fix: applying some copilot changes

Author: lachlangrose

loopstructural/gui/data_conversion/configuration.py

@@ -1,4 +1,4 @@
-"""configuration helpers used by the data conversion UI."""
+"""Configuration helpers used by the data conversion UI."""
 
 from __future__ import annotations
 

loopstructural/gui/data_conversion/data_conversion_widget.py

@@ -7,6 +7,7 @@
 from dataclasses import dataclass
 from typing import Any, Dict, Iterable, List, Mapping, Optional, Tuple
 
+from LoopDataConverter import Datatype, InputData, LoopConverter, SurveyName
 from PyQt5.QtCore import Qt, QTimer
 from PyQt5.QtWidgets import (
     QComboBox,
@@ -25,7 +26,6 @@
 
 from ...main.helpers import ColumnMatcher
 from ...main.vectorLayerWrapper import QgsLayerFromDataFrame, QgsLayerFromGeoDataFrame
-from LoopDataConverter import Datatype, InputData, LoopConverter, SurveyName
 
 try:
     from geopandas import GeoDataFrame
@@ -34,7 +34,7 @@
 
 try:
     from pandas import DataFrame
-except Exception:  # pragma: no cover - pandas may be unavailable in tests
+except ImportException:  # pragma: no cover - pandas may be unavailable in tests
     DataFrame = None
 
 
@@ -165,18 +165,27 @@ def _normalise_converters(converters: Optional[Iterable[Any]]) -> List[Converter
             )
             label = str(raw.get("label") or raw.get("name") or identifier)
             description = str(raw.get("description") or "")
-            normalised.append(ConverterOption(identifier=identifier, label=label, description=description))
+            normalised.append(
+                ConverterOption(identifier=identifier, label=label, description=description)
+            )
             continue
 
         text = str(raw)
         normalised.append(ConverterOption(identifier=text, label=text, description=""))
     return normalised
 
+
 class AutomaticConversionWidget(QWidget):
     """Widget showing the automatic conversion workflow."""
 
     SUPPORTED_DATA_TYPES: Tuple[str, ...] = ("GEOLOGY", "STRUCTURE", "FAULT", "FOLD")
-    OUTPUT_DATA_TYPES: Tuple[str, ...] = ("GEOLOGY", "STRUCTURE", "FAULT", "FOLD", "FAULT_ORIENTATION")
+    OUTPUT_DATA_TYPES: Tuple[str, ...] = (
+        "GEOLOGY",
+        "STRUCTURE",
+        "FAULT",
+        "FOLD",
+        "FAULT_ORIENTATION",
+    )
     OUTPUT_GROUP_NAME = "Loop-Ready Data"
 
     def __init__(
@@ -208,7 +217,9 @@ def __init__(
         self.summary_text.setMinimumHeight(80)
         layout.addWidget(self.summary_text)
 
-        source_description = QLabel("Select the layers that correspond to each dataset required by the converter.")
+        source_description = QLabel(
+            "Select the layers that correspond to each dataset required by the converter."
+        )
         source_description.setWordWrap(True)
         layout.addWidget(source_description)
 
@@ -221,6 +232,9 @@ def __init__(
             try:
                 self.project.layersAdded.connect(self._guess_layers)
             except Exception:
+                # Best-effort: if the project object does not provide a compatible
+                # layersAdded signal (e.g., in certain QGIS versions or test stubs),
+                # silently skip automatic layer guessing rather than failing the UI.
                 pass
 
         actions_widget = QWidget()
@@ -288,6 +302,8 @@ def _build_data_source_inputs(self) -> None:
                 try:
                     combo.setProject(self.project)
                 except Exception:
+                    # Some QGIS/Qt environments may not support setProject or may raise here;
+                    # failure to bind the project is non-fatal, so we intentionally ignore
                     pass
             combo.setFilters(self._layer_filter_for_data_type(data_type))
             combo.setAllowEmptyLayer(True)
@@ -327,9 +343,7 @@ def _guess_layers(self) -> None:
                 if layer is not None:
                     combo.setLayer(layer)
 
