bohr-agent-sdk 0.1.101__py3-none-any.whl → 0.1.103__py3-none-any.whl

bohr_agent_sdk-0.1.103.dist-info/METADATA

@@ -0,0 +1,292 @@
+Metadata-Version: 2.4
+Name: bohr-agent-sdk
+Version: 0.1.103
+Summary: SDK for scientific agents
+Home-page: https://github.com/dptech-corp/bohr-agent-sdk/
+Author: DP Technology
+Maintainer-email: liupeng <liupeng@dp.tech>, zjgemi <liuxzj@dp.tech>
+License: MIT
+Project-URL: Homepage, https://github.com/dptech-corp/bohr-agent-sdk
+Project-URL: repository, https://github.com/dptech-corp/bohr-agent-sdk
+Project-URL: Bug Reports, https://github.com/dptech-corp/bohr-agent-sdk/issues
+Keywords: agent SDK,AI for science
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: click>=8.0.0
+Requires-Dist: mcp
+Requires-Dist: python-dotenv>=1.0.0
+Requires-Dist: typing-extensions>=4.8.0
+Requires-Dist: dpdispatcher>=0.6.8
+Requires-Dist: lbg>=1.2.29
+Requires-Dist: jsonpickle>=3.0.3
+Requires-Dist: psutil>=5.9.6
+Requires-Dist: paho-mqtt>=2.1.0
+Requires-Dist: redis>=6.2.0
+Requires-Dist: twine>=6.1.0
+Requires-Dist: build>=1.2.2.post1
+Requires-Dist: watchdog>=6.0.0
+Requires-Dist: fastapi>=0.116.0
+Requires-Dist: bohrium-open-sdk
+Provides-Extra: device
+Requires-Dist: pywinauto-recorder>=0.1.0; extra == "device"
+Provides-Extra: cloud
+Requires-Dist: paho-mqtt>=1.6.1; extra == "cloud"
+Requires-Dist: redis>=5.0.1; extra == "cloud"
+Requires-Dist: aiohttp>=3.9.1; extra == "cloud"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4.0; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.23.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
+Requires-Dist: black>=23.11.0; extra == "dev"
+Requires-Dist: isort>=5.12.0; extra == "dev"
+Requires-Dist: mypy>=1.7.0; extra == "dev"
+Requires-Dist: pylint>=3.0.0; extra == "dev"
+Requires-Dist: google-adk; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.2.0; extra == "docs"
+Requires-Dist: sphinx-rtd-theme>=1.3.0; extra == "docs"
+Provides-Extra: all
+Requires-Dist: bohr-agent-sdk[bohrium,cloud,dev,device,dispatcher,docs]; extra == "all"
+Dynamic: home-page
+Dynamic: requires-python
+
+# Bohrium Science Agent SDK
+
+[English](README.md) | [简体中文](README_CN.md)
+
+**Transform Scientific Software into AI Assistants — 3 Steps to Intelligent Transformation**
+
+## 📖 Introduction
+
+The Bohrium platform introduces the **bohr-agent-sdk Scientific Agent Development Kit**, enabling AI systems to truly execute professional scientific tasks and helping developers quickly build their own specialized research agents. Through a three-step process — **Invoking MCP Tools, Orchestrating Agent Workflows, and Deploying Services** — any scientific software can be rapidly transformed into an AI assistant.
+
+## ✨ Core Features
+
+### 🎯 Intelligent Task Management: Simplified Development, Standardized Output
+With a decorator pattern, just a few annotations can quickly transform scientific computing programs into MCP standard services. Built-in application templates turn scattered research code into standardized, reusable intelligent components.
+
+### 🔧 Multi-Backend Framework Support
+Supports mainstream Agent open frameworks including Google ADK, Langraph, and Camel, providing flexible choices for developers familiar with different technology stacks.
+
+### ☁️ Flexible Deployment: Local Development, Cloud Production
