Add cd-hit & mmseqs installation to codeql_analysis and test_coverage CI #91

	name: Test Coverage

	on:
	push:
	branches:
	- master
	pull_request:
	branches:
	- master

	jobs:
	test:
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4

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

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -r requirements.txt
	pip install pytest pytest-cov

	- name: Install cd-hit and mmseqs2
	run: \|
	sudo apt-get update
	sudo apt-get install -y cd-hit
	sudo apt-get install -y mmseqs2

	- name: Run tests with coverage and generate XML report
	run: \|
	pytest --cov=./ --cov-report=xml

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v3
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: ./coverage.xml
	fail_ci_if_error: true
	env:
	MPLBACKEND: Agg

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