From 9a2fec020eb8b03cca5699c0ab61a152482a85e9 Mon Sep 17 00:00:00 2001 From: Frank Loesche Date: Tue, 8 Sep 2026 14:53:05 -0400 Subject: [PATCH] fix code formatting, update dependencies --- pixi.lock | 1823 +++++++++-------- .../builders/page_generator_builder.py | 3 - src/neuview/cache.py | 2 - src/neuview/dataset_adapters.py | 4 - src/neuview/facade/neu_view_facade.py | 6 +- src/neuview/managers.py | 13 - src/neuview/models/domain_models.py | 2 - src/neuview/models/page_generation.py | 2 - src/neuview/neuprint_connector.py | 4 - src/neuview/page_generator.py | 10 - src/neuview/result.py | 3 - src/neuview/services/brain_region_service.py | 6 +- src/neuview/services/cache_service.py | 3 - src/neuview/services/citation_service.py | 2 - .../services/column_analysis_service.py | 4 +- .../services/connection_test_service.py | 1 - .../services/data_processing_service.py | 2 - .../services/database_query_service.py | 1 - src/neuview/services/file_service.py | 6 - .../services/jinja_template_service.py | 7 - src/neuview/services/neuron_name_service.py | 1 - src/neuview/services/neuron_search_service.py | 4 +- .../services/neuron_selection_service.py | 4 +- .../services/neuron_statistics_service.py | 4 +- .../services/partner_analysis_service.py | 3 - src/neuview/services/queue_processor.py | 2 - .../services/resource_manager_service.py | 10 +- .../services/roi_combination_service.py | 5 +- src/neuview/services/threshold_config.py | 5 - src/neuview/services/threshold_service.py | 4 - .../services/url_generation_service.py | 6 - src/neuview/utils/text_utils.py | 2 - src/neuview/visualization/color/palette.py | 1 - src/neuview/visualization/config_manager.py | 7 - .../visualization/coordinate_system.py | 1 - .../data_processing/column_data_manager.py | 13 - .../data_processing/metric_calculator.py | 12 +- .../data_processing/threshold_calculator.py | 2 - .../data_processing/validation_manager.py | 3 - .../visualization/data_transfer_objects.py | 6 +- .../visualization/dependency_injection.py | 6 - 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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) - diff --git a/src/neuview/cache.py b/src/neuview/cache.py index 58af7d4b..a523cd9b 100644 --- a/src/neuview/cache.py +++ b/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. diff --git a/src/neuview/dataset_adapters.py b/src/neuview/dataset_adapters.py index e41cbaa6..fd794fd5 100644 --- a/src/neuview/dataset_adapters.py +++ b/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. diff --git a/src/neuview/facade/neu_view_facade.py b/src/neuview/facade/neu_view_facade.py index 875f2b36..3b14be33 100644 --- a/src/neuview/facade/neu_view_facade.py +++ b/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") diff --git a/src/neuview/managers.py b/src/neuview/managers.py index cd541479..a0488307 100644 --- a/src/neuview/managers.py +++ b/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()) - - diff --git a/src/neuview/models/domain_models.py b/src/neuview/models/domain_models.py index 058e31d0..82ed4de9 100644 --- a/src/neuview/models/domain_models.py +++ b/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: diff --git a/src/neuview/models/page_generation.py b/src/neuview/models/page_generation.py index 7e33e06b..a54665e8 100644 --- a/src/neuview/models/page_generation.py +++ b/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: """ diff --git a/src/neuview/neuprint_connector.py b/src/neuview/neuprint_connector.py index 50aa0deb..341086a7 100644 --- a/src/neuview/neuprint_connector.py +++ b/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 {} - diff --git a/src/neuview/page_generator.py b/src/neuview/page_generator.py index 57dd2d36..28a1db7f 100644 --- a/src/neuview/page_generator.py +++ b/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) diff --git a/src/neuview/result.py b/src/neuview/result.py index aa70fd06..5dd2eaa6 100644 --- a/src/neuview/result.py +++ b/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 - - diff --git a/src/neuview/services/brain_region_service.py b/src/neuview/services/brain_region_service.py index 25c8e088..4dd84fc4 100644 --- a/src/neuview/services/brain_region_service.py +++ b/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: diff --git a/src/neuview/services/cache_service.py b/src/neuview/services/cache_service.py index 49fecdf0..cc668fed 