Upload folder using huggingface_hub

.devcontainer/Dockerfile

@@ -0,0 +1,15 @@
+FROM ghcr.io/astral-sh/uv:python3.13-bookworm-slim
+
+ENV UV_COMPILE_BYTECODE=1
+ENV UV_NO_CACHE=1
+
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    build-essential \
+    cmake \
+    curl \
+    gcc \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /workspaces/opensymbiose

.devcontainer/devcontainer.json

@@ -0,0 +1,16 @@
+{
+  "name": "OpenSymbiose DevContainer",
+  "build": {
+    "dockerfile": "Dockerfile",
+    "context": "."
+  },
+  "forwardPorts": [
+    8000
+  ],
+  "postCreateCommand": "uv sync && make commit",
+  "remoteUser": "root",
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {}
+  },
+  "workspaceFolder": "/workspaces/opensymbiose"
+}

.env.sample

@@ -0,0 +1 @@
+MISTRAL_API_KEY=azerty

.github/workflows/ci.yml

@@ -0,0 +1,29 @@
+name: Deploy Documentation
+on:
+  push:
+    branches:
+      - master
+      - main
+permissions:
+  contents: write
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
+      - uses: actions/cache@v4
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material mkdocstrings mkdocstrings-python mkdocs-include-markdown-plugin
+      - run: mkdocs gh-deploy --force

.github/workflows/update_space.yml

@@ -0,0 +1,29 @@
+name: Deploy to HuggingFace
+
+on:
+  push:
+    branches:
+      - main
+      - master
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: '3.13'
+
+      - name: Install Gradio
+        run: python -m pip install gradio
+
+      - name: Log in to Hugging Face
+        run: python -c 'import huggingface_hub; huggingface_hub.login(token="${{ secrets.hf_token }}")'
+
+      - name: Deploy to Spaces
+        run: gradio deploy

.gitignore

@@ -0,0 +1,188 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# Boiletplate
+venv/
+env/
+.env/
+.venv/
+.ruff_cache/
+**/.pytest_cache/
+**/__pycache__/
+dist/
+.coverage
+.gradio
+.idea
+.DS_Store

.pre-commit-config.yaml

@@ -0,0 +1,8 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.11.10
+    hooks:
+      - id: ruff-check
+        args: [ --fix, --config=pyproject.toml ]
+      - id: ruff-format
+        args: [ --config=pyproject.toml ]

.python-version

@@ -0,0 +1 @@
+3.13

CHANGELOG.md

@@ -0,0 +1,3 @@
+# v0.0.1
+
+- Prototype with two agents with tool calling, handoff, streaming of answer and state. 

Dockerfile

@@ -0,0 +1,23 @@
+FROM ghcr.io/astral-sh/uv:python3.13-bookworm-slim
+
+ENV UV_COMPILE_BYTECODE=1
+ENV UV_NO_CACHE=1
+
+RUN apt update && \
+    apt install -y --no-install-recommends \
+    build-essential \
+    cmake \
+    curl \
+    gcc \
+    git \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /app
+COPY README.md /app/
+COPY pyproject.toml /app/
+RUN uv sync --no-install-project --no-dev
+COPY src/opensymbiose /app/opensymbiose
+
+EXPOSE 8000
+
+CMD ["uv", "run", "opensymbiose/main.py"]

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2025 Corentin Meyer
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

