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> Use this file to discover all available pages before exploring further.

# Overview

## High-level description

This file contains unit tests for the `cassiopeia.critique.compare` module, specifically focusing on the comparison of phylogenetic trees. It uses various tree structures, including balanced trees, multifurcating trees, and rake-shaped trees, to test the accuracy of the comparison metrics.

## Code Structure

The `TestTreeComparisons` class contains multiple test methods, each designed to test a specific aspect of the tree comparison functionality. The `setUp` method initializes various tree structures used throughout the tests. The test methods then utilize these trees to calculate and validate different comparison metrics.

## Symbols

### `TestTreeComparisons`

#### Description

A class containing unit tests for tree comparison functions in the `cassiopeia.critique.compare` module.

#### Inputs

None

#### Outputs

None (test results are outputted to the console)

#### Internal Logic

This class utilizes the `unittest` framework in Python. Each test method within this class is executed independently and checks for specific outcomes from the tree comparison functions. Assertions are used to validate the expected results.

##### `setUp`

###### Description

Initializes various `CassiopeiaTree` objects with different tree structures for testing purposes.

###### Inputs

None

###### Outputs

None (sets up instance variables)

##### `test_out_group`

###### Description

Tests the `get_outgroup` function, which identifies the outlier node in a triplet.

###### Inputs

None

###### Outputs

None (assertions are used to validate the output of `get_outgroup`)

##### `test_same_tree_gives_perfect_triplets_correct`

###### Description

Tests the `triplets_correct` function when comparing a tree to itself, expecting perfect agreement.

###### Inputs

None

###### Outputs

None (assertions are used to validate the output of `triplets_correct`)

##### `test_triplets_correct_different_trees`

###### Description

Tests the `triplets_correct` function with different trees, expecting variations in agreement.

###### Inputs

None

###### Outputs

None (assertions are used to validate the output of `triplets_correct`)

##### `test_triplets_correct_multifurcating_same_tree`

###### Description

Tests the `triplets_correct` function with a multifurcating tree compared to itself, considering unresolvable triplets.

###### Inputs

None

###### Outputs

None (assertions are used to validate the output of `triplets_correct`)

##### `test_triplets_correct_multifurcating_different_trees`

###### Description

Tests the `triplets_correct` function with different multifurcating trees, considering unresolvable triplets.

###### Inputs

None

###### Outputs

None (assertions are used to validate the output of `triplets_correct`)

##### `test_rake_tree`

###### Description

Tests the `triplets_correct` function with a rake-shaped tree, which has all nodes at the same depth.

###### Inputs

None

###### Outputs

None (assertions are used to validate the output of `triplets_correct`)

##### `test_robinson_foulds_same_tree_bifurcating`

###### Description

Tests the `robinson_foulds` function, which calculates the Robinson-Foulds distance between trees.

###### Inputs

None

###### Outputs

None (assertions are used to validate the output of `robinson_foulds`)

## References

This code references the following symbols from other files:

* `cassiopeia.critique.critique_utilities.get_outgroup`
* `cassiopeia.critique.triplets_correct`
* `cassiopeia.critique.robinson_foulds`
* `cassiopeia.data.CassiopeiaTree`

## Dependencies

| Dependency | Purpose                                                                               |
| :--------- | :------------------------------------------------------------------------------------ |
| unittest   | Provides the framework for writing and running unit tests.                            |
| networkx   | Used for creating and manipulating graph structures, representing phylogenetic trees. |
| numpy      | Used for numerical operations and array manipulation.                                 |
| pandas     | Used for data manipulation and analysis, particularly with DataFrames.                |
| cassiopeia | The core library for single-cell lineage tracing analysis.                            |