100644 --- a/src/neuview/services/cache_service.py +++ b/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]]]: diff --git a/src/neuview/services/citation_service.py b/src/neuview/services/citation_service.py index 4834e429..9f50d565 100644 --- a/src/neuview/services/citation_service.py +++ b/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. diff --git a/src/neuview/services/column_analysis_service.py b/src/neuview/services/column_analysis_service.py index d398153c..02794a00 100644 --- a/src/neuview/services/column_analysis_service.py +++ b/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"] diff --git a/src/neuview/services/connection_test_service.py b/src/neuview/services/connection_test_service.py index 66b6d936..ea1f935f 100644 --- a/src/neuview/services/connection_test_service.py +++ b/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)}") - diff --git a/src/neuview/services/data_processing_service.py b/src/neuview/services/data_processing_service.py index 3a977682..94c2905c 100644 --- a/src/neuview/services/data_processing_service.py +++ b/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 - diff --git a/src/neuview/services/database_query_service.py b/src/neuview/services/database_query_service.py index 13ebe5bf..79e0b800 100644 --- a/src/neuview/services/database_query_service.py +++ b/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. diff --git a/src/neuview/services/file_service.py b/src/neuview/services/file_service.py index d8bc4a69..63c1d781 100644 --- a/src/neuview/services/file_service.py +++ b/src/neuview/services/file_service.py @@ -5,8 +5,6 @@ file paths for the page generation system. """ -from pathlib import Path - class FileService: """ @@ -84,7 +82,3 @@ def sanitize_filename(filename: str) -> str: sanitized = sanitized.strip("_") return sanitized - - - - diff --git a/src/neuview/services/jinja_template_service.py b/src/neuview/services/jinja_template_service.py index 6ae1e2a1..28cbb48e 100644 --- a/src/neuview/services/jinja_template_service.py +++ b/src/neuview/services/jinja_template_service.py @@ -212,8 +212,6 @@ def render_template(self, template_name: str, context: Dict[str, Any]) -> str: template = self.get_template(template_name) return template.render(**context) - - def list_templates(self) -> list[str]: """ Get a list of all available templates. @@ -231,8 +229,6 @@ def list_templates(self) -> list[str]: return self.env.list_templates() - - def get_environment(self) -> Optional[Environment]: """ Get the Jinja2 environment instance. @@ -242,8 +238,6 @@ def get_environment(self) -> Optional[Environment]: """ return self.env - - def add_global(self, name: str, value: Any) -> None: """ Add a global variable to the template environment. @@ -262,4 +256,3 @@ def add_global(self, name: str, value: Any) -> None: self.env.globals[name] = value logger.debug(f"Added global variable: {name}") - diff --git a/src/neuview/services/neuron_name_service.py b/src/neuview/services/neuron_name_service.py index ab0e3bd2..e80f394f 100644 --- a/src/neuview/services/neuron_name_service.py +++ b/src/neuview/services/neuron_name_service.py @@ -20,7 +20,6 @@ def neuron_name_to_filename(self, neuron_name: str) -> str: """Convert neuron name to filename format (same logic as PageGenerator._generate_filename).""" return neuron_name.replace("/", "_").replace(" ", "_") - def filename_to_neuron_name(self, filename: str, connector=None) -> str: """Convert filename back to original neuron name using database lookup.""" # Since filename conversion is not reliably reversible ('/' and ' ' become '_'), diff --git a/src/neuview/services/neuron_search_service.py b/src/neuview/services/neuron_search_service.py index 4839cbe5..95f0c33e 100644 --- a/src/neuview/services/neuron_search_service.py +++ b/src/neuview/services/neuron_search_service.py @@ -9,7 +9,7 @@ import logging from datetime import datetime from pathlib import Path -from typing import Any, Dict, List, Optional +from typing import List from ..utils import atomic_write @@ -214,5 +214,3 @@ def get_output_path(self) -> Path: Path object for the output file """ return self.output_dir / "static" / "js" / "neuron-search.js" - - diff --git a/src/neuview/services/neuron_selection_service.py b/src/neuview/services/neuron_selection_service.py index c2c1199f..e8ee499a 100644 --- a/src/neuview/services/neuron_selection_service.py +++ b/src/neuview/services/neuron_selection_service.py @@ -8,7 +8,7 @@ import logging import time -from typing import Dict, Any, Optional, List +from typing import Dict, Optional, List import pandas as pd from .file_service import FileService @@ -502,5 +502,3 @@ def _select_specific_soma_side( logger.warning(f"Could not select neuron: {e}") return selected_bodyids - - diff --git a/src/neuview/services/neuron_statistics_service.py b/src/neuview/services/neuron_statistics_service.py index 8b0323ab..c44ae637 100644 --- a/src/neuview/services/neuron_statistics_service.py +++ b/src/neuview/services/neuron_statistics_service.py @@ -6,7 +6,7 @@ """ import logging -from typing import Dict, Optional, Any +from typing import Dict, Optional from dataclasses import dataclass from ..models import NeuronTypeName, NeuronTypeStatistics @@ -252,5 +252,3 @@ async def get_comprehensive_statistics( f"Failed to get comprehensive statistics for {neuron_type}: {e}" ) return Err(f"Failed to get comprehensive statistics: {str(e)}") - - diff --git a/src/neuview/services/partner_analysis_service.py b/src/neuview/services/partner_analysis_service.py index 914c980d..e56169ac 100644 --- a/src/neuview/services/partner_analysis_service.py +++ b/src/neuview/services/partner_analysis_service.py @@ -251,6 +251,3 @@ def _unique_preserving_order(self, sequence: List[Any]) -> List[Any]: result.append(item) return result - - - diff --git a/src/neuview/services/queue_processor.py b/src/neuview/services/queue_processor.py index b06ded71..73f7c134 100644 --- a/src/neuview/services/queue_processor.py +++ b/src/neuview/services/queue_processor.py @@ -149,5 +149,3 @@ async def _process_generate_command( except Exception as e: return Err(f"Failed to process generate command: {str(e)}") - - diff --git a/src/neuview/services/resource_manager_service.py b/src/neuview/services/resource_manager_service.py index 00e7f811..c4c858ab 100644 --- a/src/neuview/services/resource_manager_service.py +++ b/src/neuview/services/resource_manager_service.py @@ -9,7 +9,7 @@ import logging import shutil from pathlib import Path -from typing import Any, Dict, List, Optional +from typing import Dict, List from ..utils import get_project_root, get_static_dir, get_templates_dir from .neuroglancer_js_service import NeuroglancerJSService @@ -441,7 +441,6 @@ def _should_copy_js_files(self, source_dir: Path, dest_dir: Path) -> bool: logger.debug(f"Error checking JS file existence, will copy: {e}") return True - def clean_dynamic_files( self, neuron_type: str = None, soma_side: str = None ) -> bool: @@ -504,8 +503,6 @@ def clean_dynamic_files( logger.error(f"Failed to clean dynamic files: {e}") return False - - def ensure_directory_exists(self, directory_path: Path) -> bool: """ Ensure a directory exists, creating it if necessary. @@ -523,7 +520,6 @@ def ensure_directory_exists(self, directory_path: Path) -> bool: logger.error(f"Failed to create directory {directory_path}: {e}") return False - def list_directory_contents( self, directory_path: Path, pattern: str = "*", recursive: bool = False ) -> List[Path]: @@ -550,7 +546,3 @@ def list_directory_contents( except Exception as e: logger.error(f"Failed to list directory contents for {directory_path}: {e}") return [] - - - - diff --git a/src/neuview/services/roi_combination_service.py b/src/neuview/services/roi_combination_service.py index 718ff028..c285cc97 100644 --- a/src/neuview/services/roi_combination_service.py +++ b/src/neuview/services/roi_combination_service.py @@ -8,7 +8,7 @@ import logging import re -from typing import Dict, List, Any, Optional +from typing import Dict, List, Any from collections import defaultdict logger = logging.getLogger(__name__) @@ -216,7 +216,6 @@ def _recalculate_percentages(self, rois: List[Dict[str, Any]]) -> None: else: roi["post_percentage"] = 0.0 - def is_sided_roi(self, roi_name: str) -> bool: """ Check if an ROI name contains side information. @@ -237,7 +236,6 @@ def is_sided_roi(self, roi_name: str) -> bool: return False - def get_statistics( self, original_data: List[Dict[str, Any]], combined_data: List[Dict[str, Any]] ) -> Dict[str, Any]: @@ -271,4 +269,3 @@ def count_sided_rois(data): "reduction": original_counts["total"] - combined_counts["total"], "sided_rois_combined": original_counts["sided"] - combined_counts["sided"], } - diff --git