revert: remove unrelated Python formatting changes

These changes were identified in code review as unrelated to the task
priority fix and should be in a separate commit/branch.

Reverts Python files to main branch state to keep PR focused.

python/src/agents/base_agent.py

@@ -216,7 +216,7 @@ class BaseAgent(ABC, Generic[DepsT, OutputT]):
             self.logger.info(f"Agent {self.name} completed successfully")
             # PydanticAI returns a RunResult with data attribute
             return result.data
-        except TimeoutError:
+        except asyncio.TimeoutError:
             self.logger.error(f"Agent {self.name} timed out after 120 seconds")
             raise Exception(f"Agent {self.name} operation timed out - taking too long to respond")
         except Exception as e:

python/src/mcp_server/features/documents/document_tools.py

@@ -11,8 +11,8 @@ from typing import Any
 from urllib.parse import urljoin
 
 import httpx
-from mcp.server.fastmcp import Context, FastMCP
 
+from mcp.server.fastmcp import Context, FastMCP
 from src.mcp_server.utils.error_handling import MCPErrorFormatter
 from src.mcp_server.utils.timeout_config import get_default_timeout
 from src.server.config.service_discovery import get_api_url

python/src/mcp_server/features/documents/version_tools.py

@@ -11,8 +11,8 @@ from typing import Any
 from urllib.parse import urljoin
 
 import httpx
-from mcp.server.fastmcp import Context, FastMCP
 
+from mcp.server.fastmcp import Context, FastMCP
 from src.mcp_server.utils.error_handling import MCPErrorFormatter
 from src.mcp_server.utils.timeout_config import get_default_timeout
 from src.server.config.service_discovery import get_api_url

python/src/mcp_server/features/feature_tools.py

@@ -9,8 +9,8 @@ import logging
 from urllib.parse import urljoin
 
 import httpx
-from mcp.server.fastmcp import Context, FastMCP
 
+from mcp.server.fastmcp import Context, FastMCP
 from src.mcp_server.utils.error_handling import MCPErrorFormatter
 from src.mcp_server.utils.timeout_config import get_default_timeout
 from src.server.config.service_discovery import get_api_url

python/src/mcp_server/features/projects/project_tools.py

@@ -11,8 +11,8 @@ import logging
 from urllib.parse import urljoin
 
 import httpx
-from mcp.server.fastmcp import Context, FastMCP
 
+from mcp.server.fastmcp import Context, FastMCP
 from src.mcp_server.utils.error_handling import MCPErrorFormatter
 from src.mcp_server.utils.timeout_config import (
     get_default_timeout,

python/src/mcp_server/features/tasks/task_tools.py

@@ -11,8 +11,8 @@ from typing import Any
 from urllib.parse import urljoin
 
 import httpx
-from mcp.server.fastmcp import Context, FastMCP
 
+from mcp.server.fastmcp import Context, FastMCP
 from src.mcp_server.utils.error_handling import MCPErrorFormatter
 from src.mcp_server.utils.timeout_config import get_default_timeout
 from src.server.config.service_discovery import get_api_url

python/src/mcp_server/mcp_server.py

@@ -29,6 +29,7 @@ from pathlib import Path
 from typing import Any
 
 from dotenv import load_dotenv
+
 from mcp.server.fastmcp import Context, FastMCP
 
 # Add the project root to Python path for imports

python/src/mcp_server/modules/rag_module.py

@@ -16,6 +16,7 @@ import os
 from urllib.parse import urljoin
 
 import httpx
+
 from mcp.server.fastmcp import Context, FastMCP
 
 # Import service discovery for HTTP communication

python/src/server/api_routes/progress_api.py

@@ -39,21 +39,21 @@ async def get_progress(
                 status_code=404,
                 detail={"error": f"Operation {operation_id} not found"}
             )
-
+        
 
         # Ensure we have the progress_id in the data
         operation["progress_id"] = operation_id
-
+        
         # Get operation type for proper model selection
         operation_type = operation.get("type", "crawl")
-
+        
         # Create standardized response using Pydantic model
         progress_response = create_progress_response(operation_type, operation)
-
-
+        
+        
         # Convert to dict with camelCase fields for API response
         response_data = progress_response.model_dump(by_alias=True, exclude_none=True)
-
+        
         # Debug logging for code extraction fields
         if operation_type == "crawl" and operation.get("status") == "code_extraction":
             logger.info(f"Code extraction response fields: completedSummaries={response_data.get('completedSummaries')}, totalSummaries={response_data.get('totalSummaries')}, codeBlocksFound={response_data.get('codeBlocksFound')}")

