brownian_spatial_simulator_test.py

High-level description

This file contains unit tests for the BrownianSpatialDataSimulator class, which is part of the Cassiopeia package. The tests verify the initialization of the simulator and its ability to overlay spatial data onto a CassiopeiaTree object, both with and without existing cell metadata.

Code Structure

The code defines a single test class TestBrownianSpatialDataSimulator that inherits from unittest.TestCase. It contains a setUp method to initialize test data and several test methods to verify different aspects of the BrownianSpatialDataSimulator class.

Symbols

TestBrownianSpatialDataSimulator

Description

A test class for the BrownianSpatialDataSimulator class, containing multiple test methods to verify its functionality.

Internal Logic

1. Sets up test data in the setUp method, including a basic tree and a tree with cell metadata.
2. Tests the initialization of the simulator with various parameters.
3. Tests the overlay of spatial data onto a basic tree and verifies the results.
4. Tests the overlay of spatial data without scaling to unit area.
5. Tests the overlay of spatial data onto a tree with existing cell metadata.

setUp

Description

Initializes test data, including a basic tree and a tree with cell metadata.

Internal Logic

1. Creates a directed graph representing a tree topology.
2. Initializes a CassiopeiaTree object with the topology.
3. Sets node times for the tree.
4. Creates a DataFrame with cell metadata for some nodes.
5. Initializes another CassiopeiaTree object with the topology and cell metadata.

test_init

Description

Tests the initialization of the BrownianSpatialDataSimulator with various parameters.

Internal Logic

1. Attempts to initialize the simulator with invalid parameters (dimension 0 and negative diffusion coefficient) and expects DataSimulatorError to be raised.
2. Initializes the simulator with valid parameters and verifies the attribute values.

test_overlay_data

Description

Tests the overlay_data method of the BrownianSpatialDataSimulator on a basic tree.

Internal Logic

1. Initializes the simulator with 2 dimensions and a diffusion coefficient of 1.
2. Overlays spatial data onto the basic tree.
3. Verifies the generated spatial coordinates for each node.
4. Checks that the cell metadata is correctly updated with spatial coordinates.

test_overlay_data_without_scale

Description

Tests the overlay_data method without scaling the coordinates to unit area.

Internal Logic

1. Initializes the simulator with scale_unit_area=False.
2. Overlays spatial data onto the basic tree.
3. Verifies the generated spatial coordinates for each node.
4. Checks that the cell metadata is correctly updated with spatial coordinates.

test_overlay_data_with_existing_cell_meta

Description

Tests the overlay_data method on a tree with existing cell metadata.

Internal Logic

1. Initializes the simulator with 2 dimensions and a diffusion coefficient of 1.
2. Overlays spatial data onto the tree with existing cell metadata.
3. Verifies the generated spatial coordinates for each node.
4. Checks that the cell metadata is correctly updated with spatial coordinates while preserving existing metadata.

Dependencies

Dependency	Purpose
unittest	Provides the testing framework
networkx	Used for creating and manipulating graph structures
numpy	Used for numerical operations and testing
pandas	Used for handling DataFrames and testing
cassiopeia	The package being tested

Error Handling

The tests use self.assertRaises to verify that the BrownianSpatialDataSimulator raises DataSimulatorError when initialized with invalid parameters.

Notes

• The tests use a fixed random seed (0) to ensure reproducibility of the generated spatial coordinates.
• The expected coordinates in the tests are hardcoded, which might make the tests brittle if the underlying implementation changes.