Test

Updated pyproject.toml #61

	name: Test
	on: [push, pull_request]

	jobs:
	test:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2

	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.x'

	- name: Install R
	run: \|
	sudo apt-get update
	sudo apt-get install -y r-base r-base-dev

	- name: Cache pip dependencies
	uses: actions/cache@v2
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-

	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install numpy scipy pandas pytest bitarray duckdb pyarrow rpy2

	# Step to set up R
	- name: Install R
	uses: r-lib/actions/setup-r@v2

	# Step to install R packages
	- name: Install R dependencies
	run: \|
	Rscript -e 'install.packages(c("data.table", "coloc"), repos = "https://cloud.r-project.org/")'

	- name: Download and install plink
	run: \|
	PLINK_URL="https://s3.amazonaws.com/plink1-assets/plink_linux_x86_64_20231211.zip"
	wget -q $PLINK_URL -O plink_linux_x86_64.zip
	unzip plink_linux_x86_64.zip -d plink
	sudo mv plink/plink /usr/local/bin/
	rm -rf plink_linux_x86_64.zip plink

	- name: Run unit tests
	run: pytest tests/unit_tests_mr_link_2.py

	- name: Run integration tests
	run: pytest tests/integration_tests_mr_link_2.py

	- name: Run comparison_tests_with_r_imlementation
	run: pytest tests/test_for_r_and_python_concordance.py

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