britekit 0.0.9__tar.gz → 0.0.11__tar.gz

{britekit-0.0.9 → britekit-0.0.11}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: britekit
-Version: 0.0.9
+Version: 0.0.11
 Summary: Core functions for bioacoustic recognizers.
 Project-URL: Documentation, https://github.com/jhuus/BriteKit#readme
 Project-URL: Issues, https://github.com/jhuus/BriteKit/issues
@@ -120,7 +120,7 @@ train:
 This overrides the default values for model_type, learning_rate, drop_rate and num_epochs. When using the API, you can update configuration parameters like this:
 ```
 import britekit as bk
-cfg, _ = bk.get_config()
+cfg = bk.get_config()
 cfg.train.model_type = "effnet.4"
 ```
 ## Downloading Recordings

{britekit-0.0.9 → britekit-0.0.11}/README.md

@@ -81,7 +81,7 @@ train:
 This overrides the default values for model_type, learning_rate, drop_rate and num_epochs. When using the API, you can update configuration parameters like this:
 ```
 import britekit as bk
-cfg, _ = bk.get_config()
+cfg = bk.get_config()
 cfg.train.model_type = "effnet.4"
 ```
 ## Downloading Recordings

{britekit-0.0.9 → britekit-0.0.11}/britekit/__about__.py

@@ -1,4 +1,4 @@
 # SPDX-FileCopyrightText: 2025-present Jan Huus <jhuus1@gmail.com>
 #
 # SPDX-License-Identifier: MIT
-__version__ = "0.0.9"
+__version__ = "0.0.11"

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_analyze.py

@@ -47,7 +47,7 @@ def analyze(
     from britekit.core.analyzer import Analyzer
 
     util.set_logging()
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     try:
         if rtype not in {"audacity", "csv", "both"}:
             logging.error(f"Error. invalid rtype value: {rtype}")

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_ckpt_ops.py

@@ -142,7 +142,7 @@ def ckpt_onnx(
     import torch
     from britekit.models.model_loader import load_from_checkpoint
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     base, _ = os.path.splitext(input_path)
     output_path = base + ".onnx"
     model = load_from_checkpoint(input_path)

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_db_add.py

@@ -23,7 +23,7 @@ def add_cat(db_path: Optional[str]=None, name: str="") -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -63,7 +63,7 @@ def add_stype(db_path: Optional[str]=None, name: str="") -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -103,7 +103,7 @@ def add_src(db_path: Optional[str]=None, name: str="") -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -154,7 +154,7 @@ def add_class(
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_db_delete.py

@@ -25,7 +25,7 @@ def del_cat(db_path: Optional[str]=None, name: Optional[str]=None) -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -78,7 +78,7 @@ def del_class(db_path: Optional[str]=None, name: Optional[str]=None) -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -128,7 +128,7 @@ def del_rec(db_path: Optional[str]=None, file_name: Optional[str]=None) -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -172,7 +172,7 @@ def del_sgroup(db_path: Optional[str]=None, name: Optional[str]=None) -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -217,7 +217,7 @@ def del_stype(db_path: Optional[str]=None, name: Optional[str]=None) -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -262,7 +262,7 @@ def del_src(db_path: Optional[str]=None, name: Optional[str]=None) -> None:
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 
@@ -311,7 +311,7 @@ def del_seg(db_path: Optional[str]=None, class_name: Optional[str]=None, dir_pat
     """
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if db_path is None:
         db_path = cfg.train.train_db
 

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_embed.py

@@ -57,7 +57,7 @@ def embed(
     from britekit.models.model_loader import load_from_checkpoint
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if db_path is None:
         db_path = cfg.train.train_db
 

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_ensemble.py

@@ -68,7 +68,6 @@ def ensemble(
     metric: str = "micro_roc",
     annotations_path: str = "",
     recordings_path: Optional[str] = None,
-    output_path: str = "",
 ) -> None:
     """
     Find the best ensemble of a given size from a group of checkpoints.
@@ -84,7 +83,6 @@ def ensemble(
         metric (str): Metric to use to compare ensembles (default=micro_roc).
         annotations_path (str): Path to CSV file containing ground truth annotations.
         recordings_path (str, optional): Directory containing audio recordings. Defaults to annotations directory.
-        output_path (str): Directory where reports will be saved.
     """
     import glob
     import itertools
@@ -95,7 +93,7 @@ def ensemble(
         logging.error(f"Error: invalid metric ({metric})")
         return
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     ckpt_paths = sorted(glob.glob(os.path.join(ckpt_path, "*.ckpt")))
     num_ckpts = len(ckpt_paths)
     if num_ckpts == 0:
@@ -145,6 +143,7 @@ def ensemble(
 
     logging.info(f"Best score = {best_score:.4f}")
 
