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# 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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