fix code formatting, update dependencies

src/neuview/builders/page_generator_builder.py

@@ -107,7 +107,6 @@ def with_dependency_injection(self, use_container: bool = True):
         self._use_container = use_container
         return self
 
-
     def build(self):
         """
         Build and return configured PageGenerator instance.
@@ -129,7 +128,6 @@ def build(self):
         else:
             return self._build_with_factory()
 
-
     def build_with_minimal_container(self):
         """
         Build PageGenerator with minimal dependency injection container for testing.
@@ -339,4 +337,3 @@ def default_config(cls, config: Config, output_dir: str):
             Configured builder ready to build
         """
         return cls().with_config(config).with_output_directory(output_dir)
-

src/neuview/cache.py

@@ -318,7 +318,6 @@ def load_neuron_type_cache(self, neuron_type: str) -> Optional[NeuronTypeCacheDa
             logger.warning(f"Failed to load cache for {neuron_type}: {e}")
             return None
 
-
     def list_cached_neuron_types(self) -> List[str]:
         """Get list of neuron types that have valid cache files (lazy - no file loading).
 
@@ -364,7 +363,6 @@ def list_cached_neuron_types(self) -> List[str]:
 
         return sorted(cached_types)
 
-
     def get_cached_data_lazy(self) -> "LazyCacheDataDict":
         """Get a lazy-loading dictionary for cached neuron type data.
 

src/neuview/dataset_adapters.py

@@ -473,7 +473,6 @@ def get_synapse_counts(self, neurons_df: pd.DataFrame) -> Tuple[int, int]:
         return int(pre_total), int(post_total)
 
 
-
 class HemibrainAdapter(DatasetAdapter):
     """Adapter for Hemibrain dataset."""
 
@@ -540,7 +539,6 @@ def get_synapse_counts(self, neurons_df: pd.DataFrame) -> Tuple[int, int]:
         return int(pre_total), int(post_total)
 
 
-
 class OpticLobeAdapter(DatasetAdapter):
     """Adapter for Optic Lobe dataset."""
 
@@ -620,7 +618,6 @@ def get_synapse_counts(self, neurons_df: pd.DataFrame) -> Tuple[int, int]:
         return int(pre_total), int(post_total)
 
 
-
 class FafbAdapter(DatasetAdapter):
     """Adapter for FlyWire FAFB dataset."""
 
@@ -758,7 +755,6 @@ def get_synapse_counts(self, neurons_df: pd.DataFrame) -> Tuple[int, int]:
         return int(pre_total), int(post_total)
 
 
-
 class WaspAdapter(DatasetAdapter):
     """Adapter for the wasp3 dataset.
 

src/neuview/facade/neu_view_facade.py

@@ -8,7 +8,7 @@
 
 import logging
 from pathlib import Path
-from typing import Optional, Dict, Any, List
+from typing import Optional, Dict, Any
 
 from ..config import Config
 from ..builders.page_generator_builder import PageGeneratorBuilder
@@ -68,7 +68,6 @@ def create(
 
         return cls(config=config, output_dir=output_dir)
 
-
     def with_queue_service(self, queue_service) -> "NeuViewFacade":
         """
         Configure the facade with a queue service.
@@ -227,8 +226,6 @@ def generate_page(self, neuron_type: str, **kwargs) -> Dict[str, Any]:
                 "metadata": {},
             }
 
-
-
     def validate_configuration(self) -> Dict[str, Any]:
         """
         Validate the current configuration.
@@ -276,7 +273,6 @@ def validate_configuration(self) -> Dict[str, Any]:
 
         return {"valid": len(errors) == 0, "errors": errors, "warnings": warnings}
 
-
     def cleanup(self) -> None:
         """Clean up resources and reset the facade."""
         logger.info("Cleaning up neuView facade")

src/neuview/managers.py

@@ -424,7 +424,6 @@ def get_template_dependencies(self, template_path: str) -> List[str]:
 
         return list(dependencies)
 
-
     def _find_circular_dependencies(self) -> List[List[str]]:
         """Find circular dependencies in the template graph."""
         visited = set()
@@ -502,8 +501,6 @@ def clear_cache(self) -> None:
             # Clear everything (cache strategies don't support pattern clearing)
             self._cache_strategy.clear()
 
-
-
     def add_custom_filter(self, name: str, filter_func: callable) -> None:
         """
         Add a custom filter to template strategies that support it.
@@ -534,7 +531,6 @@ def add_global_variable(self, name: str, value: Any) -> None:
             if hasattr(strategy, "add_global"):
                 strategy.add_global(name, value)
 
-
     def get_template_info(self, template_path: str) -> Dict[str, Any]:
         """
         Get comprehensive information about a template.
@@ -925,7 +921,6 @@ def copy_resource(self, source_path: str, dest_path: str) -> bool:
 
         return False
 
-
     def invalidate_resource(self, resource_path: str) -> None:
         """
         Invalidate cache for a specific resource.
@@ -961,10 +956,6 @@ def clear_cache(self) -> None:
                 strategy.clear_cache()
 
