Merge pull request #51 from cov-lineages/dev #109

	name: scorpio
	on: [push, pull_request]
	defaults:
	run:
	shell: bash -l {0}

	jobs:
	run_pangolin_test:
	name: Scorpio test on ${{ matrix.os }}
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: ["ubuntu-latest", "macos-latest"]
	steps:
	- uses: actions/checkout@v2
	- uses: conda-incubator/setup-miniconda@v2
	with:
	environment-file: environment.yml
	activate-environment: scorpio
	channels: conda-forge,bioconda,defaults
	- name: Install scorpio
	run: pip install -e .
	- name: Install pytest
	run: pip install pytest
	- name: Check scorpio version
	run: scorpio --version
	- name: Run scorpio unittests
	run: pytest 2>&1 \| tee scorpio_pytests.log
	- name: Run scorpio in pangolin mode with test data
	run: scorpio classify -i scorpio/tests/data/type_constellations/test.fa --pangolin --output-counts --long 2>&1 \| tee scorpio_pangolin.log
	# add more tests here

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