fix: resolve remaining type check issues

src/batdetect2/compat/data.py

@@ -102,19 +102,19 @@ def convert_to_annotation_group(
         x_inds.append(0)
         y_inds.append(0)
 
-        annotations.append(
-            Annotation(
-                start_time=start_time,
-                end_time=end_time,
-                low_freq=low_freq,
-                high_freq=high_freq,
-                class_prob=1.0,
-                det_prob=1.0,
-                individual="0",
-                event=event,
-                class_id=class_id,
-            )
-        )
+        annotation_entry: Annotation = {
+            "start_time": start_time,
+            "end_time": end_time,
+            "low_freq": low_freq,
+            "high_freq": high_freq,
+            "class_prob": 1.0,
+            "det_prob": 1.0,
+            "individual": "0",
+            "event": event,
+            "class": get_recording_class_name(recording),
+            "class_id": class_id,
+        }
+        annotations.append(annotation_entry)
 
     return {
         "id": str(recording.path),

src/batdetect2/core/registries.py

@@ -53,7 +53,7 @@ class Registry(Generic[T_Type, P_Type]):
     def __init__(self, name: str, discriminator: str = "name"):
         self._name = name
         self._registry: dict[
-            str, Callable[Concatenate[..., P_Type], T_Type]
+            str, Callable[Concatenate[Any, P_Type], T_Type]
         ] = {}
         self._discriminator = discriminator
         self._config_types: dict[str, Type[BaseModel]] = {}
@@ -80,7 +80,7 @@ class Registry(Generic[T_Type, P_Type]):
             )
 
         def decorator(
-            func: Callable[Concatenate[T_Config, P_Type], T_Type],
+            func: Callable[..., T_Type],
         ):
             self._registry[name] = func
             return func
@@ -102,8 +102,8 @@ class Registry(Generic[T_Type, P_Type]):
     def build(
         self,
         config: BaseModel,
-        *args: P_Type.args,
-        **kwargs: P_Type.kwargs,
+        *args: Any,
+        **kwargs: Any,
     ) -> T_Type:
         """Builds a logic instance from a config object."""
 

src/batdetect2/evaluate/config.py

@@ -12,13 +12,15 @@ __all__ = [
 ]
 
 
+def _default_tasks() -> list[TaskConfig]:
+    return [
+        DetectionTaskConfig(),
+        ClassificationTaskConfig(),
+    ]
+
+
 class EvaluationConfig(BaseConfig):
-    tasks: List[TaskConfig] = Field(
-        default_factory=lambda: [
-            DetectionTaskConfig(),
-            ClassificationTaskConfig(),
-        ]
-    )
+    tasks: List[TaskConfig] = Field(default_factory=_default_tasks)
 
 
 def get_default_eval_config() -> EvaluationConfig:

src/batdetect2/evaluate/tasks/classification.py

@@ -25,11 +25,15 @@ from batdetect2.postprocess.types import ClipDetections, Detection
 from batdetect2.targets.types import TargetProtocol
 
 
+def _default_metrics() -> list[ClassificationMetricConfig]:
+    return [ClassificationAveragePrecisionConfig()]
+
+
 class ClassificationTaskConfig(BaseSEDTaskConfig):
     name: Literal["sound_event_classification"] = "sound_event_classification"
     prefix: str = "classification"
     metrics: list[ClassificationMetricConfig] = Field(
-        default_factory=lambda: [ClassificationAveragePrecisionConfig()]
+        default_factory=_default_metrics
     )
     plots: list[ClassificationPlotConfig] = Field(default_factory=list)
     include_generics: bool = True

src/batdetect2/evaluate/tasks/clip_classification.py

@@ -23,13 +23,15 @@ from batdetect2.postprocess.types import ClipDetections
 from batdetect2.targets.types import TargetProtocol
 
 
+def _default_metrics() -> list[ClipClassificationMetricConfig]:
+    return [ClipClassificationAveragePrecisionConfig()]
+
+
 class ClipClassificationTaskConfig(BaseTaskConfig):
     name: Literal["clip_classification"] = "clip_classification"
     prefix: str = "clip_classification"
     metrics: list[ClipClassificationMetricConfig] = Field(
-        default_factory=lambda: [
-            ClipClassificationAveragePrecisionConfig(),
-        ]
+        default_factory=_default_metrics
     )
     plots: list[ClipClassificationPlotConfig] = Field(default_factory=list)
 

src/batdetect2/evaluate/tasks/clip_detection.py

@@ -22,13 +22,15 @@ from batdetect2.postprocess.types import ClipDetections
 from batdetect2.targets.types import TargetProtocol
 
