scmcp-shared 0.3.0__py3-none-any.whl → 0.3.6__py3-none-any.whl

scmcp_shared/__init__.py

@@ -1,3 +1,3 @@
 
-__version__ = "0.3.0"
+__version__ = "0.3.6"
 

scmcp_shared/cli.py

@@ -1,77 +1,89 @@
-import typer
-from typing import Optional, Union, Type
+import argparse
+from typing import Optional, Union, Type, Dict, Callable
 from enum import Enum
-from .util import add_figure_route, set_env,setup_mcp
-
-
-class TransportEnum(str, Enum):
-    STDIO = "stdio"
-    SSE = "sse"
-    SHTTP = "shttp"
-
-    @property
-    def transport_value(self) -> str:
-        """Get the actual transport value to use."""
-        if self == TransportEnum.SHTTP:
-            return "streamable-http"
-        return self.value
-
-
-class ModuleEnum(str, Enum):
-    """Base class for module types."""
-    ALL = "all"
-
+from .util import add_figure_route, set_env
+import os
 
 
 class MCPCLI:
     """Base class for CLI applications with support for dynamic modules and parameters."""
     
-    def __init__(self, name: str, help_text: str, manager=None, modules=ModuleEnum):
+    def __init__(self, name: str, help_text: str, mcp=None, manager=None):
         self.name = name
-        self.modules = modules
+        self.mcp = mcp
         self.manager = manager
-        self.app = typer.Typer(
-            name=name,
-            help=help_text,
-            add_completion=False,
-            no_args_is_help=True,
+        self.parser = argparse.ArgumentParser(
+            description=help_text,
+            prog=name
         )
+        self.subcommands: Dict[str, tuple[argparse.ArgumentParser, Callable]] = {}
         self._setup_commands()
     
     def _setup_commands(self):
         """Setup the main commands for the CLI."""
-        self.app.command(name="run", help="Start the server with the specified configuration")(self.run_command())
-        self.app.callback()(self._callback)
-
-    def run_command(self):
-        def _run_command(
-            log_file: Optional[str] = typer.Option(None, "--log-file", help="log file path, use stdout if None"),
-            transport: TransportEnum = typer.Option(TransportEnum.STDIO, "-t", "--transport", help="specify transport type", 
-                                        case_sensitive=False),
-            port: int = typer.Option(8000, "-p", "--port", help="transport port"),
-            host: str = typer.Option("127.0.0.1", "--host", help="transport host"),
-            forward: str = typer.Option(None, "-f", "--forward", help="forward request to another server"),
-            module: list[self.modules] = typer.Option(
-                [self.modules.ALL], 
-                "-m", 
-                "--module", 
-                help="specify module to run"
-            ),
-        ):
-            """Start the server with the specified configuration."""
-            if "all" in module:
-                modules = None
-            elif isinstance(module, list) and bool(module):
-                modules = [m.value for m in module]
-            self.mcp =  self.manager(self.name, include_modules=modules).mcp
-
-            self.run_mcp(log_file, forward, transport, host, port)
-        return _run_command
+        subparsers = self.parser.add_subparsers(dest='command', help='Available commands')        
+        run_parser = subparsers.add_parser('run', help='Start the server with the specified configuration')
+        self._setup_run_command(run_parser)
+        self.subcommands['run'] = (run_parser, self._run_command)
         