Makefile

@@ -0,0 +1,62 @@
+.PHONY: help
+
+help:
+	@echo "Usage:"
+	@echo "  make dev                Run the package with developer settings"
+	@echo "  make prod               Run the pacakge with production settings"
+	@echo "  make test               CI: Run tests"
+	@echo "  make cov                CI: Run test and calculate coverage"
+	@echo "  make check              CI: Lint the code"
+	@echo "  make format             CI: Format the code"
+	@echo "  make type               CI: Check typing"
+	@echo "  make doc                Run local documentation server"
+	@echo "  make build              Build the package wheel before publishing to Pypi"
+	@echo "  make publish            Publish package to Pypi"
+	@echo "  make dockerbuild        Build the docker image"
+	@echo "  make dockerrun          Run the docker image"
+	@echo "  make allci              Run all CI steps (check, format, type, test coverage)"
+
+dev:
+	uv run --env-file=.env gradio src/opensymbiose/gradio/app.py
+
+prod:
+	uv run --env-file=.env opensymbiose
+
+test:
+	uv run --env-file=.env pytest tests/
+
+cov:
+	uv run --env-file=.env pytest --cov=src/opensymbiose tests/ --cov-report=term-missing
+
+check:
+	uv run ruff check $$(git diff --name-only --cached -- '*.py')
+
+format:
+	uv run ruff format $$(git diff --name-only --cached -- '*.py')
+
+type:
+	uv run ty check $$(git diff --name-only --cached -- '*.py')
+
+doc:
+	uvx --with mkdocstrings  --with mkdocs-material --with mkdocstrings-python --with mkdocs-include-markdown-plugin mkdocs serve
+
+build:
+	uv build
+
+publish:
+	uv publish
+
+commit:
+	uv run pre-commit
+
+dockerbuild:
+	docker build -t opensymbiose:latest .
+
+dockerrun:
+	docker run --rm opensymbiose:latest
+
+allci:
+	$(MAKE) check
+	$(MAKE) format
+	$(MAKE) type
+	$(MAKE) cov

README.md

@@ -1,12 +1,20 @@
 ---
-title: Opensymbiose
-emoji: 🦀
-colorFrom: pink
-colorTo: gray
+title: opensymbiose
+app_file: src/opensymbiose/gradio/app.py
 sdk: gradio
 sdk_version: 5.31.0
-app_file: app.py
-pinned: false
 ---
+# OpenSymbiose: Open Source Biotechnology AI Agent
+
+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]>
+
+## Installation
+
+From PyPi: `pip install opensymbiose`
+
+## Usage
+
+Placeholder
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference

docs/index.md

@@ -0,0 +1,20 @@
+---
+title: Home
+description: OpenSymbiose
+hide:
+  - navigation
+---
+
+# OpenSymbiose: Open Source Biotechnology AI Agent
+
+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]>
+
+## Installation
+
+From PyPi: `pip install opensymbiose`
+
+## Usage
+
+Placeholder

docs/reference.md

@@ -0,0 +1,7 @@
+# API Reference
+
+::: opensymbiose.main
+handler: python
+options:
+show_root_heading: true
+show_source: true

mkdocs.yml

@@ -0,0 +1,71 @@
+site_name: OpenSymbiose
+site_url: https://github.com/lambda-science/OpenSymbiose
+site_author: Corentin Meyer
+site_description: OpenSymbiose
+theme:
+  font:
+    text: Inter
+    code: JetBrains Mono
+  icon:
+    logo: material/file-document-multiple-outline
+  palette:
+    # Palette toggle for light mode
+    - scheme: default
+      primary: white
+      toggle:
+        icon: material/lightbulb
+        name: Switch to dark mode
+
+    # Palette toggle for dark mode
+    - scheme: slate
+      primary: black
+      toggle:
+        icon: material/lightbulb-outline
+        name: Switch to light mode
+  name: material
+  features:
+    - navigation.instant
+    - navigation.top
+    - navigation.tabs
+    - search.suggest
+    - search.highlight
+
+plugins:
+  - search
+  - tags
+  - mkdocstrings:
+      default_handler: python
+      handlers:
+        python:
+          paths: [ "src" ]
+          options:
+            annotations_path: brief
+            docstring_style: google
+  - include-markdown:
+      preserve_includer_indent: true
+nav:
+  - Home: index.md
+  - API Reference: reference.md
+markdown_extensions:
+  - attr_list
+  - admonition
+  - pymdownx.details
+  - pymdownx.superfences
+  - tables
+  - md_in_html
+  - pymdownx.highlight:
+      anchor_linenums: true
+  - pymdownx.inlinehilite
+  - pymdownx.snippets
+  - pymdownx.superfences
+  - pymdownx.emoji:
+      emoji_index: !!python/name:material.extensions.emoji.twemoji
+      emoji_generator: !!python/name:material.extensions.emoji.to_svg
+
+repo_url: https://github.com/lambda-science/OpenSymbiose
+extra:
+  social:
+    - icon: material/web
+      link: https://cmeyer.fr/
+    - icon: fontawesome/brands/x-twitter
+      link: https://x.com/corentinm_py

