Testing Guide#

This guide covers testing practices and guidelines for PhyloZoo.

Setup#

Testing Dependencies#

PhyloZoo uses a small set of testing tools:

pytest >= 7.0.0
pytest-cov >= 4.0.0

You can install them directly:

pip install pytest pytest-cov

or as part of the development extra when working on PhyloZoo itself:

pip install -e ".[dev]"

Test Organization#

Test Framework#

PhyloZoo uses pytest as the testing framework. Tests are located in the tests/ directory and mirror the source code structure.

Test Structure#

Tests are organized to mirror the source code structure:

tests/core/ - Tests for core modules (networks, quartets, splits, sequences, distance)
tests/viz/ - Tests for visualization
tests/utils/ - Tests for utility modules
tests/conftest.py - Shared fixtures and pytest configuration

Running Tests#

Run all tests:

pytest

Run tests with coverage:

pytest --cov=phylozoo --cov-report=html

Run specific test files:

pytest tests/core/network/test_dnetwork.py

Run tests matching a pattern:

pytest -k "test_split"

Run tests and show print statements:

pytest -s

Run tests in verbose mode:

pytest -v

Writing Tests#

Guidelines#

When adding new tests:

Create a test file named test_<module_name>.py in the appropriate subdirectory
Import the module you’re testing
Use descriptive test function names starting with test_
Use pytest fixtures from conftest.py when appropriate
Add docstrings to test classes and functions explaining what they test
Use type hints for test functions

Example:

def test_my_function() -> None:
    """Test that my_function works correctly."""
    result = my_function(input)
    assert result == expected_output

Test Classes#

Group related tests in test classes:

class TestMyClass:
    """Test cases for MyClass."""

    def test_basic_functionality(self) -> None:
        """Test basic functionality."""
        # Test code here
        pass

    def test_edge_case(self) -> None:
        """Test edge case handling."""
        # Test code here
        pass

Fixtures#

Shared fixtures are defined in tests/conftest.py. Use fixtures for common test data:

def test_with_fixture(sample_network) -> None:
    """Test using a fixture."""
    assert sample_network.num_nodes > 0

Best Practices#

Test both success and failure cases: Test that functions work correctly and handle errors appropriately
Use descriptive assertions: Include clear error messages in assertions when possible
Test edge cases: Test with empty inputs, single elements, boundary conditions
Keep tests independent: Each test should be able to run independently
Use fixtures for common setup: Avoid duplicating test setup code