Update cd-hit and mmseq installation #543

	name: Unit Tests

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

	jobs:
	test:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	os: [ubuntu-latest, windows-latest]
	python-version: ['3.9', '3.10', '3.11', '3.12']

	steps:
	- uses: actions/checkout@v4

	- name: Cache Python dependencies
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-${{ matrix.python-version }}-

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

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


	- name: Install cd-hit (Ubuntu)
	if: runner.os == 'Linux'
	run: \|
	sudo apt-get update
	sudo apt-get install -y cd-hit

	- name: Install mmseqs2 (Ubuntu)
	if: runner.os == 'Linux'
	run: \|
	sudo apt-get update
	sudo apt-get install -y mmseqs2

	- name: Install cd-hit (Windows)
	if: runner.os == 'Windows'
	run: \|
	curl -LO https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.zip
	tar -xf cd-hit-v4.8.1-2019-0228.zip -C $Env:Path

	- name: Install mmseqs2 (Windows)
	if: runner.os == 'Windows'
	run: \|
	curl -LO https://mmseqs.com/latest/mmseqs-win64.zip
	tar -xf mmseqs-win64.zip -C $Env:Path

	- name: Run Tests
	run: pytest tests
	env:
	HYPOTHESIS_DEADLINE: 10000000
	MPLBACKEND: Agg

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