Remove unused functions and clean up error handling

Removed the unused get_cache_info function from cache_manager.py and its references in __init__.py. Also removed the unused _handle_llm_error function from consensus.py and inlined its logic for clearer error handling. Cleaned up imports in annotate.py.

Author: cafferychen777

python/mllmcelltype/__init__.py

@@ -1,7 +1,6 @@
 """mLLMCelltype: A Python module for cell type annotation using various LLMs."""
 
 from .annotate import annotate_clusters, get_model_response
-from .cache_manager import get_cache_info
 from .consensus import (
     check_consensus,
     interactive_consensus_annotation,
@@ -50,7 +49,6 @@
     "load_from_cache",
     "clear_cache",
     "get_cache_stats",
-    "get_cache_info",
     "format_results",
     # Prompts
     "create_prompt",

python/mllmcelltype/annotate.py

@@ -2,8 +2,6 @@
 
 from __future__ import annotations
 
-import json
-import re
 import time
 from typing import Optional, Union
 

python/mllmcelltype/cache_manager.py

@@ -5,7 +5,6 @@
 
 Functions:
     clear_mllmcelltype_cache(): Interactive cache clearing
-    get_cache_info(): Get basic information about current cache (delegates to get_cache_stats)
     clear_cache_cli(): Command-line interface for cache management
 """
 
@@ -36,24 +35,6 @@ def clear_mllmcelltype_cache():
         print("No cache directory found.")
 
 
-def get_cache_info():
-    """Get basic information about the current cache state.
-
-    This is a convenience wrapper around get_cache_stats(detailed=False).
-    For detailed statistics including provider counts and timestamps,
-    use get_cache_stats() instead.
-
-    Returns:
-        dict: Cache info with keys: exists, path, count, size, size_mb
-              (also includes file_count and total_size for backward compatibility)
-    """
-    stats = get_cache_stats(detailed=False)
-    # Add backward-compatible keys
-    stats["file_count"] = stats["count"]
-    stats["total_size"] = stats["size"]
-    return stats
-
-
 def clear_cache_cli():
     """Command-line interface for cache management."""
     import sys
@@ -70,9 +51,9 @@ def clear_cache_cli():
         print(f"\nCleared {removed} cache files.")
     elif len(sys.argv) > 1 and sys.argv[1] == "--info":
         # Show cache info
-        info = get_cache_info()
+        info = get_cache_stats(detailed=False)
         print(f"\nCache directory: {info['path']}")
-        print(f"Number of cache files: {info['file_count']}")
+        print(f"Number of cache files: {info['count']}")
         print(f"Total cache size: {info['size_mb']:.2f} MB")
     else:
         # Interactive mode

python/mllmcelltype/consensus.py

@@ -48,26 +48,6 @@ def _get_api_key(provider: str, api_keys: Optional[dict[str, str]] = None) -> Op
     return load_api_key(provider)
 
 
-def _handle_llm_error(
-    error: Exception, context: str, attempt: int = 0, max_attempts: int = 1
-) -> None:
-    """Handle LLM API call errors consistently.
-
-    Args:
-        error: The exception that occurred
-        context: Context description (e.g., "Qwen attempt", "Claude fallback")
-        attempt: Current attempt number (0-based)
-        max_attempts: Maximum number of attempts
-    """
-    if attempt < max_attempts - 1:
-        write_log(f"Error on {context} {attempt + 1}: {str(error)}", level="warning")
-        write_log("Waiting before next attempt...")
-    else:
-        write_log(f"Error on {context}: {str(error)}", level="warning")
-        if "attempt" in context.lower():
-            write_log(f"All {context.split()[0]} retry attempts failed")
-
-
 def _call_llm_with_retry(
     prompt: str,
     provider: str,
@@ -119,11 +99,12 @@ def _call_llm_with_retry(
             KeyError,
             json.JSONDecodeError,
         ) as e:
-            _handle_llm_error(e, f"{provider} attempt", attempt, max_retries)
             if attempt < max_retries - 1:
+                write_log(f"Error on {provider} attempt {attempt + 1}/{max_retries}: {str(e)}", level="warning")
                 time.sleep(5 * (2**attempt))
             else:
-                write_log(f"falling back to {fallback_provider}")
+                write_log(f"All {provider} retry attempts failed: {str(e)}", level="warning")
+                write_log(f"Falling back to {fallback_provider}")
 
     # Try fallback provider
     if api_keys:
@@ -147,7 +128,7 @@ def _call_llm_with_retry(
                 KeyError,
                 json.JSONDecodeError,
             ) as e:
-                _handle_llm_error(e, f"{fallback_provider} fallback")
+                write_log(f"Error on {fallback_provider} fallback: {str(e)}", level="warning")
         else:
             write_log(f"No {fallback_provider} API key found, falling back to simple consensus")