EvoScientist/README.md

EvoScientist

🔥 News

TODO

• [27 Sep 2025] ⛳ Our preprint is now live on [arXiv] — check it out for details.

Overview

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📖 Contents

• ⛏️ Installation
• 🔑 API Key Configuration
• ⚡ Quick Start
  • CLI Inference
  • Script Inference
  • Web Interface
• 📊 Evaluation
• 📝 Citation
• 📚 Acknowledgments
• 📦 Codebase Contributors
• 📜 License

⛏️ Installation

Tip

Use uv for installation — it's faster and more reliable than pip.

For Development

# Create and activate a conda environment
conda create -n EvoSci python=3.11 -y
conda activate EvoSci

# Install in development (editable) mode
pip install EvoScientist
# or
pip install -e .

Option 1:

Install the latest version directly from GitHub for quick setup:

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Option 2:

If you plan to modify the code or contribute to the project, you can clone the repository and install it in editable mode:

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🔄 Upgrade to the latest code base

git pull
uv pip install -e .

🔑 API Key Configuration

EvoScientist requires API keys for LLM inference and web search. You can configure them in two ways:

Option A: Environment Variables (Global)

Set keys directly in your terminal session. Add these to your shell profile (~/.bashrc, ~/.zshrc, etc.) to persist across sessions:

export ANTHROPIC_API_KEY="your_anthropic_api_key_here"
export TAVILY_API_KEY="your_tavily_api_key_here"

Option B: .env File (Project-level)

Create a .env file in the project root. This keeps keys scoped to the project and out of your shell history:

cp .env.example .env

Then edit .env and fill in your keys:

ANTHROPIC_API_KEY=your_anthropic_api_key_here
TAVILY_API_KEY=your_tavily_api_key_here

Warning

Never commit .env files containing real API keys to version control. The .env file is already included in .gitignore.

Key	Required	Description
ANTHROPIC_API_KEY	Yes	Anthropic API key for Claude (console.anthropic.com)
TAVILY_API_KEY	Yes	Tavily API key for web search (app.tavily.com)

⚡ Quick Start

CLI Inference

You can perform inference directly from the command line using our CLI tool:

python -m EvoScientist 

or

EvoSci # or EvoScientist

Optional arguments:

--workdir <path>   Override workspace directory for this session
--use-cwd          Use current working directory as workspace
--thread-id <id>   Resume a conversation thread
--no-thinking      Disable thinking display

Interactive Commands:

Command	Description
/exit	Quit the session
/new	Start a new session (new workspace + thread)
/thread	Show current thread ID and workspace path
/skills	List installed user skills
/install-skill <source>	Install a skill from local path or GitHub
/uninstall-skill <name>	Uninstall a user-installed skill

Skill Installation Examples:

# Install from local path
/install-skill ./my-skill

# Install from GitHub URL
/install-skill https://github.com/owner/repo/tree/main/skill-name

# Install from GitHub shorthand
/install-skill owner/repo@skill-name

Runtime Directories

By default, the workspace is created under a hidden directory in the current project directory:

./.evoscientist/workspace/
  memory/   # shared MEMORY.md
  skills/   # user-installed skills
  runs/     # per-thread workspaces

You can force workspace to be the current directory via --use-cwd.

If you set EVOSCIENTIST_HOME, EvoScientist will place workspace/ under that directory instead of the project root:

Example with EVOSCIENTIST_HOME=~/.evoscientist:

~/.evoscientist/
  workspace/
    memory/
    skills/
    runs/

Script Inference

from EvoScientist import EvoScientist_agent
from langchain_core.messages import HumanMessage
from EvoScientist.utils import format_messages

thread = {"configurable": {"thread_id": "1"}}
question = "Hi?"
last_len = 0

for state in EvoScientist_agent.stream(
    {"messages": [HumanMessage(content=question)]},
    config=thread,
    stream_mode="values",
):
    msgs = state["messages"]
    if len(msgs) > last_len:
        format_messages(msgs[last_len:]) 
        last_len = len(msgs)

Output

╭─────────────────────────────────────────────────── 🧑 Human ────────────────────────────────────────────────────╮
│ Hi?                                                                                                             │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
╭───────────────────────────────────────────────────── 📝 AI ─────────────────────────────────────────────────────╮
│ Hi! I'm here to help you with experimental research tasks. I can assist with:                                   │
│                                                                                                                 │
│ - **Planning experiments** - designing stages, success criteria, and workflows                                  │
│ - **Running experiments** - implementing baselines, training models, analyzing results                          │
│ - **Research** - finding papers, methods, datasets, and baselines                                               │
│ - **Analysis** - computing metrics, creating visualizations, interpreting results                               │
│ - **Writing** - drafting experimental reports and documentation                                                 │
│                                                                                                                 │
│ What would you like to work on today?                                                                           │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

Web Interface

TODO

📊 Evaluation

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📝 Citation

If you find our paper and code useful in your research and applications, please cite using this BibTeX:

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📚 Acknowledgments

This project builds upon the following outstanding open-source works:

• Deep Agents — A framework for building AI agents that can interact with various tools and environments.
• Deep Agents UI — A user interface for visualising and managing Deep Agents.

We thank the authors for their valuable contributions to the open-source community.

📦 Codebase Contributors

Yougang Lyu

Xi Zhang

For any enquiries or collaboration opportunities, please contact: youganglyu@gmail.com

📜 License

This project is licensed under the MIT License - see the LICENSE file for details.