EvoScientist 0.0.1.dev6

EvoScientist: Towards Self-Evolving AI Scientists for End-to-End Scientific Discovery

EvoScientist

🔥 News

TODO

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

Overview

TODO

📖 Contents

• 🤖 Supported Models
• ⛏️ Installation
• 🔑 API Key Configuration
• ⚡ Quick Start
  • CLI Inference
  • Script Inference
  • Web Interface
• 🔌 MCP Tools
• 📊 Evaluation
• 📝 Citation
• 📚 Acknowledgments
• 📦 EvoScientist Team
• 📜 License

🤖 Supported Models

Provider	Short Name	Model ID
Anthropic	claude-opus-4-6	claude-opus-4-6
Anthropic	claude-opus-4-5	claude-opus-4-5-20251101
Anthropic	claude-sonnet-4-5	claude-sonnet-4-5-20250929
Anthropic	claude-haiku-4-5	claude-haiku-4-5-20251001
OpenAI	gpt-4o	gpt-4o
OpenAI	gpt-4o-mini	gpt-4o-mini
OpenAI	o1	o1
OpenAI	o1-mini	o1-mini
Google	gemini-3-pro	gemini-3-pro-preview
Google	gemini-3-flash	gemini-3-flash-preview
Google	gemini-2.5-pro	gemini-2.5-pro
Google	gemini-2.5-flash	gemini-2.5-flash
Google	gemini-2.5-flash-lite	gemini-2.5-flash-lite
NVIDIA	glm4.7	z-ai/glm4.7
NVIDIA	deepseek-v3.1	deepseek-ai/deepseek-v3.1-terminus
NVIDIA	nemotron-nano	nvidia/nemotron-3-nano-30b-a3b

You can also use any full model ID directly — the provider will be inferred automatically.

⛏️ 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:

TODO

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:

TODO

🔄 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 three ways:

Option A: Interactive Setup Wizard (Recommended)

EvoSci onboard

The wizard guides you through selecting a provider, entering API keys, choosing a model, and configuring workspace settings. Keys are validated automatically.

Option B: 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"

# Optional: OpenAI, Google, or NVIDIA provider
export OPENAI_API_KEY="your_openai_api_key_here"
export GOOGLE_API_KEY="your_google_api_key_here"
export NVIDIA_API_KEY="your_nvidia_api_key_here"

Option C: .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	For Anthropic	Anthropic API key for Claude (console.anthropic.com)
GOOGLE_API_KEY	For Google	Google API key for Gemini models (aistudio.google.com)
OPENAI_API_KEY	For OpenAI	OpenAI API key for GPT models (platform.openai.com)
NVIDIA_API_KEY	For NVIDIA	NVIDIA API key for NIM models (build.nvidia.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:

--mode <mode>      Workspace mode: 'daemon' (persistent) or 'run' (isolated per-session)
-n, --name <name>  Name for the run directory (requires --mode run; duplicates get _1, _2, …)
--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
-p, --prompt <q>   Single-shot mode: execute query and exit

Configuration commands:

EvoSci onboard                # Interactive setup wizard
EvoSci onboard --skip-validation  # Skip API key validation
EvoSci config                 # List all configuration values
EvoSci config get <key>       # Get a single value
EvoSci config set <key> <val> # Set a single value
EvoSci config reset --yes     # Reset to defaults
EvoSci config path            # Show config file path

Interactive Commands:

Command	Description
/exit	Quit the session
/new	Start a new session (new workspace + thread)
/thread	Show current thread ID and workspace path
/channel	Start iMessage channel (shares agent session)
/skills	List installed user skills
/install-skill <source>	Install a skill from local path or GitHub
/uninstall-skill <name>	Uninstall a user-installed skill
/mcp	List configured MCP servers and tool routing

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

iMessage Channel

EvoScientist can be controlled remotely via iMessage. The channel shares the same agent and conversation thread as the CLI — messages from your phone go through the same session.

# Enable during onboard
EvoSci onboard        # Step 7 configures iMessage

# Or enable manually
EvoSci config set imessage_enabled true
EvoSci config set imessage_allowed_senders "[phone]"

The channel can also be started manually with /channel in the interactive CLI.

