Merge branch 'main' into issue-440 #1316

	name: Python CQA

	on: [push, pull_request]


	# TODO: separate lint and test jobs; lint first, test "needs" lint
	# https://docs.github.com/en/actions/reference/workflow-syntax-for-github-actions#jobs

	jobs:
	test:

	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10", "3.11", "3.12"]
	env:
	SEQREPO_ROOT_DIR: ./tests/data/seqrepo/latest

	steps:
	- uses: actions/checkout@v4
	with:
	submodules: recursive
	- uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-test-${{ hashFiles('pyproject.toml') }}
	restore-keys: \|
	${{ runner.os }}-pip-
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	- name: Update pip and setuptools
	run: \|
	python -m pip install --upgrade pip setuptools
	- name: Install dependencies
	run: \|
	pip install -e .[dev,extras]
	- name: Test with pytest
	run: \|
	python -m pytest

	precommit_hooks:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: actions/setup-python@v5
	- uses: pre-commit/action@v3.0.1

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