiomic
	- name: Test with pytest
	run: \|
	uv run coverage run -m pytest --maxfail=10 -m "not gpu" -m "not no_github_ci"
	uv run coverage xml
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v5
	with:
	fail_ci_if_error: true
	token: ${{ secrets.CODECOV_TOKEN }}

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