percolation_test.py

Here’s a detailed documentation of the target file test/solver_tests/percolation_test.py:

High-level description

This file contains unit tests for the PercolationSolver in Cassiopeia’s solver module. It tests the solver’s ability to construct phylogenetic trees from character matrices using different joining solvers and dissimilarity functions.

Code Structure

The main class PercolationSolverTest inherits from unittest.TestCase and contains several test methods. These methods create character matrices, solve them using different configurations of the PercolationSolver, and compare the resulting trees to expected structures.

Symbols

find_triplet_structure

Description

This function determines the structure of a triplet of nodes in a given tree.

Inputs

Name	Type	Description
triplet	tuple	A tuple of three node labels
T	networkx.DiGraph	The tree to analyze

Outputs

Name	Type	Description
structure	str	The structure of the triplet (“ab”, “ac”, “bc”, or ”-“)

Internal Logic

1. Find ancestors for each node in the triplet.
2. Count common ancestors between pairs of nodes.
3. Determine the structure based on which pair has the most common ancestors.

neg_hamming_similarity_without_missing

Description

This function computes the negative Hamming similarity between two sequences, ignoring missing data.

Inputs

Name	Type	Description
s1	np.array	First sequence
s2	np.array	Second sequence
missing_state_indicator	int	Value indicating missing data
weights	Optional[Dict[int, Dict[int, float]]]	Optional weights for states

Outputs

Name	Type	Description
similarity	float	Negative Hamming similarity

class PercolationSolverTest(unittest.TestCase)

Description

This class contains unit tests for the PercolationSolver.

Test Methods

test_NJ_negative_similarity

Tests the PercolationSolver using NeighborJoiningSolver with negative Hamming similarity.

test_NJ_weighted_hamming_distance

Tests the PercolationSolver using NeighborJoiningSolver with weighted Hamming distance.

test_Greedy

Tests the PercolationSolver using VanillaGreedySolver.

test_priors_case

Tests the PercolationSolver with prior probabilities for mutations.

Internal Logic

For each test:

1. Create a character matrix.
2. Initialize a CassiopeiaTree with the character matrix.
3. Set up a joining solver (NeighborJoiningSolver or VanillaGreedySolver).
4. Create a PercolationSolver with the joining solver.
5. Solve the tree.
6. Compare the resulting tree structure with the expected structure using triplet comparisons.

Dependencies

Dependency	Purpose
unittest	For creating and running unit tests
itertools	For generating combinations
networkx	For graph operations
numba	For JIT compilation of functions
numpy	For numerical operations
pandas	For data manipulation
cassiopeia	The main package being tested

Error Handling

The tests use assertions to check if the resulting tree structures match the expected structures. If any assertion fails, the test will raise an AssertionError.

Logging

This file does not implement any explicit logging. However, the unittest framework will log test results.

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