Working basic double agent handoff and streaming

Author: lambda-science

.gitignore

@@ -183,4 +183,6 @@ env/
 **/__pycache__/
 dist/
 .coverage
-
+.gradio
+.idea
+.DS_Store

Makefile

@@ -17,16 +17,16 @@ help:
 	@echo "  make allci              Run all CI steps (check, format, type, test coverage)"
 
 dev:
-	uv run opensymbiose
+	uv run --env-file=.env gradio src/opensymbiose/gradio/app.py
 
 prod:
-	uv run opensymbiose
+	uv run --env-file=.env opensymbiose
 
 test:
-	uv run pytest tests/
+	uv run --env-file=.env pytest tests/
 
 cov:
-	uv run pytest --cov=src/opensymbiose tests/ --cov-report=term-missing
+	uv run --env-file=.env pytest --cov=src/opensymbiose tests/ --cov-report=term-missing
 
 check:
 	uv run ruff check $$(git diff --name-only --cached -- '*.py')

README.md

@@ -1,6 +1,12 @@
+---
+title: opensymbiose
+app_file: src/opensymbiose/gradio/app.py
+sdk: gradio
+sdk_version: 5.31.0
+---
 # OpenSymbiose: Open Source Biotechnology AI Agent
 
-OpenSymbiose in an open-source biotechnology / biology research AI agent designed to support researcher.
+OpenSymbiose is an open-source biotechnology / biology research AI agent designed to support researcher.
 
 Creator and Maintainer: [**Corentin Meyer**, PhD](https://cmeyer.fr/) - <[email protected]>
 

docs/index.md

@@ -7,7 +7,7 @@ hide:
 
 # OpenSymbiose: Open Source Biotechnology AI Agent
 
-OpenSymbiose in an open-source biotechnology / biology research AI agent designed to support researcher.
+OpenSymbiose is an open-source biotechnology / biology research AI agent designed to support researcher.
 
 Creator and Maintainer: [**Corentin Meyer**, PhD](https://cmeyer.fr/) - <[email protected]>
 

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "opensymbiose"
 version = "0.0.0"
-description = "OpenSymbiose in an open-source biotechnology / biology research AI agent designed to support researcher."
+description = "OpenSymbiose is an open-source biotechnology / biology research AI agent designed to support researcher."
 readme = "README.md"
 requires-python = ">=3.13"
 authors = [
@@ -11,8 +11,11 @@ maintainers = [
     { name = "Corentin Meyer", email = "[email protected]" }
 ]
 dependencies = [
+    "biopython>=1.85",
+    "bioservices>=1.12.1",
     "gradio>=5.31.0",
     "mistralai>=1.8.0",
+    "python-dotenv>=1.1.0",
 ]
 
 [project.urls]
@@ -41,7 +44,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 
 [project.scripts]
-opensymbiose = "opensymbiose.main:hello_world"
+opensymbiose = "opensymbiose.gradio.app:demo.launch"
 
 [tool.ruff]
 target-version = "py313"

requirements.txt

@@ -0,0 +1,7 @@
+# For HuggingFace Space Gradio App
+opensymbiose
+mistralai
+python-dotenv
+gradio
+bioservices
+biopython

src/opensymbiose/__init__.py

@@ -0,0 +1,3 @@
+from dotenv import load_dotenv
+
+load_dotenv()

src/opensymbiose/agents/__init__.py

@@ -0,0 +1,11 @@
+"""
+Opensymbiose Agents package.
+
+This package provides classes and functions for managing Mistral AI agents.
+"""
+
+from opensymbiose.agents.agent import Agent
+from opensymbiose.agents.agent_manager import AgentManager
+from opensymbiose.agents.create_agents import setup_agents, get_agents
+
+__all__ = ['Agent', 'AgentManager', 'setup_agents', 'get_agents']

src/opensymbiose/agents/agent.py

@@ -0,0 +1,91 @@
+"""
+Agent class to represent individual Mistral AI agents.
+"""
+from typing import Any
+
+from mistralai import Mistral
+
+
+class Agent:
+    """
+    Represents a Mistral AI agent with its properties and capabilities.
+    """
+
+    def __init__(self, agent_data: Any):
+        """
+        Initialize an Agent object from Mistral API agent data.
+        
+        Args:
+            agent_data: The agent data returned from Mistral API
+        """
+        self.id = agent_data.id
+        self.name = agent_data.name
+        self.description = agent_data.description
+        self.model = agent_data.model
+        self.tools = agent_data.tools
+        self.handoffs = agent_data.handoffs if hasattr(agent_data, 'handoffs') else []
+        self._raw_data = agent_data
+
+    @property
+    def raw_data(self) -> Any:
+        """
+        Get the raw agent data from Mistral API.
+        
+        Returns:
+            The raw agent data
+        """
+        return self._raw_data
+
+    def add_handoff(self, agent_id: str, client: Mistral) -> None:
+        """
+        Add a handoff to another agent.
+        
+        Args:
+            agent_id: The ID of the agent to handoff to
+            client: The Mistral client instance
+        """
+        if agent_id not in self.handoffs:
+            self.handoffs.append(agent_id)
+            updated_agent = client.beta.agents.update(
+                agent_id=self.id,
+                handoffs=self.handoffs
+            )
+            # Update the raw data with the updated agent
+            self._raw_data = updated_agent
+
+    def remove_handoff(self, agent_id: str, client: Mistral) -> None:
+        """
+        Remove a handoff to another agent.
+        
+        Args:
+            agent_id: The ID of the agent to remove handoff from
+            client: The Mistral client instance
+        """
+        if agent_id in self.handoffs:
+            self.handoffs.remove(agent_id)
+            updated_agent = client.beta.agents.update(
+                agent_id=self.id,
+                handoffs=self.handoffs
+            )
+            # Update the raw data with the updated agent
+            self._raw_data = updated_agent
+
+    def __str__(self) -> str:
+        """
+        String representation of the agent.
+        
+        Returns:
+            A string representation of the agent
+        """
+        return f"Agent(id={self.id}, name={self.name}, model={self.model})"
+
+    def __repr__(self) -> str:
+        """
+        Detailed representation of the agent.
+        
+        Returns:
+            A detailed representation of the agent
+        """
+        return (f"Agent(id={self.id}, name={self.name}, "
+                f"description={self.description}, model={self.model}, "
+                f"tools={self.tools}, handoffs={self.handoffs})")

