Fixed linting errors

Makefile

@@ -32,7 +32,7 @@ lint:             ## Run ruff, black, mypy linters.
 	$(ENV_PREFIX)ruff $(PROJECT_NAME)/
 	$(ENV_PREFIX)black --check $(PROJECT_NAME)/
 	$(ENV_PREFIX)black --check tests/
-	$(ENV_PREFIX)mypy $(PROJECT_NAME)/
+	$(ENV_PREFIX)mypy $(PROJECT_NAME)/ --config-file pyproject.toml
 
 .PHONY: test-watch
 test-watch:    ## Run tests and generate coverage report.

pyproject.toml

@@ -3,12 +3,9 @@ name = "soundevent"
 version = "0.7.0"
 description = "soundevent is an open-source Python package for the computational biocoustic community, providing standardized tools for sound event analysis and data management."
 authors = [
-  { name = "Santiago Martinez", email = "[email protected]" },
-]
-dependencies = [
-    "pydantic>=2.0",
-    "email-validator>=2.1.0.post1",
+    { name = "Santiago Martinez", email = "[email protected]" },
 ]
+dependencies = ["pydantic>=2.0", "email-validator>=2.1.0.post1"]
 requires-python = ">=3.8"
 readme = "README.md"
 license = { text = "MIT" }
@@ -87,6 +84,9 @@ profile = "black"
 
 [tool.mypy]
 ignore_missing_imports = true
+show_error_codes = true
+show_error_code_links = true
+disable_error_code = ["call-overload", "misc"]
 
 [tool.coverage.run]
 branch = true

src/soundevent/audio/io.py

@@ -3,18 +3,17 @@
 Currently only supports reading and writing of .wav files.
 """
 
-import os
+from pathlib import Path
 from typing import Dict, Optional, Tuple
 
 import numpy as np
 import soundfile as sf
 import xarray as xr
 
+from soundevent import data
 from soundevent.audio.chunks import parse_into_chunks
 from soundevent.audio.media_info import extract_media_info_from_chunks
 from soundevent.audio.raw import RawData
-from soundevent.data.clips import Clip
-from soundevent.data.recordings import PathLike, Recording
 
 __all__ = [
     "load_audio",
@@ -35,7 +34,7 @@
 
 
 def load_audio(
-    path: PathLike,
+    path: data.PathLike,
     offset: int = 0,
     samples: Optional[int] = None,
 ) -> Tuple[np.ndarray, int]:
@@ -99,8 +98,8 @@ def load_audio(
 
 
 def load_recording(
-    recording: Recording,
-    audio_dir: Optional[PathLike] = None,
+    recording: data.Recording,
+    audio_dir: Optional[data.PathLike] = None,
 ) -> xr.DataArray:
     """Load a recording from a file.
 
@@ -121,7 +120,7 @@ def load_recording(
     path = recording.path
 
     if audio_dir is not None:
-        path = os.path.join(audio_dir, path)
+        path = Path(audio_dir) / path
 
     data, _ = load_audio(path)
     return xr.DataArray(
@@ -147,8 +146,8 @@ def load_recording(
 
 
 def load_clip(
-    clip: Clip,
-    audio_dir: Optional[PathLike] = None,
+    clip: data.Clip,
+    audio_dir: Optional[data.PathLike] = None,
 ) -> xr.DataArray:
     """Load a clip from a file.
 
@@ -177,7 +176,7 @@ def load_clip(
 
     path = recording.path
     if audio_dir is not None:
-        path = os.path.join(audio_dir, path)
+        path = Path(audio_dir) / path
 
     data, _ = load_audio(
         path,

src/soundevent/io/aoef/annotation_project.py

@@ -9,7 +9,7 @@
 class AnnotationProjectObject(AnnotationSetObject):
     """Schema definition for an annotation project object in AOEF format."""
 
