fixed all linting issues from new ruff settings

Author: mbsantiago

back/pyproject.toml

@@ -79,7 +79,7 @@ dev-dependencies = [
     "httpx>=0.23.3",
     "tox>=4.7.0",
     "flake8>=6.1.0",
-    "pyright>=1.1.320",
+    "pyright>=1.1.363",
     "ruff>=0.1.7",
     "icecream>=2.1.3",
     "pytest-xdist>=3.5.0",

back/src/whombat/api/annotation_projects.py

@@ -225,8 +225,7 @@ async def from_soundevent(
         session: AsyncSession,
         data: data.AnnotationProject,
     ) -> schemas.AnnotationProject:
-        """Convert a soundevent Annotation Project to a Whombat annotation
-        project.
+        """Convert a soundevent Annotation Project to a Whombat annotation project.
 
         Parameters
         ----------
@@ -263,8 +262,7 @@ async def to_soundevent(
         obj: schemas.AnnotationProject,
         audio_dir: Path | None = None,
     ) -> data.AnnotationProject:
-        """Convert a Whombat annotation project to a soundevent annotation
-        project.
+        """Convert a Whombat annotation project to a soundevent annotation project.
 
         Parameters
         ----------

back/src/whombat/api/audio.py

@@ -23,8 +23,8 @@ def load_audio(
     recording: schemas.Recording,
     start_time: float | None = None,
     end_time: float | None = None,
-    audio_dir: Path = Path.cwd(),
-    audio_parameters: schemas.AudioParameters = schemas.AudioParameters(),
+    audio_dir: Path | None = None,
+    audio_parameters: schemas.AudioParameters | None = None,
 ):
     """Load audio.
 
@@ -46,6 +46,12 @@ def load_audio(
     bytes
         Audio data.
     """
+    if audio_dir is None:
+        audio_dir = Path().cwd()
+
+    if audio_parameters is None:
+        audio_parameters = schemas.AudioParameters()
+
     # Set start and end times.
     if start_time is None:
         start_time = 0.0
@@ -233,7 +239,6 @@ def generate_wav_header(
     The structure of the WAV header is described in
     (WAV PCM soundfile format)[http://soundfile.sapp.org/doc/WaveFormat/].
     """
-
     byte_rate = samplerate * channels * bit_depth // 8
     block_align = channels * bit_depth // 8
 

back/src/whombat/api/clip_evaluations.py

@@ -239,8 +239,7 @@ async def to_soundevent(
         audio_dir: Path | None = None,
         evaluations: Sequence[schemas.SoundEventEvaluation] | None = None,
     ) -> data.ClipEvaluation:
-        """Create a clip evaluation in soundevent format from a clip evaluation
-        in whombat format.
+        """Create a clip evaluation in soundevent format from a clip evaluation in whombat format.
 
         Parameters
         ----------

back/src/whombat/api/clips.py

@@ -112,7 +112,7 @@ async def create_many_without_duplicates(
         clip_features = await self._create_clip_features(session, clips)
         return [
             clip.model_copy(update=dict(features=features))
-            for clip, features in zip(clips, clip_features)
+            for clip, features in zip(clips, clip_features, strict=False)
         ]
 
     async def add_feature(
@@ -298,7 +298,6 @@ async def _create_clip_features(
         list[list[schemas.Feature]]
             List of features created for each clip.
         """
-
         clip_features = [
             [
                 schemas.Feature(name=name, value=value)
@@ -309,7 +308,7 @@ async def _create_clip_features(
 
         create_values = [
             (clip.id, feature.name, feature.value)
-            for clip, features in zip(clips, clip_features)
+            for clip, features in zip(clips, clip_features, strict=False)
             for feature in features
         ]
 

back/src/whombat/api/common/base.py

@@ -366,7 +366,7 @@ def _clear_from_cache(self, obj: WhombatSchema) -> None:
         self._cache.pop(pk, None)
 
     def _get_pk_condition(self, pk: PrimaryKey) -> _ColumnExpressionArgument:
-        column = getattr(self._model, "uuid")
+        column = self._model.uuid  # type: ignore
         if not column:
             raise NotImplementedError(
                 f"The model {self._model.__name__} does not have a column named"
@@ -375,7 +375,7 @@ def _get_pk_condition(self, pk: PrimaryKey) -> _ColumnExpressionArgument:
         return column == pk
 
     def _get_pk_from_obj(self, obj: WhombatSchema) -> PrimaryKey:
-        pk = getattr(obj, "uuid")
+        pk = obj.uuid  # type: ignore
         if not pk:
             raise NotImplementedError(
                 "The primary key could not be retrieved from the object. "

back/src/whombat/api/datasets.py

@@ -310,7 +310,8 @@ async def add_recordings(
             if not recording.path.is_relative_to(obj.audio_dir):
                 warnings.warn(
                     "The recording is not part of the dataset audio "
-                    f"directory. \ndataset = {obj}\nrecording = {recording}"
+                    f"directory. \ndataset = {obj}\nrecording = {recording}",
+                    stacklevel=2,
                 )
                 continue
 

