feat: add Memory Store for AI agent project knowledge persistence (v0.6)

.backup/start_mcp_v1.py.bak

@@ -0,0 +1,160 @@
+#!/usr/bin/env python3
+"""
+MCP server for knowledge graph
+Provide knowledge graph query service for AI
+"""
+
+import sys
+from pathlib import Path
+from loguru import logger
+from config import settings,get_current_model_info
+
+# add project root to Python path
+project_root = Path(__file__).parent
+sys.path.insert(0, str(project_root))
+
+def check_dependencies():
+    """check necessary dependencies"""
+    required_packages = [
+        "fastmcp",
+        "neo4j", 
+        "ollama",
+        "loguru"
+    ]
+
+    missing_packages = []
+
+    for package in required_packages:
+        try:
+            __import__(package)
+            logger.info(f"✓ {package} is available")
+        except ImportError:
+            missing_packages.append(package)
+            logger.error(f"✗ {package} is missing")
+
+    if missing_packages:
+        logger.error(f"Missing packages: {', '.join(missing_packages)}")
+        logger.error("Please install missing packages:")
+        logger.error(f"pip install {' '.join(missing_packages)}")
+        return False
+
+    return True
+
+def check_services():
+    """check necessary services"""
+    from config import validate_neo4j_connection, validate_ollama_connection, validate_openrouter_connection, settings
+
+    logger.info("Checking service connections...")
+
+    # check Neo4j connection
+    if validate_neo4j_connection():
+        logger.info("✓ Neo4j connection successful")
+    else:
+        logger.error("✗ Neo4j connection failed")
+        logger.error("Please ensure Neo4j is running and accessible")
+        return False
+
+    # Conditionally check LLM provider connections
+    if settings.llm_provider == "ollama" or settings.embedding_provider == "ollama":
+        if validate_ollama_connection():
+            logger.info("✓ Ollama connection successful")
+        else:
+            logger.error("✗ Ollama connection failed")
+            logger.error("Please ensure Ollama is running and accessible")
+            return False
+
+    if settings.llm_provider == "openrouter" or settings.embedding_provider == "openrouter":
+        if validate_openrouter_connection():
+            logger.info("✓ OpenRouter connection successful")
+        else:
+            logger.error("✗ OpenRouter connection failed")
+            logger.error("Please ensure OpenRouter API key is configured correctly")
+            return False
+
+    return True
+
+def print_mcp_info():
+    """print MCP server info"""
+    from config import settings
+
+    logger.info("=" * 60)
+    logger.info("Knowledge Graph MCP Server")
+    logger.info("=" * 60)
+    logger.info(f"App Name: {settings.app_name}")
+    logger.info(f"Version: {settings.app_version}")
+    logger.info(f"Neo4j URI: {settings.neo4j_uri}")
+    logger.info(f"Ollama URL: {settings.ollama_base_url}")
+    logger.info(f"Model: {get_current_model_info()}")
+    logger.info("=" * 60)
+
+    logger.info("Available MCP Tools:")
+    tools = [
+        "query_knowledge - Query the knowledge base with RAG",
+        "search_documents - Search for documents",
+        "search_code - Search for code snippets", 
+        "search_relations - Search for relationships",
+        "add_document - Add a document to knowledge base",
+        "add_file - Add a file to knowledge base",
+        "add_directory - Add directory contents to knowledge base",
+        "get_statistics - Get knowledge base statistics"
+    ]
+
+    for tool in tools:
+        logger.info(f"  • {tool}")
+
+    logger.info("\nAvailable MCP Resources:")
+    resources = [
+        "knowledge://config - System configuration",
+        "knowledge://status - System status and health",
+        "knowledge://recent-documents/{limit} - Recent documents"
+    ]
+
+    for resource in resources:
+        logger.info(f"  • {resource}")
+
+    logger.info("\nAvailable MCP Prompts:")
+    prompts = [
+        "suggest_queries - Generate query suggestions for different domains"
+    ]
+
+    for prompt in prompts:
+        logger.info(f"  • {prompt}")
+
+    logger.info("=" * 60)
+
+def main():
+    """main function"""
+    logger.info("Starting Knowledge Graph MCP Server...")
+
+    # check dependencies
+    if not check_dependencies():
+        logger.error("Dependency check failed. Exiting.")
+        sys.exit(1)
+
+    # check services
+    if not check_services():
+        logger.error("Service check failed. Exiting.")
+        sys.exit(1)
+
+    # print service info
+    print_mcp_info()
+
+    # start MCP server
+    try:
+        logger.info("Starting MCP server...")
+        logger.info("The server will run in STDIO mode for MCP client connections")
+        logger.info("To test the server, run: python test_mcp_client.py")
+        logger.info("Press Ctrl+C to stop the server")
+
+        # import and run MCP server
+        from mcp_server import mcp
+        mcp.run()
+
+    except KeyboardInterrupt:
+        logger.info("Server stopped by user")
+    except Exception as e:
+        logger.error(f"Server error: {e}")
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main() 