 
-
-
-
-
 class DependencyManager:
     """
     Manager for handling dependencies between templates and resources.
@@ -988,8 +979,6 @@ def __init__(
         self._dependency_graph = defaultdict(set)
         self._reverse_dependency_graph = defaultdict(set)
 
-
-
     def get_dependents(self, item: str, item_type: str = "template") -> Set[str]:
         """
         Get all items that depend on the given item.
@@ -1003,5 +992,3 @@ def get_dependents(self, item: str, item_type: str = "template") -> Set[str]:
         """
         dep_key = f"{item_type}:{item}"
         return self._reverse_dependency_graph.get(dep_key, set())
-
-

src/neuview/models/domain_models.py

@@ -166,7 +166,6 @@ def has_soma_location(self) -> bool:
         )
 
 
-
 @dataclass
 class NeuronCollection:
     """Entity representing a collection of neurons of the same type."""
@@ -215,7 +214,6 @@ def body_ids(self) -> List[BodyId]:
         """List of all body IDs."""
         return [neuron.body_id for neuron in self.neurons]
 
-
     def get_synapse_statistics(self) -> Dict[str, float]:
         """Calculate synapse statistics for the collection."""
         if not self.neurons:

src/neuview/models/page_generation.py

@@ -118,7 +118,6 @@ class AnalysisResults:
     layer_analysis: Optional[Dict[str, Any]] = None
     column_analysis: Optional[Dict[str, Any]] = None
 
-
     def to_dict(self) -> Dict[str, Any]:
         """Convert to dictionary for template context."""
         # Always provide expected keys to prevent template errors
@@ -162,7 +161,6 @@ class PageGenerationContext:
     additional_context: Dict[str, Any] = field(default_factory=dict)
 
 
-
 @dataclass
 class PageGenerationResponse:
     """

src/neuview/neuprint_connector.py

@@ -440,7 +440,6 @@ def clear_neuron_data_cache(self, neuron_type: str = None):
             else:
                 self._soma_sides_cache.clear()
 
-
     def get_database_metadata(self) -> Dict[str, Any]:
         """
         Get database metadata including lastDatabaseEdit.
@@ -545,7 +544,6 @@ def get_database_metadata(self) -> Dict[str, Any]:
                     "uuid": "Unknown",
                 }
 
-
     def get_cache_stats(self) -> Dict[str, Any]:
         """
         Get cache performance statistics.
@@ -1458,7 +1456,6 @@ def get_available_types(self) -> List[str]:
         except Exception as e:
             raise RuntimeError(f"Failed to fetch available neuron types: {e}")
 
-
     def get_soma_sides_for_type(self, neuron_type: str) -> List[str]:
         """
         Get soma sides for a specific neuron type with caching to avoid repeated queries.
@@ -1817,4 +1814,3 @@ def _get_roi_hierarchy(self) -> dict:
         except Exception as e:
             logger.warning(f"Failed to fetch ROI hierarchy: {e}")
             return {}
-

src/neuview/page_generator.py

@@ -301,7 +301,6 @@ def _get_partner_body_ids(self, partner_data, direction, connected_bids):
             partner_data, direction, connected_bids
         )
 
-
     def _generate_neuron_search_js(self):
         """Generate neuron-search.js with embedded neuron types data."""
         # Delegate to neuron search service
@@ -331,9 +330,6 @@ def _generate_neuroglancer_url(
             neuron_type, neuron_data, soma_side, connector
         )
 
-
-
-
     def _generate_neuprint_url(
         self, neuron_type: str, neuron_data: Dict[str, Any]
     ) -> str:
@@ -352,7 +348,6 @@ def _generate_neuprint_url(
             neuron_type, neuron_data
         )
 
-
     def generate_page_unified(self, request: PageGenerationRequest):
         """
         Generate an HTML page using the unified orchestrator workflow.
@@ -469,7 +464,6 @@ def _get_columns_from_neuron_cache(self, neuron_type: str):
         """
         return self.cache_service.get_columns_from_neuron_cache(neuron_type)
 
-
     def _load_persistent_columns_cache(self, cache_key):
         """Load persistent cache for all columns dataset query."""
         return self.cache_service.load_persistent_columns_cache(cache_key)
@@ -522,7 +516,6 @@ def _analyze_column_roi_data(
             spacing_factor,
         )
 
-
     def _compute_thresholds(self, df: pd.DataFrame, n_bins: int = 5):
         """
         Compute threshold lists for synapse and neuron counts at different aggregation levels.
@@ -609,7 +602,6 @@ def _generate_region_hexagonal_grids(
 
         return result.region_grids
 
-
     def clean_dynamic_files_for_neuron(
         self, neuron_type: str, soma_side: str = None
     ) -> bool:
@@ -644,7 +636,6 @@ def generate_filename(neuron_type: str, soma_side: str) -> str:
         """
         return FileService.generate_filename(neuron_type, soma_side)
 
