Merge branch 'master' of https://github.com/bigbio/py-pgatk into spec… #309

	# 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: Python package

	on:
	push:
	branches: [ spectrumAI ]
	pull_request:
	branches: [ spectrumAI ]

	jobs:
	build:

	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: [3.7, 3.8]

	steps:
	- uses: actions/checkout@v2
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v1
	with:
	python-version: ${{ matrix.python-version }}
	- name: Setup Miniconda
	uses: conda-incubator/[email protected]
	with:
	use-mamba: true
	auto-activate-base: true
	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	conda install --channel conda-forge --channel bioconda bedtools htslib
	python -m pip install --upgrade pip
	pip install flake8 pytest
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Lint with flake8
	shell: bash -l {0}
	run: \|
	# stop the build if there are Python syntax errors or undefined names
	flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
	flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
	- name: Test with pytest
	shell: bash -l {0}
	run: \|
	python setup.py install
	cd pypgatk
	python -s tests/pypgatk_tests.py

Provide feedback