pyproject.toml

@@ -0,0 +1,53 @@
+[project]
+name = "opensymbiose"
+version = "0.0.1"
+description = "OpenSymbiose is an open-source biotechnology / biology research AI agent designed to support researcher."
+readme = "README.md"
+requires-python = ">=3.13"
+authors = [
+    { name = "Corentin Meyer", email = "[email protected]" },
+]
+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]
+Homepage = "https://github.com/lambda-science/OpenSymbiose"
+Documentation = "https://lambda-science.github.io/OpenSymbiose/"
+Repository = "https://github.com/lambda-science/OpenSymbiose"
+Issues = "https://github.com/lambda-science/OpenSymbiose/issues"
+
+[dependency-groups]
+dev = [
+    "ruff",
+    "pytest",
+    "pytest-cov",
+    "ty",
+    "pre-commit",
+]
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/opensymbiose"]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project.scripts]
+opensymbiose = "opensymbiose.gradio.app:demo.launch"
+
+[tool.ruff]
+target-version = "py313"
+
+[tool.coverage.run]
+omit = ["tests/*"]

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

src/opensymbiose/agents/create_agents.py

@@ -0,0 +1,56 @@
+"""
+Module for creating and managing Mistral AI agents.
+This module provides a simple interface to create and manage agents using the AgentManager class.
+"""
+from opensymbiose.agents.agent_manager import AgentManager
+
+
+def setup_agents():
+    """
+    Set up the agents for the application.
+
+    Returns:
+        A dictionary of agent names to Agent objects
+    """
+    # Initialize the agent manager (Singleton pattern ensures only one instance)
+    agent_manager = AgentManager()
+
+    # Get or create the test agent with web search tool
+    test_agent = agent_manager.get_or_create_agent(
+        agent_name="Test Agent Tools",
+        model="mistral-medium-latest",
+        description="An agent with tools",
+        tools=[{"type": "web_search"}]
+    )
+
+    # Get or create the calculating agent with code interpreter tool
+    calculating_agent = agent_manager.get_or_create_agent(
+        agent_name="Calculating Agent",
+        model="mistral-medium-latest",
+        description="A calculating agent with tools",
+        tools=[{"type": "code_interpreter"}]
+    )
+
+    # Create handoff from test agent to calculating agent
+    agent_manager.create_handoff("Test Agent Tools", "Calculating Agent")
+
+    # Return a dictionary of agent names to Agent objects
+    return {
+        "test_agent_tools": test_agent,
+        "calculating_agent": calculating_agent
+    }
+
+
+# Create a convenience function to get the agents
+def get_agents():
+    """
+    Get the agents for the application.
+
+    Returns:
+        A dictionary of agent names to Agent objects
+    """
+    return setup_agents()
+
+
+# For backwards compatibility and direct script execution
+symbiose_agents = setup_agents() if __name__ == "__main__" else {}

