scmcp-shared 0.3.7__tar.gz → 0.4.0__tar.gz

{scmcp_shared-0.3.7 → scmcp_shared-0.4.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.3.7
+Version: 0.4.0
 Summary: A shared function libray for scmcphub
 Project-URL: Homepage, http://scmcphub.org/
 Project-URL: Repository, https://github.com/scmcphub/scmcp-shared
@@ -39,6 +39,7 @@ Keywords: AI,agent,bioinformatics,llm,mcp,model context protocol,scRNA-seq,singl
 Requires-Python: >=3.10
 Requires-Dist: fastmcp>=2.7.0
 Requires-Dist: igraph
+Requires-Dist: instructor>=1.8.3
 Requires-Dist: leidenalg
 Requires-Dist: mcp>=1.8.0
 Requires-Dist: nest-asyncio

{scmcp_shared-0.3.7 → scmcp_shared-0.4.0}/pyproject.toml

@@ -27,6 +27,7 @@ dependencies = [
     "mcp>=1.8.0",
     "fastmcp>=2.7.0",
     "nest_asyncio",
+    "instructor>=1.8.3",
 ]
 
 [build-system]
@@ -51,4 +52,4 @@ Documentation = "https://docs.scmcphub.org/"
 
 [tool.pytest.ini_options]
 asyncio_mode = "strict"
-asyncio_default_fixture_loop_scope = "function"
+asyncio_default_fixture_loop_scope = "function"

scmcp_shared-0.4.0/src/scmcp_shared/__init__.py

@@ -0,0 +1,3 @@
+
+__version__ = "0.4.0"
+

scmcp_shared-0.4.0/src/scmcp_shared/agent.py

@@ -0,0 +1,30 @@
+import instructor
+from openai import OpenAI
+from scmcp_shared.schema.tool import ToolList
+import os
+
+
+
+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": f"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
+            },  
+        ],
+        response_model=ToolList,
+    )
+    return response.tools

{scmcp_shared-0.3.7 → scmcp_shared-0.4.0}/src/scmcp_shared/cli.py

@@ -35,6 +35,7 @@ class MCPCLI:
         parser.add_argument('--host', default='127.0.0.1', help='transport host')
         parser.add_argument('-f', '--forward', help='forward request to another server')
         parser.add_argument('-wd', '--working-dir', default=".", help='working directory')
+        parser.add_argument('--tool-mode', choices=["auto", "normal"], default="normal", help='tool selection mode')
         parser.add_argument('--log-file', help='log file path, use stdout if None')
     
     def add_command(self, name: str, help_text: str, handler: Callable) -> argparse.ArgumentParser:
@@ -78,6 +79,15 @@ class MCPCLI:
             modules = None
         if self.manager is not None:
             self.mcp = self.manager(self.name, include_modules=modules).mcp
+            all_tools = self.mcp._tool_manager._tools
+            auto_tools = {tool: all_tools[tool] for tool in all_tools if all_tools[tool].name in ["search_tool", "run_tool"]}
+            if args.tool_mode == "auto":
+                all_tools = self.mcp._tool_manager._tools
+                self.mcp._tool_manager._all_tools = all_tools
+                self.mcp._tool_manager._tools = auto_tools
+            else:
+                for name in auto_tools:
+                    self.mcp._tool_manager.remove_tool(name)
         elif self.mcp is not None:
             pass
         else:

scmcp_shared-0.4.0/src/scmcp_shared/schema/tool.py

@@ -0,0 +1,11 @@
+from pydantic import BaseModel, Field
+from typing import List
+
+
+class Tool(BaseModel):
+    name: str = Field(description="The name of the tool")
+    description: str = Field(description="The description of the tool")
+
+
+class ToolList(BaseModel):
+    tools: List[Tool]

scmcp_shared-0.4.0/src/scmcp_shared/server/auto.py

@@ -0,0 +1,52 @@
+from fastmcp import FastMCP
+from fastmcp.server.dependencies import get_context
+from ..agent import select_tool
+from pydantic import Field
+
+auto_mcp = FastMCP("SmartMCP-select-Server")
+
+
+@auto_mcp.tool()
+def search_tool(
+    task: str= Field(description="The tasks or questions that needs to be solved using available tools")
+):
+    """search the tools 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
+    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:
+        tool = tool.model_dump()
+        tool["parameters"] = all_tools[tool["name"]].parameters
+        tool_list.append(tool)
+    fastmcp._tool_manager._tools = auto_tools
+    return tool_list
+
+
+@auto_mcp.tool()
+async def run_tool(
+    name: str= Field(description="The name of the tool to run"),  
+    parameter: dict = Field(description="The parameters to pass to the tool")
+):
+    """run the tool with the given name and parameters. Only start call the tool when last tool is finished."""
+    ctx = get_context()
+    fastmcp = ctx.fastmcp
+    all_tools = fastmcp._tool_manager._all_tools
+    auto_tools = fastmcp._tool_manager._tools
+    fastmcp._tool_manager._tools =  all_tools
+
+    try:
+        result = await fastmcp._tool_manager.call_tool(name, parameter)
+    except Exception as e:
+        fastmcp._tool_manager._tools = auto_tools
+        result = {"error": str(e)}
+
+    return result

{scmcp_shared-0.3.7 → scmcp_shared-0.4.0}/src/scmcp_shared/server/base.py

@@ -6,7 +6,7 @@ from collections.abc import AsyncIterator
 from contextlib import asynccontextmanager
 import asyncio
 from typing import Optional, List, Any, Iterable
-
+from .auto import auto_mcp
 
 class BaseMCP:
     """Base class for all Scanpy MCP classes."""

{scmcp_shared-0.3.7 → scmcp_shared-0.4.0}/src/scmcp_shared/server/pp.py

@@ -120,12 +120,16 @@ class ScanpyPreprocessingMCP(BaseMCP):
                 func_kwargs = filter_args(request, sc.pp.calculate_qc_metrics)
                 ads = get_ads()
                 adata = ads.get_adata(adinfo=adinfo)
+                if request.qc_vars:
+                    for var in request.qc_vars:
+                        if var not in adata.var.columns:
+                            return f"Cound find {var} in adata.var, consider to use mark_var tool to mark the variable"
                 func_kwargs["inplace"] = True
                 try:
                     sc.pp.calculate_qc_metrics(adata, **func_kwargs)
                     add_op_log(adata, sc.pp.calculate_qc_metrics, func_kwargs, adinfo)
                 except KeyError as e:
-                    raise KeyError(f"Cound find {e} in adata.var")
+                    raise KeyError(f"Cound find {e} in adata.var, consider to use mark_var tool to mark the variable")
                 return [generate_msg(adinfo, adata, ads)]
             except ToolError as e:
                 raise ToolError(e)

scmcp_shared-0.3.7/src/scmcp_shared/__init__.py

@@ -1,3 +0,0 @@
-
-__version__ = "0.3.7"
-