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Here’s a high-level description and documentation of the provided code:

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High-level description

This file contains unit tests for the utilities stored in cassiopeia/data/utilities.py. It tests various functions related to bootstrapping character matrices and allele tables, converting trees to Newick format, computing phylogenetic weight matrices, and calculating inter-cluster distances.

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Code Structure

The code defines a TestDataUtilities class that inherits from unittest.TestCase. This class contains multiple test methods, each testing a specific functionality of the data utilities module.

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Symbols

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TestDataUtilities

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Description

A test class containing various unit tests for the data utilities module.

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Internal Logic

The class sets up test data in the setUp method and defines multiple test methods to verify the functionality of different utility functions.

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test_bootstrap_character_matrices_no_priors

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Description

Tests the sample_bootstrap_character_matrices function without providing priors.

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test_bootstrap_character_matrices_with_priors

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Description

Tests the sample_bootstrap_character_matrices function with provided priors.

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test_bootstrap_allele_tables

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Description

Tests the sample_bootstrap_allele_tables function for standard allele tables.

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test_bootstrap_allele_tables_non_cassiopeia_allele_table

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Description

Tests the sample_bootstrap_allele_tables function for non-standard allele tables.

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test_bootstrap_allele_tables_priors

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Description

Tests the sample_bootstrap_allele_tables function with provided indel priors.

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test_to_newick_no_branch_lengths

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Description

Tests the to_newick function without including branch lengths.

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test_to_newick_branch_lengths

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Description

Tests the to_newick function including branch lengths.

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test_lca_characters

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Description

Tests the get_lca_characters function for finding the lowest common ancestor characters.

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test_lca_characters_ambiguous

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Description

Tests the get_lca_characters function with ambiguous character states.

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test_lca_characters_ambiguous2

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Description

Another test for the get_lca_characters function with different ambiguous character states.

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test_lca_characters_ambiguous_and_missing

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Description

Tests the get_lca_characters function with both ambiguous and missing character states.

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test_resolve_most_abundant

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Description

Tests the resolve_most_abundant function for resolving the most common state in an ambiguous character.

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test_simple_phylogenetic_weights_matrix

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Description

Tests the compute_phylogenetic_weight_matrix function for a simple tree.

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test_simple_phylogenetic_weights_matrix_inverse

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Description

Tests the compute_phylogenetic_weight_matrix function with inverse weights.

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test_phylogenetic_weights_matrix_inverse_fn

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Description

Tests the compute_phylogenetic_weight_matrix function with a custom inverse function.

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test_net_relatedness_index

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Description

Tests the net_relatedness_index function for calculating the Net Relatedness Index.

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test_inter_cluster_distance_basic

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Description

Tests the compute_inter_cluster_distances function for basic inter-cluster distance calculation.

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test_inter_cluster_distance_custom_input

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Description

Tests the compute_inter_cluster_distances function with custom input data.

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Dependencies

  • unittest
  • networkx
  • numpy
  • pandas
  • cassiopeia.data.CassiopeiaTree
  • cassiopeia.data.utilities
  • cassiopeia.mixins.errors.CassiopeiaError
  • cassiopeia.preprocess.utilities
This test suite ensures that the data utility functions in the Cassiopeia package are working correctly and handling various edge cases appropriately.