Tests #26

	name: Tests

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

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	max-parallel: 5
	matrix:
	python: [3.8, 3.9, '3.10']
	fail-fast: false

	steps:

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

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

	- name: Set up Python 3.X
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python }}

	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH

	- name: conda
	run: \|
	conda install -c conda-forge -c bioconda --quiet -y python=${{ matrix.python }} seqtk
	conda install -c conda-forge -y ncurses
	- name: Install dependencies
	run: \|
	pip install coveralls pytest-cov pytest pytest-xdist

	- name: install package itself
	run: \|
	pip install .

	- name: testing
	run: \|
	pytest -v --cov-report term-missing --cov=sequana_pipelines.revcomp

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

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