lint

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>

Author: james-leinas

src/allotropy/allotrope/schema_mappers/adm/binding_affinity_analyzer/benchling/_2024/_12/binding_affinity_analyzer.py

@@ -109,6 +109,7 @@ class DeviceControlDocument:
 @dataclass(frozen=True)
 class ProcessedData:
     """Represents a single processed data document (one analysis model)."""
+
     model_name: str
     binding_on_rate_measurement_datum__kon_: float | None = None
     binding_off_rate_measurement_datum__koff_: float | None = None
@@ -310,7 +311,9 @@ def _get_surface_plasmon_resonance_measurement_document(
                         proc_data.maximum_binding_capacity__rmax_,
                     ),
                     # Only include report points in the first processed data document
-                    report_point_aggregate_document=report_point_aggregate if idx == 0 else None,
+                    report_point_aggregate_document=report_point_aggregate
+                    if idx == 0
+                    else None,
                 )
                 processed_data_documents.append(
                     add_custom_information_document(

src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_data_creator.py

@@ -140,18 +140,14 @@ def _get_measurements(
                     equilibrium_dissociation_constant__kd_=(
                         kinetics.equilibrium_dissociation_constant
                     ),
-                    maximum_binding_capacity__rmax_=(
-                        kinetics.maximum_binding_capacity
-                    ),
+                    maximum_binding_capacity__rmax_=(kinetics.maximum_binding_capacity),
                     processed_data_custom_info=_clean_custom_info(
                         {
                             chi_squared_label: quantity_or_none(
                                 TQuantityValueSquareResponseUnit,
                                 kinetics.kinetics_chi_squared,
                             ),
-                            "tc": quantity_or_none(
-                                TQuantityValueUnitless, kinetics.tc
-                            ),
+                            "tc": quantity_or_none(TQuantityValueUnitless, kinetics.tc),
                             "U-value": quantity_or_none(
                                 TQuantityValueUnitless, kinetics.u_value
                             ),
@@ -176,7 +172,11 @@ def _get_measurements(
             processed_data_list.append(
                 ProcessedData(
                     model_name="N/A",  # No model when there's no kinetics data
-                    data_processing_document=_clean_custom_info(data_processing_document) if data_processing_document else None,
+                    data_processing_document=_clean_custom_info(
+                        data_processing_document
+                    )
+                    if data_processing_document
+                    else None,
                 )
             )
 

src/allotropy/parsers/cytiva_biacore_insight/cytiva_biacore_insight_structure.py

@@ -408,8 +408,12 @@ def create_from_kinetics_model(kinetics_data: SeriesData) -> KineticsData | None
             curve_markers=kinetics_data.get(str, "Curve markers"),
             binding_on_rate_measurement_datum=kinetics_data.get(float, "ka (1/Ms)"),
             binding_off_rate_measurement_datum=kinetics_data.get(float, "kd (1/s)"),
-            equilibrium_dissociation_constant=kinetics_data.get(float, "KD (M)", duplicate_strategy="first"),
-            maximum_binding_capacity=kinetics_data.get(float, "Rmax (RU)", duplicate_strategy="first"),
+            equilibrium_dissociation_constant=kinetics_data.get(
+                float, "KD (M)", duplicate_strategy="first"
+            ),
+            maximum_binding_capacity=kinetics_data.get(
+                float, "Rmax (RU)", duplicate_strategy="first"
+            ),
             kinetics_chi_squared=kinetics_data.get(float, "Kinetics Chi² (RU²)"),
             u_value=kinetics_data.get(float, "U-value"),
             tc=kinetics_data.get(float, "tc"),
@@ -428,8 +432,12 @@ def create_from_affinity_model(kinetics_data: SeriesData) -> KineticsData | None
             model_name=model,
             acceptance_state=kinetics_data.get(str, "Acceptance state"),
             curve_markers=kinetics_data.get(str, "Curve markers"),
-            equilibrium_dissociation_constant=kinetics_data.get(float, "KD (M)", duplicate_strategy="last"),
-            maximum_binding_capacity=kinetics_data.get(float, "Rmax (RU)", duplicate_strategy="last"),
+            equilibrium_dissociation_constant=kinetics_data.get(
+                float, "KD (M)", duplicate_strategy="last"
+            ),
+            maximum_binding_capacity=kinetics_data.get(
+                float, "Rmax (RU)", duplicate_strategy="last"
+            ),
             kinetics_chi_squared=kinetics_data.get(float, "Affinity Chi² (RU²)"),
             offset=kinetics_data.get(float, "offset (RU)"),
             tc=kinetics_data.get(float, "tc"),
@@ -447,7 +455,9 @@ def _get_key(row: pd.Series[Any]) -> str:
             # Build key with all available capture solutions
             capture_solution = row.get("Capture 1 Solution", "")
             # Handle None, NaN, or pd.NA values for capture_solution
-            if capture_solution is None or (isinstance(capture_solution, float) and np.isnan(capture_solution)):
+            if capture_solution is None or (
+                isinstance(capture_solution, float) and np.isnan(capture_solution)
+            ):
                 capture_solution = ""
             analyte_solution = row.get("Analyte 1 Solution", "")
             return f"{channel_or_flowcell} {capture_solution} {analyte_solution}"
@@ -460,9 +470,13 @@ def _get_key(row: pd.Series[Any]) -> str:
 
