[pre-commit.ci] pre-commit autoupdate #89

	name: Test and build

	on:
	push:
	branches: [main]
	release:
	types: [published]
	branches: [main]
	pull_request:
	workflow_dispatch:

	jobs:
	check-links:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: gaurav-nelson/github-action-markdown-link-check@v1
	name: Check links in markdown files
	with:
	use-quiet-mode: 'yes'
	use-verbose-mode: 'yes'

	test:
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: [ windows-latest, ubuntu-latest, macos-latest ]
	python-version: [ "3.11" ]

	steps:
	- uses: actions/checkout@v4
	with:
	submodules: true

	- uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}

	- name: Install system dependencies in Linux
	if: matrix.os == 'ubuntu-latest'
	run: \|
	sudo apt update

	- name: Install Poetry
	uses: abatilo/[email protected]
	with:
	poetry-version: 1.2.2

	- name: Install dependencies
	run: poetry install

	- name: Run tests
	run: poetry run pytest --cov-report=xml

	- name: Upload coverage to Codecov
	if: matrix.os == 'ubuntu-latest' && success()
	uses: codecov/codecov-action@v3

	- name: Run Snakemake with example data
	if: "!cancelled()" # Run this step, even if the previous one fails
	run: poetry run snakemake --cores all

Provide feedback