scmcp-shared 0.4.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

scmcp_shared/server/base.py

@@ -1,148 +0,0 @@
-import inspect
-from fastmcp import FastMCP
-from ..schema import AdataInfo
-from ..util import filter_tools
-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."""
-    
-    def __init__(self, name: str, include_tools: list = None, exclude_tools: list = None, AdataInfo = AdataInfo):
-        """
-        Initialize BaseMCP with optional tool filtering.
-        
-        Args:
-            name (str): Name of the MCP server
-            include_tools (list, optional): List of tool names to include. If None, all tools are included.
-            exclude_tools (list, optional): List of tool names to exclude. If None, no tools are excluded.
-            AdataInfo: The AdataInfo class to use for type annotations.
-        """
-        self.mcp = FastMCP(name)
-        self.include_tools = include_tools
-        self.exclude_tools = exclude_tools
-        self.AdataInfo = AdataInfo
-        self._register_tools()
-
-    def _register_tools(self):
-        """Register all tool methods with the FastMCP instance based on include/exclude filters"""
-        # Get all methods of the class
-        methods = inspect.getmembers(self, predicate=inspect.ismethod)
-        
-        # Filter methods that start with _tool_
-        tool_methods = [tl_method() for name, tl_method in methods if name.startswith('_tool_')]
-        
-        # Filter tools based on include/exclude lists
-        if self.include_tools is not None:
-            tool_methods = [tl for tl in tool_methods if tl.name in self.include_tools]
-        
-        if self.exclude_tools is not None:
-            tool_methods = [tl for tl in tool_methods if tl.name not in self.exclude_tools]
-
-        # Register filtered tools
-        for tool in tool_methods:
-            # Get the function returned by the tool method
-            if tool is not None:
-                self.mcp.add_tool(tool)
-
-
-class AdataState:
-    def __init__(self, add_adtypes=None):
-        self.adata_dic = {"exp": {}, "activity": {}, "cnv": {}, "splicing": {}}
-        if isinstance(add_adtypes, str):
-            self.adata_dic[add_adtypes] = {}
-        elif isinstance(add_adtypes, Iterable):
-            self.adata_dic.update({adtype: {} for adtype in add_adtypes})
-        self.active_id = None
-        self.metadatWa = {}
-        self.cr_kernel = {}
-        self.cr_estimator = {}
-        
-    def get_adata(self, sampleid=None, adtype="exp", adinfo=None):
-        if adinfo is not None:
-            kwargs = adinfo.model_dump()
-            sampleid = kwargs.get("sampleid", None)
-            adtype = kwargs.get("adtype", "exp")
-        try:
-            if self.active_id is None:
-                return None
-            sampleid = sampleid or self.active_id
-            return self.adata_dic[adtype][sampleid]
-        except KeyError as e:
-            raise KeyError(f"Key {e} not found in adata_dic[{adtype}].Please check the sampleid or adtype.")
-        except Exception as e:
-            raise Exception(f"fuck {e} {type(e)}")
-    
-    def set_adata(self, adata, sampleid=None, sdtype="exp", adinfo=None):
-        if adinfo is not None:
-            kwargs = adinfo.model_dump()
-            sampleid = kwargs.get("sampleid", None)
-            sdtype = kwargs.get("adtype", "exp")
-        sampleid = sampleid or self.active_id
-        if sdtype not in self.adata_dic:
-            self.adata_dic[sdtype] = {}
-        self.adata_dic[sdtype][sampleid] = adata
-
-
-class BaseMCPManager:
-    """Base class for MCP module management."""
-    
-    def __init__(self, 
-        name: str, 
-        include_modules: Optional[List[str]] = None, 
-        exclude_modules: Optional[List[str]] = None,
-        include_tools: Optional[List[str]] = None,
-        exclude_tools: Optional[List[str]] = None,
-    ):
-        """
-        Initialize BaseMCPManager with optional module filtering.
-        
-        Args:
-            name (str): Name of the MCP server
-            include_modules (List[str], optional): List of module names to include. If None, all modules are included.
-            exclude_modules (List[str], optional): List of module names to exclude. If None, no modules are excluded.
-            include_tools (List[str], optional): List of tool names to include. If None, all tools are included.
-            exclude_tools (List[str], optional): List of tool names to exclude. If None, no tools are excluded.
-        """
-        self.ads = AdataState()
-        self.mcp = FastMCP(name, lifespan=self.adata_lifespan)
-        self.include_modules = include_modules
-        self.exclude_modules = exclude_modules
-        self.include_tools = include_tools
-        self.exclude_tools = exclude_tools
-        self.available_modules = {}
-        self._init_modules()
-        self._register_modules()
-
-    def _init_modules(self):
-        """Initialize available modules. To be implemented by subclasses."""
-        raise NotImplementedError("Subclasses must implement _init_modules")
-
-    def _register_modules(self):
-        """Register modules based on include/exclude filters."""
-        # Filter modules based on include/exclude lists
-        if self.include_modules is not None:
-            self.available_modules = {k: v for k, v in self.available_modules.items() if k in self.include_modules}
-        
-        if self.exclude_modules is not None:
-            self.available_modules = {k: v for k, v in self.available_modules.items() if k not in self.exclude_modules}
-
-        # Register each module
-        for module_name, mcpi in self.available_modules.items():
-            if isinstance(mcpi, FastMCP):
-                if self.include_tools is not None and module_name in self.include_tools:
-                    mcpi = filter_tools(mcpi, include_tools= self.include_tools[module_name])
-                if self.exclude_tools is not None and module_name in self.exclude_tools:
-                    mcpi = filter_tools(mcpi, exclude_tools=self.exclude_tools[module_name])
-
-                asyncio.run(self.mcp.import_server(module_name, mcpi))
-            else:
-                asyncio.run(self.mcp.import_server(module_name, mcpi().mcp))
-
-    @asynccontextmanager
-    async def adata_lifespan(self, server: FastMCP) -> AsyncIterator[Any]:
-        """Context manager for AdataState lifecycle."""
-        yield self.ads