back/src/whombat/api/evaluation_sets.py

@@ -404,7 +404,6 @@ async def _update_from_soundevent(
         data: data.EvaluationSet,
     ) -> schemas.EvaluationSet:
         """Update an evaluation set from an object in `soundevent` format."""
-
         _existing_tags = {(t.key, t.value) for t in obj.tags}
         for t in data.evaluation_tags:
             if (t.key, t.value) not in _existing_tags:

back/src/whombat/api/io/aoef/annotation_tasks.py

@@ -89,7 +89,9 @@ async def _create_annotation_tasks(
 
     missing = [
         (t, proj_uuid)
-        for (t, proj_uuid) in zip(annotation_tasks, annotation_project_uuids)
+        for (t, proj_uuid) in zip(
+            annotation_tasks, annotation_project_uuids, strict=False
+        )
         if t.uuid not in mapping
     ]
     if not missing:

back/src/whombat/api/io/aoef/clip_annotations.py

@@ -136,7 +136,6 @@ async def _create_clip_annotation_notes(
     users: dict[UUID, UUID],
 ) -> None:
     """Create clip annotation notes."""
-
     notes = [
         note
         for annotation in clip_annotations

back/src/whombat/api/io/aoef/clip_evaluations.py

@@ -92,7 +92,9 @@ async def _create_clip_evaluations(
 
     missing = [
         (clip_evals, eval_uuid)
-        for clip_evals, eval_uuid in zip(clip_evaluations, evaluations_uuids)
+        for clip_evals, eval_uuid in zip(
+            clip_evaluations, evaluations_uuids, strict=False
+        )
         if clip_evals.uuid not in mapping
     ]
     if not missing:

back/src/whombat/api/io/aoef/datasets.py

@@ -99,7 +99,7 @@ async def import_dataset(
 
 
 def normalize_path(path: Path, dataset_dir: Path) -> Path:
-    """Normalize a path to a dataset directory"""
+    """Normalize a path to a dataset directory."""
     if path.is_absolute():
         return path.relative_to(dataset_dir)
     return path

back/src/whombat/api/io/aoef/recordings.py

@@ -61,7 +61,7 @@ async def import_recordings(
     users: dict[UUID, UUID],
     feature_names: dict[str, int],
     audio_dir: Path | None = None,
-    base_audio_dir: Path = Path.home(),
+    base_audio_dir: Path | None = None,
 ) -> dict[UUID, int]:
     """Import a set of recordings in AOEF format into the database.
 
@@ -74,6 +74,9 @@ async def import_recordings(
     if not recordings:
         return {}
 
+    if base_audio_dir is None:
+        base_audio_dir = Path.home()
+
     if not audio_dir:
         # If no audio directory is given, assume that the paths are relative
         # to the base audio directory

back/src/whombat/api/io/aoef/sound_event_annotations.py

@@ -122,7 +122,9 @@ async def _create_sound_event_annotations(
 
     missing = [
         (s, ca_uuid)
-        for s, ca_uuid in zip(sound_events_annotations, clip_annotation_uuids)
+        for s, ca_uuid in zip(
+            sound_events_annotations, clip_annotation_uuids, strict=False
+        )
         if s.uuid not in mapping
     ]
     if not missing:

back/src/whombat/api/io/aoef/sound_event_evaluations.py

@@ -100,7 +100,9 @@ async def _create_sound_event_evaluations(
 
     missing = [
         (match, eval_uuid)
-        for match, eval_uuid in zip(matches, clip_evaluation_uuids)
+        for match, eval_uuid in zip(
+            matches, clip_evaluation_uuids, strict=False
+        )
         if match.uuid not in mapping
     ]
 

back/src/whombat/api/io/aoef/sound_event_predictions.py

@@ -109,7 +109,9 @@ async def _create_sound_event_predictions(
 
     missing = [
         (s, ca_uuid)
-        for s, ca_uuid in zip(sound_events_predictions, clip_prediction_uuids)
+        for s, ca_uuid in zip(
+            sound_events_predictions, clip_prediction_uuids, strict=False
+        )
         if s.uuid not in mapping
     ]
     if not missing:

back/src/whombat/api/io/aoef/tags.py

@@ -11,7 +11,7 @@ async def import_tags(
     session: AsyncSession,
     tags: list[TagObject],
 ) -> dict[int, int]:
-    """Import tags from a list of dicts"""
+    """Import tags from a list of dicts."""
     if not tags:
         return {}
 

back/src/whombat/api/recordings.py

@@ -2,16 +2,16 @@
 
 import datetime
 import logging
-import soundfile as sf
 from functools import partial
 from multiprocessing import Pool
 from pathlib import Path
 from typing import Sequence
 from uuid import UUID
 
