Merge pull request #7 from zpliu1126/patch-1 #61

	name: thoraxe

	on: [push]

	jobs:
	build:

	runs-on: ubuntu-20.04
	strategy:
	matrix:
	python-version: ["3.6", "3.7", "3.8"] # https://devguide.python.org/versions/#versions

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	- name: Install dependencies
	run: \|
	git clone https://github.com/PhyloSofS-Team/ProGraphMSA.git prographmsa
	chmod a+x ./prographmsa/bin/ProGraphMSA_64
	sudo cp ./prographmsa/bin/ProGraphMSA_64 /bin/ProGraphMSA
	rm -fr prographmsa # clean up
	sudo apt-get install -y lcov
	python -m pip install --upgrade pip
	python -m pip install 'numpy==1.19.5'
	pip install pytest pylint
	python -m pip install coveralls codecov
	pip install -r requirements.txt
	python -m pip install .
	python -m pip install sphinx sphinx_rtd_theme sphinx-argparse
	- name: Test, Lint and Coverage
	run: \|
	export PYTEST_ADDOPTS="--pylint"
	python setup.py test
	coveralls --service=github
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	- name: Documentation
	run: \|
	export SPHINX_APIDOC_OPTIONS=members
	sphinx-apidoc -o docs/source/api thoraxe
	sphinx-build docs/source docs/build/html
	- name: Deploy
	uses: peaceiris/actions-gh-pages@v3
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	publish_dir: ./docs/build/html/

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