Release v1.1.6: update server.json for MCP Registry and refine spatial tools

- Sync server.json version to 1.1.6, add title field for MCP Registry
- Unify parameter defaults and top-k utility in spatial tools

Author: cafferychen777

chatspatial/__init__.py

@@ -5,7 +5,7 @@
 Integrates 60 methods from Python and R ecosystems via Model Context Protocol.
 """
 
-__version__ = "1.1.5"
+__version__ = "1.1.6"
 
 # Import configuration to set up environment
 from . import config as config  # noqa: F401

chatspatial/models/data.py

@@ -6,7 +6,7 @@
 
 from typing import Annotated, Literal, Optional, Union
 
-from pydantic import BaseModel, ConfigDict, Field, model_validator
+from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
 from typing_extensions import Self
 
 # =============================================================================
@@ -1445,6 +1445,22 @@ class SpatialVariableGenesParameters(BaseModel):
     )
     warn_housekeeping: bool = True  # Warn if >30% of top genes are housekeeping genes
 
+    @field_validator("n_top_genes")
+    @classmethod
+    def validate_n_top_genes(cls, v: int | None) -> int | None:
+        if v is not None and v <= 0:
+            raise ValueError("n_top_genes must be positive")
+        return v
+
+    @field_validator("sparkx_percentage")
+    @classmethod
+    def validate_sparkx_percentage(cls, v: float) -> float:
+        if not (0 < v < 1):
+            raise ValueError(
+                "sparkx_percentage must be between 0 and 1"
+            )
+        return v
+
 
 class CellCommunicationParameters(BaseModel):
     """Cell-cell communication analysis parameters model with explicit user control"""

chatspatial/tools/spatial_domains.py

@@ -8,13 +8,16 @@
 function, which handles data preparation and dispatches to the selected method.
 """
 
+import logging
 from collections import Counter
 from typing import TYPE_CHECKING, Any
 
 import numpy as np
 import pandas as pd
 import scanpy as sc
 
+logger = logging.getLogger(__name__)
+
 if TYPE_CHECKING:
     from ..spatial_mcp_adapter import ToolContext
 
@@ -90,6 +93,12 @@ async def identify_spatial_domains(
 
         # Step 1: Determine gene subset (no copy yet)
         use_hvg = params.use_highly_variable and "highly_variable" in adata.var.columns
+        if params.use_highly_variable and "highly_variable" not in adata.var.columns:
+            logger.warning(
+                "use_highly_variable=True but 'highly_variable' "
+                "column not found in adata.var. "
+                "Using all genes instead."
+            )
         hvg_mask = adata.var["highly_variable"] if use_hvg else None
 
         # Step 2: Check data quality on original adata (read-only)

chatspatial/tools/spatial_genes.py

@@ -72,6 +72,14 @@ def _calculate_sparse_gene_stats(X) -> tuple[np.ndarray, np.ndarray]:
         gene_totals = np.asarray(X.sum(axis=0)).flatten()
         n_expressed = np.asarray((X > 0).sum(axis=0)).flatten()
 
+    # Guard against NaN/Inf values from degenerate inputs
+    gene_totals = np.nan_to_num(
+        gene_totals, nan=0.0, posinf=0.0, neginf=0.0
+    )
+    n_expressed = np.nan_to_num(
+        n_expressed, nan=0.0, posinf=0.0, neginf=0.0
+    )
+
     return gene_totals, n_expressed
 
 

chatspatial/utils/compute.py

@@ -423,6 +423,16 @@ def gmm_clustering(
     # Fit and predict
     labels = gmm.fit_predict(data)
 
+    if not gmm.converged_:
+        import warnings
+
+        warnings.warn(
+            f"GMM did not converge after {gmm.n_iter_} iterations. "
+            "Results may be unreliable. Consider increasing max_iter.",
+            UserWarning,
+            stacklevel=2,
+        )
+
     # Convert to 1-indexed labels (mclust compatibility)
     # mclust returns labels starting from 1, sklearn from 0
     labels = labels + 1

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "chatspatial"
-version = "1.1.5"
+version = "1.1.6"
 description = "ChatSpatial: Natural language-driven spatial transcriptomics analysis via Model Context Protocol (MCP) integration"
 readme = "README.md"
 license = {text = "MIT"}

server.json

@@ -1,17 +1,18 @@
 {
   "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
   "name": "io.github.cafferychen777/chatspatial",
+  "title": "ChatSpatial",
   "description": "Natural language-driven spatial transcriptomics analysis with 60+ methods via MCP",
   "repository": {
     "url": "https://github.com/cafferychen777/ChatSpatial",
     "source": "github"
   },
-  "version": "1.0.3",
+  "version": "1.1.6",
   "packages": [
     {
       "registryType": "pypi",
       "identifier": "chatspatial",
-      "version": "1.0.3",
+      "version": "1.1.6",
       "transport": {
         "type": "stdio"
       },