sharedmutationjoiner_test.py
Here’s a detailed documentation of the target file test/solver_tests/sharedmutationjoiner_test.py:
High-level description
This file contains unit tests for the SharedMutationJoiningSolver in Cassiopeia’s solver module. It tests various aspects of the solver, including initialization, cherry finding, similarity map updating, and tree solving for different scenarios.
Code Structure
The main class TestSharedMutationJoiningSolver inherits from unittest.TestCase and contains multiple test methods. The setUp method initializes test data and solver instances used across different tests.
Symbols
find_triplet_structure
Description
A helper function that determines the structure of a triplet in a given tree.
Inputs
| Name | Type | Description |
|---|---|---|
| triplet | tuple | A tuple of three node names |
| T | networkx.DiGraph | The tree to analyze |
Outputs
| Name | Type | Description |
|---|---|---|
| structure | str | The structure of the triplet (”-”, “ab”, “ac”, or “bc”) |
Internal Logic
- Find ancestors for each node in the triplet
- Count common ancestors between pairs
- Determine the structure based on which pair has the most common ancestors
TestSharedMutationJoiningSolver
Description
The main test class containing various test methods for the SharedMutationJoiningSolver.
Internal Logic
setUp: Initializes test data and solver instances- Test methods: Each method tests a specific aspect of the solver
TestSharedMutationJoiningSolver.setUp
Description
Initializes test data and solver instances used across different tests.
Internal Logic
- Creates character matrices and dissimilarity maps for different test scenarios
- Initializes CassiopeiaTrees with the test data
- Creates SharedMutationJoiningSolver instances with different configurations
TestSharedMutationJoiningSolver.test_init
Description
Tests the initialization of the SharedMutationJoiningSolver.
Internal Logic
- Checks if the similarity function is numbaized when possible
- Checks if a warning is raised when the similarity function can’t be numbaized
TestSharedMutationJoiningSolver.test_find_cherry
Description
Tests the find_cherry method of the solver.
Internal Logic
- Calls
find_cherryon a test similarity map - Checks if the returned cherry is correct
TestSharedMutationJoiningSolver.test_create_similarity_map
Description
Tests the creation of a similarity map with weighted priors.
Internal Logic
- Creates a similarity map using test data and priors
- Checks if the similarity values are correct
TestSharedMutationJoiningSolver.test_update_similarity_map_and_character_matrix
Description
Tests the updating of the similarity map and character matrix after joining nodes.
Internal Logic
- Updates the similarity map and character matrix for different joining scenarios
- Checks if the updated maps and matrices are correct
TestSharedMutationJoiningSolver.test_basic_solver
Description
Tests the basic functionality of the solver on a simple tree.
Internal Logic
- Solves a basic tree
- Checks if the original data is unaltered
- Verifies the structure of the solved tree
TestSharedMutationJoiningSolver.test_solver_no_numba
Description
Tests the solver functionality without Numba optimization.
Internal Logic
Similar to test_basic_solver, but uses a solver instance without Numba optimization.
TestSharedMutationJoiningSolver.test_smj_solver_weights
Description
Tests the solver with weighted priors.
Internal Logic
- Solves trees with weighted priors
- Checks the structure of the solved trees
TestSharedMutationJoiningSolver.test_pp_solver
Description
Tests the solver on a perfect phylogeny scenario.
Internal Logic
- Solves a perfect phylogeny tree
- Checks the structure of the solved tree
- Tests with collapsing mutationless edges
TestSharedMutationJoiningSolver.test_duplicate
Description
Tests the solver’s behavior with duplicate and missing data.
Internal Logic
- Solves a tree with duplicate and missing data
- Checks the structure of the solved tree
Dependencies
- unittest
- functools (partial)
- typing (Dict)
- itertools
- networkx (nx)
- numba
- numpy (np)
- pandas (pd)
- scipy
- cassiopeia.data (CassiopeiaTree, utilities)
- cassiopeia.solver (SharedMutationJoiningSolver, dissimilarity_functions, solver_utilities)
Error Handling
The test methods use various assertions to check if the solver behaves correctly. If any assertion fails, the test will raise an AssertionError.