Features:

• Thinking content and todo lists are forwarded to iMessage as intermediate messages
• Media files (images, PDFs) are auto-sent when the agent writes (write_file) or reads (read_file) them — no extra commands needed

Runtime Directories

By default, the workspace is created under the current directory:

./workspace/
  memory/   # shared MEMORY.md (persistent across sessions)
  skills/   # user-installed skills
  runs/     # per-session workspaces

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

Override individual paths via environment variables:

Variable	Default	Description
EVOSCIENTIST_WORKSPACE_DIR	./workspace	Root workspace directory
EVOSCIENTIST_RUNS_DIR	./workspace/runs	Per-session run directories
EVOSCIENTIST_MEMORY_DIR	./workspace/memory	Shared memory storage
EVOSCIENTIST_SKILLS_DIR	./workspace/skills	User-installed skills

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

🔌 MCP Tools

EvoScientist supports MCP servers, allowing you to extend agents with external tools (databases, APIs, etc.).

Adding Servers

The quickest way to add an MCP server is from the CLI:

# stdio transport (auto-detected from command)
EvoSci mcp add filesystem npx -- -y @modelcontextprotocol/server-filesystem /tmp

# http transport (auto-detected from URL)
EvoSci mcp add brave-search http://localhost:8080/mcp -H "Authorization:Bearer ${BRAVE_API_KEY}"

# sse transport, routed to a specific agent
EvoSci mcp add my-sse http://localhost:9090/sse --transport sse -e research-agent

# With tool allowlist
EvoSci mcp add fs npx -- -y @modelcontextprotocol/server-filesystem /tmp -t read_file,write_file

Or from the interactive CLI:

/mcp add filesystem npx -y @modelcontextprotocol/server-filesystem /tmp
/mcp remove filesystem
/mcp list

Options:

Flag	Description
--tools, -t	Comma-separated tool allowlist (omit = all tools)
--expose-to, -e	Comma-separated target agents (default: main)
--header, -H	HTTP header as Key:Value (repeatable)
--env	Env var as KEY=VALUE for stdio (repeatable)

YAML Configuration

Servers are stored in ~/.config/evoscientist/mcp.yaml. You can also edit this file directly:

filesystem:
  transport: stdio
  command: npx
  args: ["-y", "@modelcontextprotocol/server-filesystem", "/path/to/dir"]
  tools: [read_file, write_file]     # optional allowlist (omit = all tools)
  expose_to: [main, code-agent]      # optional routing (omit = ["main"])

brave-search:
  transport: http
  url: "http://localhost:8080/mcp"
  headers:
    Authorization: "Bearer ${BRAVE_API_KEY}"
  expose_to: [research-agent]

Use ${VAR} syntax to reference environment variables in config values.

Supported Transports

Transport	Config Fields
stdio	command, args, env (optional)
http	url, headers (optional)
sse	url, headers (optional)
websocket	url

Tool Routing

Use expose_to to control which agents receive each server's tools:

• main — the main EvoScientist orchestrator agent
• Any subagent name (code-agent, research-agent, debug-agent, planner-agent, data-analysis-agent, writing-agent)

Tools routed to subagents are injected automatically — no need to edit subagent.yaml. All MCP tools are also registered in the tool registry, so they can be referenced by name in subagent.yaml if needed.

Editing Servers

Update individual fields on an existing server without re-adding it:

# Change routing
EvoSci mcp edit filesystem --expose-to main,code-agent

# Set a tool allowlist
EvoSci mcp edit filesystem --tools read_file,write_file

# Clear a tool allowlist (pass all tools)
EvoSci mcp edit filesystem --tools none

# Change URL
EvoSci mcp edit my-api --url http://new-host:9090/mcp

Or interactively: /mcp edit filesystem --expose-to main,code-agent

Management Commands

EvoSci mcp              # List configured servers
EvoSci mcp list         # List configured servers
EvoSci mcp add ...      # Add a server
EvoSci mcp edit ...     # Edit an existing server
EvoSci mcp remove ...   # Remove a server

All commands also work interactively: /mcp, /mcp list, /mcp add ..., /mcp edit ..., /mcp remove <name>.

📊 Evaluation

TODO

📝 Citation

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

TODO

📚 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.

📦 EvoScientist Team

Xi Zhang†

Yougang Lyu

Dinos Papakostas

^† Project Leader

For any enquiries or collaboration opportunities, please contact: [e-mail]

📜 License

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