-    collection_type: Literal["annotation_project"] = "annotation_project"
+    collection_type: Literal["annotation_project"] = "annotation_project"  # type: ignore
     name: str
     description: Optional[str] = None
     instructions: Optional[str] = None
@@ -32,7 +32,10 @@ def __init__(
             )
         )
 
-    def to_aoef(self, obj: data.AnnotationProject) -> AnnotationProjectObject:
+    def to_aoef(
+        self,
+        obj: data.AnnotationProject,  # type: ignore
+    ) -> AnnotationProjectObject:
         tasks = [
             self.annotation_task_adapter.to_aoef(task)
             for task in obj.tasks or []
@@ -63,7 +66,7 @@ def to_aoef(self, obj: data.AnnotationProject) -> AnnotationProjectObject:
 
     def to_soundevent(
         self,
-        obj: AnnotationProjectObject,
+        obj: AnnotationProjectObject,  # type: ignore
     ) -> data.AnnotationProject:
         annotation_set = super().to_soundevent(obj)
 

src/soundevent/io/aoef/dataset.py

@@ -8,15 +8,15 @@
 class DatasetObject(RecordingSetObject):
     """Schema definition for a dataset object in AOEF format."""
 
-    collection_type: Literal["dataset"] = "dataset"
+    collection_type: Literal["dataset"] = "dataset"  # type: ignore
     name: str
     description: Optional[str] = None
 
 
 class DatasetAdapter(RecordingSetAdapter):
     def to_aoef(
         self,
-        obj: data.Dataset,
+        obj: data.Dataset,  # type: ignore
     ) -> DatasetObject:
         recording_set = super().to_aoef(obj)
         return DatasetObject(
@@ -31,7 +31,7 @@ def to_aoef(
 
     def to_soundevent(
         self,
-        obj: DatasetObject,
+        obj: DatasetObject,  # type: ignore
     ) -> data.Dataset:
         recording_set = super().to_soundevent(obj)
         return data.Dataset(

src/soundevent/io/aoef/evaluation.py

@@ -193,19 +193,16 @@ def to_soundevent(
                 sound_event_annotation
             )
 
-        for clip_annotations in obj.clip_annotations or []:
-            self.clip_annotations_adapter.to_soundevent(clip_annotations)
+        clip_annotations = [
+            self.clip_annotations_adapter.to_soundevent(clip_predictions)
+            for clip_predictions in obj.clip_annotations or []
+        ]
 
         for sound_event_prediction in obj.sound_event_predictions or []:
             self.sound_event_prediction_adapter.to_soundevent(
                 sound_event_prediction
             )
 
-        clip_annotations = [
-            self.clip_annotations_adapter.to_soundevent(clip_predictions)
-            for clip_predictions in obj.clip_annotations or []
-        ]
-
         clip_predictions = [
             self.clip_predictions_adapter.to_soundevent(evaluated_clip)
             for evaluated_clip in obj.clip_predictions or []

src/soundevent/io/aoef/evaluation_set.py

@@ -8,14 +8,17 @@
 class EvaluationSetObject(AnnotationSetObject):
     """Schema definition for an evaluation set object in AOEF format."""
 
-    collection_type: Literal["evaluation_set"] = "evaluation_set"
+    collection_type: Literal["evaluation_set"] = "evaluation_set"  # type: ignore
     name: str
     description: Optional[str] = None
     evaluation_tags: Optional[List[int]] = None
 
 
 class EvaluationSetAdapter(AnnotationSetAdapter):
-    def to_aoef(self, obj: data.EvaluationSet) -> EvaluationSetObject:
+    def to_aoef(
+        self,
+        obj: data.EvaluationSet,  # type: ignore
+    ) -> EvaluationSetObject:
         annotation_set = super().to_aoef(obj)
         return EvaluationSetObject(
             uuid=annotation_set.uuid,
@@ -36,7 +39,10 @@ def to_aoef(self, obj: data.EvaluationSet) -> EvaluationSetObject:
             else None,
         )
 
-    def to_soundevent(self, obj: EvaluationSetObject) -> data.EvaluationSet:
+    def to_soundevent(
+        self,
+        obj: EvaluationSetObject,  # type: ignore
+    ) -> data.EvaluationSet:
         annotation_set = super().to_soundevent(obj)
         return data.EvaluationSet(
             **{

src/soundevent/io/aoef/model_run.py

@@ -6,14 +6,14 @@
 
 
 class ModelRunObject(PredictionSetObject):
-    collection_type: Literal["model_run"] = "model_run"
+    collection_type: Literal["model_run"] = "model_run"  # type: ignore
     name: str
     version: Optional[str] = None
     description: Optional[str] = None
 
 
 class ModelRunAdapter(PredictionSetAdapter):
-    def to_aoef(self, obj: data.ModelRun) -> ModelRunObject:
+    def to_aoef(self, obj: data.ModelRun) -> ModelRunObject:  # type: ignore
         prediction_set = super().to_aoef(obj)
         return ModelRunObject(
             uuid=prediction_set.uuid,
@@ -30,7 +30,7 @@ def to_aoef(self, obj: data.ModelRun) -> ModelRunObject:
             description=obj.description,
         )
 