-
-    def _callback(self):
-        """Liana MCP CLI root command."""
-        pass
+    def _setup_run_command(self, parser: argparse.ArgumentParser):
+        """Setup run command arguments."""
+        parser.add_argument('-t', '--transport', default="stdio",
+                          choices=["stdio", "shttp", "sse"],
+                          help='specify transport type')
+        parser.add_argument('-p', '--port', type=int, default=8000, help='transport port')
+        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('--log-file', help='log file path, use stdout if None')
+    
+    def add_command(self, name: str, help_text: str, handler: Callable) -> argparse.ArgumentParser:
+        """add new subcommand
+        
+        Args:
+            name: subcommand name
+            help_text: help text
+            handler: handler function
+            
+        Returns:
+            ArgumentParser: parser for the subcommand
+        """
+        subparsers = self.parser._subparsers._group_actions[0]
+        parser = subparsers.add_parser(name, help=help_text)
+        self.subcommands[name] = (parser, handler)
+        return parser
+    
+    def get_command_parser(self, name: str) -> Optional[argparse.ArgumentParser]:
+        """get the parser for the subcommand
+        
+        Args:
+            name: subcommand name
+            
+        Returns:
+            ArgumentParser: parser for the subcommand, return None if the subcommand does not exist
+        """
+        if name in self.subcommands:
+            return self.subcommands[name][0]
+        return None
+    
+    def _run_command(self, args):
+        """Start the server with the specified configuration."""
+        os.chdir(args.working_dir)
+        if hasattr(args, 'module'):
+            if "all" in args.module:
+                modules = None
+            elif isinstance(args.module, list) and bool(args.module):
+                modules = args.module
+        else:
+            modules = None
+        if self.manager is not None:
+            self.mcp = self.manager(self.name, include_modules=modules).mcp
+        elif self.mcp is not None:
+            pass
+        else:
+            raise ValueError("No manager or mcp provided")
+        transport = args.transport
+        self.run_mcp(args.log_file, args.forward, transport, args.host, args.port)
 
     def run_mcp(self, log_file, forward, transport, host, port):
         set_env(log_file, forward, transport, host, port)
@@ -80,8 +92,8 @@ class MCPCLI:
         if transport == "stdio":
             self.mcp.run()
         elif transport in ["sse", "shttp"]:
+            transport = "streamable-http" if transport == "shttp" else transport
             add_figure_route(self.mcp)
-            transport = transport.transport_value
             self.mcp.run(
                 transport=transport,
                 host=host, 
@@ -89,8 +101,11 @@ class MCPCLI:
                 log_level="info"
             )
  
-    def run_cli(self, mcp=None, module_dic=None):
+    def run(self):
         """Run the CLI application."""
-        self.mcp = mcp
-        self.module_dic = module_dic
-        self.app()
+        args = self.parser.parse_args()
+        if args.command in self.subcommands:
+            handler = self.subcommands[args.command][1]
+            handler(args)
+        else:
+            self.parser.print_help()

scmcp_shared/schema/io.py

@@ -30,9 +30,9 @@ class ReadModel(BaseModel):
         default=False,
         description="Assume the first column stores row names. This is only necessary if these are not strings: strings in the first column are automatically assumed to be row names."
     )
-    first_column_obs: bool = Field(
-        default=True,
-        description="If True, assume the first column stores observations (cell or barcode) names when provide text file. If False, the data will be transposed."
+    transpose: bool = Field(
+        default=False,
+        description="If True, the data will be transposed."
     )
     backup_url: str = Field(
         default=None,

scmcp_shared/schema/tl.py

@@ -938,6 +938,11 @@ class PCAModel(BaseModel):
         gt=0
     )
     
+    key_added: str = Field(
+        default="X_pca",
+        description="PCA embedding stored key in adata.obsm."
+    )
+    
     @field_validator('n_comps', 'chunk_size')
     def validate_positive_integers(cls, v: Optional[int]) -> Optional[int]:
         """Validate positive integers"""