.github/CONTRIBUTING.md

@@ -0,0 +1,233 @@
+# Contributing to Codebase RAG
+
+Thank you for your interest in contributing! This document provides guidelines for contributing to the project.
+
+## Getting Started
+
+### Prerequisites
+
+- Python 3.11, 3.12, or 3.13
+- [uv](https://github.com/astral-sh/uv) (recommended) or pip
+- Git
+
+### Setup Development Environment
+
+```bash
+# Clone the repository
+git clone https://github.com/yourusername/codebase-rag.git
+cd codebase-rag
+
+# Install dependencies
+uv pip install -e .
+
+# Or using pip
+pip install -e .
+```
+
+## Testing
+
+### Running Tests
+
+We have comprehensive unit tests for all MCP handlers. Tests are required for all new features and bug fixes.
+
+```bash
+# Run all unit tests
+pytest tests/test_mcp_*.py -v
+
+# Run specific test file
+pytest tests/test_mcp_handlers.py -v
+
+# Run with coverage report
+pytest tests/test_mcp_*.py --cov=mcp_tools --cov-report=html
+
+# Run only unit tests (no external dependencies)
+pytest tests/ -v -m "unit"
+
+# Run integration tests (requires Neo4j)
+pytest tests/ -v -m "integration"
+```
+
+### Writing Tests
+
+When adding new features, please include tests:
+
+1. **Unit Tests**: Test individual functions in isolation
+   - Mock all external dependencies
+   - Test success and failure cases
+   - Test edge cases and validation
+
+2. **Integration Tests**: Test with real services (optional)
+   - Mark with `@pytest.mark.integration`
+   - Require Neo4j or other external services
+
+Example test:
+
+```python
+import pytest
+from unittest.mock import AsyncMock
+from mcp_tools.knowledge_handlers import handle_query_knowledge
+
+@pytest.mark.asyncio
+async def test_handle_query_knowledge_success(mock_knowledge_service):
+    """Test successful knowledge query"""
+    # Arrange
+    mock_knowledge_service.query.return_value = {
+        "success": True,
+        "answer": "Test response"
+    }
+
+    # Act
+    result = await handle_query_knowledge(
+        args={"question": "test question"},
+        knowledge_service=mock_knowledge_service
+    )
+
+    # Assert
+    assert result["success"] is True
+    assert result["answer"] == "Test response"
+    mock_knowledge_service.query.assert_called_once()
+```
+
+## Code Quality
+
+### Formatting and Linting
+
+We use `black`, `isort`, and `ruff` for code quality:
+
+```bash
+# Format code with black
+black .
+
+# Sort imports with isort
+isort .
+
+# Lint with ruff
+ruff check .
+
+# Auto-fix issues
+ruff check --fix .
+```
+
+### Pre-commit Checks
+
+Before committing:
+
+1. Run tests: `pytest tests/test_mcp_*.py -v`
+2. Format code: `black . && isort .`
+3. Check linting: `ruff check .`
+
+## Pull Request Process
+
+### Creating a Pull Request
+
+1. **Fork the repository** and create a new branch:
+   ```bash
+   git checkout -b feature/your-feature-name
+   ```
+
+2. **Make your changes** with clear, descriptive commits:
+   ```bash
+   git commit -m "feat: add new feature X"
+   git commit -m "fix: resolve issue with Y"
+   ```
+
+3. **Write tests** for your changes
+
+4. **Run tests locally**:
+   ```bash
+   pytest tests/test_mcp_*.py -v
+   ```
+
+5. **Push to your fork**:
+   ```bash
+   git push origin feature/your-feature-name
+   ```
+
+6. **Create a Pull Request** on GitHub
+
+### PR Requirements
+
+For your PR to be merged:
+
+- ✅ All tests must pass
+- ✅ Code coverage should not decrease
+- ✅ Code must be formatted (black, isort)
+- ✅ Linting should pass (ruff)
+- ✅ Clear description of changes
+- ✅ Tests for new features
+
+### GitHub Actions
+
+When you create a PR, GitHub Actions will automatically:
+
+1. **Run unit tests** on Python 3.11, 3.12, and 3.13
+2. **Check code quality** (black, isort, ruff)
+3. **Generate coverage report**
+4. **Report results** in the PR
+
+**PR cannot be merged until all checks pass.**
+
+### Commit Message Format
+
+We follow conventional commits:
+
+- `feat:` New feature
+- `fix:` Bug fix
+- `docs:` Documentation changes
+- `test:` Adding or updating tests
+- `refactor:` Code refactoring
+- `chore:` Maintenance tasks
+
+Examples:
+```
+feat: add streaming support for MCP tools
+fix: resolve memory leak in task queue
+docs: update MCP server architecture guide
+test: add tests for memory handlers
+refactor: extract handlers to modules
+```
+
+## Code Organization
+
+### Project Structure
+
+```
+codebase-rag/
+├── api/                    # FastAPI routes
+├── core/                   # Core application logic
+├── services/              # Business logic services
+├── mcp_tools/             # MCP handler modules
+│   ├── knowledge_handlers.py
+│   ├── code_handlers.py
+│   ├── memory_handlers.py
+│   ├── task_handlers.py
+│   └── system_handlers.py
+├── tests/                 # Test suite
+│   ├── test_mcp_handlers.py
+│   ├── test_mcp_utils.py
+│   └── test_mcp_integration.py
+└── docs/                  # Documentation
+```
+
+### Adding New MCP Tools
+
+1. Add handler function to appropriate `mcp_tools/*.py` file
+2. Add tool definition to `mcp_tools/tool_definitions.py`
+3. Update routing in `mcp_server.py`
+4. Write tests in `tests/test_mcp_handlers.py`
+5. Update documentation
+
+## Getting Help
+
+- 📖 Read the documentation in `docs/`
+- 🐛 Report bugs via GitHub Issues
+- 💬 Ask questions in Discussions
+- 📧 Contact maintainers
+
+## License
+
+By contributing, you agree that your contributions will be licensed under the same license as the project.
+
+---
+
+Thank you for contributing! 🎉