Split-read SV calling improvements #198

	name: build tests

	on:
	push:
	branches: [ "main" ]
	pull_request:
	branches: [ "main" ]

	jobs:
	build-and-test:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3

	- name: Download assets
	uses: dsaltares/[email protected]
	with:
	repo: 'WGLab/ContextSV'
	version: 'tags/v0.1.0'
	file: 'TestData.zip'

	- name: Unzip assets
	shell: bash --login {0}
	run: unzip TestData.zip

	- name: Set up conda environment
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: contextsv
	environment-file: environment.yml
	python-version: 3.9
	auto-activate-base: false

	- name: Install samtools and bcftools using sudo apt-get
	run: \|
	sudo apt-get update
	sudo apt-get install -y samtools bcftools

	- name: Build C++ code
	shell: bash --login {0} # --login enables PATH variable access
	run: \|
	make

	- name: Run unit tests
	shell: bash --login {0}
	run: \|
	mkdir -p tests/output
	python -m pytest -s -v tests/test_general.py

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