Tests

put the step attribution of reads in apart mode : rescue: 5 #11

	name: Tests

	on:
	push:
	branches: [main, master]
	pull_request:
	branches: [main, master]

	jobs:
	test:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.10'

	- name: Install system dependencies (bowtie2, samtools)
	run: \|
	sudo apt-get update
	sudo apt-get install -y bowtie2 samtools

	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -e .
	pip install pytest pytest-cov

	- name: Run tests with coverage
	id: pytest
	continue-on-error: true
	run: python -m pytest tests/ --cov=hicberg --cov-report=xml --cov-report=term-missing

	- name: Upload coverage to Codecov
	if: always()
	uses: codecov/codecov-action@v4
	with:
	files: ./coverage.xml
	fail_ci_if_error: false
	token: ${{ secrets.CODECOV_TOKEN }}

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