+Dual-mode architecture supports seamless transition between development and production. Local environments enable rapid iteration and feature validation, while Bohrium's cloud GPU clusters handle production-grade computing tasks. The SDK automatically manages the complete workflow of task scheduling, status monitoring, and result collection, with built-in file transfer mechanisms for handling large-scale data uploads and downloads. Developers focus on core algorithm implementation while infrastructure management is fully automated.
+
+### 🖼️ Visual Interactive Interface: Professional Presentation, Intuitive Operation
+Based on the modern React framework, deploy fully-featured web applications with one click. Built-in 3D molecular visualization engine supports multiple structure formats and rendering modes for interactive molecular structure display. Real-time data synchronization ensures instant computing status updates, while multi-session management supports parallel task processing. Integrated with enterprise-grade features including file management, project switching, and permission control. Transform command-line tools into professional visual applications, significantly enhancing user experience and tool usability.
+
+## 🖼️ Interface Showcase
+
+### Scientific Computing Master Console
+<div align="center">
+
+![SCIMaster](image/SCIMaster.PNG)
+
+*Powerful scientific computing task management and monitoring platform*
+
+</div>
+
+### Visual Interactive Interface
+<div align="center">
+
+![UI](image/UI.png)
+
+*Modern web application interface providing intuitive user experience*
+
+</div>
+
+## 🚀 Quick Start
+
+### Installation
+
+```bash
+pip install bohr-agent-sdk -i https://pypi.org/simple --upgrade
+```
+
+### Build Your Research Agent in 3 Steps
+
+#### Step 1: Get Project Templates
+
+```bash
+# Get calculation project template
+dp-agent fetch scaffolding --type=calculation
+
+# Get device control project template
+dp-agent fetch scaffolding --type=device
+
+# Get configuration file
+dp-agent fetch config
+```
+
+#### Step 2: Develop Your Agent
+
+**Lab Mode Development Example**
+
+```python
+from typing import Dict, TypedDict
+from dp.agent.device.device import Device, action, BaseParams, SuccessResult
+
+class TakePictureParams(BaseParams):
+    """Picture taking parameters"""
+    horizontal_width: str  # Image horizontal width
+
+class PictureData(TypedDict):
+    """Picture data structure"""
+    image_id: str
+
+class PictureResult(SuccessResult):
+    """Picture taking result"""
+    data: PictureData
+
+class MyDevice(Device):
+    """Custom device class"""
+    device_name = "my_device"
+
+    @action("take_picture")
+    def take_picture(self, params: TakePictureParams) -> PictureResult:
+        """
+        Execute picture taking action
+
+        Through the @action decorator, automatically register this method as an MCP standard service
+        """
+        hw = params.get("horizontal_width", "default")
+        # Execute actual device control logic
+        return PictureResult(
+            message=f"Picture taken with {self.device_name}",
+            data={"image_id": "image_123"}
+        )
+```
+
+**Cloud Mode Development Example**
+
+```python
+"""
+MCP protocol-based cloud device control example
+"""
+import signal
+import sys
+from dp.agent.cloud import mcp, get_mqtt_cloud_instance
+from dp.agent.device.device import TescanDevice, register_mcp_tools
