test_coverage.yml

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