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)

test_transitive_deps.py

@@ -3,7 +3,7 @@
 
 import asyncio
 import sys
-import json
+
 from pypi_query_mcp.tools.package_query import query_package_dependencies
 
 
@@ -12,10 +12,14 @@ async def test_direct_dependencies():
     print("Testing direct dependencies for 'requests'...")
     try:
         result = await query_package_dependencies("requests", include_transitive=False)
-        print(f"✓ Direct dependencies found: {len(result.get('runtime_dependencies', []))}")
+        print(
+            f"✓ Direct dependencies found: {len(result.get('runtime_dependencies', []))}"
+        )
         print(f"  Package: {result.get('package_name')}")
         print(f"  Version: {result.get('version')}")
-        print(f"  Runtime deps: {result.get('runtime_dependencies', [])[:3]}...")  # Show first 3
+        print(
+            f"  Runtime deps: {result.get('runtime_dependencies', [])[:3]}..."
+        )  # Show first 3
         return True
     except Exception as e:
         print(f"✗ Error testing direct dependencies: {e}")
@@ -27,44 +31,44 @@ async def test_transitive_dependencies():
     print("\nTesting transitive dependencies for 'requests'...")
     try:
         result = await query_package_dependencies(
-            "requests", 
-            include_transitive=True, 
-            max_depth=3,
-            python_version="3.10"
+            "requests", include_transitive=True, max_depth=3, python_version="3.10"
         )
-        
-        print(f"✓ Transitive analysis completed")
+
+        print("✓ Transitive analysis completed")
         print(f"  Include transitive: {result.get('include_transitive')}")
         print(f"  Package: {result.get('package_name')}")
         print(f"  Version: {result.get('version')}")
-        
+
         # Check transitive dependency structure
-        transitive = result.get('transitive_dependencies', {})
-        all_packages = transitive.get('all_packages', {})
+        transitive = result.get("transitive_dependencies", {})
+        all_packages = transitive.get("all_packages", {})
         print(f"  Total packages in tree: {len(all_packages)}")
-        
+
         # Check summary
-        summary = result.get('dependency_summary', {})
+        summary = result.get("dependency_summary", {})
         print(f"  Direct runtime deps: {summary.get('direct_runtime_count', 0)}")
-        print(f"  Total transitive packages: {summary.get('total_transitive_packages', 0)}")
+        print(
+            f"  Total transitive packages: {summary.get('total_transitive_packages', 0)}"
+        )
         print(f"  Max depth: {summary.get('max_dependency_depth', 0)}")
-        
+
         # Check analysis
-        analysis = result.get('analysis', {})
-        performance = analysis.get('performance_impact', {})
+        analysis = result.get("analysis", {})
+        performance = analysis.get("performance_impact", {})
         print(f"  Performance level: {performance.get('performance_level', 'unknown')}")
-        
-        complexity = summary.get('complexity_score', {})
+
+        complexity = summary.get("complexity_score", {})
         print(f"  Complexity level: {complexity.get('level', 'unknown')}")
-        
+
         # Check circular dependencies
-        circular = transitive.get('circular_dependencies', [])
+        circular = transitive.get("circular_dependencies", [])
         print(f"  Circular dependencies found: {len(circular)}")
-        
+
         return True
     except Exception as e:
         print(f"✗ Error testing transitive dependencies: {e}")
         import traceback
+
         traceback.print_exc()
         return False
 
@@ -74,19 +78,17 @@ async def test_small_package():
     print("\nTesting transitive dependencies for 'six' (smaller package)...")
     try:
         result = await query_package_dependencies(
-            "six", 
-            include_transitive=True, 
-            max_depth=2
+            "six", include_transitive=True, max_depth=2
         )
-        
-        transitive = result.get('transitive_dependencies', {})
-        all_packages = transitive.get('all_packages', {})
-        print(f"✓ Analysis completed for 'six'")
+
+        transitive = result.get("transitive_dependencies", {})
+        all_packages = transitive.get("all_packages", {})
+        print("✓ Analysis completed for 'six'")
         print(f"  Total packages: {len(all_packages)}")
-        
-        summary = result.get('dependency_summary', {})
+
+        summary = result.get("dependency_summary", {})
         print(f"  Direct runtime deps: {summary.get('direct_runtime_count', 0)}")
-        
+
         return True
     except Exception as e:
         print(f"✗ Error testing 'six': {e}")
@@ -97,21 +99,21 @@ async def main():
     """Run all tests."""
     print("Testing PyPI Query MCP Server - Transitive Dependencies")
     print("=" * 60)
-    
+
     results = []
-    
+
     # Test 1: Direct dependencies (existing functionality)
     results.append(await test_direct_dependencies())
-    
+
     # Test 2: Transitive dependencies (new functionality)
     results.append(await test_transitive_dependencies())
-    
+
     # Test 3: Small package test
     results.append(await test_small_package())
-    
+
     print("\n" + "=" * 60)
     print(f"Test Results: {sum(results)}/{len(results)} passed")
-    
+
     if all(results):
         print("✓ All tests passed! Transitive dependency functionality is working.")
         return 0
@@ -121,4 +123,4 @@ async def main():
 
 
 if __name__ == "__main__":
-    sys.exit(asyncio.run(main()))
+    sys.exit(asyncio.run(main()))