Add cd-hit & mmseqs installation to codeql_analysis and test_coverage CI #599

	name: CodeQL

	on:
	push:
	branches:
	- master
	pull_request:
	branches:
	- master
	schedule:
	- cron: '0 0 * * 0'

	jobs:
	analyze:
	name: Analyze
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v4
	- name: Initialize CodeQL
	uses: github/codeql-action/init@v3
	with:
	languages: "python"
	- name: Perform CodeQL Analysis
	uses: github/codeql-action/analyze@v3

	code-quality:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: 3.9

	- name: Cache Python dependencies
	uses: actions/cache@v4
	with:
	path: ~/.cache/pip
	key: ${{ runner.os }}-pip-3.9-${{ hashFiles('**/requirements.txt') }}
	restore-keys: \|
	${{ runner.os }}-pip-3.9-

	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install flake8 mypy pylint

	- 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 flake8 (check style)
	run: flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics

	- name: Run mypy (check static typing)
	run: mypy aaanalysis/__init__.py --follow-imports=skip

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