build

test v0.2.2 #26

	name: build
	on:
	push:
	branches:
	- main
	pull_request:
	branches:
	- main

	jobs:
	build:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v2

	- name: Set up Miniconda
	uses: conda-incubator/setup-miniconda@v2
	with:
	miniconda-version: "latest"
	activate-environment: test-env
	python-version: "3.10"

	- name: Install dependencies
	shell: bash -l {0}
	run: \|
	# Remove tmp files
	sudo rm -rf /tmp/*

	# Install conda packages
	conda env list
	conda info
	conda config --add channels defaults
	conda config --add channels bioconda
	conda config --add channels conda-forge
	conda install pandas==2.2.2
	conda install maturin
	conda install rust
	conda install pylint
	conda install coveralls
	conda install pytest
	conda install pytest-cov
	conda install pysam==0.22.0
	conda install numpy==1.26.2
	pip install pyensembl

	# Install vstol
	pip install . --verbose

	- name: Download ensembl data
	shell: bash -l {0}
	run: \|
	pyensembl install --release 95 --species human

	- name: Run linter
	shell: bash -l {0}
	run: \|
	chmod +x lint.sh
	bash lint.sh

	- name: Run unit tests
	shell: bash -l {0}
	run: \|
	chmod +x unittest.sh
	bash unittest.sh

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