scmcp_shared/server/io.py

@@ -33,7 +33,7 @@ class ScanpyIOMCP(BaseMCP):
                 elif file.is_file():
                     func_kwargs = filter_args(request, sc.read)
                     adata = sc.read(**func_kwargs)
-                    if not kwargs.get("first_column_obs", True):
+                    if not kwargs.get("transpose", True):
                         adata = adata.T
                 else:
                     raise FileNotFoundError(f"{kwargs['filename']} does not exist")
@@ -47,8 +47,18 @@ class ScanpyIOMCP(BaseMCP):
                 adata.layers["counts"] = adata.X
                 adata.var_names_make_unique()
                 adata.obs_names_make_unique()
+                adata.obs["scmcp_sampleid"] = adinfo.sampleid or ads.active_id
                 ads.set_adata(adata, adinfo=adinfo)
-                return generate_msg(adinfo, adata, ads)
+                return [
+                    {
+                        "sampleid": adinfo.sampleid or ads.active_id, 
+                        "adtype": adinfo.adtype, 
+                        "adata": adata,
+                        "adata.obs_names[:10]": adata.obs_names[:10],
+                        "adata.var_names[:10]": adata.var_names[:10],
+                        "notice": "check obs_names and var_names. transpose the data if needed"
+                    }
+                    ]
             except ToolError as e:
                 raise ToolError(e)
             except Exception as e:

scmcp_shared/server/pp.py

@@ -86,12 +86,12 @@ class ScanpyPreprocessingMCP(BaseMCP):
                     if request.var_max is not None:
                         mask = mask & (adata.var[request.var_key] <= request.var_max)        
                     adata = adata[:, mask]
-                    if request.highly_variable is not None:
-                        adata = adata[:, adata.var.highly_variable]
+                    if request.highly_variable:
+                        adata = adata[:, mask & adata.var.highly_variable]
                     add_op_log(adata, "subset_genes", 
                         {
-                        "var_key": request.var_key, "var_value": request.var_value, 
-                        "var_min": request.var_min, "var_max": request.var_max, "hpv":  request.highly_variable
+                        "var_key": request.var_key,  "var_min": request.var_min, "var_max": request.var_max, 
+                        "hpv":  request.highly_variable
                         }, adinfo
                     )
                 ads.set_adata(adata, adinfo=adinfo)
@@ -133,7 +133,7 @@ class ScanpyPreprocessingMCP(BaseMCP):
         return _calculate_qc_metrics
 
     def _tool_log1p(self):
-        def _log1p(request: Log1PModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _log1p(request: Log1PModel=Log1PModel(), adinfo: self.AdataInfo=self.AdataInfo()):
             """Logarithmize the data matrix"""
             try:
                 result = forward_request("pp_log1p", request, adinfo)

scmcp_shared/server/tl.py

@@ -23,7 +23,7 @@ class ScanpyToolsMCP(BaseMCP):
         super().__init__("ScanpyMCP-TL-Server", include_tools, exclude_tools, AdataInfo)
 
     def _tool_tsne(self):
-        def _tsne(request: TSNEModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _tsne(request: TSNEModel=TSNEModel(), adinfo: self.AdataInfo=self.AdataInfo()):
             """t-distributed stochastic neighborhood embedding (t-SNE) for visualization"""
             try:
                 result = forward_request("tl_tsne", request, adinfo)
@@ -45,7 +45,7 @@ class ScanpyToolsMCP(BaseMCP):
         return _tsne
 
     def _tool_umap(self):
-        def _umap(request: UMAPModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _umap(request: UMAPModel=UMAPModel(), adinfo: self.AdataInfo=self.AdataInfo()):
             """Uniform Manifold Approximation and Projection (UMAP) for visualization"""
             try:
                 result = forward_request("tl_umap", request, adinfo)
@@ -134,7 +134,7 @@ class ScanpyToolsMCP(BaseMCP):
         return _embedding_density
 
     def _tool_leiden(self):
-        def _leiden(request: LeidenModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _leiden(request: LeidenModel=LeidenModel(), adinfo: self.AdataInfo=self.AdataInfo()):
             """Leiden clustering algorithm for community detection"""
             try:
                 result = forward_request("tl_leiden", request, adinfo)
@@ -156,7 +156,7 @@ class ScanpyToolsMCP(BaseMCP):
         return _leiden
 
