Fix sonarqube issues (#328)

* fix pytest.raises syntax in audio test

* fix pytest.raises syntax in core_api_base test

* fix pytest.raises syntax in mseed test

* replace float equality asserts with np.isclose()

* pass AudioData.write() subtype parameter as keyword-only

* extract nested conditions

* fix multirule noqa syntax

* set subtype as keyword-only parameter

* remove double negation in equality test

* remove nested conditions

* set sx as keyword-only parameter in write() method

* use typing.Generator in return type

* remove redundant return

* extract nested conditions

* use list comprehension

* rename builtin format variable

* comment empty function rather than raw pass

* rename unused request variable with _

* remove redundant list comprehension

* refactor pytest.raise call

* add typing.Generator annotation

* add docstring in empty dunder override

* fix pytest raises syntax

* remove unnecessary list assignment

* fix pytest syntax

* replace unused var name with _

* test_spectro linting

* fix pytest raises syntax

Author: Gautzilla

src/osekit/core_api/audio_data.py

@@ -263,8 +263,8 @@ def get_value_calibrated(self) -> np.ndarray:
     def write(
         self,
         folder: Path,
-        subtype: str | None = None,
         *,
+        subtype: str | None = None,
         link: bool = False,
     ) -> None:
         """Write the audio data to file.
@@ -349,13 +349,12 @@ def split(
             The list of ``AudioData`` subdata objects.
 
         """
-        normalization_values = (
-            None
-            if not pass_normalization
-            else self.normalization_values
-            if any(self.normalization_values.values())
-            else self.get_normalization_values()
-        )
+        if not pass_normalization:
+            normalization_values = None
+        elif any(self.normalization_values.values()):
+            normalization_values = self.normalization_values
+        else:
+            normalization_values = self.get_normalization_values()
         return super().split(
             nb_subdata=nb_subdata,
             normalization_values=normalization_values,
@@ -440,13 +439,12 @@ def split_frames(
             if stop_frame == -1
             else self.begin + Timedelta(seconds=stop_frame / self.sample_rate)
         )
-        normalization_values = (
-            None
-            if not pass_normalization
-            else self.normalization_values
-            if any(self.normalization_values.values())
-            else self.get_normalization_values()
-        )
+        if not pass_normalization:
+            normalization_values = None
+        elif any(self.normalization_values.values()):
+            normalization_values = self.normalization_values
+        else:
+            normalization_values = self.get_normalization_values()
         return AudioData.from_files(
             list(self.files),
             start_timestamp,

src/osekit/core_api/audio_dataset.py

@@ -100,12 +100,13 @@ def instrument(self, instrument: Instrument | None) -> None:
         for data in self.data:
             data.instrument = instrument
 
+    @staticmethod
     def _write_audio(
-        self,
         data: AudioData,
         folder: Path,
         subtype: str | None = None,
-        link: bool = False,  # noqa: FBT001, FBT002,
+        *,
+        link: bool = False,
     ) -> AudioData:
         """Write audio data to disk."""
         data.write(folder=folder, subtype=subtype, link=link)
@@ -114,28 +115,29 @@ def _write_audio(
     def write(
         self,
         folder: Path,
-        subtype: str | None = None,
-        link: bool = False,  # noqa: FBT001, FBT002,
         first: int = 0,
         last: int | None = None,
+        *,
+        subtype: str | None = None,
+        link: bool = False,
     ) -> None:
         """Write all data objects in the specified folder.
 
         Parameters
         ----------
         folder: Path
             Folder in which to write the data.
+        first: int
+            Index of the first ``AudioData`` object to write.
+        last: int | None
+            Index after the last ``AudioData`` object to write.
         subtype: str | None
             Subtype as provided by the soundfile module.
             Defaulted as the default 16-bit PCM for WAV audio files.
         link: bool
             If ``True``, each ``AudioData`` will be bound to the corresponding written file.
             Their items will be replaced with a single item, which will match the whole
             new ``AudioFile``.
-        first: int
-            Index of the first ``AudioData`` object to write.
-        last: int | None
-            Index after the last ``AudioData`` object to write.
 
