| # Reference Repositories | |
| This directory contains reference implementations that inform our architecture. These repos are **git-ignored** and should be cloned locally. | |
| ## Clone Commands | |
| ```bash | |
| cd reference_repos | |
| # PydanticAI Research Agent (Brave Search + Agent patterns) | |
| git clone --depth 1 https://github.com/coleam00/PydanticAI-Research-Agent.git pydanticai-research-agent | |
| rm -rf pydanticai-research-agent/.git | |
| # PubMed MCP Server (Production-grade, TypeScript) | |
| git clone --depth 1 https://github.com/cyanheads/pubmed-mcp-server.git pubmed-mcp-server | |
| rm -rf pubmed-mcp-server/.git | |
| # Microsoft AutoGen (Multi-agent orchestration) | |
| git clone --depth 1 https://github.com/microsoft/autogen.git autogen-microsoft | |
| rm -rf autogen-microsoft/.git | |
| # Claude Agent SDK (Anthropic's agent framework) | |
| git clone --depth 1 https://github.com/anthropics/claude-agent-sdk-python.git claude-agent-sdk | |
| rm -rf claude-agent-sdk/.git | |
| ``` | |
| ## What Each Repo Provides | |
| | Repository | Key Patterns | Reference In Docs | | |
| |------------|--------------|-------------------| | |
| | **pydanticai-research-agent** | @agent.tool decorator, Brave Search, dependency injection | Section 16 | | |
| | **pubmed-mcp-server** | PubMed E-utilities, MCP server patterns, research agent | Section 16 | | |
| | **autogen-microsoft** | Multi-agent orchestration, reflect_on_tool_use | Sections 14, 15 | | |
| | **claude-agent-sdk** | @tool decorator, hooks system, in-process MCP | Sections 14, 15 | | |
| ## Quick Reference Files | |
| ### PydanticAI Research Agent | |
| - `agents/research_agent.py` - Agent with @agent.tool pattern | |
| - `tools/brave_search.py` - Brave Search implementation | |
| - `models/research_models.py` - Pydantic models | |
| ### PubMed MCP Server | |
| - `src/mcp-server/tools/pubmedSearchArticles/` - PubMed search | |
| - `src/mcp-server/tools/pubmedResearchAgent/` - Research orchestrator | |
| - `src/services/NCBI/` - NCBI E-utilities client | |
| ### AutoGen | |
| - `python/packages/autogen-agentchat/` - Agent patterns | |
| - `python/packages/autogen-core/` - Core abstractions | |
| ### Claude Agent SDK | |
| - `src/claude_agent_sdk/client.py` - SDK client | |
| - `examples/mcp_calculator.py` - @tool decorator example | |