Merge pull request #27 from Clinical-Genomics/update-lint #195

	name: Build
	on: [push, pull_request]

	jobs:
	build:
	name: Test Crunchy (${{ matrix.python-version }}, ${{ matrix.os }})
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.9", "3.10"]

	steps:

	- name: Git checkout
	uses: actions/checkout@v2.5.0

	- name: Get Conda
	uses: conda-incubator/setup-miniconda@v2.2.0
	with:
	auto-update-conda: true
	python-version: ${{ matrix.python-version }}

	# Need to add shell to make conda environments work
	- name: Install spring
	shell: bash -l {0}
	run: \|
	conda install -c bioconda spring

	- name: Install samtools
	shell: bash -l {0}
	run: \|
	conda install -c bioconda samtools

	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	python -m pip install --upgrade pip
	python setup.py install

	- name: Test with pytest
	shell: bash -l {0}
	run: \|
	pip install pytest
	pip install pytest-mock
	py.test -rxs tests/

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