     def _tool_louvain(self):
-        def _louvain(request: LouvainModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _louvain(request: LouvainModel=LouvainModel(), adinfo: self.AdataInfo=self.AdataInfo()):
             """Louvain clustering algorithm for community detection"""
             try:
                 result = forward_request("tl_louvain", request, adinfo)
@@ -376,7 +376,7 @@ class ScanpyToolsMCP(BaseMCP):
         return _score_genes_cell_cycle
 
     def _tool_pca(self):
-        def _pca(request: PCAModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _pca(request: PCAModel=PCAModel(), adinfo: self.AdataInfo=self.AdataInfo()):
             """Compute PCA (Principal Component Analysis)."""
             try:
                 result = forward_request("tl_pca", request, adinfo)

scmcp_shared/server/util.py

@@ -87,7 +87,7 @@ class ScanpyUtilMCP(BaseMCP):
         return _mark_var
 
     def _tool_list_var(self):
-        def _list_var(request: ListVarModel, adinfo: self.AdataInfo=self.AdataInfo()):
+        def _list_var(request: ListVarModel=ListVarModel(), 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)
@@ -95,7 +95,7 @@ class ScanpyUtilMCP(BaseMCP):
                     return result
                 adata = get_ads().get_adata(adinfo=adinfo)
                 columns = list(adata.var.columns)
-                add_op_log(adata, list_var, {}, adinfo)
+                add_op_log(adata, "list_var", {}, adinfo)
                 return columns
             except ToolError as e:
                 raise ToolError(e)
@@ -115,7 +115,7 @@ class ScanpyUtilMCP(BaseMCP):
                     return result    
                 adata = get_ads().get_adata(adinfo=adinfo)
                 columns = list(adata.obs.columns)
-                add_op_log(adata, list_obs, {}, adinfo)
+                add_op_log(adata, "list_obs", {}, adinfo)
                 return columns
             except ToolError as e:
                 raise ToolError(e)
@@ -135,8 +135,12 @@ class ScanpyUtilMCP(BaseMCP):
                     return result     
                 adata = get_ads().get_adata(adinfo=adinfo)
                 var_names = request.var_names
-                result = {v: v in adata.var_names for v in var_names}
-                add_op_log(adata, check_var, {"var_names": var_names}, adinfo)
+                if adata.raw is not None:
+                    all_var_names = adata.raw.to_adata().var_names
+                else:
+                    all_var_names = adata.var_names
+                result = {v: v in all_var_names for v in var_names}
+                add_op_log(adata, "check_var", {"var_names": var_names}, adinfo)
                 return result
             except ToolError as e:
                 raise ToolError(e)
@@ -157,7 +161,7 @@ class ScanpyUtilMCP(BaseMCP):
                 ads = get_ads()
                 adata = ads.get_adata(adinfo=adinfo)
                 kwargs = {k: v for k, v in request.model_dump().items() if v is not None}
-                merged_adata = adata.concat(list(ads.adata_dic[dtype].values()), **kwargs)
+                merged_adata = adata.concat(ads.adata_dic, **kwargs)
                 ads.adata_dic[dtype] = {}
                 ads.active_id = "merged_adata"
                 add_op_log(merged_adata, ad.concat, kwargs, adinfo)

scmcp_shared/util.py

@@ -104,6 +104,10 @@ def savefig(axes, func=None, **kwargs):
     args = []
     for k,v in kwargs.items():
         if isinstance(v, (tuple, list, set)):
+            v = v[:3]  ## show first 3 elements
+            args.append(f"{k}-{'-'.join([str(i) for i in v])}")
+        elif isinstance(v, dict):
+            v = list(v.keys())[:3]  ## show first 3 elements
             args.append(f"{k}-{'-'.join([str(i) for i in v])}")
         else:
             args.append(f"{k}-{v}")
@@ -209,7 +213,7 @@ def get_ads():
 
 
 def generate_msg(adinfo, adata, ads):
-    return {"sampleid": adinfo.sampleid or ads.active_id, "dtype": adinfo.adtype, "adata": adata}
+    return {"sampleid": adinfo.sampleid or ads.active_id, "adtype": adinfo.adtype, "adata": adata}
 