-    def _build_layer_candidate_map(
-        self, combo: QgsMapLayerComboBox
-    ) -> Dict[str, QgsVectorLayer]:
+    def _build_layer_candidate_map(self, combo: QgsMapLayerComboBox) -> Dict[str, QgsVectorLayer]:
         candidates: Dict[str, QgsVectorLayer] = {}
         for layer in self._layers_for_combo(combo):
             if not isinstance(layer, QgsVectorLayer) or not layer.isValid():
@@ -473,9 +487,7 @@ def _handle_run_conversion(self) -> bool:
             return False
 
         if added_layers:
-            message = (
-                f"Conversion completed: {added_layers} layer(s) added to '{self.OUTPUT_GROUP_NAME}'."
-            )
+            message = f"Conversion completed: {added_layers} layer(s) added to '{self.OUTPUT_GROUP_NAME}'."
         elif result not in (None, True):
             message = f"Conversion completed: {result}"
         else:

loopstructural/gui/loop_widget.py

@@ -72,4 +72,3 @@ def get_visualisation_widget(self):
             The visualisation widget.
         """
         return self.visualisation_widget
-

loopstructural/gui/map2loop_tools/thickness_calculator_widget.py

@@ -1,8 +1,8 @@
 """Widget for thickness calculator."""
 
 import os
-import pandas as pd
 
+import pandas as pd
 from PyQt5.QtWidgets import QMessageBox, QWidget
 from qgis.core import QgsMapLayerProxyModel
 from qgis.PyQt import uic
@@ -151,7 +151,7 @@ def _guess_layers(self):
         if structure_layer_match:
             structure_layer = self.data_manager.find_layer_by_name(structure_layer_match)
             self.structureLayerComboBox.setLayer(structure_layer)
-            
+
         # Attempt to find cross-sections layer
         cross_sections_layer_names = get_layer_names(self.crossSectionLayerComboBox)
         cross_sections_matcher = ColumnMatcher(cross_sections_layer_names)
@@ -221,14 +221,14 @@ def _on_calculator_type_changed(self):
             self.maxLineLengthSpinBox.setVisible(True)
             self.crossSectionLayerLabel.setVisible(False)
             self.crossSectionLayerComboBox.setVisible(False)
-            
-        if calculator_type == "InterpolatedStructure":
+
+        elif calculator_type == "InterpolatedStructure":
             self.maxLineLengthLabel.setVisible(False)
             self.maxLineLengthSpinBox.setVisible(False)
             self.crossSectionLayerLabel.setVisible(False)
             self.crossSectionLayerComboBox.setVisible(False)
-            
-        if calculator_type == "AlongSection":
+
+        elif calculator_type == "AlongSection":
             self.crossSectionLayerLabel.setVisible(True)
             self.crossSectionLayerComboBox.setVisible(True)
             self.maxLineLengthLabel.setVisible(False)
@@ -247,7 +247,7 @@ def _restore_selection(self):
             ('basal_contacts_layer', self.basalContactsComboBox),
             ('sampled_contacts_layer', self.sampledContactsComboBox),
             ('structure_layer', self.structureLayerComboBox),
-            ("cross_sections_layer", self.crossSectionLayerComboBox)
+            ("cross_sections_layer", self.crossSectionLayerComboBox),
         ):
             if layer_name := settings.get(key):
                 layer = self.data_manager.find_layer_by_name(layer_name)
@@ -335,13 +335,12 @@ def _run_calculator(self):
             if not self.structureLayerComboBox.currentLayer():
                 QMessageBox.warning(self, "Missing Input", "Please select a structure layer.")
                 return False
-        
+
         elif calculator_type == "AlongSection":
             if not self.crossSectionLayerComboBox.currentLayer():
                 QMessageBox.warning(self, "Missing Input", "Please select a cross-sections layer.")
                 return False
 