+
+def signal_handler(sig, frame):
+    """Graceful shutdown handling"""
+    print("Shutting down...")
+    get_mqtt_cloud_instance().stop()
+    sys.exit(0)
+
+def main():
+    """Start cloud services"""
+    print("Starting Tescan Device Twin Cloud Services...")
+
+    # Register signal handler
+    signal.signal(signal.SIGINT, signal_handler)
+
+    # Create device instance
+    device = TescanDevice(mcp, device)
+
+    # Automatically register device tools to MCP server
+    # register_mcp_tools implements automatic registration through Python introspection
+    register_mcp_tools(device)
+
+    # Start MCP server
+    print("Starting MCP server...")
+    mcp.run(transport="sse")
+
+if __name__ == "__main__":
+    main()
+```
+
+#### Step 3: Run and Deploy
+
+```bash
+# Local lab environment
+dp-agent run tool device
+
+# Cloud computing environment
+dp-agent run tool cloud
+
+# Scientific calculation mode
+dp-agent run tool calculation
+
+# Start agent (with Web UI)
+dp-agent run agent --config
+
+# Debug mode
+dp-agent run debug
+```
+
+## 🏗️ Project Structure
+
+After running `dp-agent fetch scaffolding`, you'll get a standardized project structure:
+
+```
+your-project/
+├── lab/                    # Lab mode
+│   ├── __init__.py
+│   └── tescan_device.py    # Device control implementation
+├── cloud/                  # Cloud mode
+│   ├── __init__.py
+│   └── mcp_server.py       # MCP service implementation
+├── calculation/            # Calculation mode
+│   └── __init__.py
+├── .env                    # Environment configuration
+└── main.py                 # Main program entry
+```
+
+## ⚙️ Configuration
+
+Configure necessary environment variables in the `.env` file:
+
+```bash
+# MQTT connection configuration
+MQTT_INSTANCE_ID=your_instance_id
+MQTT_ENDPOINT=your_endpoint
+MQTT_DEVICE_ID=your_device_id
+MQTT_GROUP_ID=your_group_id
+MQTT_AK=your_access_key
+MQTT_SK=your_secret_key
+
+# Computing resource configuration
+BOHRIUM_USERNAME=your_username
+BOHRIUM_PASSWORD=your_password
+```
+
+Note: The `dp-agent fetch config` command automatically downloads configuration files and replaces dynamic variables (such as MQTT_DEVICE_ID). For security reasons, this feature is only available in internal network environments.
+
+## 🎯 Application Scenarios
+
+- **Materials Science Computing**: Molecular dynamics simulation, first-principles calculations
+- **Bioinformatics Analysis**: Gene sequence analysis, protein structure prediction
+- **Laboratory Equipment Control**: Intelligent control of research equipment such as electron microscopes and X-ray diffractometers
+- **Data Processing Workflows**: Automated data cleaning, analysis, and visualization
+- **Machine Learning Training**: Model training, hyperparameter optimization, result evaluation
+
+## 🔧 Advanced Features
+
+### File Management
+
+```bash
+# Upload files to cloud
+dp-agent artifact upload <path>
+
+# Download cloud files
+dp-agent artifact download <artifact_id>
+```
+
+### Task Monitoring
+
+The SDK provides real-time task status monitoring, supporting:
+- Task queue management
+- Computing resource scheduling
+- Automatic result collection
+- Exception handling and retry mechanisms
+
+## 📚 Documentation & Support
+
+- 📖 [Detailed Documentation](https://dptechnology.feishu.cn/wiki/ZSj9wbLJEiwdNek0Iu7cKsFanuW)
+