src/opensymbiose/agents/test_agent_manager.py

@@ -0,0 +1,83 @@
+"""
+Test script for the AgentManager and Agent classes.
+"""
+import os
+import sys
+
+# Add the parent directory to the path to allow importing the modules
+sys.path.insert(0, os.path.abspath(os.path.join(os.path.dirname(__file__), '../../..')))
+
+from opensymbiose.agents.agent_manager import AgentManager
+from opensymbiose.agents.create_agents import setup_agents, get_agents
+
+
+def test_agent_manager():
+    """
+    Test the AgentManager class.
+    """
+    print("Testing AgentManager...")
+
+    # Test singleton pattern
+    manager1 = AgentManager()
+    manager2 = AgentManager()
+    assert manager1 is manager2, "Singleton pattern failed"
+    print("✓ Singleton pattern works")
+
+    # Test listing agents
+    agents = manager1.list_agents()
+    print(f"Found {len(agents)} agents")
+
+    # Test refreshing agents
+    manager1.refresh_agents()
+    print(f"Refreshed agents, found {len(manager1.agents)} agents")
+
+    # Test getting an agent
+    if manager1.agents:
+        agent_name = list(manager1.agents.keys())[0]
+        agent = manager1.get_agent(agent_name)
+        print(f"Got agent: {agent}")
+
+    print("AgentManager tests completed successfully")
+
+
+def test_create_agents():
+    """
+    Test the create_agents module.
+    """
+    print("\nTesting create_agents module...")
+
+    # Test setup_agents function
+    agents = setup_agents()
+    assert "test_agent_tools" in agents, "Test agent not created"
+    assert "calculating_agent" in agents, "Calculating agent not created"
+
+    print(f"✓ setup_agents created {len(agents)} agents")
+
+    # Test get_agents function
+    agents2 = get_agents()
+    assert agents2["test_agent_tools"].id == agents["test_agent_tools"].id, "get_agents returned different agents"
+
+    print("✓ get_agents works correctly")
+
+    # Test handoffs
+    test_agent = agents["test_agent_tools"]
+    calc_agent = agents["calculating_agent"]
+
+    assert calc_agent.id in test_agent.handoffs, "Handoff not created"
+
+    print(f"✓ Handoff from {test_agent.name} to {calc_agent.name} created successfully")
+
+    print("create_agents tests completed successfully")
+
+
+if __name__ == "__main__":
+    # Check if MISTRAL_API_KEY is set
+    if not os.environ.get("MISTRAL_API_KEY"):
+        print("Error: MISTRAL_API_KEY environment variable is not set")
+        print("Please set it before running this test script")
+        sys.exit(1)
+
+    test_agent_manager()
+    test_create_agents()
+
+    print("\nAll tests completed successfully!")

src/opensymbiose/config.py

@@ -0,0 +1,3 @@
+import os
+
+MISTRAL_API_KEY = os.getenv("MISTRAL_API_KEY")

