Merge pull request #34 from Clinical-Genomics/fix-cli-pip-install #30

	name: Crunchy CI
	on: [push, pull_request]

	jobs:
	test-coverage:
	name: Test Crunchy
	runs-on: ubuntu-latest
	strategy:
	fail-fast: false
	matrix:
	python-version: ["3.10"]

	steps:

	- name: Git checkout
	uses: actions/[email protected]

	- name: Install and configure Poetry
	uses: snok/install-poetry@v1

	- name: Install Dependencies
	run: poetry install

	- name: Get Conda
	uses: conda-incubator/[email protected]
	with:
	auto-update-conda: true

	# 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: Unit tests and coverage
	run: \|
	poetry run pytest --cov=./ --cov-report xml --cov-report term

	- name: Upload coverage to Codecov
	uses: codecov/[email protected]
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: unittests

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