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# vanillagreedy_test.py

## High-level description

This file contains unit tests for the VanillaGreedySolver class, which is part of the Cassiopeia package for phylogenetic tree reconstruction. The tests cover various aspects of the solver, including frequency dictionary computation, missing data handling, ambiguous state handling, and tree reconstruction with different input scenarios.

## Code Structure

The main class `VanillaGreedySolverTest` inherits from `unittest.TestCase` and contains multiple test methods. Each test method focuses on a specific aspect of the VanillaGreedySolver's functionality, such as frequency dictionary computation, missing data handling, and tree reconstruction. The tests use sample character matrices and expected tree structures to verify the solver's behavior.

## Symbols

### VanillaGreedySolverTest

#### Description

A test class that contains unit tests for the VanillaGreedySolver class.

#### Internal Logic

The class contains multiple test methods, each focusing on a specific aspect of the VanillaGreedySolver's functionality:

1. Frequency dictionary computation
2. Missing data handling
3. Ambiguous state handling
4. Tree reconstruction with various input scenarios

### 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 containing 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

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

### test\_basic\_freq\_dict

#### Description

Tests the computation of mutation frequencies for a basic character matrix.

#### Internal Logic

1. Create a sample character matrix
2. Initialize a VanillaGreedySolver
3. Compute mutation frequencies
4. Assert the correctness of the frequency dictionary

### test\_duplicate\_freq\_dict

#### Description

Tests the computation of mutation frequencies for a character matrix with duplicate rows.

#### Internal Logic

Similar to test\_basic\_freq\_dict, but with a character matrix containing duplicate rows.

### test\_ambiguous\_freq\_dict

#### Description

Tests the computation of mutation frequencies for a character matrix with ambiguous states.

#### Internal Logic

Similar to test\_basic\_freq\_dict, but with a character matrix containing ambiguous states (tuples).

### test\_ambiguous\_duplicate\_freq\_dict

#### Description

Tests the computation of mutation frequencies for a character matrix with ambiguous states and duplicate rows.

#### Internal Logic

Similar to test\_ambiguous\_freq\_dict, but with duplicate rows.

### test\_average\_missing\_data

#### Description

Tests the average missing data imputation method.

#### Internal Logic

1. Create a sample character matrix with missing data
2. Apply the average missing data imputation method
3. Assert the correctness of the resulting partitions

### test\_average\_missing\_data\_priors

#### Description

Tests the average missing data imputation method with priors.

#### Internal Logic

Similar to test\_average\_missing\_data, but includes priors for weighting.

### test\_all\_duplicates\_base\_case

#### Description

Tests the solver's behavior when all samples are identical.

#### Internal Logic

1. Create a character matrix with identical rows
2. Solve the tree
3. Verify the resulting tree structure

### test\_case\_1, test\_case\_2

#### Description

Tests the solver's behavior with more complex character matrices.

#### Internal Logic

1. Create a complex character matrix
2. Solve the tree
3. Verify the resulting tree structure using triplet comparisons

### test\_weighted\_case\_trivial

#### Description

Tests the solver's behavior with a weighted case (using priors).

#### Internal Logic

Similar to test\_case\_2, but includes priors for weighting.

### test\_priors\_case

#### Description

Tests the solver's behavior with more complex priors.

#### Internal Logic

Similar to test\_weighted\_case\_trivial, but with more complex priors.

### test\_ambiguous\_no\_missing, test\_ambiguous\_with\_missing, test\_ambiguous\_with\_missing\_and\_duplicates

#### Description

Tests the solver's behavior with ambiguous states, missing data, and duplicates.

#### Internal Logic

1. Create character matrices with ambiguous states, missing data, and/or duplicates
2. Solve the tree
3. Verify the resulting tree structure using triplet comparisons

## Dependencies

| Dependency | Purpose                                   |
| :--------- | :---------------------------------------- |
| unittest   | Provides the testing framework            |
| itertools  | Used for generating combinations          |
| networkx   | Used for tree representation and analysis |
| pandas     | Used for character matrix representation  |
| cassiopeia | The main package being tested             |

## Error Handling

The test cases use assertions to verify the correctness of the solver's output. If any assertion fails, the test case will raise an AssertionError.

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