 import cachetools
+import soundfile as sf
 from soundevent import data
-from soundevent.audio import compute_md5_checksum, get_media_info, MediaInfo
+from soundevent.audio import MediaInfo, compute_md5_checksum, get_media_info
 from sqlalchemy import and_
 from sqlalchemy.ext.asyncio import AsyncSession
 

back/src/whombat/api/sound_event_annotations.py

@@ -306,7 +306,6 @@ async def _create_from_soundevent(
         schemas.SoundEventAnnotation
             The created annotation.
         """
-
         user = None
         if data.created_by is not None:
             user = await users.from_soundevent(session, data.created_by)

back/src/whombat/api/sound_event_predictions.py

@@ -265,8 +265,7 @@ async def _create_from_soundevent(
         data: data.SoundEventPrediction,
         clip_prediction: schemas.ClipPrediction,
     ) -> schemas.SoundEventPrediction:
-        """Create a new Whombat sound event prediction from a sound event
-        prediction in soundevent format.
+        """Create a sound event prediction from one in soundevent format.
 
         Parameters
         ----------

back/src/whombat/api/spectrograms.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 
 import numpy as np
-from soundevent import audio, arrays
+from soundevent import arrays, audio
 
 import whombat.api.audio as audio_api
 from whombat import schemas
@@ -20,7 +20,7 @@ def compute_spectrogram(
     end_time: float,
     audio_parameters: schemas.AudioParameters,
     spectrogram_parameters: schemas.SpectrogramParameters,
-    audio_dir: Path = Path.cwd(),
+    audio_dir: Path | None = None,
 ) -> np.ndarray:
     """Compute a spectrogram for a recording.
 
@@ -42,6 +42,9 @@ def compute_spectrogram(
     DataArray
         Spectrogram image.
     """
+    if audio_dir is None:
+        audio_dir = Path.cwd()
+
     wav = audio_api.load_audio(
         recording,
         start_time,

back/src/whombat/core/spectrograms.py

@@ -30,7 +30,6 @@ def normalize_spectrogram(
     xr.DataArray
         Normalized array.
     """
-
     attrs = spectrogram.attrs
     min_val = attrs.get("min_dB")
     if min_val is None or relative:

back/src/whombat/filters/annotation_tasks.py

@@ -23,7 +23,6 @@ class RecordingTagFilter(base.Filter):
 
     def filter(self, query: Select) -> Select:
         """Filter the query."""
-
         if self.key is None and self.value is None:
             return query
 

back/src/whombat/migrations/env.py

@@ -86,8 +86,7 @@ def do_run_migrations(connection: Connection) -> None:
 
 
 def run_migrations() -> None:
-    """In this scenario we need to create an Engine and associate a connection
-    with the context."""
+    """Run migrations synchronously."""
     configuration = get_configurations()
 
     connectable = engine_from_config(
@@ -102,8 +101,7 @@ def run_migrations() -> None:
 
 
 async def run_async_migrations() -> None:
-    """In this scenario we need to create an Engine and associate a connection
-    with the context."""
+    """Run migrations asynchronously."""
     configuration = get_configurations()
 
     connectable = async_engine_from_config(

back/src/whombat/migrations/versions/03a1d239e06e_first_migration.py

@@ -1,4 +1,4 @@
-"""first migration
+"""first migration.
 
 Revision ID: 03a1d239e06e
 Revises:

back/src/whombat/models/clip_annotation.py

@@ -34,7 +34,9 @@ class ClipAnnotation(Base):
         The sound events annotated in the clip.
     tags
         The tags attached to the annotation.
-    notes
+
+    Notes
+    -----
         The notes attached to the annotation.
     clip
         The clip to which the annotation belongs.

back/src/whombat/models/recording.py

@@ -76,7 +76,9 @@ class Recording(Base):
         The time expansion factor of the recording.
     rights
         A string describing the usage rights of the recording.
-    notes
+
+    Notes
+    -----
         A list of notes associated with the recording.
     tags
         A list of tags associated with the recording.

back/src/whombat/models/sound_event_annotation.py

@@ -38,7 +38,9 @@ class SoundEventAnnotation(Base):
         The sound event annotated by the annotation.
     tags
         A list of tags associated with the annotation.
-    notes
+
+    Notes
+    -----
         A list of notes associated with the annotation.
     clip_annotation
         The clip annotation to which the annotation belongs.

back/src/whombat/plugins.py

@@ -35,11 +35,16 @@ def load_plugins() -> Generator[tuple[str, ModuleType], None, None]:
         module = importlib.import_module(name)
 
         if not hasattr(module, "__description__"):
-            warnings.warn(f"Plugin {name} has no __description__ attribute.")
+            warnings.warn(
+                f"Plugin {name} has no __description__ attribute.",
+                stacklevel=2,
+            )
             continue
 
         if not hasattr(module, "__version__"):
-            warnings.warn(f"Plugin {name} has no __version__ attribute.")
+            warnings.warn(
+                f"Plugin {name} has no __version__ attribute.", stacklevel=2
+            )
 
         yield name[8:], module