scmcp-shared 0.3.6__py3-none-any.whl → 0.3.7__py3-none-any.whl

scmcp_shared/server/util.py

@@ -4,8 +4,9 @@ from pathlib import Path
 import scanpy as sc
 from fastmcp import FastMCP , Context
 from fastmcp.exceptions import ToolError
+from fastmcp.tools.tool import Tool
 from ..schema.util import *
-from ..schema import AdataModel, AdataInfo
+from ..schema import AdataInfo
 from ..util import filter_args, forward_request, get_ads, generate_msg,add_op_log
 from .base import BaseMCP
 
@@ -24,7 +25,7 @@ class ScanpyUtilMCP(BaseMCP):
 
 
     def _tool_query_op_log(self):
-        def _query_op_log(request: QueryOpLogModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _query_op_log(request: QueryOpLogParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Query the adata operation log"""
             adata = get_ads().get_adata(adinfo=adinfo)
             op_dic = adata.uns["operation"]["op"]
@@ -33,10 +34,10 @@ class ScanpyUtilMCP(BaseMCP):
             for opid in opids:
                 op_list.append(op_dic[opid])
             return op_list
-        return _query_op_log
+        return Tool.from_function(_query_op_log, name="query_op_log")
 
     def _tool_mark_var(self):
-        def _mark_var(request: MarkVarModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _mark_var(request: MarkVarParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """
             Determine if each gene meets specific conditions and store results in adata.var as boolean values.
             For example: mitochondrion genes startswith MT-.
@@ -84,10 +85,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _mark_var
+        return Tool.from_function(_mark_var, name="mark_var")
 
     def _tool_list_var(self):
-        def _list_var(request: ListVarModel=ListVarModel(), adinfo: self.AdataInfo=self.AdataInfo()):
+        def _list_var(request: ListVarParams=ListVarParams(), adinfo: self.AdataInfo=self.AdataInfo()):
             """List key columns in adata.var. It should be called for checking when other tools need var key column names as input."""
             try:
                 result = forward_request("ul_list_var", request, adinfo)
@@ -104,10 +105,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _list_var
+        return Tool.from_function(_list_var, name="list_var")
 
     def _tool_list_obs(self):
-        def _list_obs(request: ListObsModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _list_obs(request: ListObsParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """List key columns in adata.obs. It should be called before other tools need obs key column names input."""
             try:
                 result = forward_request("ul_list_obs", request, adinfo)
@@ -124,10 +125,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _list_obs
+        return Tool.from_function(_list_obs, name="list_obs")
 
     def _tool_check_var(self):
-        def _check_var(request: VarNamesModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _check_var(request: VarNamesParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Check if genes/variables exist in adata.var_names. This tool should be called before gene expression visualizations or color by genes."""
             try:
                 result = forward_request("ul_check_var", request, adinfo)
@@ -149,10 +150,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _check_var
+        return Tool.from_function(_check_var, name="check_var")
 
     def _tool_merge_adata(self):
-        def _merge_adata(request: ConcatBaseModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _merge_adata(request: ConcatBaseParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Merge multiple adata objects."""
             try:
                 result = forward_request("ul_merge_adata", request, adinfo)
@@ -174,10 +175,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _merge_adata
+        return Tool.from_function(_merge_adata, name="merge_adata")
 
     def _tool_set_dpt_iroot(self):
-        def _set_dpt_iroot(request: DPTIROOTModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _set_dpt_iroot(request: DPTIROOTParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Set the iroot cell"""
             try:
                 result = forward_request("ul_set_dpt_iroot", request, adinfo)
@@ -205,10 +206,10 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _set_dpt_iroot
+        return Tool.from_function(_set_dpt_iroot, name="set_dpt_iroot")
 
     def _tool_add_layer(self):
-        def _add_layer(request: AddLayerModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _add_layer(request: AddLayerParams, adinfo: self.AdataInfo=self.AdataInfo()):
             """Add a layer to the AnnData object."""
             try:
                 result = forward_request("ul_add_layer", request, adinfo)
@@ -237,7 +238,7 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _add_layer
+        return Tool.from_function(_add_layer, name="add_layer")
 
     def _tool_check_samples(self):
         def _check_samples(request: None, adinfo: self.AdataInfo=self.AdataInfo()):
@@ -252,4 +253,4 @@ class ScanpyUtilMCP(BaseMCP):
                     raise ToolError(e.__context__)
                 else:
                     raise ToolError(e)
-        return _check_samples
+        return Tool.from_function(_check_samples, name="check_samples")

