supercellular_sampler_test.py

Here’s a detailed documentation of the test/simulator_tests/supercellular_sampler_test.py file:

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High-level description

This file contains unit tests for the SupercellularSampler class, which is a subclass of LeafSubsampler. The tests verify the functionality of the SupercellularSampler, including its initialization, error handling, and leaf subsampling behavior.

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Code Structure

The main class SupercellularSamplerTest inherits from unittest.TestCase and contains several test methods. The setUp method initializes a test network and character matrix used in multiple tests.

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Symbols

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SupercellularSamplerTest

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Description

A test class that contains unit tests for the SupercellularSampler class.

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Internal Logic

The class sets up a test network and character matrix in the setUp method, which are used across multiple test cases.

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setUp

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Description

Initializes the test environment by creating a test network and character matrix.

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Internal Logic

• Creates a directed graph (self.test_network) representing a tree structure.
• Defines a character matrix (self.character_matrix) with sample data for testing.

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test_bad_parameters

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Description

Tests the SupercellularSampler initialization with invalid parameters.

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Internal Logic

• Attempts to create a SupercellularSampler with both ratio and number_of_merges specified, which should raise a LeafSubsamplerError.
• Attempts to create a SupercellularSampler with neither ratio nor number_of_merges specified, which should also raise a LeafSubsamplerError.

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test_bad_number_of_samples

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Description

Tests the subsample_leaves method with invalid inputs.

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Internal Logic

• Creates a CassiopeiaTree with the test network and character matrix.
• Attempts to subsample leaves with invalid number_of_merges values (10, 0, and 2 for a tree without a character matrix), which should raise appropriate errors.

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test_subsample_balanced_tree

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Description

Tests the subsample_leaves method with valid inputs and verifies the output.

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Internal Logic

• Creates a CassiopeiaTree with the test network and character matrix.
• Subsamples leaves using SupercellularSampler with number_of_merges=2.
• Verifies the resulting character matrix and edges against expected values.
• Repeats the test with collapse_duplicates=False and verifies the results.

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Dependencies

• unittest
• networkx
• numpy
• pandas
• cassiopeia.data.CassiopeiaTree
• cassiopeia.simulator.LeafSubsampler
• cassiopeia.simulator.SupercellularSampler
• cassiopeia.data.utilities

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Error Handling

The tests check for various error conditions, including:

• Incorrect initialization parameters for SupercellularSampler
• Invalid number of merges in subsample_leaves method
• Attempting to subsample leaves on a tree without a character matrix

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TODOs

There are no explicit TODOs in this file.

This test file ensures that the SupercellularSampler class behaves correctly under various conditions and produces expected outputs when subsampling leaves from a CassiopeiaTree.