Fix import formatting and add missing noqa in tools

Standardizes import formatting in preprocessing.py and adds missing noqa directive for error handling import in visualization.py. Also makes a minor style fix in integration.py for consistency.

Author: cafferychen777

chatspatial/tools/integration.py

@@ -314,7 +314,7 @@ def integrate_multiple_samples(adatas, batch_key="batch", method="harmony", n_pc
         mean_squared = np.array(X_squared.mean(axis=0)).flatten()
 
         # Variance = E[X²] - E[X]²
-        gene_var = mean_squared - mean_per_gene ** 2
+        gene_var = mean_squared - mean_per_gene**2
     else:
         # Dense matrix: use standard variance calculation
         gene_var = np.var(combined.X, axis=0)

chatspatial/tools/preprocessing.py

@@ -14,7 +14,8 @@
 from mcp.server.fastmcp import Context
 
 from ..models.analysis import PreprocessingResult
-from ..models.data import PreprocessingParameters, ResolVIPreprocessingParameters
+from ..models.data import (PreprocessingParameters,
+                           ResolVIPreprocessingParameters)
 from ..utils.data_adapter import standardize_adata
 from ..utils.tool_error_handling import mcp_tool_error_handler
 

chatspatial/tools/visualization.py

@@ -39,7 +39,7 @@
 # Import error handling utilities
 from ..utils.error_handling import DataCompatibilityError  # noqa: E402
 from ..utils.error_handling import DataNotFoundError  # noqa: E402
-from ..utils.error_handling import InvalidParameterError, ProcessingError
+from ..utils.error_handling import InvalidParameterError, ProcessingError  # noqa: E402
 # Import standardized image utilities
 from ..utils.image_utils import optimize_fig_to_image_with_cache  # noqa: E402
 # Import path utilities for safe file operations