unifom_leaf_subsampler_test.py

Here’s a detailed documentation of the target file:

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High-level description

This file contains unit tests for the UniformLeafSubsampler class, which is responsible for uniformly subsampling leaves from a CassiopeiaTree. The tests cover various scenarios including parameter validation, error handling, and the correctness of the subsampling process.

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Symbols

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UniformLeafSubsamplerTest

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Description

A test class that inherits from unittest.TestCase, containing multiple test methods to verify the functionality of the UniformLeafSubsampler class.

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Internal Logic

The class contains three main test methods:

1. test_bad_parameters: Tests error handling for invalid initialization parameters.
2. test_bad_number_of_samples: Tests error handling for invalid sample sizes.
3. test_subsample_balanced_tree: Tests the subsampling process on a balanced tree.
4. test_subsample_custom_tree: Tests the subsampling process on a custom tree.

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test_bad_parameters

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Description

Tests that the UniformLeafSubsampler raises appropriate errors when initialized with invalid parameters.

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Internal Logic

1. Attempts to create a UniformLeafSubsampler with both ratio and number_of_leaves specified, expecting a LeafSubsamplerError.
2. Attempts to create a UniformLeafSubsampler with neither ratio nor number_of_leaves specified, expecting a LeafSubsamplerError.

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test_bad_number_of_samples

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Description

Tests that the UniformLeafSubsampler raises appropriate errors when attempting to subsample with invalid sample sizes.

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Internal Logic

1. Creates a balanced tree using networkx.
2. Attempts to subsample with 0 leaves, expecting a LeafSubsamplerError.
3. Attempts to subsample with a very small ratio (0.0001), expecting a LeafSubsamplerError.

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test_subsample_balanced_tree

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Description

Tests the subsampling process on a balanced tree, verifying the correctness of the resulting subsampled tree.

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Internal Logic

1. Creates a balanced tree using networkx.
2. Performs subsampling with a fixed number of leaves (3) and verifies the resulting tree structure.
3. Performs subsampling with a ratio (0.65) and verifies the resulting tree structure.

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test_subsample_custom_tree

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Description

Tests the subsampling process on a custom tree, verifying the correctness of the resulting subsampled tree, including branch lengths and node times.

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Internal Logic

1. Creates a custom tree using networkx.
2. Performs subsampling with a ratio (0.5) and verifies the resulting tree structure, branch lengths, and node times.
3. Performs subsampling with a fixed number of leaves (6) and verifies the resulting tree structure.

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Dependencies

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Error Handling

The tests specifically check for proper error handling in the following cases:

1. Invalid initialization parameters for UniformLeafSubsampler.
2. Attempting to subsample with invalid sample sizes (0 or very small ratio).

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Notes

• The tests use fixed random seeds (np.random.seed(10) and np.random.seed(11)) to ensure reproducibility of the random subsampling process.
• The tests cover both the case of subsampling with a fixed number of leaves and with a ratio of the total leaves.
• The tests verify not only the structure of the resulting subsampled tree but also the correctness of branch lengths and node times in the custom tree test case.