-    def to_soundevent(self, obj: ModelRunObject) -> data.ModelRun:
+    def to_soundevent(self, obj: ModelRunObject) -> data.ModelRun:  # type: ignore
         prediction_set = super().to_soundevent(obj)
         return data.ModelRun(
             **dict(prediction_set),

src/soundevent/io/load.py

@@ -9,16 +9,16 @@
 if sys.version_info >= (3, 8):
     from typing import Literal
 else:
-    from typing_extensions import Literal
+    from typing_extensions import Literal  # pragma: no cover
 
 
 @overload
 def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["dataset"] = "dataset",
-) -> data.Dataset:
+    type: Literal["recording_set"] = "recording_set",  # type: ignore
+) -> data.RecordingSet:  # type: ignore
     ...
 
 
@@ -27,8 +27,8 @@ def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["annotation_set"] = "annotation_set",
-) -> data.AnnotationSet:
+    type: Literal["dataset"] = "dataset",  # type: ignore
+) -> data.Dataset:  # type: ignore
     ...
 
 
@@ -37,8 +37,8 @@ def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["annotation_project"] = "annotation_project",
-) -> data.AnnotationProject:
+    type: Literal["annotation_set"] = "annotation_set",  # type: ignore
+) -> data.AnnotationSet:  # type: ignore
     ...
 
 
@@ -47,8 +47,8 @@ def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["prediction_set"] = "prediction_set",
-) -> data.PredictionSet:
+    type: Literal["annotation_project"] = "annotation_project",  # type: ignore
+) -> data.AnnotationProject:  # type: ignore
     ...
 
 
@@ -57,8 +57,8 @@ def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["model_run"] = "model_run",
-) -> data.ModelRun:
+    type: Literal["prediction_set"] = "prediction_set",  # type: ignore
+) -> data.PredictionSet:  # type: ignore
     ...
 
 
@@ -67,8 +67,8 @@ def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["evaluation_set"] = "evaluation_set",
-) -> data.EvaluationSet:
+    type: Literal["model_run"] = "model_run",  # type: ignore
+) -> data.ModelRun:  # type: ignore
     ...
 
 
@@ -77,8 +77,8 @@ def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["evaluation"] = "evaluation",
-) -> data.Evaluation:
+    type: Literal["evaluation_set"] = "evaluation_set",  # type: ignore
+) -> data.EvaluationSet:  # type: ignore
     ...
 
 
@@ -87,17 +87,17 @@ def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Literal["recording_set"] = "recording_set",
-) -> data.RecordingSet:
+    type: Literal["evaluation"] = "evaluation",  # type: ignore
+) -> data.Evaluation:  # type: ignore
     ...
 
 
 def load(
     path: data.PathLike,
     audio_dir: Optional[data.PathLike] = None,
     format: Optional[str] = "aoef",
-    type: Optional[DataType] = None,
-) -> DataObject:
+    type: Optional[DataType] = None,  # type: ignore
+) -> DataObject:  # type: ignore
     if format is None:
         format = infer_format(path)
 

src/soundevent/plot/tags.py

@@ -1,7 +1,7 @@
 """Functions for plotting tags."""
 
 from itertools import cycle
-from typing import Optional
+from typing import Dict, Optional, List
 
 import numpy as np
 from matplotlib.axes import Axes
@@ -26,7 +26,7 @@ def __init__(
         num_colors: int = 20,
     ):
         """Initialize color mapper."""
-        self._tags = {}
+        self._tags: Dict[data.Tag, str] = {}
 
         colormap = get_cmap(cmap)
         self._colors = cycle(
@@ -75,7 +75,7 @@ def add_tags_legend(
     for tag in color_mapper._tags:
         color = color_mapper.get_color(tag)
         handles.append(ax.scatter([], [], color=color))
-        labels.append(tag)
+        labels.append(str(tag))
 
     ax.legend(handles, labels, loc="upper right")
 

tox.ini

@@ -8,6 +8,7 @@ extras = all
 deps =
     pytest>=6
     hypothesis
+    html5lib
 commands =
     pytest {tty:--color=yes} {posargs:tests}