> ## Documentation Index
> Fetch the complete documentation index at: https://demo.agenticlabs.com/llms.txt
> Use this file to discover all available pages before exploring further.

# cas9_lineage_tracing_simulator_test.py

Here's a high-level description and documentation for the target file:

## High-level description

This file contains unit tests for the Cas9-based lineage tracing data simulator in the Cassiopeia package. It tests various aspects of the simulator, including basic setup, error handling, and data generation functionality.

## Code Structure

The main class `TestCas9LineageTracingDataSimulator` contains multiple test methods that check different aspects of the `Cas9LineageTracingDataSimulator` class. The tests cover basic setup, error handling, and data generation functionality.

## Symbols

### TestCas9LineageTracingDataSimulator

#### Description

A unittest.TestCase class that contains test methods for the Cas9LineageTracingDataSimulator.

#### Internal Logic

The class sets up a basic tree structure and several instances of Cas9LineageTracingDataSimulator with different configurations in the `setUp` method. It then tests various aspects of the simulator in separate test methods.

### setUp

#### Description

Sets up the test environment by creating a basic tree structure and initializing several Cas9LineageTracingDataSimulator instances with different configurations.

### test\_basic\_setup

#### Description

Tests the basic setup of the Cas9LineageTracingDataSimulator, including the number of characters, mutation rates, and priors.

### test\_setup\_errors

#### Description

Tests various error conditions in the setup of Cas9LineageTracingDataSimulator, such as invalid input parameters.

### test\_get\_cassettes

#### Description

Tests the `get_cassettes` method of the Cas9LineageTracingDataSimulator.

### test\_introduce\_states

#### Description

Tests the `introduce_states` method of the Cas9LineageTracingDataSimulator.

### test\_silence\_cassettes

#### Description

Tests the `silence_cassettes` method of the Cas9LineageTracingDataSimulator.

### test\_collapse\_sites

#### Description

Tests the `collapse_sites` method of the Cas9LineageTracingDataSimulator.

### test\_simulator\_basic

#### Description

Tests the basic functionality of the Cas9LineageTracingDataSimulator by overlaying data on a tree and checking the resulting character matrix.

### test\_no\_collapse

#### Description

Tests the Cas9LineageTracingDataSimulator without collapsing sites.

### test\_no\_resection

#### Description

Tests the Cas9LineageTracingDataSimulator without resection.

### test\_simulator\_with\_state\_generating\_distribution

#### Description

Tests the Cas9LineageTracingDataSimulator with a state-generating distribution.

### test\_simulator\_with\_per\_character\_priors

#### Description

Tests the Cas9LineageTracingDataSimulator with per-character priors.

### test\_simulator\_with\_per\_character\_rates

#### Description

Tests the Cas9LineageTracingDataSimulator with per-character mutation rates.

## Dependencies

* unittest
* networkx
* numpy
* pandas
* cassiopeia

## Error Handling

The test methods use assertions to check for expected behavior and raise exceptions for unexpected results.

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