CodeMutator 0.0.16

A comprehensive Python framework for building coding agents using GenAI

Mutator Framework

A comprehensive Python framework for building AI-powered coding agents that can execute complex coding tasks using Large Language Models (LLMs).

Features

Core Capabilities

• LLM Integration: Support for multiple LLM providers via LiteLLM (OpenAI, Anthropic, Google, etc.)
• LangChain-Powered Execution: Built on LangChain for robust agent orchestration, tool calling, and streaming
• Intelligent Task Planning: Simplified planning system where the LLM decides when to break down complex tasks
• Extensible Tool System: Modern @tool decorator for easy tool creation with built-in file operations, shell commands, and Git integration
• Context Management: Vector-based project context with ChromaDB for intelligent code understanding
• Dual Execution Modes: Chat mode (read-only) and Agent mode (full code modification)
• Safety Features: Configurable safety checks and user confirmations
• Sub-Agent Delegation: Automatic delegation of complex tasks to specialized sub-agents
• Streaming Support: Real-time streaming of agent responses and tool execution via LangGraph

Advanced Features

• MCP Server Integration: Support for Model Context Protocol servers
• Configuration Management: Flexible configuration system with validation
• Event-Driven Architecture: Real-time execution monitoring and control
• CLI Interface: Rich command-line interface with interactive features
• Extensible Design: Easy to add custom tools and integrations
• Tool Management: Disable built-in tools to avoid conflicts with custom implementations

Installation

pip install CodeMutator

Development Installation

git clone https://github.com/code-mutator/mutator.git
cd mutator
pip install -e .

Quick Start

Basic Usage

import asyncio
from mutator import Mutator, AgentConfig, ExecutionMode

async def main():
    # Create and initialize agent
    config = AgentConfig(working_directory="./my_project")
    agent = Mutator(config)
    await agent.initialize()
    
    # Execute a simple task
    async for event in agent.execute_task(
        "Add error handling to the main.py file",
        execution_mode=ExecutionMode.AGENT
    ):
        print(f"{event.event_type}: {event.data}")

asyncio.run(main())

Chat Mode

import asyncio
from mutator import Mutator, AgentConfig

async def main():
    config = AgentConfig(working_directory="./my_project")
    agent = Mutator(config)
    await agent.initialize()
    
    # Chat without making changes
    response = await agent.chat("What does the main function do?")
    print(response.content)

asyncio.run(main())

CLI Usage

# Execute a task
mutator execute "Add unit tests for the authentication module" --project ./my_project

# Interactive chat
mutator chat --project ./my_project

# Single chat message
mutator chat "Explain the database schema" --project ./my_project

# Check agent status
mutator status --project ./my_project

# List available tools
mutator tools

Configuration

API Key Setup

The framework supports multiple LLM providers. Set up your API keys using environment variables:

# OpenAI
export OPENAI_API_KEY="your-openai-api-key"

# Anthropic
export ANTHROPIC_API_KEY="your-anthropic-api-key"

# Google
export GOOGLE_API_KEY="your-google-api-key"

# Azure OpenAI
export AZURE_API_KEY="your-azure-api-key"
export AZURE_API_BASE="https://your-resource.openai.azure.com/"
export AZURE_API_VERSION="2023-05-15"

Provider Usage

# Use OpenAI (default)
mutator chat --model gpt-4-turbo-preview

# Use Anthropic Claude
mutator chat --provider anthropic --model claude-3-sonnet-20240229

# Use Google Gemini
mutator chat --provider google --model gemini-pro

# Use Azure OpenAI
mutator chat --provider azure --model gpt-4

Creating Configuration

# Create default configuration
mutator config create --output my_config.json

# Validate configuration
mutator config validate my_config.json

# Show configuration
mutator config show my_config.json

Configuration Structure

{
  "llm_config": {
    "model": "gpt-4-turbo-preview",
    "provider": "openai",
    "api_key": "your-api-key",
    "max_tokens": 2000,
    "temperature": 0.1
  },
  "context_config": {
    "project_path": "./",
    "max_context_files": 20,
    "ignore_patterns": ["*.pyc", "__pycache__", ".git"]
  },
  "safety_config": {
    "confirmation_level": "medium",
    "allowed_shell_commands": ["ls", "cat", "git"],
    "blocked_shell_commands": ["rm", "sudo", "wget"]
  },
  "execution_config": {
    "default_mode": "agent",
    "max_iterations": 50,
    "retry_on_failure": true
  },
  "disabled_tools": [
    "git_status",
    "git_add",
    "run_shell"
  ]
}