{scmcp_shared-0.3.6.dist-info → scmcp_shared-0.3.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.3.6
+Version: 0.3.7
 Summary: A shared function libray for scmcphub
 Project-URL: Homepage, http://scmcphub.org/
 Project-URL: Repository, https://github.com/scmcphub/scmcp-shared
@@ -37,7 +37,9 @@ License: BSD 3-Clause License
 License-File: LICENSE
 Keywords: AI,agent,bioinformatics,llm,mcp,model context protocol,scRNA-seq,single cell
 Requires-Python: >=3.10
-Requires-Dist: fastmcp>=2.3.4
+Requires-Dist: fastmcp>=2.7.0
+Requires-Dist: igraph
+Requires-Dist: leidenalg
 Requires-Dist: mcp>=1.8.0
 Requires-Dist: nest-asyncio
 Requires-Dist: scanpy

scmcp_shared-0.3.7.dist-info/RECORD

@@ -0,0 +1,21 @@
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+scmcp_shared/cli.py,sha256=KYHp5_VE2JVVT4Su57ELzQa1lI2P8Gw0b4ruBP_Dtxk,4396
+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/util.py,sha256=fMZxTNf9Bv_xDzrW7YK08q0tCoC3L7ofqPY0K2ykG8k,4824
+scmcp_shared/server/__init__.py,sha256=4KE2Y_gDenF0ZyTGicQW0fTgJfMIQYZfpRP4hQ4rFYs,416
+scmcp_shared/server/base.py,sha256=o6NSi39I6xe7p-00-7FMR3gYwRCsM8D2WQhwWvlJcrU,6400
+scmcp_shared/server/io.py,sha256=kGBbtd3ltj0ypd0kgMy1l2zT2AVf5yXCHAebQR-ZtUA,4033
+scmcp_shared/server/pl.py,sha256=GVu7GQKW67jz3ig43HLX0d2cjGDPJDXdxMSf6b72kAA,15558
+scmcp_shared/server/pp.py,sha256=_U2ZSLIo-u_z3psg8Sw2gJEAaxhp3gW_-YMq4q9kCe8,15984
+scmcp_shared/server/tl.py,sha256=LeKcR6F4PNRHZomlD3-igrF44YBQW6Kg7h75psGl9c0,19112
+scmcp_shared/server/util.py,sha256=b6gG1dfXe5GdhM4yUtpxBqx1gMRyQVu3dytmzJeD9zs,12590
+scmcp_shared-0.3.7.dist-info/METADATA,sha256=vK9jmNEbuZCt-DhGbLMyGhFd6_HXZpkxAy2a1XgvH58,2402
+scmcp_shared-0.3.7.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+scmcp_shared-0.3.7.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
+scmcp_shared-0.3.7.dist-info/RECORD,,

scmcp_shared-0.3.6.dist-info/RECORD

@@ -1,21 +0,0 @@
-scmcp_shared/__init__.py,sha256=uRdcgGfRb4TRwNLKx3spJv6bL90b8RrAvcbq2RJ2TFI,24
-scmcp_shared/cli.py,sha256=KYHp5_VE2JVVT4Su57ELzQa1lI2P8Gw0b4ruBP_Dtxk,4396
-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=hmKMr5A8YRtPmGD3pwN9RPA8Urhp1WEMzEaNt7SnD7k,4636
-scmcp_shared/schema/pl.py,sha256=rzE09wHMY3JR56HZc-QfIUUM0fGXRKd-7Dh3CrQrFB0,29547
-scmcp_shared/schema/pp.py,sha256=48F6oKf-I8IZuNQDfq_Lpp3fLLKA4PruqRje_ZrtTyw,21664
-scmcp_shared/schema/tl.py,sha256=DaZUce33OW67h-caK9BW4sD9zhlehmj3mCq1P-3vllM,34407
-scmcp_shared/schema/util.py,sha256=x_2GPsmliHabi9V5C6YEv_M8ZHJsinDZJ6ePWrLPmcI,4815
-scmcp_shared/server/__init__.py,sha256=4KE2Y_gDenF0ZyTGicQW0fTgJfMIQYZfpRP4hQ4rFYs,416
-scmcp_shared/server/base.py,sha256=kaOfi4yHLWr_AdBdpKzDrJiwRmbHF2jbsfI5g2qqgRA,6576
-scmcp_shared/server/io.py,sha256=tBi1D3ItOxuQmuq2fV9c9t9-J7JuaiPMcBB9UT-S-PM,3928
-scmcp_shared/server/pl.py,sha256=HdhjrZfEx-IzCkZ03IGCW-mjUItfNvKdSOFbJ2_-2XQ,14854
-scmcp_shared/server/pp.py,sha256=xWwW5Y5h-XdMYmSZjvACnoY7-4SfjharwI1GB6FcDPQ,15383
-scmcp_shared/server/tl.py,sha256=qmWuSNplJtoa_92ivzAeCeyclGq2sW4Ao71_MHyk3es,18384
-scmcp_shared/server/util.py,sha256=BGYbkbRKABlCgLAstqD1LutJwfiES0GfIOqMSpLw4FI,12205
-scmcp_shared-0.3.6.dist-info/METADATA,sha256=byQeLeLTMtp_77wrbPORvmY4KLVKSRWxpDJW_Yo18PA,2355
-scmcp_shared-0.3.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-scmcp_shared-0.3.6.dist-info/licenses/LICENSE,sha256=YNr1hpea195yq-wGtB8j-2dGtt7A5G00WENmxa7JGco,1495
-scmcp_shared-0.3.6.dist-info/RECORD,,