bohr_agent_sdk-0.1.103.dist-info/RECORD

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dp/agent/cli/cli.py

@@ -8,7 +8,18 @@ import signal
 import uuid
 import requests
 
+try:
+    from dotenv import load_dotenv
+    env_file = Path('.env')
+    if not env_file.exists():
+        env_file = Path(__file__).parent.parent.parent.parent.parent / '.env'
+    if env_file.exists():
+        load_dotenv(env_file)
+except ImportError:
+    pass
+
 from ..server.storage import storage_dict
+from .templates.ui.ui_utils import UIConfigManager, UIProcessManager
 
 @click.group()
 def cli():
@@ -29,37 +40,34 @@ def scaffolding(type):
     """Fetch scaffolding for the science agent."""
     click.echo(f"Generating {type} project scaffold...")
     
-    # 获取模板目录路径
     templates_dir = Path(__file__).parent / 'templates'
-    
-    # 获取用户当前工作目录
     current_dir = Path.cwd()
     
     
-    # 创建必要的目录结构
+    # Create necessary directory structure
     if type == 'device':
-        project_dirs = project_dirs = ['cloud', 'device']
+        project_dirs = ['cloud', 'device']
     elif type == 'calculation':
-        project_dirs = project_dirs = ['calculation']
+        project_dirs = ['calculation']
         
     for dir_name in project_dirs:
         dst_dir = current_dir / dir_name
         
         if dst_dir.exists():
-            click.echo(f"Warning: {dir_name} already exists，skipping...")
-            click.echo(f"If you want to create a new scaffold, please delete the existing project folder first.")
+            click.echo(f"Warning: {dir_name} already exists, skipping...")
+            click.echo(f"To create a new scaffold, please delete the existing folder first.")
             continue
             
-        # 只创建目录，不复制SDK文件
+        # Create directory only
         dst_dir.mkdir(parents=True, exist_ok=True)
     
-    # 创建__init__.py文件以使目录成为Python包
+    # Create __init__.py files to make directories Python packages
     for dir_name in project_dirs:
         init_file = current_dir / dir_name / '__init__.py'
         if not init_file.exists():
             init_file.write_text('')
     
-    # 从模板创建main.py文件
+    # Create main.py from template
     main_template = templates_dir / 'main.py.template'
     main_file = current_dir / 'main.py'
     if not main_file.exists():
@@ -78,11 +86,11 @@ def scaffolding(type):
         calculation_file = current_dir / 'calculation' / 'simple.py'
         if not calculation_file.exists():
             shutil.copy2(calculation_template, calculation_file)
-            click.echo("\nCreated calculation example implementation in calculation/calculation.py")
-            click.echo("Please modify this file according to your actual calculation control requirements.")
+            click.echo("\nCreated calculation example implementation in calculation/simple.py")
+            click.echo("Please modify this file according to your actual calculation requirements.")
     
-    click.echo("\nSucceed for fetching scaffold!")
-    click.echo("Now you can use dp-agent run-cloud or dp-agent run-device to run this project!")
+    click.echo("\nSuccessfully created scaffold!")
+    click.echo("Now you can use dp-agent run tool cloud/device/calculation to run this project!")
 
 @fetch.command()
 def config():
@@ -104,7 +112,6 @@ def config():
         response = requests.get(remote_env_url)
         with open(env_file, 'w') as f:
             f.write(response.text)
-        #shutil.copy2(env_template, env_file)
         click.echo("Configuration file .env has been created.")
         click.echo("\nIMPORTANT: Please update the following configurations in your .env file:")
         click.echo("1. MQTT_INSTANCE_ID - Your Aliyun MQTT instance ID")
@@ -172,16 +179,109 @@ def calculation():
         sys.exit(1)
 