src/opensymbiose/agents/agent_manager.py

@@ -0,0 +1,152 @@
+"""
+AgentManager class to manage Mistral AI agents.
+"""
+import os
+from typing import Dict, List, Optional
+
+from mistralai import Mistral
+
+from opensymbiose.agents.agent import Agent
+
+
+class AgentManager:
+    """
+    Manages Mistral AI agents, including creation, retrieval, and handoffs.
+    Implements the Singleton pattern to ensure only one instance exists.
+    """
+
+    _instance = None
+
+    def __new__(cls, api_key: Optional[str] = None):
+        """
+        Create a new instance of AgentManager or return the existing one (Singleton pattern).
+        
+        Args:
+            api_key: The Mistral API key. If not provided, it will be read from the environment.
+        
+        Returns:
+            The AgentManager instance
+        """
+        if cls._instance is None:
+            cls._instance = super(AgentManager, cls).__new__(cls)
+            cls._instance._initialized = False
+        return cls._instance
+
+    def __init__(self, api_key: Optional[str] = None):
+        """
+        Initialize the AgentManager with the Mistral API key.
+        
+        Args:
+            api_key: The Mistral API key. If not provided, it will be read from the environment.
+        """
+        # Skip initialization if already initialized (part of Singleton pattern)
+        if self._initialized:
+            return
+
+        self.api_key = api_key or os.environ.get("MISTRAL_API_KEY")
+        if not self.api_key:
+            raise ValueError(
+                "Mistral API key is required. Provide it as an argument or set the MISTRAL_API_KEY environment variable.")
+
+        self.client = Mistral(self.api_key)
+        self.agents: Dict[str, Agent] = {}
+        self._initialized = True
+
+    def list_agents(self) -> List[Agent]:
+        """
+        List all agents from the Mistral API.
+        
+        Returns:
+            A list of Agent objects
+        """
+        agent_list = self.client.beta.agents.list()
+        return [Agent(agent) for agent in agent_list]
+
+    def refresh_agents(self) -> None:
+        """
+        Refresh the local cache of agents from the Mistral API.
+        """
+        self.agents = {}
+        agent_list = self.client.beta.agents.list()
+        for agent_data in agent_list:
+            agent = Agent(agent_data)
+            self.agents[agent.name] = agent
+
+    def get_agent(self, agent_name: str) -> Optional[Agent]:
+        """
+        Get an agent by name.
+        
+        Args:
+            agent_name: The name of the agent
+            
+        Returns:
+            The Agent object if found, None otherwise
+        """
+        # Refresh agents if not already loaded
+        if not self.agents:
+            self.refresh_agents()
+
+        return self.agents.get(agent_name)
+
+    def get_or_create_agent(
+            self,
+            agent_name: str,
+            model: str,
+            description: str,
+            tools: List[Dict[str, str]]
+    ) -> Agent:
+        """
+        Get an agent by name or create it if it doesn't exist.
+        
+        Args:
+            agent_name: The name of the agent
+            model: The model to use for the agent
+            description: The description of the agent
+            tools: The tools to enable for the agent
+            
+        Returns:
+            The Agent object
+        """
+        # Refresh agents if not already loaded
+        if not self.agents:
+            self.refresh_agents()
+
+        # Check if agent exists
+        agent = self.agents.get(agent_name)
+
+        # Create agent if it doesn't exist
+        if not agent:
+            agent_data = self.client.beta.agents.create(
+                model=model,
+                description=description,
+                name=agent_name,
+                tools=tools
+            )
+            agent = Agent(agent_data)
+            self.agents[agent_name] = agent
+            print(f"Created new agent: {agent}")
+        else:
+            print(f"Using existing agent: {agent}")
+
+        return agent
+
+    def create_handoff(self, from_agent_name: str, to_agent_name: str) -> None:
+        """
+        Create a handoff from one agent to another.
+        
+        Args:
+            from_agent_name: The name of the agent to handoff from
+            to_agent_name: The name of the agent to handoff to
+        """
+        from_agent = self.get_agent(from_agent_name)
+        to_agent = self.get_agent(to_agent_name)
+
+        if not from_agent:
+            raise ValueError(f"Agent '{from_agent_name}' not found")
+        if not to_agent:
+            raise ValueError(f"Agent '{to_agent_name}' not found")
+
+        from_agent.add_handoff(to_agent.id, self.client)
+
+        # Update the local cache
+        self.agents[from_agent_name] = from_agent