Tests

Merge pull request #80 from rabix/bugfix/sbpack_argparse #187

	name: Tests

	on:
	push:
	branches: [ master ]
	pull_request:
	branches: [ master ]

	concurrency:
	group: build-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	build:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-latest, macos-latest, windows-latest]
	python-version: [3.7, 3.8, 3.9, "3.10"]

	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 wheel
	python -m pip install --upgrade "pip!=22.0.1" "pip!=22.0.2" "pip!=22.0.0" setuptools
	python -m pip install .
	- name: Lint with flake8
	run: \|
	pip install flake8
	# 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: Install test dependencies
	run: \|
	pip install -r test-requirements.txt
	pip install pipx
	pipx install cwltool>=3.0
	pip uninstall -y pytest-workflow
	pipx ensurepath
	# Need a new shell so that ensurepath takes
	- name: Test with pytest
	env:
	SB_AUTH_TOKEN: ${{ secrets.API_KEY }}
	SB_API_ENDPOINT: https://api.sbgenomics.com/v2
	run: \|
	echo $PATH
	cd tests
	py.test --cov=./ --cov-report=xml
	- name: Upload coverage to Codecov
	uses: codecov/[email protected]
	with:
	fail_ci_if_error: true

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