Provider-Specific Configuration Examples

OpenAI Configuration

{
  "llm_config": {
    "provider": "openai",
    "model": "gpt-4-turbo-preview",
    "api_key": "your-openai-api-key",
    "max_tokens": 4000,
    "temperature": 0.1
  }
}

Anthropic Configuration

{
  "llm_config": {
    "provider": "anthropic",
    "model": "claude-3-sonnet-20240229",
    "api_key": "your-anthropic-api-key",
    "max_tokens": 4000,
    "temperature": 0.1
  }
}

Google Configuration

{
  "llm_config": {
    "provider": "google",
    "model": "gemini-pro",
    "api_key": "your-google-api-key",
    "max_tokens": 2048,
    "temperature": 0.1
  }
}

Azure OpenAI Configuration

{
  "llm_config": {
    "provider": "azure",
    "model": "gpt-4",
    "api_key": "your-azure-api-key",
    "base_url": "https://your-resource.openai.azure.com/",
    "api_version": "2023-05-15",
    "max_tokens": 4000,
    "temperature": 0.1
  }
}

Examples

Complex Task Execution

import asyncio
from mutator import Mutator, AgentConfig, ExecutionMode

async def refactor_codebase():
    config = AgentConfig(working_directory="./my_project")
    agent = Mutator(config)
    await agent.initialize()
    
    task = """
    Refactor the user authentication system:
    1. Extract authentication logic into a separate service
    2. Add comprehensive error handling
    3. Implement rate limiting
    4. Add unit tests for all new components
    5. Update documentation
    """
    
    async for event in agent.execute_task(
        task, 
        execution_mode=ExecutionMode.AGENT
    ):
        if event.event_type == "task_started":
            print(f"Starting: {event.data}")
        elif event.event_type == "tool_call_completed":
            print(f"Completed: {event.data['tool_name']}")
        elif event.event_type == "task_completed":
            print("Task completed successfully!")

asyncio.run(refactor_codebase())

Custom Tool Creation (Modern @tool Decorator)

from mutator import Mutator, AgentConfig
from mutator.tools.decorator import tool

@tool
def calculate_complexity(file_path: str) -> dict:
    """Calculate code complexity metrics for a file."""
    try:
        with open(file_path, 'r') as f:
            content = f.read()
        
        lines = len(content.splitlines())
        functions = content.count('def ')
        classes = content.count('class ')
        
        return {
            "file_path": file_path,
            "lines_of_code": lines,
            "functions": functions,
            "classes": classes,
            "complexity_score": lines + functions * 2 + classes * 3
        }
    except Exception as e:
        return {"error": f"Failed to analyze file: {str(e)}"}

@tool
def format_json(data: str, indent: int = 2) -> dict:
    """Format JSON data with proper indentation."""
    try:
        import json
        parsed = json.loads(data)
        formatted = json.dumps(parsed, indent=indent)
        return {
            "formatted_json": formatted,
            "original_length": len(data),
            "formatted_length": len(formatted)
        }
    except Exception as e:
        return {"error": f"Invalid JSON: {str(e)}"}

async def main():
    # Create agent
    config = AgentConfig()
    agent = Mutator(config)
    await agent.initialize()
    
    # Register custom tools
    agent.tool_manager.register_function(calculate_complexity)
    agent.tool_manager.register_function(format_json)
    
    # Use the tools
    result = await agent.tool_manager.execute_tool("calculate_complexity", {"file_path": "main.py"})
    print(f"Complexity analysis: {result}")
    
    # Or let the LLM use them in tasks
    async for event in agent.execute_task(
        "Analyze the complexity of all Python files in the src directory and format the results as JSON"
    ):
        print(f"{event.event_type}: {event.data}")

asyncio.run(main())

