ccphylo_solver_test.py

​

High-level description

This file contains unit tests for the CCPhylo solver implementations in the Cassiopeia package. It compares the results of CCPhylo solvers (NJ, DNJ, HNJ, and UPGMA) against standard Neighbor Joining (NJ) and UPGMA implementations for phylogenetic tree reconstruction.

​

Code Structure

The code defines a test class TestCCPhyloSolver that inherits from unittest.TestCase. It includes several test methods to compare different solver implementations and their behavior under various conditions.

​

Symbols

​

find_triplet_structure

​

Description

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

​

Inputs

​

Outputs

​

Internal Logic

1. Find ancestors for each node in the triplet
2. Calculate the number of common ancestors for each pair
3. Determine the structure based on which pair has the most common ancestors

​

delta_fn

​

Description

This function calculates the dissimilarity between two arrays.

​

Inputs

​

Outputs

​

TestCCPhyloSolver

​

Description

This is the main test class containing various test methods for CCPhylo solvers.

​

Internal Logic

1. Sets up test data and solver instances in the setUp method
2. Defines test methods for different solver implementations and scenarios
3. Compares the results of CCPhylo solvers with standard implementations

​

Test Methods

1. test_ccphylo_invalid_input: Tests error handling for invalid solver inputs
2. test_ccphylo_nj_solver: Compares CCPhylo NJ solver with standard NJ solver
3. test_ccphylo_dnj_solver: Compares CCPhylo DNJ solver with standard NJ solver
4. test_ccphylo_hnj_solver: Compares CCPhylo HNJ solver with standard NJ solver
5. test_ccphylo_upgma_solver: Compares CCPhylo UPGMA solver with standard UPGMA solver
6. test_collapse_mutationless_edges_ccphylo: Tests collapsing mutationless edges in CCPhylo NJ solver
7. test_duplicate_sample_ccphylo: Tests CCPhylo NJ solver with duplicate samples

​

Dependencies

​

Configuration

The tests check for the existence of a config.ini file and a ccphylo_path setting to determine if CCPhylo is configured.

​

Error Handling

The code uses unittest.skipUnless to skip tests if CCPhylo is not configured. It also tests for DistanceSolverError when invalid inputs are provided to solvers.