test_linux.yml

name: Run Unit Tests

on: [pull_request]

jobs:
  test:
    runs-on: ubuntu-latest

    steps:
    - name: Checkout repository
      uses: actions/checkout@main

    - name: Set up Python
      uses: actions/setup-python@main
      with:
        python-version: '3.11'

    - name: Install dependencies
      run: |
        sudo apt update
        sudo apt install libopenmpi-dev
        python -m pip install --upgrade pip
        python -m pip install flake8 pytest pytest-cov
        pip install -e .[all]

    - name: lint with flake8
      run: |
        # stop the build if there are Python syntax errors or undefined names
        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics

    - name: Run unit tests
      run: |
        python -m pytest tests/ -v --tb=short

    - name: Run unit tests with coverage (optional)
      run: |
        python -m pytest tests/ --cov=uq_physicell --cov-report=term-missing --cov-report=xml
      continue-on-error: true

    - name: Upload coverage to Codecov (optional)
      if: success()
      uses: codecov/codecov-action@main
      with:
        file: ./coverage.xml
        flags: unittests
        name: codecov-umbrella
      continue-on-error: true