scmcp-shared 0.5.0__py3-none-any.whl → 0.6.2__py3-none-any.whl

scmcp_shared/__init__.py

@@ -1 +1 @@
-__version__ = "0.5.0"
+__version__ = "0.6.2"

scmcp_shared/agent.py

@@ -1,12 +1,10 @@
-import instructor
-from openai import OpenAI
-from scmcp_shared.schema.tool import ToolList
+from .schema.tool import ToolList
 import os
 
 
 from agno.agent import Agent
 from agno.models.openai import OpenAILike
-from scmcp_shared.kb import load_kb
+from .kb import load_kb
 
 model = OpenAILike(
     id=os.getenv("MODEL"),
@@ -15,43 +13,24 @@ model = OpenAILike(
 )
 
 
-def rag_agent(task, software=None):
+def rag_agent(task, software="scmcp"):
     knowledge_base = load_kb(software=software)
     agent = Agent(
         model=model,
         knowledge=knowledge_base,
         show_tool_calls=True,
         search_knowledge=True,
+        instructions="""
+        MUST query the knowledge base, and return the code example that can be used to solve the task.
+        """,
     )
     query = f"""
     <task>
     {task}
     </task>
-    拆分任务，分别查询知识库，查找完成每个子任务所需要的函数以及参数, 给出一个总的用于解决任务的代码示例。返回结果格式为：
-    <function_list>
-        <function>
-            <package>.<module>.<function_name>
-            <package>.<module>.<function_name>(<param1>[, <param2>=<default>][, ...][, **kwargs])
-            <一句话描述函数的主要功能>。
-
-            <可选：补充说明/实现细节/依赖等>
-
-            Parameters
-            :
-            <param1> (<type>) – <param1 的说明>
-
-            <param2> (<type> (default: <default>)) – <param2 的说明>
-
-            <param3> (<type> (default: <default>)) – <param3 的说明>
-
-            ...（按需继续列出其他参数）
-
-            **kwargs – <对底层实现传递的其他关键字参数的说明；如无需说明可简写为“其他关键字参数”。>
-        </function>
-                        ...
-    </function_list>
+    查询知识库，给出一个用于解决任务的代码示例。返回结果格式为：
     <code_example>
-    [code_example]
+        [code_example]
     </code_example>
     """
     rep = agent.run(query)
@@ -59,22 +38,13 @@ def rag_agent(task, software=None):
 
 
 def select_tool(query):
-    API_KEY = os.environ.get("API_KEY", None)
-    BASE_URL = os.environ.get("BASE_URL", None)
-    MODEL = os.environ.get("MODEL", None)
-
-    client = OpenAI(api_key=API_KEY, base_url=BASE_URL)
-    client = instructor.from_openai(client)
-
-    response = client.chat.completions.create(
-        model=MODEL,
-        messages=[
-            {
-                "role": "system",
-                "content": "you are a bioinformatician, you are given a task and a list of tools, you need to select the most directly relevant tools to use to solve the task",
-            },
-            {"role": "user", "content": query},
-        ],
+    agent = Agent(
+        model=model,
         response_model=ToolList,
+        use_json_mode=True,
+        instructions="""
+        you are a bioinformatician, you are given a task and a list of tools, you need to select the most directly relevant tools to use to solve the task
+        """,
     )
-    return response.tools
+    rep = agent.run(query)
+    return rep.content

scmcp_shared/kb.py

@@ -3,9 +3,13 @@ from agno.embedder.openai import OpenAIEmbedder
 from agno.models.deepseek import DeepSeek
 from agno.vectordb.lancedb import LanceDb
 from agno.knowledge.agent import AgentKnowledge
-import importlib.resources
 import os
+import requests
+import zipfile
+from pathlib import Path
+import logging
 
+logger = logging.getLogger(__name__)
 
 embedder_id = os.getenv("EMBEDDER_MODEL")
 embedder_api_key = os.getenv("EMBEDDER_API_KEY")
@@ -15,10 +19,77 @@ model_api_key = os.getenv("API_KEY")
 model_base_url = os.getenv("BASE_URL")
 
