Tests

Fix genomecov and support long reads #127

	name: Tests

	on:
	push:
	branches:
	- main
	- dev
	workflow_dispatch:
	pull_request:
	branches-ignore: []
	schedule:
	- cron: '0 0 1 * *'

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5
	matrix:
	python: [ 3.9, '3.10', '3.11']
	fail-fast: false


	steps:

	- name: install graphviz
	run: \|
	sudo apt-get install -y graphviz

	- name: checkout git repo
	uses: actions/checkout@v2

	- name: conda/mamba
	uses: mamba-org/setup-micromamba@v1
	with:
	environment-file: environment.yml
	create-args: >-
	python=${{ matrix.python }}

	- name: install package itself
	shell: bash -l {0}
	run: \|
	pip install .
	pip install "pulp==2.7.0" --no-deps


	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	pip install coveralls pytest-cov pytest pytest-xdist

	- name: testing
	shell: bash -l {0}
	run: \|
	pytest -v --cov-report term-missing --cov=sequana_pipelines.variant_calling

	- name: coveralls
	shell: bash -l {0}
	run: \|
	echo $COVERALLS_REPO_TOKEN
	coveralls --service=github
	env:
	GITHUB_TOKEN: ${{ github.token }}

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