Merge pull request #65 from bgruening/patch-1 #54

	name: pytest

	on:
	push:
	branches: ["master", "develop"]
	pull_request:
	branches: ["master", "develop"]

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	timeout-minutes: 10
	strategy:
	matrix:
	python-version: ['3.7', '3.8', '3.9']
	defaults:
	run:
	shell: bash -l {0}
	env:
	HTSLIB_CONFIGURE_OPTIONS: "--disable-libcurl"

	steps:
	- name: Checkout sinto
	uses: actions/checkout@v2

	- uses: conda-incubator/setup-miniconda@v2
	with:
	auto-update-conda: true
	auto-activate-base: false
	activate-environment: testenv
	use-only-tar-bz2: true

	- name: Install dependencies
	run: \|
	conda install -c bioconda samtools htslib
	conda install -c anaconda flake8 pytest
	python -m pip install --upgrade pip
	python -m pip install --upgrade build

	- name: Build and install package
	run: \|
	python -m build
	pip install .

	- name: Lint with flake8
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

	- name: Test with pytest
	run: \|
	REF_PATH=':' pytest

Provide feedback