chore: Use Ruff for linting and formatting (#147) #1416

	name: CI

	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main
	# Run daily at 0:01 UTC
	schedule:
	- cron: '1 0 * * *'
	workflow_dispatch:


	jobs:
	test:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-latest]
	python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']

	steps:
	- name: Checkout code
	uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install external dependencies
	run: \|
	sudo apt-get update -y
	sudo apt-get install -y graphviz libgraphviz-dev

	- name: Install Python dependencies
	# c.f. https://github.com/astral-sh/uv/issues/4333 for why snakemake lower bound
	run: \|
	python -m pip install uv
	uv pip install --system --upgrade pip wheel
	uv pip install --system '.[develop,local,reana]' 'snakemake>6.8.0'

	- name: List installed dependencies
	run: python -m pip list

	- name: Run unit tests
	run: \|
	pytest tests/

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