 
         """

src/osekit/core_api/base_item.py

@@ -81,4 +81,4 @@ def __eq__(self, other: BaseItem[TFile]) -> bool:
             return False
         if self.begin != other.begin:
             return False
-        return not self.end != other.end
+        return self.end == other.end

src/osekit/core_api/spectro_data.py

@@ -244,13 +244,8 @@ def v_lim(self) -> tuple[float, float]:
 
     @v_lim.setter
     def v_lim(self, v_lim: tuple[float, float] | None) -> None:
-        v_lim = (
-            v_lim
-            if v_lim is not None
-            else (-120.0, 0.0)
-            if self.db_type == "FS"
-            else (0.0, 170.0)
-        )
+        if v_lim is None:
+            v_lim = (-120.0, 0.0) if self.db_type == "FS" else (0.0, 170.0)
         self._v_lim = v_lim
 
     def get_value(self) -> np.ndarray:
@@ -527,8 +522,8 @@ def save_spectrogram(
     def write(
         self,
         folder: Path,
-        sx: np.ndarray | None = None,
         *,
+        sx: np.ndarray | None = None,
         link: bool = False,
     ) -> None:
         """Write the Spectro data to file.

src/osekit/logging_context.py

@@ -13,9 +13,8 @@
 """
 
 import logging
-from collections.abc import Generator
+import typing
 from contextlib import contextmanager
-from typing import Any
 
 
 class LoggingContext:
@@ -29,7 +28,7 @@ def __init__(self) -> None:
         self.logger = logging.root
 
     @contextmanager
-    def set_logger(self, logger: logging.Logger) -> Generator[None, Any, None]:
+    def set_logger(self, logger: logging.Logger) -> typing.Generator:
         """Set a contextmanager for calling utils functions with a specific logger.
 
         Parameters

src/osekit/public_api/dataset.py

@@ -616,7 +616,6 @@ def _sort_dataset(self, dataset: type[DatasetChild]) -> None:
             return
         if type(dataset) is SpectroDataset | LTASDataset:
             self._sort_spectro_dataset(dataset)
-            return
 
     def _sort_audio_dataset(self, dataset: AudioDataset) -> None:
         dataset.move_files(self._get_audio_dataset_subpath(dataset))
@@ -789,15 +788,12 @@ def from_dict(cls, dictionary: dict) -> Dataset:
         """
         datasets = {}
         for name, dataset in dictionary["datasets"].items():
-            dataset_class = (
-                AudioDataset
-                if dataset["class"] == "AudioDataset"
-                else SpectroDataset
-                if dataset["class"] == "SpectroDataset"
-                else LTASDataset
-                if dataset["class"] == "LTASDataset"
-                else BaseDataset
-            )
+            dataset_class = {
+                "AudioDataset": AudioDataset,
+                "SpectroDataset": SpectroDataset,
+                "LTASDataset": LTASDataset,
+            }[dataset["class"]]
+
             datasets[name] = {
                 "class": dataset["class"],
                 "analysis": dataset["analysis"],

src/osekit/utils/multiprocess_utils.py

@@ -41,14 +41,14 @@ def multiprocess(
 
     """
     if bypass_multiprocessing or not config.multiprocessing["is_active"]:
-        return list(
+        return [
             func(element, *args, **kwargs)
             for element in tqdm(
                 enumerable,
                 disable=os.getenv("DISABLE_TQDM", "False").lower()
                 in ("true", "1", "t"),
             )
-        )
+        ]
 
     partial_func = partial(func, *args, **kwargs)
 

tests/conftest.py

@@ -3,7 +3,7 @@
 import logging
 import os
 import sys
-from collections.abc import Generator
+import typing
 from pathlib import Path
 from unittest.mock import MagicMock
 
@@ -45,7 +45,7 @@ def audio_files(
         series_type = request.param.get("series_type", "repeat")
         sine_frequency = request.param.get("sine_frequency", 1000.0)
         magnitude = request.param.get("magnitude", 1.0)
-        format = request.param.get("format", "wav")
+        audio_format = request.param.get("format", "wav")
     else:
         sample_rate = 48_000
         duration = 1.0
@@ -54,9 +54,9 @@ def audio_files(
         series_type = "repeat"
         sine_frequency = 1000.0
         magnitude = 1.0
-        format = "wav"
+        audio_format = "wav"
 
-    nb_samples = int(round(duration * sample_rate))
+    nb_samples = round(duration * sample_rate)
     data = generate_sample_audio(
         nb_files=nb_files,
         nb_samples=nb_samples,
@@ -88,14 +88,14 @@ def audio_files(
     for index, begin_time in enumerate(file_begin_timestamps):
         time_str = begin_time.strftime(format=datetime_format)
         idx = 0
-        while (file := tmp_path / f"audio_{time_str}_{idx}.{format}").exists():
+        while (file := tmp_path / f"audio_{time_str}_{idx}.{audio_format}").exists():
             idx += 1
         files.append(file)
         kwargs = {
             "file": file,
             "data": data[index],
             "samplerate": sample_rate,
-            "subtype": "DOUBLE" if format.lower() == "wav" else "PCM_24",
+            "subtype": "DOUBLE" if audio_format.lower() == "wav" else "PCM_24",
         }
         sf.write(**kwargs)
     output = [AudioFile(path=f, strptime_format=datetime_format) for f in files]
@@ -111,7 +111,7 @@ def patch_filehandlers(
         return
 
     def disabled_filewrite(self: any, record: any) -> None:
-        pass
+        """Prevent the logger from actually writing files."""
 
