codeql_analysis.yml

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