reference_repos/README.md

Reference Repositories

This directory contains reference implementations that inform our architecture. These repos are git-ignored and should be cloned locally.

Clone Commands

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