     monkeypatch.setattr(logging.FileHandler, "emit", disabled_filewrite)
 
@@ -217,7 +217,7 @@ def mocked_get_raw_value(self: AudioData) -> np.ndarray:
 
 
 @pytest.fixture(autouse=True)
-def restore_config() -> Generator:
+def restore_config() -> typing.Generator:
     resample_quality_settings = {**config.resample_quality_settings}
     multiprocessing = {**config.multiprocessing}
     yield

tests/test_audio.py

@@ -218,7 +218,7 @@ def test_audio_file_read(
     stop: pd.Timestamp,
     expected: np.ndarray,
 ) -> None:
-    files, request = audio_files
+    files, _ = audio_files
     assert np.allclose(files[0].read(start, stop)[:, 0], expected, atol=1e-7)
 
 
@@ -448,7 +448,7 @@ def test_audio_item(
     stop: pd.Timestamp | None,
     expected: np.ndarray,
 ) -> None:
-    files, request = audio_files
+    files, _ = audio_files
     item = AudioItem(files[0], start, stop)
     assert np.array_equal(item.get_value()[:, 0], expected)
     assert item.shape == item.get_value().shape
@@ -710,7 +710,7 @@ def test_audio_resample_sample_count(
     sample_rate: int,
     expected_nb_samples: int,
 ) -> None:
-    audio_files, request = audio_files
+    audio_files, _ = audio_files
     data = AudioData.from_files(audio_files, begin=start, end=stop)
     data.sample_rate = sample_rate
     assert data.get_value().shape[0] == expected_nb_samples
@@ -1745,7 +1745,7 @@ def test_split_data_normalization_pass(patch_audio_data: None) -> None:
     ad = AudioData()
     ad.mocked_value = [1, 2, 3]
     original_normalization_values = ad.get_normalization_values()
-    assert all(v for v in original_normalization_values.values())
+    assert all(original_normalization_values.values())
 
     assert all(
         part.normalization_values == original_normalization_values
@@ -1867,10 +1867,10 @@ def test_split_frames_errors(patch_audio_data: None) -> None:
         "Start_frame must be greater than or equal to 0.",
         "Stop_frame must be lower than the length of the data.",
     ]
-    with pytest.raises(ValueError, match=error_msgs[0]) as e:
-        assert ad.split_frames(start_frame=-1, stop_frame=2) == e
-    with pytest.raises(ValueError, match=error_msgs[1]) as e:
-        assert ad.split_frames(start_frame=0, stop_frame=100) == e
+    with pytest.raises(ValueError, match=error_msgs[0]):
+        ad.split_frames(start_frame=-1, stop_frame=2)
+    with pytest.raises(ValueError, match=error_msgs[1]):
+        ad.split_frames(start_frame=0, stop_frame=100)
 
 
 @pytest.mark.parametrize(

tests/test_core_api_base.py

@@ -29,7 +29,7 @@ class DummyItem(BaseItem[DummyFile]): ...
 class DummyData(BaseData[DummyItem, DummyFile]):
     item_cls = DummyItem
 
-    def write(self, folder: Path, link: bool = False) -> None: ...
+    def write(self, folder: Path, *, link: bool = False) -> None: ...
 
     def link(self, folder: Path) -> None: ...
 
@@ -134,8 +134,8 @@ def test_base_file_with_no_begin_error() -> None:
     with pytest.raises(
         ValueError,
         match=r"Either begin or strptime_format must be specified",
-    ) as e:
-        assert DummyFile(path=r"foo") == e
+    ):
+        DummyFile(path=r"foo")
 
 
 @pytest.mark.parametrize(
@@ -503,21 +503,18 @@ def test_base_dataset_from_files_overlap_errors(overlap: float, mode: str) -> No
     with pytest.raises(
         ValueError,
         match=rf"Overlap \({overlap}\) must be between 0 and 1.",
-    ) as e:
-        assert (
-            DummyDataset.from_files(
-                [
-                    DummyFile(
-                        path=Path("foo"),
-                        begin=Timestamp("2016-02-05 00:00:00"),
-                        end=Timestamp("2016-02-05 00:10:00"),
-                    ),
-                ],
-                data_duration=Timedelta(seconds=1),
-                mode=mode,
-                overlap=overlap,
-            )
-            == e
+    ):
+        DummyDataset.from_files(
+            [
+                DummyFile(
+                    path=Path("foo"),
+                    begin=Timestamp("2016-02-05 00:00:00"),
+                    end=Timestamp("2016-02-05 00:10:00"),
+                ),
+            ],
+            data_duration=Timedelta(seconds=1),
+            mode=mode,
+            overlap=overlap,
         )