chore: upgrade all Python packages and fix linting issues

- Update all dependencies to latest versions (fastmcp, httpx, packaging, etc.)
- Downgrade click from yanked 8.2.2 to stable 8.1.7
- Fix code formatting and linting issues with ruff
- Most tests passing (2 test failures in dependency resolver need investigation)

pypi_query_mcp/core/version_utils.py

@@ -288,31 +288,31 @@ class VersionCompatibility:
 
 def sort_versions_semantically(versions: list[str], reverse: bool = True) -> list[str]:
     """Sort package versions using semantic version ordering.
-    
+
     This function properly sorts versions by parsing them as semantic versions,
     ensuring that pre-release versions (alpha, beta, rc) are ordered correctly
     relative to stable releases.
-    
+
     Args:
         versions: List of version strings to sort
         reverse: If True, sort in descending order (newest first). Default True.
-        
+
     Returns:
         List of version strings sorted semantically
-        
+
     Examples:
         >>> sort_versions_semantically(['1.0.0', '2.0.0a1', '1.5.0', '2.0.0'])
         ['2.0.0', '2.0.0a1', '1.5.0', '1.0.0']
-        
+
         >>> sort_versions_semantically(['5.2rc1', '5.2.5', '5.2.0'])
         ['5.2.5', '5.2.0', '5.2rc1']
     """
     if not versions:
         return []
-        
+
     def parse_version_safe(version_str: str) -> tuple[Version | None, str]:
         """Safely parse a version string, returning (parsed_version, original_string).
-        
+
         Returns (None, original_string) if parsing fails.
         """
         try:
@@ -320,26 +320,26 @@ def sort_versions_semantically(versions: list[str], reverse: bool = True) -> lis
         except InvalidVersion:
             logger.debug(f"Failed to parse version '{version_str}' as semantic version")
             return (None, version_str)
-    
+
     # Parse all versions, keeping track of originals
     parsed_versions = [parse_version_safe(v) for v in versions]
-    
+
     # Separate valid and invalid versions
     valid_versions = [(v, orig) for v, orig in parsed_versions if v is not None]
     invalid_versions = [orig for v, orig in parsed_versions if v is None]
-    
+
     # Sort valid versions semantically
     valid_versions.sort(key=lambda x: x[0], reverse=reverse)
-    
+
     # Sort invalid versions lexicographically as fallback
     invalid_versions.sort(reverse=reverse)
-    
+
     # Combine results: valid versions first, then invalid ones
     result = [orig for _, orig in valid_versions] + invalid_versions
-    
+
     logger.debug(
         f"Sorted {len(versions)} versions: {len(valid_versions)} valid, "
         f"{len(invalid_versions)} invalid"
     )
-    
+
     return result