+    assert best_ensemble is not None
     best_names = [Path(ckpt_path).name for ckpt_path in best_ensemble]
     logging.info(f"Best ensemble = {best_names}")
 
@@ -215,14 +214,6 @@ def ensemble(
     required=False,
     help="Recordings directory. Default is directory containing annotations file.",
 )
-@click.option(
-    "-o",
-    "--output",
-    "output_path",
-    type=click.Path(file_okay=False, dir_okay=True),
-    required=True,
-    help="Path to output directory.",
-)
 def _ensemble_cmd(
     cfg_path: Optional[str],
     ckpt_path: str,
@@ -231,7 +222,6 @@ def _ensemble_cmd(
     metric: str,
     annotations_path: str,
     recordings_path: Optional[str],
-    output_path: str,
 ) -> None:
     util.set_logging()
-    ensemble(cfg_path, ckpt_path, ensemble_size, num_tries, metric, annotations_path, recordings_path, output_path)
+    ensemble(cfg_path, ckpt_path, ensemble_size, num_tries, metric, annotations_path, recordings_path)

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_extract.py

@@ -42,7 +42,7 @@ def extract_all(
     from britekit.training_db.extractor import Extractor
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if db_path is not None:
         cfg.train.train_db = db_path
 
@@ -172,7 +172,7 @@ def extract_by_image(
     from britekit.training_db.extractor import Extractor
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if db_path is not None:
         cfg.train.train_db = db_path
 

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_find_dup.py

@@ -105,7 +105,7 @@ def find_dup(
         else:
             return False
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if db_path is None:
         db_path = cfg.train.train_db
 

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_pickle.py

@@ -37,7 +37,7 @@ def pickle(
     """
     from britekit.core.pickler import Pickler
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if db_path is None:
         db_path = cfg.train.train_db
 

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_plot.py

@@ -89,7 +89,7 @@ def plot_db(
     from britekit.core.plot import plot_spec
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if power is not None:
         cfg.audio.power = power
 
@@ -247,7 +247,7 @@ def plot_dir(
     """
     from britekit.core.audio import Audio
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if power is not None:
         cfg.audio.power = power
 
@@ -363,7 +363,7 @@ def plot_rec(
     """
     from britekit.core.audio import Audio
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if power is not None:
         cfg.audio.power = power
 

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_reextract.py

@@ -38,7 +38,7 @@ def reextract(
         spec_group (str): Spectrogram group name for storing the extracted spectrograms. Defaults to 'default'.
     """
     from britekit.core.reextractor import Reextractor
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
 
     if class_name and classes_path:
         logging.error("Only one of --name and --classes may be specified.")

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_reports.py

@@ -143,7 +143,7 @@ def rpt_db(cfg_path: Optional[str] = None,
     from britekit.training_db.training_db import TrainingDatabase
     from britekit.training_db.training_data_provider import TrainingDataProvider
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     if db_path is not None:
         cfg.train.train_db = db_path
 
@@ -214,7 +214,7 @@ def rpt_epochs(
     from britekit.core.analyzer import Analyzer
     from britekit.testing.per_segment_tester import PerSegmentTester
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     ckpt_paths = glob.glob(str(Path(input_path) / "*.ckpt"))
     if len(ckpt_paths) == 0:
         logging.error(f"No checkpoint files found in {input_path}")
@@ -403,7 +403,7 @@ def rpt_labels(
     """
     import pandas as pd
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if min_score is None:
         min_score = cfg.infer.min_score
 
@@ -556,7 +556,7 @@ def rpt_test(
     from britekit.testing.per_recording_tester import PerRecordingTester
     from britekit.testing.per_segment_tester import PerSegmentTester
 
-    cfg, _ = get_config()
+    cfg = get_config()
     try:
         if not recordings_path:
             recordings_path = str(Path(annotations_path).parent)

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_search.py

@@ -62,7 +62,7 @@ def search(
     from britekit.models.model_loader import load_from_checkpoint
     from britekit.training_db.training_db import TrainingDatabase
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
 
     if not os.path.exists(output_path):
         os.makedirs(output_path)

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_train.py

@@ -31,7 +31,7 @@ def train(
     """
     from britekit.core.trainer import Trainer
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     try:
         start_time = time.time()
         Trainer().run()
@@ -89,7 +89,7 @@ def find_lr(cfg_path: str, num_batches: int):
     """
     from britekit.core.trainer import Trainer
 
-    cfg, _ = get_config(cfg_path)
+    cfg = get_config(cfg_path)
     try:
         suggested_lr, fig = Trainer().find_lr(num_batches)
         fig.savefig("learning_rates.jpeg")