Project Analysis

import asyncio
from mutator import Mutator, AgentConfig

async def analyze_project():
    config = AgentConfig(working_directory="./my_project")
    agent = Mutator(config)
    await agent.initialize()
    
    # Get project context
    context = await agent.context_manager.get_project_context()
    print(f"Project: {context.get('project_name', 'Unknown')}")
    print(f"Files: {len(context.get('files', []))}")
    
    # Search for specific patterns
    results = await agent.context_manager.search_context("authentication", max_results=5)
    for result in results:
        print(f"Found in {result['file_path']}: {result['content'][:100]}...")

asyncio.run(analyze_project())

Configuration Management

import asyncio
from mutator import AgentConfig, LLMConfig, SafetyConfig
from mutator.core.types import ConfirmationLevel

async def custom_configuration():
    # Create custom configuration
    config = AgentConfig(
        llm_config=LLMConfig(
            model="claude-3-sonnet-20240229",
            max_tokens=4000,
            temperature=0.2
        ),
        safety_config=SafetyConfig(
            confirmation_level=ConfirmationLevel.HIGH,
            allowed_shell_commands=["git", "ls", "cat"],
            blocked_shell_commands=["rm", "sudo", "curl"]
        ),
        disabled_tools=["web_search", "fetch_url"]  # Disable web tools
    )
    
    # Create agent with custom config
    agent = Mutator(config)
    await agent.initialize()
    
    # Execute task with custom settings
    async for event in agent.execute_task(
        "Review the codebase and suggest improvements"
    ):
        print(f"{event.event_type}: {event.data}")

asyncio.run(custom_configuration())

Architecture

Core Components

1. Mutator: Main orchestrator class
2. LLMClient: Interface to language models
3. ToolManager: Tool registration and execution with @tool decorator support
4. ContextManager: Project understanding and vector search
5. TaskPlanner: Simplified task analysis and prompt creation
6. TaskExecutor: Task execution with LLM-driven tool selection

Execution Flow

Task Input → Complexity Analysis → LLM Execution → Tool Selection → Sub-Agent Delegation (if needed) → Results

Modern Tool System

The framework uses a modern @tool decorator system:

from mutator.tools.decorator import tool

@tool
def my_tool(param1: str, param2: int = 10) -> dict:
    """Tool description here."""
    # Tool implementation
    return {"result": "success"}

Features:

• Automatic schema generation from function signatures
• Type inference from annotations
• Default parameter handling
• Async support for both sync and async functions
• Error handling with structured responses

Safety Features

• Confirmation Levels: None, Low, Medium, High
• Command Filtering: Allowed/blocked shell commands
• Path Validation: Prevent dangerous file operations
• Interactive Mode: User confirmation for tool execution
• Tool Disabling: Disable specific tools to prevent conflicts

Advanced Usage

Sub-Agent Task Delegation

The framework includes a powerful task tool that automatically delegates complex operations to sub-agents:

# The LLM will automatically use the task tool for complex operations
async for event in agent.execute_task(
    "Implement a complete REST API with authentication, rate limiting, and comprehensive tests"
):
    if event.event_type == "tool_call_started" and event.data.get("tool_name") == "task":
        print("Delegating to sub-agent for complex task execution")

Event Monitoring

async def monitor_execution():
    config = AgentConfig()
    agent = Mutator(config)
    await agent.initialize()
    
    async for event in agent.execute_task("Create a new API endpoint"):
        if event.event_type == "tool_call_started":
            print(f"Executing: {event.data['tool_name']}")
        elif event.event_type == "complexity_analysis":
            print(f"Task complexity: {event.data['recommended_type']}")
        elif event.event_type == "task_failed":
            print(f"Task failed: {event.data['error']}")
            break

Context Management

# Custom context configuration
from mutator.core.config import ContextConfig

context_config = ContextConfig(
    project_path="./my_project",
    max_context_files=50,
    ignore_patterns=["*.pyc", "__pycache__", ".git", "node_modules"],
    file_size_limit=1024 * 1024  # 1MB
)

config = AgentConfig(context_config=context_config)
agent = Mutator(config)

