Merge pull request #197 from joonan-lab/develop-108 #1626

	name: CWAS CI

	on: [push, pull_request]

	jobs:
	build-linux:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: true
	max-parallel: 5

	steps:
	- uses: actions/checkout@v4
	- name: Set up Python 3.9
	uses: actions/setup-python@v4
	with:
	python-version: 3.9

	- name: Install system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y build-essential libz-dev libbz2-dev liblzma-dev

	- name: Install R and dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y r-base libtirpc-dev
	echo "R installed:"
	R --version
	export R_HOME=$(R RHOME)
	echo "R_HOME set to $R_HOME"

	- name: Add conda to system path
	run: \|
	# $CONDA is an environment variable pointing to the root of the miniconda directory
	echo $CONDA/bin >> $GITHUB_PATH
	- name: Install dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y tabix
	python -m pip install --upgrade pip
	pip install build
	pip install .
	- name: Lint with flake8
	run: \|
	conda install flake8
	# stop the build if there are Python syntax errors or undefined names
	flake8 cwas --count --select=E9,F63,F7,F82 --show-source --statistics
	# exit-zero treats all errors as warnings.
	flake8 cwas --count --exit-zero --max-line-length=80 --statistics --extend-ignore=E203
	- name: Test with pytest
	run: \|
	pytest tests

Provide feedback