Test

Fix utf-8 problem #116

	name: Test

	on:
	push:
	branches: [main, dev]
	pull_request:
	branches: [main]

	jobs:
	test:
	runs-on: ubuntu-22.04
	strategy:
	fail-fast: false
	matrix:
	python-version: ['3.9', '3.10', '3.11', '3.12']

	steps:
	- uses: actions/checkout@v4

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v5
	with:
	python-version: ${{ matrix.python-version }}
	cache: 'pip'

	- name: Install system dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y bedtools samtools ncbi-blast+

	- name: Install Python dependencies
	run: \|
	pip install --upgrade pip
	pip install setuptools
	pip install .
	pip install -r requirements-dev.txt

	- name: Verify installation
	run: \|
	which Magphi
	Magphi --check
	blastn -version
	samtools --version \| head -1
	bedtools --version

	- name: Run unit tests
	working-directory: unit_tests
	run: python Magphi_test.py

	- name: Run pylint
	run: pylint -E Magphi/*.py

	- name: Run functional tests
	run: bash functional_tests/Magphi-test.sh -p Magphi -d functional_tests/test_data -v

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