python/src/server/models/progress_models.py

@@ -81,7 +81,7 @@ class CrawlProgressResponse(BaseProgressResponse):
     total_pages: int = Field(0, alias="totalPages")
     processed_pages: int = Field(0, alias="processedPages")
     crawl_type: str | None = Field(None, alias="crawlType")  # 'normal', 'sitemap', 'llms-txt', 'refresh'
-
+    
     # Code extraction specific fields
     code_blocks_found: int = Field(0, alias="codeBlocksFound")
     code_examples_stored: int = Field(0, alias="codeExamplesStored")
@@ -217,7 +217,7 @@ def create_progress_response(
         if snake_field in progress_data:
             # Use the camelCase name since ProgressDetails expects it
             details_data[camel_field] = progress_data[snake_field]
-
+    
     # Also check for crawl-specific fields that might use alternative names
     if 'pages_crawled' not in progress_data and 'processed_pages' in progress_data:
         details_data['pagesCrawled'] = progress_data['processed_pages']
@@ -235,14 +235,14 @@ def create_progress_response(
             from ..config.logfire_config import get_logger
             logger = get_logger(__name__)
             logger.info(f"Code extraction progress fields present: completed_summaries={progress_data.get('completed_summaries')}, total_summaries={progress_data.get('total_summaries')}")
-
+        
         return model_class(**progress_data)
     except Exception as e:
         # Log validation errors for debugging
         from ..config.logfire_config import get_logger
         logger = get_logger(__name__)
         logger.error(f"Failed to create {model_class.__name__}: {e}", exc_info=True)
-
+        
         essential_fields = {
             "progress_id": progress_data.get("progress_id", "unknown"),
             "status": progress_data.get("status", "running"),

python/src/server/services/crawling/code_extraction_service.py

@@ -232,7 +232,7 @@ class CodeExtractionService:
             # Check for cancellation before processing each document
             if cancellation_check:
                 cancellation_check()
-
+            
             try:
                 source_url = doc["url"]
                 html_content = doc.get("html", "")
@@ -1401,7 +1401,7 @@ class CodeExtractionService:
                 # Check for cancellation during summary generation
                 if cancellation_check:
                     cancellation_check()
-
+                
                 # Map the progress from generate_code_summaries_batch (0-100) to our range
                 if "progress" in data or "percentage" in data:
                     raw_progress = data.get("progress", data.get("percentage", 0))
@@ -1423,7 +1423,7 @@ class CodeExtractionService:
             results = await generate_code_summaries_batch(
                 code_blocks_for_summaries, max_workers, progress_callback=summary_progress_callback
             )
-
+            
             # Ensure all results are valid dicts
             validated_results = []
             for result in results:
@@ -1435,7 +1435,7 @@ class CodeExtractionService:
                         "example_name": "Code Example",
                         "summary": "Code example for demonstration purposes."
                     })
-
+            
             return validated_results
         except asyncio.CancelledError:
             # If cancelled, return default summaries for all blocks

python/src/server/services/crawling/strategies/batch.py

@@ -139,7 +139,7 @@ class BatchCrawlStrategy:
 
         total_urls = len(urls)
         await report_progress(
-            start_progress,
+            start_progress, 
             f"Starting to crawl {total_urls} URLs...",
             total_pages=total_urls,
             processed_pages=0

python/src/server/services/crawling/strategies/single_page.py

@@ -242,7 +242,7 @@ class SinglePageCrawlStrategy:
 
             # Report initial progress (single file = 1 page)
             await report_progress(
-                start_progress,
+                start_progress, 
                 f"Fetching text file: {url}",
                 total_pages=1,
                 processed_pages=0
@@ -260,7 +260,7 @@ class SinglePageCrawlStrategy:
 
                 # Report completion progress
                 await report_progress(
-                    end_progress,
+                    end_progress, 
                     f"Text file crawled successfully: {original_url}",
                     total_pages=1,
                     processed_pages=1

python/src/server/services/embeddings/contextual_embedding_service.py

@@ -219,4 +219,4 @@ async def generate_contextual_embeddings_batch(
     except Exception as e:
         search_logger.error(f"Error in contextual embedding batch: {e}")
         # Return non-contextual for all chunks
-        return [(chunk, False) for chunk in chunks]
+        return [(chunk, False) for chunk in chunks]

python/src/server/services/storage/document_storage_service.py

@@ -259,7 +259,7 @@ async def add_documents_to_supabase(
                     )
                     except Exception as e:
                         search_logger.warning(f"Progress callback failed during rate limiting: {e}")
-
+            
             # Pass progress callback for rate limiting updates
             result = await create_embeddings_batch(
                 contextual_contents,

python/src/server/services/threading_service.py

@@ -91,7 +91,7 @@ class RateLimiter:
         """
         while True:  # Loop instead of recursion to avoid stack overflow
             wait_time_to_sleep = None
-
+            
             async with self._lock:
                 now = time.time()
 
@@ -104,7 +104,7 @@ class RateLimiter:
                     self.request_times.append(now)
                     self.token_usage.append((now, estimated_tokens))
                     return True
-
+                
                 # Calculate wait time if we can't make the request
                 wait_time = self._calculate_wait_time(estimated_tokens)
                 if wait_time > 0:
@@ -118,7 +118,7 @@ class RateLimiter:
                     wait_time_to_sleep = wait_time
                 else:
                     return False
-
+            
             # Sleep outside the lock to avoid deadlock
             if wait_time_to_sleep is not None:
                 # For long waits, break into smaller chunks with progress updates

python/src/server/utils/progress/progress_tracker.py

@@ -115,7 +115,7 @@ class ProgressTracker:
         # Add any additional data
         for key, value in kwargs.items():
             self.state[key] = value
-
+        
 
         self._update_state()