                 # Try to create both kinetics and affinity models
                 models = []
-                if kinetics_model := KineticsData.create_from_kinetics_model(series_data):
+                if kinetics_model := KineticsData.create_from_kinetics_model(
+                    series_data
+                ):
                     models.append(kinetics_model)
-                if affinity_model := KineticsData.create_from_affinity_model(series_data):
+                if affinity_model := KineticsData.create_from_affinity_model(
+                    series_data
+                ):
                     models.append(affinity_model)
 
                 if models:

src/allotropy/parsers/cytiva_biacore_t200_control/cytiva_biacore_t200_control_data_creator.py

@@ -170,9 +170,7 @@ def create_measurements(
 
         # Wrap report points in a ProcessedData object (required by new schema)
         processed_data = (
-            [ProcessedData(model_name="N/A")]
-            if report_points is not None
-            else None
+            [ProcessedData(model_name="N/A")] if report_points is not None else None
         )
 
         measurements.append(
@@ -211,7 +209,9 @@ def create_measurements(
                     ),
                     **measurement.sample_custom_info,
                 },
-                sensorgram_data_cube=_get_sensorgram_datacube(measurement.sensorgram_data),
+                sensorgram_data_cube=_get_sensorgram_datacube(
+                    measurement.sensorgram_data
+                ),
                 report_point_data=report_points,
                 processed_data=processed_data,
                 # for Mobilization experiments

src/allotropy/parsers/cytiva_biacore_t200_evaluation/cytiva_biacore_t200_evaluation_data_creator.py

@@ -385,15 +385,19 @@ def _normalize_flow_cell_id(value: Any) -> str:
         # Extract kinetic parameters
         kon = _extract_kinetic_parameter(kinetic_data, "parameters", ["ka", "kon"])
         koff = _extract_kinetic_parameter(kinetic_data, "parameters", ["kd", "koff"])
-        kd = _extract_kinetic_parameter(kinetic_data, "calculated", ["Kd_M", "KD", "kd"])
+        kd = _extract_kinetic_parameter(
+            kinetic_data, "calculated", ["Kd_M", "KD", "kd"]
+        )
         rmax = _extract_kinetic_parameter(kinetic_data, "parameters", ["Rmax", "rmax"])
 
         # Create processed data object if we have kinetic data
         processed_data_list = None
         if kinetic_data is not None:
             processed_data_list = [
                 ProcessedData(
-                    model_name=kinetic_data.get("model", "N/A") if isinstance(kinetic_data, dict) else "N/A",
+                    model_name=kinetic_data.get("model", "N/A")
+                    if isinstance(kinetic_data, dict)
+                    else "N/A",
                     binding_on_rate_measurement_datum__kon_=kon,
                     binding_off_rate_measurement_datum__koff_=koff,
                     equilibrium_dissociation_constant__kd_=kd,