 
 def sc_like_plot(plot_func, adata, request, adinfo, **kwargs):
@@ -260,17 +264,19 @@ def setup_mcp(mcp, sub_mcp_dic, modules=None):
     return mcp
 
 def _update_args(mcp, func, args_dic : dict):
-    defs = mcp._tool_manager._tools[func].parameters['$defs']
-    model_names = list(defs.keys())
-    args_model = model_names[0] if  model_names[0] != "AdataModel" else model_names[1]
     for args, property_dic in args_dic.items():
         for pk, v in property_dic.items():
-            for model in model_names:
-                if args in mcp._tool_manager._tools[func].parameters['$defs'][model]["properties"]:
-                    mcp._tool_manager._tools[func].parameters['$defs'][model]["properties"][args][pk] = v
+            mcp._tool_manager._tools[func].parameters["properties"]["request"].setdefault(pk, {})
+            mcp._tool_manager._tools[func].parameters["properties"]["request"][pk][args] = v
 
 
 def update_mcp_args(mcp, tool_args : dict):
     tools = mcp._tool_manager._tools.keys()
     for tool in tool_args: 
         _update_args(mcp, tool, tool_args[tool])
+
+
+def check_adata(adata, adinfo, ads):
+    sampleid = adinfo.sampleid or ads.active_id
+    if sampleid != adata.uns["scmcp_sampleid"]:
+        raise ValueError(f"sampleid mismatch: {sampleid} != {adata.uns['scmcp_sampleid']}")

{scmcp_shared-0.3.0.dist-info → scmcp_shared-0.3.6.dist-info}/METADATA

@@ -1,7 +1,10 @@
 Metadata-Version: 2.4
 Name: scmcp_shared
-Version: 0.3.0
+Version: 0.3.6
 Summary: A shared function libray for scmcphub
+Project-URL: Homepage, http://scmcphub.org/
+Project-URL: Repository, https://github.com/scmcphub/scmcp-shared
+Project-URL: Documentation, https://docs.scmcphub.org/
 Author-email: shuang <hsh-me@outlook.com>
 License: BSD 3-Clause License
         
@@ -32,10 +35,11 @@ License: BSD 3-Clause License
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 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: mcp>=1.8.0
-Requires-Dist: pydantic
+Requires-Dist: nest-asyncio
 Requires-Dist: scanpy
 Description-Content-Type: text/markdown
 

scmcp_shared-0.3.6.dist-info/RECORD

@@ -0,0 +1,21 @@
+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,,

scmcp_shared-0.3.0.dist-info/RECORD

@@ -1,21 +0,0 @@
-scmcp_shared/__init__.py,sha256=nSn3YFzkE-BAmUSmif33CxdohNxkgmLE9cYFNbjEu_E,24
-scmcp_shared/cli.py,sha256=NU31Vv-xev8yGtl1KHZhVswJNbK18x2AVzhhH9MR03M,3325
-scmcp_shared/logging_config.py,sha256=eCuLuyxMmbj8A1E0VqYWoKA5JPTSbo6cmjS4LOyd0RQ,872
-scmcp_shared/util.py,sha256=vxmR6_iOBa5jaBNBWl3QBysJ14kXRrqrENDRl3_TChQ,9339
-scmcp_shared/schema/__init__.py,sha256=Kwkc7kPLjExOlxt1sWEy_5qa96MvOS8sNCMlZa6yRg8,737
-scmcp_shared/schema/io.py,sha256=ZKJpKkKazDE3_ZX3GtMIT08kSaiNmy0qVaxivhN7Dx4,4744
-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=0HlZ_WQkgnc93LfIYapRCijWBBaFAdM5SV3Ioht_1wI,34281
-scmcp_shared/schema/util.py,sha256=x_2GPsmliHabi9V5C6YEv_M8ZHJsinDZJ6ePWrLPmcI,4815
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