 
+def _default_metrics() -> list[ClipDetectionMetricConfig]:
+    return [ClipDetectionAveragePrecisionConfig()]
+
+
 class ClipDetectionTaskConfig(BaseTaskConfig):
     name: Literal["clip_detection"] = "clip_detection"
     prefix: str = "clip_detection"
     metrics: list[ClipDetectionMetricConfig] = Field(
-        default_factory=lambda: [
-            ClipDetectionAveragePrecisionConfig(),
-        ]
+        default_factory=_default_metrics
     )
     plots: list[ClipDetectionPlotConfig] = Field(default_factory=list)
 

src/batdetect2/evaluate/tasks/detection.py

@@ -24,11 +24,15 @@ from batdetect2.postprocess.types import ClipDetections
 from batdetect2.targets.types import TargetProtocol
 
 
+def _default_metrics() -> list[DetectionMetricConfig]:
+    return [DetectionAveragePrecisionConfig()]
+
+
 class DetectionTaskConfig(BaseSEDTaskConfig):
     name: Literal["sound_event_detection"] = "sound_event_detection"
     prefix: str = "detection"
     metrics: list[DetectionMetricConfig] = Field(
-        default_factory=lambda: [DetectionAveragePrecisionConfig()]
+        default_factory=_default_metrics
     )
     plots: list[DetectionPlotConfig] = Field(default_factory=list)
 

src/batdetect2/evaluate/tasks/top_class.py

@@ -24,11 +24,15 @@ from batdetect2.postprocess.types import ClipDetections
 from batdetect2.targets.types import TargetProtocol
 
 
+def _default_metrics() -> list[TopClassMetricConfig]:
+    return [TopClassAveragePrecisionConfig()]
+
+
 class TopClassDetectionTaskConfig(BaseSEDTaskConfig):
     name: Literal["top_class_detection"] = "top_class_detection"
     prefix: str = "top_class"
     metrics: list[TopClassMetricConfig] = Field(
-        default_factory=lambda: [TopClassAveragePrecisionConfig()]
+        default_factory=_default_metrics
     )
     plots: list[TopClassPlotConfig] = Field(default_factory=list)
 

src/batdetect2/outputs/formats/batdetect2.py

@@ -154,17 +154,18 @@ class BatDetect2Formatter(OutputFormatterProtocol[FileAnnotation]):
         top_class_index = int(np.argmax(prediction.class_scores))
         top_class_score = float(prediction.class_scores[top_class_index])
         top_class = self.get_class_name(top_class_index)
-        return Annotation(
-            start_time=start_time,
-            end_time=end_time,
-            low_freq=low_freq,
-            high_freq=high_freq,
-            class_prob=top_class_score,
-            det_prob=float(prediction.detection_score),
-            individual="",
-            event=self.event_name,
-            **{"class": top_class},
-        )
+        annotation: Annotation = {
+            "start_time": start_time,
+            "end_time": end_time,
+            "low_freq": low_freq,
+            "high_freq": high_freq,
+            "class_prob": top_class_score,
+            "det_prob": float(prediction.detection_score),
+            "individual": "",
+            "event": self.event_name,
+            "class": top_class,
+        }
+        return annotation
 
     @output_formatters.register(BatDetect2OutputConfig)
     @staticmethod

src/batdetect2/preprocess/config.py

@@ -26,6 +26,13 @@ __all__ = [
 ]
 
 
+def _default_spectrogram_transforms() -> list[SpectrogramTransform]:
+    return [
+        PcenConfig(),
+        SpectralMeanSubtractionConfig(),
+    ]
+
+
 class PreprocessingConfig(BaseConfig):
     """Unified configuration for the audio preprocessing pipeline.
 
@@ -58,10 +65,7 @@ class PreprocessingConfig(BaseConfig):
     audio_transforms: List[AudioTransform] = Field(default_factory=list)
 
     spectrogram_transforms: List[SpectrogramTransform] = Field(
-        default_factory=lambda: [
-            PcenConfig(),
-            SpectralMeanSubtractionConfig(),
-        ]
+        default_factory=_default_spectrogram_transforms
     )
 
     stft: STFTConfig = Field(default_factory=STFTConfig)

src/batdetect2/targets/classes.py

@@ -71,7 +71,7 @@ class TargetClassConfig(BaseConfig):
 
 DEFAULT_DETECTION_CLASS = TargetClassConfig(
     name="bat",
-    match_if=AllOfConfig(  # ty: ignore[unknown-argument]
+    match_if=AllOfConfig(
         conditions=[
             HasTagConfig(tag=data.Tag(term=call_type, value="Echolocation")),
             NotConfig(