-
     def _find_youtube_video(self, neuron_type: str) -> Optional[str]:
         """
         Find YouTube video ID for a neuron type by matching against descriptions.
@@ -661,7 +652,6 @@ def _get_primary_rois(self, connector):
         """Get primary ROIs based on dataset type and available data."""
         return self.roi_analysis_service.get_primary_rois(connector)
 
-
     def _get_region_for_type(self, neuron_type: str, connector) -> str:
         """Find the type's assigned "region" - used for setting the NG view."""
         return self.roi_analysis_service.get_region_for_type(neuron_type, connector)

src/neuview/result.py

@@ -78,7 +78,6 @@ def map_err(self, func: Callable[[E], Any]) -> "Result":
             return self
 
 
-
 @dataclass
 class Ok(Result[T, E]):
     """Success variant of Result."""
@@ -109,5 +108,3 @@ def __repr__(self) -> str:
 
     def __eq__(self, other) -> bool:
         return isinstance(other, Err) and self.error == other.error
-
-

src/neuview/services/brain_region_service.py

@@ -7,7 +7,7 @@
 
 import re
 import logging
-from typing import Dict, Optional
+from typing import Dict
 
 from ..utils import get_input_dir
 
@@ -105,8 +105,6 @@ def load_brain_regions(self) -> Dict[str, str]:
             self._loaded = True
             return self.brain_regions
 
-
-
     def roi_abbr_filter(self, roi_name: str) -> str:
         """
         Convert ROI abbreviation to HTML abbr tag with full name in title.
@@ -160,8 +158,6 @@ def roi_abbr_filter(self, roi_name: str) -> str:
             logger.debug(f"Brain region abbreviation not found: {roi_name}")
             return roi_name
 
-
-
     def __len__(self) -> int:
         """Return the number of loaded brain regions."""
         if not self._loaded:

src/neuview/services/cache_service.py

@@ -14,7 +14,6 @@
 
 import pandas as pd
 
-from ..utils import atomic_write
 
 from ..commands import GeneratePageCommand
 from ..models import (
@@ -439,7 +438,6 @@ def _clean_roi_name(self, roi_name: str) -> str:
 
         return cleaned.strip()
 
-
     def load_persistent_columns_cache(
         self, cache_key: str
     ) -> Optional[Tuple[list, Dict[str, set]]]:
@@ -489,7 +487,6 @@ def load_persistent_columns_cache(
 
         return None
 
-
     def get_columns_from_neuron_cache(
         self, neuron_type: str
     ) -> Tuple[Optional[list], Optional[Dict[str, set]]]:

src/neuview/services/citation_service.py

@@ -187,8 +187,6 @@ def get_citation(self, citation_key: str) -> Optional[Tuple[str, str]]:
             self.load_citations()
         return self.citations.get(citation_key)
 
-
-
     def format_doi_url(self, doi: str) -> str:
         """
         Convert a DOI string to a full URL.

src/neuview/services/column_analysis_service.py

@@ -148,9 +148,7 @@ def analyze_column_roi_data(
             # analysis) and the R slot displays the R-hemisphere SVG (from
             # the L-soma analysis). No separate combined-mode files are
             # produced.
-            soma_side_lower = (
-                soma_side.lower() if isinstance(soma_side, str) else ""
-            )
+            soma_side_lower = soma_side.lower() if isinstance(soma_side, str) else ""
             if soma_side_lower == "combined":
                 if "somaSide" in neurons_df.columns:
                     l_neurons = neurons_df[neurons_df["somaSide"] == "L"]

src/neuview/services/connection_test_service.py

@@ -41,4 +41,3 @@ async def test_connection(
 
         except Exception as e:
             return Err(f"Connection test failed: {str(e)}")
-

src/neuview/services/data_processing_service.py

@@ -388,7 +388,6 @@ def _save_column_layer_cache(
         except Exception as e:
             logger.warning(f"Failed to save cache to {cache_path}: {e}")
 
-
     def _minmax_normalize(self, data: List[Dict]) -> List[Dict]:
         """Apply min-max normalization to numerical fields."""
         # Implementation would go here based on specific requirements
@@ -398,4 +397,3 @@ def _zscore_normalize(self, data: List[Dict]) -> List[Dict]:
         """Apply z-score normalization to numerical fields."""
         # Implementation would go here based on specific requirements
         return data
-

src/neuview/services/database_query_service.py

@@ -569,7 +569,6 @@ def get_partner_body_ids(
             logger.error(f"Error getting partner bodyIds for {neuron_type}: {e}")
             return {"downstream": {}, "upstream": {}}
 
-
     def _process_partner_results(self, result_df: pd.DataFrame) -> Dict:
         """
         Process partner query results to get top partner for each type and soma side.