PACKAGE_STRUCTURE.md

Package Structure

How Medea is organized for pip installation.

Structure

Medea/
├── medea/              # pip-installable package
│   ├── __init__.py        # Public API
│   ├── core.py            # Core functions (medea, experiment_analysis, etc.)
│   ├── agents/            # Agent implementations
│   └── tool_space/        # Tools and utilities
│
├── examples/              # Usage examples
├── evaluation/            # Benchmarks (not in package)
├── main.py                # Evaluation CLI
├── pyproject.toml         # Package config
└── README.md

Usage Modes

As a library (recommended):

from medea import medea, AgentLLM

For evaluation (development):

python main.py --task targetID --disease ra

Public API

# Core functions
from medea import medea, experiment_analysis, literature_reasoning

# Agents
from medea import ResearchPlanning, Analysis, LiteratureReasoning

# LLM
from medea import AgentLLM, LLMConfig

# Actions (if you need custom agents)
from medea import ResearchPlanDraft, CodeGenerator, LiteratureSearch

# Utils
from medea import Proposal, CodeSnippet, multi_round_discussion

Installation

pip install -e .  # Editable mode

Benefits

• ✅ Clean imports: from medea import medea
• ✅ No code duplication
• ✅ Works with existing evaluation code
• ✅ Easy to extend

Development

Edit code in medea/agents/ or medea/tool_space/ - changes apply immediately in editable mode.

Publishing (Future)

python -m build
python -m twine upload dist/*

Then users install with: pip install medea