a/src/neuview/services/threshold_config.py b/src/neuview/services/threshold_config.py index 38450406..c5520738 100644 --- a/src/neuview/services/threshold_config.py +++ b/src/neuview/services/threshold_config.py @@ -278,7 +278,6 @@ def get_profile(self, name: str) -> Optional[ThresholdProfile]: """ return self._profiles.get(name) - def get_threshold_value( self, profile_name: str, context: Optional[str] = None ) -> float: @@ -409,8 +408,6 @@ def update_computed_thresholds( ) return True - - def import_config(self, config: Dict[str, Any]) -> bool: """ Import threshold configuration. @@ -466,8 +463,6 @@ def import_config(self, config: Dict[str, Any]) -> bool: return False - - # Global threshold configuration instance _global_threshold_config: Optional[ThresholdConfig] = None diff --git a/src/neuview/services/threshold_service.py b/src/neuview/services/threshold_service.py index c7b208e2..5d2a9bc0 100644 --- a/src/neuview/services/threshold_service.py +++ b/src/neuview/services/threshold_service.py @@ -372,8 +372,6 @@ def layer_thresholds(self, values: Any, n_bins: int = 5) -> List[float]: """ return self.calculate_thresholds(values, n_bins, method="linear") - - def validate_thresholds(self, thresholds: List[float]) -> bool: """ Validate that thresholds are properly ordered and contain valid values. @@ -401,8 +399,6 @@ def validate_thresholds(self, thresholds: List[float]) -> bool: except (TypeError, ValueError): return False - - def get_roi_filtering_threshold( self, profile_name: str = "roi_filtering_default" ) -> float: diff --git a/src/neuview/services/url_generation_service.py b/src/neuview/services/url_generation_service.py index 14202166..60f4dcee 100644 --- a/src/neuview/services/url_generation_service.py +++ b/src/neuview/services/url_generation_service.py @@ -172,9 +172,3 @@ def generate_neuprint_url( # Return a fallback URL if URL generation fails logger.warning(f"Failed to generate NeuPrint URL for {neuron_type}: {e}") return f"https://{self.config.neuprint.server}/?dataset={self.config.neuprint.dataset}" - - - - - - diff --git a/src/neuview/utils/text_utils.py b/src/neuview/utils/text_utils.py index 4ba6c290..b0d6da99 100644 --- a/src/neuview/utils/text_utils.py +++ b/src/neuview/utils/text_utils.py @@ -294,5 +294,3 @@ def clean_roi_name(roi_name: str) -> str: .replace("_L", "") .replace("_R", "") ) - - diff --git a/src/neuview/visualization/color/palette.py b/src/neuview/visualization/color/palette.py index 07ca1d1d..c3140547 100644 --- a/src/neuview/visualization/color/palette.py +++ b/src/neuview/visualization/color/palette.py @@ -191,4 +191,3 @@ def hex_to_rgb(hex_color: str) -> tuple: return tuple(int(hex_color[i : i + 2], 16) for i in (0, 2, 4)) except ValueError as e: raise ValueError(f"Invalid hex color '{hex_color}': {e}") - diff --git a/src/neuview/visualization/config_manager.py b/src/neuview/visualization/config_manager.py index 4c0cc257..947d8944 100644 --- a/src/neuview/visualization/config_manager.py +++ b/src/neuview/visualization/config_manager.py @@ -224,9 +224,6 @@ def get_coordinate_system_params(self) -> Dict[str, Any]: "margin": self.margin, } - - - def __str__(self) -> str: """String representation of configuration.""" return ( @@ -318,7 +315,3 @@ def create_for_generation( } return EyemapConfiguration(**config_params) - - - - diff --git a/src/neuview/visualization/coordinate_system.py b/src/neuview/visualization/coordinate_system.py index 12e3c3cd..7805c6ef 100644 --- a/src/neuview/visualization/coordinate_system.py +++ b/src/neuview/visualization/coordinate_system.py @@ -387,7 +387,6 @@ def __init__( self.geometry = HexagonGeometry(hex_size) self.layout = HexagonGridLayout(hex_size, margin) - def convert_column_coordinates( self, columns: List[Dict], mirror_side: Optional[str] = None ) -> List[Dict]: diff --git a/src/neuview/visualization/data_processing/column_data_manager.py b/src/neuview/visualization/data_processing/column_data_manager.py index 871fc145..062becba 100644 --- a/src/neuview/visualization/data_processing/column_data_manager.py +++ b/src/neuview/visualization/data_processing/column_data_manager.py @@ -8,14 +8,11 @@ import logging from typing import List, Dict, Set, Tuple, Optional, Any -from collections import defaultdict from .data_structures import ( ColumnData, ColumnCoordinate, ColumnStatus, - MetricType, SomaSide, - RegionColumnsMap, ColumnDataMap, ) from .validation_manager import ValidationManager @@ -104,11 +101,6 @@ def organize_structured_data_by_side( ) return data_maps - - - - - def determine_column_status( self, coordinate: ColumnCoordinate, @@ -144,11 +136,6 @@ def determine_column_status( else: return ColumnStatus.EXCLUDED - - - - - def validate_data_consistency(self, columns: List[ColumnData]) -> Dict[str, Any]: """ Validate consistency of column data. diff --git a/src/neuview/visualization/data_processing/metric_calculator.py b/src/neuview/visualization/data_processing/metric_calculator.py index 41297e2f..7be4722e 100644 --- a/src/neuview/visualization/data_processing/metric_calculator.py +++ b/src/neuview/visualization/data_processing/metric_calculator.py @@ -8,9 +8,9 @@ import logging import math -from typing import List, Dict, Optional, Tuple, Any +from typing import List, Optional, Tuple import numpy as np -from .data_structures import ColumnData, MetricType, MinMaxData +from .data_structures import ColumnData, MetricType from .validation_manager import ValidationManager logger = logging.getLogger(__name__) @@ -114,12 +114,6 @@ def normalize_value( # Clamp to target range return max(target_min, min(target_max, scaled)) - - - - - - def _calculate_skewness(self, values: np.ndarray) -> float: """Calculate skewness of a distribution.""" if len(values) < 3: @@ -196,5 +190,3 @@ def _classify_layer_pattern(self, values: List[float]) -> str: return "uniform" else: return "distributed" - - diff --git a/src/neuview/visualization/data_processing/threshold_calculator.py b/src/neuview/visualization/data_processing/threshold_calculator.py index 293cdb67..adfbc6a9 100644 --- a/src/neuview/visualization/data_processing/threshold_calculator.py +++ b/src/neuview/visualization/data_processing/threshold_calculator.py @@ -169,7 +169,6 @@ def calculate_min_max_data( global_max_cells=global_max_cells, ) - def _extract_metric_values( self, column_data: List[ColumnData], @@ -420,7 +419,6 @@ def validate_thresholds(self, thresholds: ThresholdData) -> ValidationResult: """ return self.validation_manager.validate_threshold_data(thresholds) - def _score_threshold_distribution( self, values_array: np.ndarray, thresholds: List[float] ) -> float: diff --git a/src/neuview/visualization/data_processing/validation_manager.py b/src/neuview/visualization/data_processing/validation_manager.py index 543f23f3..cb0b676a 100644 --- a/src/neuview/visualization/data_processing/validation_manager.py +++ b/src/neuview/visualization/data_processing/validation_manager.py @@ -17,7 +17,6 @@ SomaSide, ColumnStatus, ThresholdData, - MinMaxData, ) logger = logging.getLogger(__name__) @@ -371,8 +370,6 @@ def _validate_threshold_list(self, thresholds: List[float]) -> bool: return True - - def validate_data_consistency( self, column_data: List[ColumnData], diff --git a/src/neuview/visualization/data_transfer_objects.py b/src/neuview/visualization/data_transfer_objects.py index f893aff4..9312dd41 100644 --- a/src/neuview/visualization/data_transfer_objects.py +++ b/src/neuview/visualization/data_transfer_objects.py @@ -112,9 +112,9 @@ class RenderingRequest: min_val: float max_val: float thresholds: Dict - plot_desc: str # e.g. "Synapses (All Columns)" - roi: str # ROI label, e.g. "ME" / "LO" / "LOP" - neuron_type: str # Cell type label, e.g. "CT1" / "Tm3" + plot_desc: str # e.g. "Synapses (All Columns)" + roi: str # ROI label, e.g. "ME" / "LO" / "LOP" + neuron_type: str # Cell type label, e.g. "CT1" / "Tm3" metric_type: str soma_side: SomaSide output_format: str = "svg" diff --git a/src/neuview/visualization/dependency_injection.py b/src/neuview/visualization/dependency_injection.py index fee84d9b..83ff1308 100644 --- a/src/neuview/visualization/dependency_injection.py +++ b/src/neuview/visualization/dependency_injection.py @@ -26,7 +26,6 @@ from .color import ColorMapper from .coordinate_system import EyemapCoordinateSystem from .rendering import RenderingManager - from .eyemap_generator import EyemapGenerator # Configuration and exceptions are safe to import at module level from .config_manager import ConfigurationManager, EyemapConfiguration @@ -322,7 +321,6 @@ def _resolve_by_string(self, service_name: str) -> Any: f"Service '{service_name}' not found", service_type=service_name ) - def is_registered(self, service_type: Type[T]) -> bool: """Check if a