scmcp_shared-0.4.0.dist-info/RECORD

@@ -1,24 +0,0 @@
-scmcp_shared/__init__.py,sha256=5DHi9fyCf-CfX64oAsNqmkR27WRUetIg-NfPin0QKBw,24
-scmcp_shared/agent.py,sha256=tWGAyOwdg3oTfYFquGPompUZMHSWqW3VQvEymywaE0o,854
-scmcp_shared/cli.py,sha256=8Am2zdn1z_gle6Jz-JQkvK-6_mOB6BFhfK05A0pNpkc,5032
-scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
-scmcp_shared/util.py,sha256=8_c6WPNpYNoxKpq6tQCC4elCQkWyk3rH-hTe1sqff4A,9535
-scmcp_shared/schema/__init__.py,sha256=Kwkc7kPLjExOlxt1sWEy_5qa96MvOS8sNCMlZa6yRg8,737
-scmcp_shared/schema/io.py,sha256=-wgL2NQBXwAcojid8rF2Y46GsKL7H6JiheKE6frMotw,4638
-scmcp_shared/schema/pl.py,sha256=7AFXgqb2GAlmeXS6m3IdJgThLz6-FTDBmrJqoAi8j98,29612
-scmcp_shared/schema/pp.py,sha256=WtaugFLP9vfusBZQCXGAYPmYu-5yWHC2wJTSZutS1XM,21674
-scmcp_shared/schema/tl.py,sha256=FEZpr218eaQ8rUp5EJzbjyw1ejqCX4Shsf9CumaKs8A,34425
-scmcp_shared/schema/tool.py,sha256=U-VFrovAEr2FklS8cSJPimfhTSTHmskmLfCO7Ee0s2o,267
-scmcp_shared/schema/util.py,sha256=fMZxTNf9Bv_xDzrW7YK08q0tCoC3L7ofqPY0K2ykG8k,4824
-scmcp_shared/server/__init__.py,sha256=4KE2Y_gDenF0ZyTGicQW0fTgJfMIQYZfpRP4hQ4rFYs,416
-scmcp_shared/server/auto.py,sha256=32SC5nC0N7JuPsDSMFRvojaPmUbpybwY1aCOrQMzaL4,1781
-scmcp_shared/server/base.py,sha256=I90L_DNdCv--VOIHDRjdVehq-3iBm9mV0Sc9OU7GAXQ,6426
-scmcp_shared/server/io.py,sha256=kGBbtd3ltj0ypd0kgMy1l2zT2AVf5yXCHAebQR-ZtUA,4033
-scmcp_shared/server/pl.py,sha256=GVu7GQKW67jz3ig43HLX0d2cjGDPJDXdxMSf6b72kAA,15558
-scmcp_shared/server/pp.py,sha256=UCzogVULgSs8JTR8PiybroGlrm2QvNRrbeAYj7ujr3E,16297
-scmcp_shared/server/tl.py,sha256=LeKcR6F4PNRHZomlD3-igrF44YBQW6Kg7h75psGl9c0,19112
-scmcp_shared/server/util.py,sha256=b6gG1dfXe5GdhM4yUtpxBqx1gMRyQVu3dytmzJeD9zs,12590
-scmcp_shared-0.4.0.dist-info/METADATA,sha256=CKca84Vmtqc5h06oOH6lxqYVDCeVNJpGypX03Y-O1iI,2435
-scmcp_shared-0.4.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scmcp_shared-0.4.0.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
-scmcp_shared-0.4.0.dist-info/RECORD,,