Development #284

	name: Unit Tests

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

	jobs:
	main_tests:
	name: 'Python ${{ matrix.python-version }} on ${{ matrix.os }}: ${{ matrix.section}})'
	runs-on: ${{ matrix.os }}
	strategy:
	fail-fast: false
	matrix:
	os: ['ubuntu-latest', 'macos-latest']
	section: ["Tools", "Core"]
	python-version: ['3.10']
	defaults:
	run:
	shell: bash -l {0}
	steps:
	- uses: actions/checkout@v2
	with:
	submodules: true
	fetch-depth: 0 # full history for setuptools_scm
	- uses: conda-incubator/setup-miniconda@v2
	with:
	# Don't update conda - performance:
	# miniconda-version: 'latest'
	# auto-update-conda: true
	python-version: ${{ matrix.python-version }}
	channels: conda-forge,bioconda
	environment-file: environment.yaml
	activate-environment: ymp
	channel-priority: strict
	mamba-version: "*"
	- name: Install
	run: \|
	pip install --no-deps .
	- name: Testing Core
	if: matrix.section == 'Core'
	run: \|
	pytest -vv -n auto --junit-xml junit/report.xml --durations=0
	- name: Testing Tools
	if: matrix.section == 'Tools'
	run: \|
	pytest -vvvs -n 1 --junit-xml junit-tools/report.xml --run-tools -m runs_tool --timeout=600 --durations=0
	- name: Upload logs
	if: failure()
	uses: actions/upload-artifact@v1
	with:
	name: Test Failure Logs ${{matrix.os}} ${{matrix.section}}
	path: test_failures
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v1
	with:
	env_vars: OS,PYTHON
	verbose: true
	files: coverage.xml
	flags: ${{matrix.section}}

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