Disabled Tools

You can disable specific built-in tools to avoid conflicts with custom implementations:

from mutator import Mutator, AgentConfig

# Disable git tools when using GitHub API
config = AgentConfig(
    disabled_tools=[
        "git_status",
        "git_add", 
        "git_commit",
        "git_log"
    ]
)

agent = Mutator(config)
await agent.initialize()

# Git tools are now disabled, use your custom GitHub API tools instead

Common use cases:

• GitHub API Integration: Disable git tools to use GitHub API instead
• Security: Disable shell tools in restricted environments
• Performance: Disable unused tools to reduce overhead

CLI Reference

Main Commands

# Execute tasks
mutator execute "task description" [options]

# Chat with agent
mutator chat [message] [options]

# Check status
mutator status [options]

# List tools
mutator tools [options]

# Configuration management
mutator config create [options]
mutator config validate <config-file>
mutator config show <config-file>

Options

--project, -p       Path to project directory
--config, -c        Path to configuration file
--mode, -m          Execution mode (chat/agent)
--type, -t          Task type (simple/complex)
--verbose, -v       Verbose output
--interactive, -i   Interactive mode with confirmations

Examples

# Execute with custom config
mutator execute "Add logging to all functions" --config my_config.json --project ./src

# Interactive chat session
mutator chat --project ./my_app

# Single chat message
mutator chat "What's the purpose of the main.py file?" --project ./my_app

# Check agent status
mutator status --project ./my_app

# List available tools
mutator tools --config my_config.json

# Create configuration
mutator config create --output ./configs/dev_config.json

# Validate configuration
mutator config validate ./configs/dev_config.json

Best Practices

Task Design

• Be Specific: Clear, actionable task descriptions
• Let the LLM Decide: The framework automatically determines when to use sub-agents
• Provide Context: Include relevant project information

Tool Development

• Use @tool Decorator: Leverage the modern tool system for easy development
• Type Annotations: Use type hints for automatic schema generation
• Error Handling: Return structured error responses
• Documentation: Include clear docstrings for tool descriptions

Safety

• Use Confirmation Levels: Appropriate safety for your environment
• Limit Shell Commands: Restrict dangerous operations
• Review Generated Code: Always review before deploying
• Disable Unused Tools: Reduce attack surface by disabling unnecessary tools

Performance

• Optimize Context: Limit context size for faster processing
• Use Appropriate Models: Balance capability with cost
• Monitor Resource Usage: Track API calls and processing time
• Disable Unused Tools: Reduce initialization overhead

Contributing

We welcome contributions to the Mutator Framework! Please follow these guidelines to ensure a smooth development experience.

Development Setup

Prerequisites

• Python 3.8+ (Python 3.11+ recommended for Apple Silicon Macs)
• Git

Quick Setup

1. Fork and Clone the Repository

   git clone https://github.com/code-mutator/mutator.git
   cd mutator
   

2. Create Virtual Environment

   # Create virtual environment
   python -m venv .venv
   
   # Activate virtual environment
   # On macOS/Linux:
   source .venv/bin/activate
   # On Windows:
   .venv\Scripts\activate
   

3. Install Dependencies

   # Upgrade pip
   pip install --upgrade pip
   
   # Install project in development mode with dev dependencies
   pip install -e ".[dev]"
   

4. Verify Installation

   # Test CLI
   mutator --help
   
   # Run tests
   pytest tests/
   

Apple Silicon (ARM64) Setup

If you're on Apple Silicon (M1/M2/M3 Mac) and encounter architecture compatibility issues:

1. Use Virtual Environment (Recommended)

   # Create and activate virtual environment
   python -m venv .venv
   source .venv/bin/activate
   
   # Install with ARM64 compatibility
   pip install --upgrade pip
   pip install -e .
   

2. Alternative: Use Homebrew Python

   # Install Homebrew Python (if not already installed)
   brew install python@3.11
   
   # Create virtual environment with Homebrew Python
   /opt/homebrew/bin/python3.11 -m venv .venv
   source .venv/bin/activate
   
   # Install dependencies
   pip install -e .
   

3. Verify Architecture

   python -c "import platform; print(f'Architecture: {platform.machine()}')"
   # Should output: arm64
   

