build

change python >=3.9 #83

	name: build

	on: [push]


	env:
	FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true # ← ajouter ça

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5

	steps:

	- name: Checkout repo
	uses: actions/checkout@v4

	- name: Create micromamba env. for package
	uses: mamba-org/setup-micromamba@v2
	with:
	generate-run-shell: true
	environment-file: environment.yml
	post-cleanup: none # ← évite les erreurs de nettoyage

	- name: Install package
	run: \|
	pip install .
	shell: micromamba-shell {0}

	- name: Check installed package
	run: \|
	hicberg --version
	bowtie2 --version
	shell: micromamba-shell {0}

	- name: Lint and test
	run: \|
	pip install pytest-pylint pytest pytest-cov pylint codecov mappy
	pytest --pylint --pylint-error-types=EF --pylint-rcfile=.pylintrc --doctest-modules hicberg
	coverage run --source=hicberg -m pytest -v tests
	coverage report -m
	coverage xml
	shell: micromamba-shell {0}

	- name: Upload coverage reports to Codecov
	uses: codecov/codecov-action@v5
	env:
	CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

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