-
         # Prepare parameters
         params = self.get_parameters()
 

loopstructural/main/m2l_api.py

@@ -8,7 +8,7 @@
     SorterObservationProjections,
     SorterUseNetworkX,
 )
-from map2loop.thickness_calculator import InterpolatedStructure, StructuralPoint, AlongSection
+from map2loop.thickness_calculator import AlongSection, InterpolatedStructure, StructuralPoint
 from osgeo import gdal
 from qgis.core import QgsVectorLayer
 
@@ -457,7 +457,7 @@ def calculate_thickness(
         else basal_contacts_gdf
     )
     sampled_contacts_gdf = qgsLayerToGeoDataFrame(sampled_contacts)
-    structure_gdf = qgsLayerToGeoDataFrame(structure) 
+    structure_gdf = qgsLayerToGeoDataFrame(structure)
     cross_sections_gdf = qgsLayerToGeoDataFrame(cross_sections)
 
     # Log parameters via DebugManager if provided
@@ -475,7 +475,6 @@ def calculate_thickness(
                 "sampled_contacts": sampled_contacts_gdf,
                 "structure": structure_gdf,
                 "cross_sections": cross_sections_gdf,
-                
             },
         )
 
@@ -485,9 +484,7 @@ def calculate_thickness(
         'maxy': geology_gdf.total_bounds[3],
         'miny': geology_gdf.total_bounds[1],
     }
-    
-    
-        
+
     # Rename unit name field if needed
     if unit_name_field and unit_name_field != 'UNITNAME':
         if unit_name_field in geology_gdf.columns:
@@ -535,8 +532,8 @@ def calculate_thickness(
         calculator = AlongSection(
             bounding_box=bounding_box,
             sections=cross_sections_gdf,
-            )
-    
+        )
+
     if unit_name_field != 'UNITNAME' and unit_name_field in geology_gdf.columns:
         geology_gdf = geology_gdf.rename(columns={unit_name_field: 'UNITNAME'})
     units = geology_gdf.copy()

loopstructural/main/vectorLayerWrapper.py

@@ -599,10 +599,18 @@ def _geometry_from_value(value):
                 try:
                     data = bytes(data)
                 except Exception:
+                    # Best-effort conversion to bytes; if this fails, leave data as-is
+
                     pass
                 try:
                     return QgsGeometry.fromWkb(data)
                 except Exception:
+                    # Best-effort conversion to bytes; if this fails, fall back to using the
+                    # original data and let the subsequent fromWkb call handle it.
+                    logger.debug(
+                        "Failed to convert WKB data to bytes in _geometry_from_value",
+                        exc_info=True,
+                    )
                     continue
     # Shapely geometries expose wkb/wkt attributes
     wkb_data = getattr(value, "wkb", None)
@@ -661,6 +669,7 @@ def _crs_from_geodataframe_crs(crs_info) -> QgsCoordinateReferenceSystem:
         if epsg:
             return QgsCoordinateReferenceSystem.fromEpsgId(int(epsg))
     except Exception:
+        logger.debug("Failed to convert EPSG code to QgsCoordinateReferenceSystem", exc_info=True)
         pass
     if isinstance(crs_info, str):
         try:
@@ -696,7 +705,9 @@ def QgsLayerFromGeoDataFrame(geodataframe, layer_name: str = "Converted Data"):
     for column in geodataframe.columns:
         if column == geometry_column:
             continue
-        attribute_fields.append(QgsField(str(column), _qvariant_type_from_dtype(geodataframe[column].dtype)))
+        attribute_fields.append(
+            QgsField(str(column), _qvariant_type_from_dtype(geodataframe[column].dtype))
+        )
     if attribute_fields:
         provider.addAttributes(attribute_fields)
         layer.updateFields()