Development Workflow

1. Create Feature Branch

   git checkout -b feature/your-feature-name
   

2. Make Changes

   • Follow the existing code style and patterns
   • Add type hints where appropriate
   • Include docstrings for new functions/classes

3. Run Tests

   # Run all tests
   pytest tests/
   
   # Run specific test file
   pytest tests/unit/test_tools.py
   
   # Run with coverage
   pytest tests/ --cov=mutator
   

4. Code Quality Checks

   # Format code (if black is installed)
   black mutator/ tests/
   
   # Sort imports (if isort is installed)
   isort mutator/ tests/
   
   # Type checking (if mypy is installed)
   mypy mutator/
   

5. Test CLI Functionality

   # Test with virtual environment
   source .venv/bin/activate
   mutator status
   mutator tools
   
   # Or use the wrapper script
   ./run_mutator.sh status
   ./run_mutator.sh tools
   

Adding New Tools

When adding new tools, use the modern @tool decorator:

from mutator.tools.decorator import tool
from typing import Optional

@tool
def my_new_tool(
    required_param: str,
    optional_param: Optional[int] = None
) -> dict:
    """
    Brief description of what the tool does.
    
    Args:
        required_param: Description of required parameter
        optional_param: Description of optional parameter
        
    Returns:
        Dictionary with results or error information
    """
    try:
        # Tool implementation
        result = f"Processed {required_param}"
        return {
            "success": True,
            "result": result,
            "optional_used": optional_param is not None
        }
    except Exception as e:
        return {
            "success": False,
            "error": str(e)
        }

Testing Guidelines

1. Unit Tests: Test individual functions and classes
2. Integration Tests: Test tool interactions and workflows
3. CLI Tests: Test command-line interface functionality
4. Architecture Tests: Ensure compatibility across platforms

Example test structure:

import pytest
from mutator.tools.your_tool import your_function

def test_your_function_success():
    """Test successful execution of your function."""
    result = your_function("test_input")
    assert result["success"] is True
    assert "result" in result

def test_your_function_error_handling():
    """Test error handling in your function."""
    result = your_function(None)  # Should cause error
    assert result["success"] is False
    assert "error" in result

Troubleshooting Development Issues

Architecture Errors on Apple Silicon:

# If you see "mach-o file, but is an incompatible architecture" errors:
# 1. Delete existing virtual environment
rm -rf .venv

# 2. Create new virtual environment
python -m venv .venv
source .venv/bin/activate

# 3. Reinstall with no cache
pip install --no-cache-dir -e .

Import Errors:

# Make sure virtual environment is activated
source .venv/bin/activate

# Reinstall in development mode
pip install -e .

CLI Not Working:

# Use the wrapper script
./run_mutator.sh --help

# Or activate virtual environment first
source .venv/bin/activate
mutator --help

Submitting Changes

1. Commit Changes

   git add .
   git commit -m "feat: add new tool for X functionality"
   

2. Push to Fork

   git push origin feature/your-feature-name
   

3. Create Pull Request

   • Include clear description of changes
   • Reference any related issues
   • Include tests for new functionality
   • Update documentation if needed

Commit Message Format

Use conventional commit format:

• feat: - New features
• fix: - Bug fixes
• docs: - Documentation changes
• test: - Test additions/changes
• refactor: - Code refactoring
• chore: - Maintenance tasks

Examples:

feat: add web scraping tool with rate limiting
fix: resolve architecture compatibility on Apple Silicon
docs: update contribution guidelines with venv setup
test: add integration tests for tool manager

Development Environment Verification

After setup, verify everything works:

# 1. Activate virtual environment
source .venv/bin/activate

# 2. Check CLI
mutator --help
mutator status

# 3. Run tests
pytest tests/ -v

# 4. Test tool functionality
python -c "
from mutator import Mutator, AgentConfig
import asyncio

async def test():
    config = AgentConfig()
    agent = Mutator(config)
    await agent.initialize()
    tools = await agent.tool_manager.list_tools()
    print(f'Available tools: {len(tools)}')

asyncio.run(test())
"

If all steps complete successfully, you're ready to contribute!

License

see LICENSE file for details.