Merge pull request #37 from Clinical-Genomics/refactor-linters #43

	name: Crunchy CI
	on: [push, pull_request]

	jobs:
	test-coverage:
	name: Test Crunchy
	runs-on: ubuntu-latest
	steps:

	- name: Git checkout
	uses: actions/checkout@v4

	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.12"


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

	- name: Install Dependencies
	run: poetry install

	- name: Get Conda
	uses: conda-incubator/setup-miniconda@v3
	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/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	flags: unittests

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