Merge branch 'master' into release/v3.1.2 #292

	# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
	# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

	name: quick-tests

	on: [push]

	jobs:
	build:
	runs-on: ubuntu-20.04
	strategy:
	matrix:
	python-version: ["3.7", "3.8", "3.9", "3.10"]
	name: python-${{ matrix.python-version }} quick
	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v2
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip setuptools wheel
	pip install .[test]
	- name: Lint with flake8
	run: \|
	pip install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 src tests --count --show-source --statistics
	- name: Lint with black
	run: \|
	pip install black
	# stop the build if black needs to be run
	black src tests -S -l 100 --check
	- name: Lint with isort
	run: \|
	pip install isort
	isort src tests --check
	- name: install bwa
	run: \|
	git clone https://github.com/lh3/bwa.git
	cd bwa
	git checkout v0.7.17
	make
	cd ..
	- name: install blat
	run: \|
	wget http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat
	chmod a+x blat
	- name: run short tests with pytest
	run: \|
	export PATH=$PATH:$(pwd):$(pwd)/bwa
	pytest tests -v \
	--junitxml=junit/test-results-${{ matrix.python-version }}.xml \
	--durations=10
	env:
	RUN_FULL: 0

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