src/opensymbiose/gradio/app.py

@@ -0,0 +1,130 @@
+import logging
+import time
+from dataclasses import asdict
+
+import gradio as gr
+from gradio import ChatMessage
+from mistralai import Mistral, ToolReferenceChunk
+
+import opensymbiose.config
+from opensymbiose.agents.create_agents import get_agents
+
+logger = logging.getLogger(__name__)
+client = Mistral(api_key=opensymbiose.config.MISTRAL_API_KEY)
+model = "mistral-medium-latest"
+
+
+def get_mistral_answer(message: str, history):
+    # Start global execution timer
+    global_start_time = time.time()
+
+    # Dictionary to track tool execution times
+    tool_timers = {}
+
+    agents = get_agents()
+    main_agent = agents["test_agent_tools"]
+    stream_response = client.beta.conversations.start_stream(
+        agent_id=main_agent.id, inputs=message, store=False
+    )
+    messages = []
+    # Add an initial empty message for the assistant's response
+    messages.append(asdict(ChatMessage(role="assistant", content="")))
+    yield messages
+    full_response = ""
+    for chunk in stream_response:
+        print(chunk)
+        if chunk.event == "message.output.delta":
+            if isinstance(chunk.data.content, str):
+                full_response += chunk.data.content
+            if isinstance(chunk.data.content, ToolReferenceChunk):
+                full_response += f"([{chunk.data.content.title}]({chunk.data.content.url})) "
+            # Update the last message with the current full response
+            messages[-1] = asdict(ChatMessage(role="assistant", content=full_response))
+            yield messages
+        elif chunk.event == "tool.execution.started":
+            # Start timer for this tool
+            tool_timers[chunk.data.name] = time.time()
+            # Add a new message for tool execution start
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={"title": f"🛠️ Using tool {chunk.data.name}..."})))
+            yield messages
+        elif chunk.event == "tool.execution.done":
+            # Calculate tool execution duration
+            tool_duration = time.time() - tool_timers.get(chunk.data.name, time.time())
+            # Add a new message for tool execution completion
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={"title": f"🛠️ Finished using {chunk.data.name}.",
+                                                         "duration": round(tool_duration, 2)})))
+            # Add a new empty message for the continuing assistant response
+            messages.append(asdict(ChatMessage(role="assistant", content=full_response)))
+            yield messages
+        elif chunk.event == "agent.handoff.started":
+            # Start timer for agent handoff
+            tool_timers["agent_handoff"] = time.time()
+            # Add a new message for agent handoff start
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={
+                                                   "title": f"🔄 Handing off from agent {chunk.data.previous_agent_name}..."})))
+            yield messages
+        elif chunk.event == "agent.handoff.done":
+            # Calculate handoff duration
+            handoff_duration = time.time() - tool_timers.get("agent_handoff", time.time())
+            # Add a new message for agent handoff completion
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={
+                                                   "title": f"✅ Handoff complete. Now using agent {chunk.data.next_agent_name}.",
+                                                   "duration": round(handoff_duration, 2)})))
+            # Add a new empty message for the continuing assistant response
+            messages.append(asdict(ChatMessage(role="assistant", content=full_response)))
+            yield messages
+        elif chunk.event == "function.call.delta":
+            # Start timer for function call
+            function_start_time = time.time()
+            # Add function call information to the response
+            function_info = f"Calling function: {chunk.data.name} with arguments: {chunk.data.arguments}"
+            # Store the function name for potential future duration calculation
+            tool_timers[f"function_{chunk.data.name}"] = function_start_time
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={"title": f"📞 {function_info}"})))
+            yield messages
+        elif chunk.event == "conversation.response.started":
+            # Add a new message for conversation response start
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={"title": f"🚀 Symbiose agent is starting...",
+                                                         "log": f"{chunk.data.conversation_id}"})))
+            yield messages
+        elif chunk.event == "conversation.response.done":
+            # Calculate global execution duration
+            global_duration = time.time() - global_start_time
+            # Add a new message for conversation response completion
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={"title": f"✅ Conversation response complete.",
+                                                         "log": f"Tokens: Prompt: {chunk.data.usage.prompt_tokens}, Completion: {chunk.data.usage.completion_tokens}, Total: {chunk.data.usage.total_tokens} Connectors: {chunk.data.usage.connector_tokens}",
+                                                         "duration": round(global_duration, 2)})))
+            yield messages
+        elif chunk.event == "conversation.response.error":
+            # Add a new message for conversation response error
+            error_message = f"Error: {chunk.data.message} (Code: {chunk.data.code})"
+            messages.append(asdict(ChatMessage(role="assistant", content="",
+                                               metadata={"title": f"❌ {error_message}"})))
+            yield messages
+        else:
+            # For other events, just update the last message
+            messages[-1] = asdict(ChatMessage(role="assistant", content=full_response))
+            yield messages
+
+
+with gr.Blocks() as demo:
+    gr.ChatInterface(
+        fn=get_mistral_answer,
+        type="messages",
+        title="Open-Symbiose🧬",
+        description="OpenSymbiose is an open-source biotechnology / biology research AI agent designed to support researcher",
+        examples=["search internet: CEO of google", "Use your calculator agent to do 1273*3/12^2"],
+        save_history=True,
+        flagging_mode="manual"
+
+    )
+
+if __name__ == "__main__":
+    demo.launch()

src/opensymbiose/main.py

@@ -0,0 +1,7 @@
+def hello_world() -> str:
+    """Prints a hello world message."""
+    return "Hello from OpenSymbiose!"
+
+
+if __name__ == "__main__":
+    hello_world()

tests/test_main.py

@@ -0,0 +1,7 @@
+from opensymbiose.main import hello_world
+
+
+def test_hello_world():
+    """Test that hello_world prints the expected message."""
+    output = hello_world()
+    assert output == "Hello from OpenSymbiose!"