service type is registered. @@ -337,7 +335,6 @@ def clear_scoped(self) -> None: self._scoped_instances.clear() logger.debug("Cleared scoped service instances") - def _create_instance(self, descriptor: ServiceDescriptor) -> Any: """ Create an instance using the service descriptor. @@ -501,7 +498,6 @@ def _register_eyemap_generator(self) -> None: logger.debug("Registered EyemapGenerator service") - # Global container instance for convenience _default_container: Optional[EyemapServiceContainer] = None @@ -528,8 +524,6 @@ def get_default_container() -> EyemapServiceContainer: return _default_container - - def reset_default_container() -> None: """Reset the default container to None, forcing recreation on next access.""" global _default_container diff --git a/src/neuview/visualization/exceptions.py b/src/neuview/visualization/exceptions.py index 6b35216e..476c249a 100644 --- a/src/neuview/visualization/exceptions.py +++ b/src/neuview/visualization/exceptions.py @@ -7,7 +7,7 @@ """ import logging -from typing import Any, Dict, List, Optional, Union, Type +from typing import Any, Dict, List, Optional, Type from pathlib import Path logger = logging.getLogger(__name__) @@ -233,14 +233,6 @@ def validate_type(value: Any, expected_type: Type, field_name: str) -> None: ) - - - - - - - - def safe_operation(operation_name: str, operation_func, *args, **kwargs): """ Execute an operation with comprehensive error handling and logging. diff --git a/src/neuview/visualization/eyemap_generator.py b/src/neuview/visualization/eyemap_generator.py index 5a7adbaf..91d3e103 100644 --- a/src/neuview/visualization/eyemap_generator.py +++ b/src/neuview/visualization/eyemap_generator.py @@ -7,7 +7,7 @@ import logging import time -from typing import Any, Dict, List, Optional, Union +from typing import Dict, List, Optional from .color import ColorMapper, ColorPalette from .config_manager import EyemapConfiguration @@ -31,7 +31,7 @@ SingleRegionGridRequest, create_rendering_request, ) -from .dependency_injection import EyemapServiceContainer, get_default_container +from .dependency_injection import EyemapServiceContainer from .exceptions import ( DataProcessingError, ErrorContext, @@ -154,8 +154,6 @@ def __init__( logger.error(f"Failed to resolve services from container: {e}") raise - - @performance_timer("generate_comprehensive_region_hexagonal_grids") @performance_timer("comprehensive_grid_generation") def generate_comprehensive_region_hexagonal_grids( @@ -677,9 +675,7 @@ def generate_comprehensive_single_region_grid( thresholds=rendering_request.thresholds, save_to_files=rendering_request.save_to_file, min_max_data=rendering_request.min_max_data, - page_soma_side=getattr( - rendering_request, "page_soma_side", None - ), + page_soma_side=getattr(rendering_request, "page_soma_side", None), ) # Create temporary manager with updated config @@ -744,7 +740,6 @@ def generate_comprehensive_single_region_grid( operation="single_region_grid_generation", ) from e - def _determine_value_range(self, thresholds: Optional[Dict]) -> Dict[str, float]: """ Determine the value range from thresholds. @@ -1030,9 +1025,6 @@ def _generate_tooltips_for_hexagons( return processed_hexagons - - - def _determine_mirror_side_with_context( self, soma_side: SomaSide, current_side: str = None ) -> str: diff --git a/src/neuview/visualization/file_output_manager.py b/src/neuview/visualization/file_output_manager.py index 863d11bf..47581c5a 100644 --- a/src/neuview/visualization/file_output_manager.py +++ b/src/neuview/visualization/file_output_manager.py @@ -7,9 +7,8 @@ """ import logging -import os from pathlib import Path -from typing import Dict, Optional, Union +from typing import Dict, Optional from .rendering import OutputFormat @@ -148,9 +147,7 @@ def _save_grids_to_files( # contralateral when the page's original soma side differs from the # hemisphere being drawn. page_soma = getattr(request, "page_soma_side", None) - is_contralateral = ( - page_soma is not None and page_soma != request.soma_side - ) + is_contralateral = page_soma is not None and page_soma != request.soma_side synapse_filename = self._generate_filename( region, request.neuron_type, side, "synapse_density", is_contralateral ) @@ -257,16 +254,11 @@ def get_output_path( return None - - - - class FileOutputManagerFactory: """ Factory class for creating FileOutputManager instances. """ - @staticmethod def create_from_config(config) -> FileOutputManager: """ @@ -281,4 +273,3 @@ def create_from_config(config) -> FileOutputManager: return FileOutputManager( output_dir=config.output_dir, eyemaps_dir=config.eyemaps_dir ) - diff --git a/src/neuview/visualization/performance/memory.py b/src/neuview/visualization/performance/memory.py index 4130faf5..6a1a7f4f 100644 --- a/src/neuview/visualization/performance/memory.py +++ b/src/neuview/visualization/performance/memory.py @@ -473,5 +473,3 @@ def memory_limit_context(limit_mb: int): f"Memory limit exceeded: {final_memory:.1f}MB > {limit_mb}MB" ) optimizer.force_garbage_collection() - - diff --git a/src/neuview/visualization/performance/monitoring.py b/src/neuview/visualization/performance/monitoring.py index 8cd3b296..510ff0ad 100644 --- a/src/neuview/visualization/performance/monitoring.py +++ b/src/neuview/visualization/performance/monitoring.py @@ -13,7 +13,7 @@ from contextlib import contextmanager from dataclasses import dataclass, field from functools import wraps -from typing import Any, Callable, Dict, List, Optional, Union +from typing import Any, Callable, Dict, List, Optional import psutil @@ -180,7 +180,6 @@ def get_current_memory_mb(self) -> float: """Get current memory usage in MB.""" return self._process.memory_info().rss / 1024 / 1024 - def get_recent_metrics(self, limit: int = 100) -> List[Dict[str, Any]]: """Get recent performance metrics.""" with self._lock: @@ -203,7 +202,6 @@ def get_memory_intensive_operations(self, limit: int = 10) -> List[Dict[str, Any ) return [metric.to_dict() for metric in sorted_metrics[:limit]] - def clear_metrics(self) -> None: """Clear all recorded metrics.""" with self._lock: @@ -374,8 +372,6 @@ def __init__(self, monitor: PerformanceMonitor): self.monitor = monitor - - # Global performance monitor instance _global_monitor = None diff --git a/src/neuview/visualization/performance/optimizers.py b/src/neuview/visualization/performance/optimizers.py index 23b54fd1..10515094 100644 --- a/src/neuview/visualization/performance/optimizers.py +++ b/src/neuview/visualization/performance/optimizers.py @@ -9,7 +9,7 @@ import hashlib import logging from abc import ABC -from typing import Dict, List, Optional, Tuple +from typing import Dict, List, Optional from .cache import get_cache_manager from .memory import MemoryOptimizer, StreamingHexagonProcessor @@ -68,7 +68,6 @@ def __init__(self, **kwargs): ) @performance_timer("coordinate_conversion") - def _generate_coordinate_cache_key( self, columns: List[Dict], soma_side: Optional[str] ) -> str: @@ -198,7 +197,6 @@ def compute_color_optimized( return color - def _generate_color_cache_key( self, value: float, min_value: float, max_value: float ) -> str: @@ -234,7 +232,6 @@ def __init__(self, **kwargs): ) @performance_timer("metadata_generation") - def _generate_metadata_cache_key(self, request) -> str: """Generate cache key for metadata based on request parameters.""" key_components = [ @@ -290,7 +287,6 @@ def __init__(self, batch_size: int = 1000, **kwargs): ) @performance_timer("hexagon_collection_creation") - def _create_hexagons_streaming( self, processing_result, coord_to_pixel, request, value_range, color_optimizer ): diff --git a/src/neuview/visualization/region_grid_processor.py b/src/neuview/visualization/region_grid_processor.py index 50762594..31eb5de8 100644 --- a/src/neuview/visualization/region_grid_processor.py +++ b/src/neuview/visualization/region_grid_processor.py @@ -276,8 +276,6 @@ def determine_mirror_side(self, soma_side: str, current_side: str) -> str: return "right" # No mirroring for left soma side - - class RegionGridProcessorFactory: """ Factory class for creating RegionGridProcessor instances. @@ -295,4 +293,3 @@ def create_processor(data_processor: DataProcessor) -> RegionGridProcessor: New RegionGridProcessor instance """ return RegionGridProcessor(data_processor) - diff --git a/src/neuview/visualization/rendering/layout_calculator.py b/src/neuview/visualization/rendering/layout_calculator.py index dc18ef1e..742c9ee4 100644 --- a/src/neuview/visualization/rendering/layout_calculator.py +++ b/src/neuview/visualization/rendering/layout_calculator.py @@ -297,6 +297,3 @@ def _calculate_layer_control_position( control_y = svg_height - total_control_height / 2 - self.margin return control_x, control_y - - - diff --git a/src/neuview/visualization/rendering/png_renderer.py b/src/neuview/visualization/rendering/png_renderer.py index f3b501b2..ee993569 100644 --- a/src/neuview/visualization/rendering/png_renderer.py +++ b/src/neuview/visualization/rendering/png_renderer.py @@ -12,7 +12,6 @@ import logging import cairosvg -from PIL import Image from .base_renderer import BaseRenderer from .svg_renderer import SVGRenderer @@ -155,9 +154,6 @@ def _convert_svg_to_png(self, svg_content: str) -> str: logger.error(f"Failed to convert SVG to PNG: {e}") raise ValueError(f"SVG to PNG conversion failed: {e}") - - - def update_config(self, **config_updates) -> None: """ Update rendering configuration and reset cached components. @@ -173,4 +169,3 @@ def update_config(self, **config_updates) -> None: } if svg_config_updates: self.svg_renderer.update_config(**svg_config_updates) - diff --git a/src/neuview/visualization/rendering/region_config.py b/src/neuview/visualization/rendering/region_config.py index dbde5200..de2a7157 100644 --- a/src/neuview/visualization/rendering/region_config.py +++ b/src/neuview/visualization/rendering/region_config.py @@ -114,7 +114,6 @@ def get_config(cls, region: str) -> RegionConfig: # Return default config for unknown regions return cls._default_config - @classmethod def get_display_layer_name(cls, region: str, layer_num: int) -> str: """ @@ -141,6 +140,3 @@ def get_control_dimensions(cls, region: str) -> Dict[str, float]: Dictionary with control dimension parameters """ return cls.get_config(region).calculate_control_dimensions() - - - diff --git a/src/neuview/visualization/rendering/rendering_config.py b/src/neuview/visualization/rendering/rendering_config.py index a09bc710..cfdf5ab1 100644 --- a/src/neuview/visualization/rendering/rendering_config.py +++ b/src/neuview/visualization/rendering/rendering_config.py @@ -53,11 +53,11 @@ class RenderingConfig: png_scale: float = 1.0 # Content configuration - plot_desc: str = "" # metric label, e.g. "Synapses (All Columns)" + plot_desc: str = "" # metric label, e.g. "Synapses (All Columns)" metric_type: str = "" soma_side: Optional[SomaSide] = None - neuron_type: Optional[str] = None # cell type label, e.g. "CT1" - region_name: Optional[str] = None # ROI label, e.g. "ME" + neuron_type: Optional[str] = None # cell type label, e.g. "CT1" + region_name: Optional[str] = None # ROI label, e.g. "ME" # The page's original soma side. When it differs from ``soma_side`` the # rendered hemisphere is contralateral to the soma side; the SVG template # uses the difference to colour the two header badges differently. diff --git a/src/neuview/visualization/rendering/rendering_manager.py b/src/neuview/visualization/rendering/rendering_manager.py index 98604498..82678301 100644 --- a/src/neuview/visualization/rendering/rendering_manager.py +++ b/src/neuview/visualization/rendering/rendering_manager.py @@ -141,7 +141,6 @@ def _get_renderer(self, output_format: OutputFormat) -> BaseRenderer: return self._renderers[output_format] - def update_config(self, **config_updates) -> None: """ Update rendering configuration for all renderers. @@ -162,8 +161,6 @@ def update_config(self, **config_updates) -> None: for renderer in self._renderers.values(): renderer.update_config(**config_updates) - - def validate_configuration(self) -> List[str]: """ Validate the current configuration and return any issues. diff --git a/test/services/test_scatterplot_service.py b/test/services/test_scatterplot_service.py index e410b712..1ad12439 100644 --- a/test/services/test_scatterplot_service.py +++ b/test/services/test_scatterplot_service.py @@ -28,8 +28,6 @@ from __future__ import annotations import logging -import os -import sys from copy import deepcopy from dataclasses import dataclass, field from types import SimpleNamespace @@ -535,9 +533,7 @@ def test_mixed_input_returns_ctx_with_only_in_range(self, caplog): ctx = svc._prepare(svc.scatter_config, points, region="ME", side="L") assert ctx is not None assert sorted(p["name"] for p in ctx["points"]) == ["kept_a", "kept_b"] - assert _warnings_about_range(caplog), ( - "expected an out-of-range warning to fire" - ) + assert _warnings_about_range(caplog), "expected an out-of-range warning to fire" def test_ctx_has_render_metadata_for_kept_points(self): """Each kept point gets sx / sy / color / r / tooltip metadata for the