Reference data refactor #2687

	name: unit tests

	# Run the test suite on pushes (incl. merges) to main and dev
	# Run the test suite when a PR is opened, pushed to, or reopened
	on:
	push:
	branches:
	- dev
	- main
	pull_request:
	types: [opened, synchronize, reopened]

	jobs:
	unit_tests:
	runs-on: ubuntu-latest
	strategy:
	matrix:
	python-version: ['3.10']

	steps:
	- uses: actions/checkout@v3
	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'
	cache-dependency-path: 'requirements**.txt'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements.txt
	pip install -r requirements-dev.txt
	- name: Check Ruff Format
	run: ruff format --check v03_pipeline --diff
	- name: Check Ruff
	run: ruff . --output-format github
	- name: Run ShellCheck
	uses: ludeeus/action-shellcheck@master
	with:
	severity: error
	scandir: './v03_pipeline/bin'
	- name: Unit Tests
	run: \|
	export GRCH37_TO_GRCH38_LIFTOVER_REF_PATH=v03_pipeline/var/test/liftover/grch37_to_grch38.over.chain.gz
	export GRCH38_TO_GRCH37_LIFTOVER_REF_PATH=v03_pipeline/var/test/liftover/grch38_to_grch37.over.chain.gz
	export ACCESS_PRIVATE_REFERENCE_DATASETS=1
	export INCLUDE_PIPELINE_VERSION_IN_PREFIX=1
	export PYSPARK_SUBMIT_ARGS='--driver-memory 8G pyspark-shell'
	nosetests --with-coverage --cover-package v03_pipeline/lib v03_pipeline/lib
	coverage report --omit 'test' --fail-under=75

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