{britekit-0.0.9 → britekit-0.0.11}/britekit/commands/_tune.py

@@ -58,7 +58,7 @@ def tune(
     from britekit.core.tuner import Tuner
 
     try:
-        cfg, _ = get_config(cfg_path)
+        cfg = get_config(cfg_path)
         if extract and skip_training:
             logging.error(
                 "Performing spectrogram extract is incompatible with skipping training."
@@ -104,6 +104,10 @@ def tune(
             to_path = os.path.join(output_path, Path(cfg_path).name)
             shutil.copy(cfg_path, to_path)
 
+        if param_path:
+            to_path = os.path.join(output_path, Path(param_path).name)
+            shutil.copy(param_path, to_path)
+
         elapsed_time = util.format_elapsed_time(start_time, time.time())
         logging.info(f"Elapsed time = {elapsed_time}")
 

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/analyzer.py

@@ -16,7 +16,7 @@ class Analyzer:
     """
 
     def __init__(self):
-        self.cfg, self.fn_cfg = get_config()
+        self.cfg = get_config()
         self.dataframes = []
 
     def _save_manifest(self, output_path: str, predictor):

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/audio.py

@@ -51,7 +51,7 @@ class Audio:
         import torchaudio as ta
 
         if cfg is None:
-            self.cfg, _ = get_config()
+            self.cfg = get_config()
         else:
             self.cfg = cfg
 

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/config_loader.py

@@ -6,7 +6,7 @@ _base_config: Optional[BaseConfig] = None
 _func_config: Optional[FunctionConfig] = None
 
 
-def get_config(cfg_path: Optional[str] = None) -> tuple[BaseConfig, FunctionConfig]:
+def get_config(cfg_path: Optional[str] = None) -> BaseConfig:
     from omegaconf import OmegaConf, DictConfig
 
     if cfg_path is None:
@@ -16,21 +16,27 @@ def get_config(cfg_path: Optional[str] = None) -> tuple[BaseConfig, FunctionConf
         return get_config_with_dict(yaml_cfg)
 
 
-def get_config_with_dict(
-    cfg_dict=None,
-) -> tuple[BaseConfig, FunctionConfig]:
+def get_func_config() -> FunctionConfig:
+    global _func_config
+    if _func_config is None:
+        _func_config = FunctionConfig()
+
+    return _func_config
+
+
+def get_config_with_dict(cfg_dict=None) -> BaseConfig:
     from omegaconf import OmegaConf
 
-    global _base_config, _func_config
+    global _base_config
     if _base_config is None:
         _base_config = OmegaConf.structured(BaseConfig())
-        _func_config = FunctionConfig()
+
     # allow late merges/overrides even if already initialized
     if cfg_dict is not None:
         _base_config = cast(
             BaseConfig, OmegaConf.merge(_base_config, OmegaConf.create(cfg_dict))
         )
-    return cast(tuple[BaseConfig, FunctionConfig], (_base_config, _func_config))
+    return _base_config
 
 
 def set_base_config(cfg: BaseConfig) -> None:

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/data_module.py

@@ -13,7 +13,7 @@ class DataModule(LightningDataModule):
         super().__init__()
         from britekit.core.dataset import SpectrogramDataset
 
-        self.cfg, _ = get_config()
+        self.cfg = get_config()
         self.train_data = None
         self.val_data = None
         self.test_data = None

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/dataset.py

@@ -59,7 +59,7 @@ class SpectrogramDataset(Dataset):
         self.noise_class_index = noise_class_index
         self.is_training = is_training
 
-        self.cfg, _ = get_config()
+        self.cfg = get_config()
 
         # get indexes of all specs that contain only noise
         self.noise_indexes = []

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/pickler.py

@@ -30,7 +30,7 @@ class Pickler:
     ):
         from britekit.training_db.training_db import TrainingDatabase
 
-        self.cfg, self.fn_cfg = get_config()
+        self.cfg = get_config()
         self.classes_path = classes_path
         self.output_path = output_path
         self.max_per_class = max_per_class

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/plot.py

@@ -28,7 +28,7 @@ def plot_spec(
     import matplotlib.pyplot as plt
     import numpy as np
 
-    cfg, _ = get_config()
+    cfg = get_config()
     assert cfg.audio.freq_scale in {"linear", "log", "mel"}
 
     if spec_duration is None:

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/predictor.py

@@ -37,7 +37,7 @@ class Predictor:
         """
         from britekit.core.audio import Audio
 
-        self.cfg, _ = get_config()
+        self.cfg = get_config()
         self.audio = Audio()
         self.class_names: Optional[List[str]] = None
         self.class_codes: Optional[List[str]] = None

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/reextractor.py

@@ -61,7 +61,7 @@ class Reextractor:
         import numpy as np
         import pandas as pd
 
-        cfg, _ = get_config()
+        cfg = get_config()
 
         with TrainingDatabase(self.db_path) as db:
             if self.class_name is None and self.classes_path is None:

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/trainer.py

@@ -14,7 +14,7 @@ class Trainer:
         import pytorch_lightning as pl
         import torch
 
-        self.cfg, _ = get_config()
+        self.cfg = get_config()
         torch.set_float32_matmul_precision("medium")
         if self.cfg.train.seed is not None:
             pl.seed_everything(self.cfg.train.seed, workers=True)

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/tuner.py

@@ -42,7 +42,7 @@ class Tuner:
         from britekit.core.pickler import Pickler
         from britekit.core.reextractor import Reextractor
 
-        self.cfg, self.fn_cfg = get_config()
+        self.cfg = get_config()
         self.original_seed = self.cfg.train.seed
         self.recording_dir = recording_dir
         self.output_dir = output_dir

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/core/util.py

@@ -101,7 +101,7 @@ def get_device() -> str:
     """Return the device for pytorch to use."""
     import torch
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if cfg.misc.force_cpu:
         return "cpu"  # for performance comparisons
     elif torch.cuda.is_available():
@@ -362,7 +362,7 @@ def get_source_name(filename: str) -> str:
     if not filename:
         return "default"
 
-    cfg, _ = get_config()
+    cfg = get_config()
     if not cfg.misc.source_regexes:
         return "default"
 
@@ -432,7 +432,7 @@ def expand_spectrogram(spec: bytes):
         raise TypeError("spec must be bytes")
 
     try:
-        cfg, _ = get_config()
+        cfg = get_config()
         bytes_data = zlib.decompress(spec)
         spec_array = np.frombuffer(bytes_data, dtype=np.uint8) / 255
         spec_array = spec_array.astype(np.float32)

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/models/base_model.py

@@ -72,7 +72,7 @@ class BaseModel(pl.LightningModule):
             )
 
         self.save_hyperparameters()
-        self.cfg, _ = get_config()
+        self.cfg = get_config()
 
         # Save parameters
         self.model_type = model_type

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/models/model_loader.py

@@ -22,7 +22,7 @@ def load_new_model(
     from britekit.models.hgnet import HGNetModel
     from britekit.models.vovnet import VovNetModel
 
-    cfg, _ = get_config()
+    cfg = get_config()
     device = get_device()
 
     # create a dict of optional keyword arguments

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/models/timm_model.py

@@ -39,7 +39,7 @@ class TimmModel(BaseModel):
 
         # head replacement is not supported here since it
         # would be very complicated with so many model types
-        cfg, _ = get_config()
+        cfg = get_config()
         assert model_type.startswith("timm.")
         self.backbone = timm.create_model(
             model_type[5:],  # strip off the "timm." prefix

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/testing/per_minute_tester.py

@@ -62,7 +62,7 @@ class PerMinuteTester(BaseTester):
         self.threshold = threshold
         self.gen_pr_table = gen_pr_table
 
-        self.cfg, self.fn_cfg = get_config()
+        self.cfg = get_config()
 
     # ============================================================================
     # Public methods - Main execution

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/testing/per_recording_tester.py

@@ -56,7 +56,7 @@ class PerRecordingTester(BaseTester):
         self.tp_secs_at_precision = tp_secs_at_precision
         self.per_recording = True
 
-        self.cfg, self.fn_cfg = get_config()
+        self.cfg = get_config()
 
     # ============================================================================
     # Public methods - Main execution

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/testing/per_segment_tester.py

@@ -68,7 +68,7 @@ class PerSegmentTester(BaseTester):
         self.coefficient = coef
         self.intercept = inter
 
-        self.cfg, self.fn_cfg = get_config()
+        self.cfg = get_config()
 
     def _get_recording_info(self):
         """

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/training_db/extractor.py

@@ -43,7 +43,7 @@ class Extractor:
         self.spec_group = spec_group if spec_group is not None else "default"
 
         self.provider = TrainingDataProvider(self.db)
-        self.cfg, _ = get_config()
+        self.cfg = get_config()
         self.audio = audio.Audio()
 
         if overlap is None:

{britekit-0.0.9 → britekit-0.0.11}/src/britekit/training_db/training_db.py

@@ -6,7 +6,6 @@ from types import SimpleNamespace
 from typing import Optional
 
 from britekit.core.exceptions import DatabaseError
-from britekit.core.config_loader import get_config
 
 
 class TrainingDatabase:
@@ -20,7 +19,6 @@ class TrainingDatabase:
 
     def __init__(self, db_path: str = os.path.join("data", "training.db")):
         self.today = datetime.today().strftime("%Y-%m-%d")
-        _, self.fn_cfg = get_config()
         try:
             self.conn = sqlite3.connect(db_path)
             self.conn.execute("PRAGMA foreign_keys = ON")