 
-def load_kb(software=None):
+def download_vector_db(source="huggingface"):
+    """
+    下载向量数据库文件
+
+    Args:
+        source: 下载源 ("huggingface" 或 "github")
+    """
+
+    local_dir = Path(__file__).parent
+    local_dir.mkdir(exist_ok=True)
+
+    # 检查是否已存在
+    if (local_dir / "scmcp.lance").exists():
+        logger.info("Vector database already exists locally")
+        return str(local_dir)
+
+    logger.info(f"Downloading vector database from {source}...")
+
+    # 下载文件
+    if source == "huggingface":
+        url = "https://huggingface.co/datasets/huangshing/scmcp_vector_db/resolve/main/vector_db.zip"
+    else:
+        raise ValueError(f"Unsupported source: {source}")
+
+    logger.info(f"Downloading from: {url}")
+    response = requests.get(url, stream=True)
+    response.raise_for_status()
+
+    # 下载到目标目录
+    zip_path = local_dir / "vector_db.zip"
+    with open(zip_path, "wb") as f:
+        for chunk in response.iter_content(chunk_size=8192):
+            f.write(chunk)
+
+    # 解压文件
+    logger.info("Extracting downloaded archive...")
+    with zipfile.ZipFile(zip_path, "r") as zip_ref:
+        zip_ref.extractall(local_dir)
+
+    # 删除zip文件
+    zip_path.unlink()
+
+    logger.info(f"Vector database downloaded and extracted to: {local_dir}")
+    return str(local_dir)
+
+
+def load_kb(software=None, auto_download=True, download_source="huggingface"):
+    """
+    加载知识库
+
+    Args:
+        software: 软件名称
+        auto_download: 是否自动下载向量数据库
+        download_source: 下载源 ("huggingface" 或 "github")
+    """
+    # 获取向量数据库路径
+    vector_db_path = Path(__file__).parent / "vector_db"
+
+    # 如果不存在且允许自动下载，则下载
+    if not (vector_db_path / "scmcp.lance").exists():
+        if auto_download:
+            logger.info("Vector database not found, downloading...")
+            download_vector_db(download_source)
+        else:
+            raise FileNotFoundError(
+                "Vector database not found. Set auto_download=True to download automatically."
+            )
+
     vector_db = LanceDb(
         table_name=software,
-        uri=importlib.resources.path("scmcp_shared", "vector_db"),
+        uri=vector_db_path,
         embedder=OpenAIEmbedder(
             id=embedder_id,
             base_url=embedder_base_url,

scmcp_shared/server/__init__.py

@@ -1 +1,8 @@
 from __future__ import annotations
+
+from .auto import auto_mcp
+from .rag import rag_mcp
+from abcoder.server import nb_mcp
+from . import preset
+
+__all__ = ["auto_mcp", "rag_mcp", "nb_mcp", "preset"]

scmcp_shared/server/auto.py

@@ -15,17 +15,19 @@ def search_tool(
     """search the tools and get tool parameters that can be used to solve the  user's tasks or questions"""
     ctx = get_context()
     fastmcp = ctx.fastmcp
-    all_tools = fastmcp._tool_manager._all_tools
+    if hasattr(fastmcp._tool_manager, "_all_tools"):
+        all_tools = fastmcp._tool_manager._all_tools
+    else:
+        all_tools = fastmcp._tool_manager._tools
     auto_tools = fastmcp._tool_manager._tools
     fastmcp._tool_manager._tools = all_tools
     query = f"<task>{task}</task>\n"
     for name in all_tools:
         tool = all_tools[name]
         query += f"<Tool>\n<name>{name}</name>\n<description>{tool.description}</description>\n</Tool>\n"
-
     results = select_tool(query)
     tool_list = []
-    for tool in results:
+    for tool in results.tools:
         tool = tool.model_dump()
         tool["parameters"] = all_tools[tool["name"]].parameters
         tool_list.append(tool)

scmcp_shared/server/rag.py

@@ -0,0 +1,13 @@
+from fastmcp import FastMCP
+from ..agent import rag_agent
+from pydantic import Field
+
+rag_mcp = FastMCP("RAG-Server")
+
+
+@rag_mcp.tool(tags={"rag"})
+def retrieve_knowledge(
+    task: str = Field(description="The tasks or questions that needs to be solved"),
+):
+    """search guide or code example that can be used to solve the user's tasks or questions"""
+    return rag_agent(task, software="scmcp")

{scmcp_shared-0.5.0.dist-info → scmcp_shared-0.6.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.5.0
+Version: 0.6.2
 Summary: A shared function libray for scmcphub
 Project-URL: Homepage, http://scmcphub.org/
 Project-URL: Repository, https://github.com/scmcphub/scmcp-shared
@@ -38,12 +38,15 @@ License-File: LICENSE
 Keywords: AI,agent,bioinformatics,llm,mcp,model context protocol,scRNA-seq,single cell
 Requires-Python: >=3.10
 Requires-Dist: abcoder
+Requires-Dist: agno
 Requires-Dist: fastmcp>=2.7.0
 Requires-Dist: igraph
-Requires-Dist: instructor>=1.8.3
+Requires-Dist: lancedb
 Requires-Dist: leidenalg
 Requires-Dist: mcp>=1.8.0
 Requires-Dist: nest-asyncio
+Requires-Dist: openai
+Requires-Dist: requests
 Requires-Dist: scanpy
 Description-Content-Type: text/markdown
 

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