 @run.command()
-def agent():
-    """Run the science agent."""
-    click.echo("Starting agent...")
-    click.echo("Agent started.")
+@click.option('--ui/--no-ui', default=True, help='Enable/disable Web UI interface')
+@click.option('--config', help='Configuration file path (default: agent-config.json)')
+@click.option('--port', type=int, help='Server port (default from config)')
+@click.option('--module', help='Agent module path (default: agent)')
+@click.option('--agent-name', help='Agent variable name (default: root_agent)')
+@click.option('--dev/--prod', default=False, help='Development mode (default: production)')
+def agent(ui, config, port, module, agent_name, dev):
+    """Run the science agent with optional UI interface."""
+    if not ui:
+        click.echo("Starting agent in console mode...")
+        click.echo("Console mode not yet implemented.")
+        return
+    
+    current_dir = Path.cwd()
+    config_path = Path(config) if config else current_dir / "agent-config.json"
+    config_manager = UIConfigManager(config_path if config_path.exists() else None)
+    
+    if module:
+        config_manager.config['agent']['module'] = module
+    
+    agent_module = config_manager.config['agent']['module']
+    
+    if '/' in agent_module or '\\' in agent_module or agent_module.endswith('.py'):
+        file_path = Path(agent_module)
+
+        if not file_path.is_absolute():
+            file_path = current_dir / file_path
+
+        if not file_path.exists():
+            click.echo(f"Error: Agent file not found: {file_path}")
+            click.echo("\nPlease ensure:")
+            click.echo("1. File path is correct")
+            click.echo("2. File exists and is accessible")
+            sys.exit(1)
+    else:
+        module_parts = agent_module.split('.')
+        module_dir = current_dir / Path(*module_parts[:-1])
+        module_file = current_dir / Path(*module_parts[:-1]) / f"{module_parts[-1]}.py"
+        module_init = module_dir / "__init__.py"
+        
+        if not (module_dir.exists() or module_file.exists()):
+            click.echo(f"Error: Module {agent_module} not found.")
+            click.echo(f"Tried to find: {module_dir} or {module_file}")
+            click.echo("\nPlease ensure:")
+            click.echo("1. You have created the agent module")
+            click.echo("2. The 'agent.module' path is correctly configured in config.json")
+            click.echo("3. Or use --module parameter to specify the correct module path")
+            sys.exit(1)
+    
+    if os.environ.get('UI_TEMPLATE_DIR'):
+        ui_dir = Path(os.environ.get('UI_TEMPLATE_DIR'))
+    else:
+        try:
+            current_file = Path(__file__).resolve()
+
+            if 'site-packages' in str(current_file):
+                ui_dir = Path(__file__).parent / "templates" / "ui"
+            else:
+                ui_dir = current_file.parent / "templates" / "ui"
+                click.echo(f"🔧 Development mode detected, using source path: {ui_dir}")
+
+        except Exception:
+            ui_dir = Path(__file__).parent / "templates" / "ui"
+    
+    if not ui_dir.exists():
+        click.echo(f"Error: UI template directory not found: {ui_dir}")
+        click.echo("Tip: You can specify template path via UI_TEMPLATE_DIR environment variable")
+        sys.exit(1)
+    
+    if agent_name:
+        config_manager.config['agent']['rootAgent'] = agent_name
+    if port:
+        config_manager.config['server']['port'] = port
+
+    temp_config = ui_dir / "config" / "agent-config.temp.json"
+    config_manager.save_config(temp_config)
+
+    os.environ['AGENT_CONFIG_PATH'] = str(temp_config)
+    os.environ['PYTHONPATH'] = f"{current_dir}:{os.environ.get('PYTHONPATH', '')}"
+    
+    try:
+        process_manager = UIProcessManager(ui_dir, config_manager.config)
+
+        process_manager.start_websocket_server()
+        process_manager.start_frontend_server(dev_mode=dev)
+
+        click.echo("\nPress Ctrl+C to stop the service...")
+        process_manager.wait_for_processes()
+
+    except KeyboardInterrupt:
+        click.echo("\nShutting down services...")
+        if 'process_manager' in locals():
+            process_manager.cleanup()
+        sys.exit(0)
+    except Exception as e:
+        click.echo(f"Error: {e}")
+        if 'process_manager' in locals():
+            process_manager.cleanup()
+        sys.exit(1)
+    finally:
+        if 'temp_config' in locals() and temp_config.exists():
+            temp_config.unlink()
 
-@run.command()
-def debug():
-    """Debug the science agent in cloud environment."""
-    click.echo("Starting cloud environment in debug mode...")
-    click.echo("Cloud environment debug mode started.")
 
 @cli.group()
 def artifact():
@@ -229,6 +329,7 @@ def download(**kwargs):
     path = storage.download(key, path)
     click.echo("%s has been downloaded to %s" % (uri, path))
 
+
 def main():
     cli()
 

dp/agent/cli/templates/__init__.py

@@ -0,0 +1 @@
+# CLI 模板包

dp/agent/cli/templates/calculation/simple.py.template

@@ -0,0 +1,15 @@
+from dp.agent.server import CalculationMCPServer
+
+# 创建 MCP Server 实例
+mcp = CalculationMCPServer("Demo", host="0.0.0.0", port=5001)
+
+# 用装饰器注册远程调用函数
+@mcp.tool()
+def add_numbers(a: int, b: int) -> int:
+    """Add two numbers."""
+    return a + b
+
+def run():
+    print("Starting MCP server on http://127.0.0.1:5001 ...")
+    mcp.run(transport="streamable-http")
+