bioacoustic-ai/bacpipe: BacPipe v1.3.4 Release Notes
Zenodo (CERN European Organization for Nuclear Research)
Abstract
🚀 bacpipe v1.3.4 Release Notes We are excited to announce bacpipe v1.3.4! This release focuses on polishing the API and developer experience, adding BirdNET v3 support, a comprehensive documentation overhaul, a refreshed set of example notebooks, and a large expansion of the test suite to lock in stability. 🔥 Key Highlights 🦜 BirdNET v3 Support A new birdnet_v3 feature extractor brings the BirdNET+ V3.0 model into bacpipe, powered by the BirdNET+_V3.0-preview3.1_Global_11K_Labels.csv label set. It operates at 32 kHz with a default 3 s segment length and produces 1280-dimensional embeddings. 📚 Documentation Overhaul Extensive docstrings and usage examples were added across the public API, the Sphinx documentation build was restructured and updated (including a revamped API reference and Read the Docs configuration), and the README.md was significantly expanded. 📓 Revamped & New Example Notebooks The basic examples were reorganized — the old simple use cases.ipynb was rewritten as simple_use_cases.ipynb, and a brand new using_different_bacpipe_functions.ipynb walks through the individual bacpipe functions. The advanced examples (clustering, extending_an_existing_model, probing_a_model, using_a_custom_model) were updated, and notebook workflows are now covered by automated tests. 🐛 Key Bug Fixes Fixed a perch_v2 bug by removing incorrect audio normalization and using softmax instead of sigmoid. Fixed a classifier prediction leak and a crash when indexing single-bin classes. Better handling of annotation files containing duplicate start/end times. 🍎 Improved Mac (MPS) Support Better support for Apple's Metal Performance Shaders (MPS — CUDA for Mac) so GPU acceleration works more smoothly on Apple silicon. 🧰 Friendlier API & Configuration Handling Improved and more consistent handling of kwargs and settings.yaml configuration, so options cascade correctly through functions and modules. Several API points were re-exposed for more convenient programmatic use. 📊 Better Dashboard & Prediction Visualization Predictions render more cleanly above spectrograms and now include hover information. The dashboard dynamically loads only what is visible, and overview plots were fixed. ⚙️ New / Updated Settings Parameters The following options in your settings.yaml (or via bacpipe.settings) were added or changed: # Minimum annotation duration (in seconds) required for inclusion in ground truth. min_annotation_length: 0 # Maximum number of labels kept per timestamp (reduces prediction file size). max_labels_per_timestamp: 30 # Choose 2D or 3D embedding plots. visualization_dimensions: 2 # Number of top classifier predictions shown above spectrograms. nr_predictions_to_display: 3 # Maximum discrete categories rendered with distinct colors before using a colorbar. max_nr_categories: 55 Other notable changes: model_base_path was renamed from bacpipe/model_checkpoints to bacpipe_model_checkpoints to avoid conflicts with the package name. rm_embedding_on_keyboard_interrupt now defaults to False, so embeddings are kept when a run is interrupted. Metadata labels were renamed from default_label_keys to metadata_label_keys, with week_of_year added as a new key. 📦 Dependency & Installation Changes Requirements were split into requirements_no_tf.txt and requirements_no_cuda.txt for lighter environments that do not need TensorFlow or GPU support. kaleido (>= 1) was added for static plot/picture export. onnxruntime was added to support ONNX-based models (e.g. BirdNET v3 and the ONNX version of Perch v2). ❤️ Acknowledgements & Contributor Thanks A massive thank you to everyone who contributed code, feedback, and models for this release! Justin Chu and the Perch/BirdNET communities for maintaining the ONNX conversions and model checkpoints that power perch_v2 and the new birdnet_v3 support. A warm thank you to all researchers, model creators, testers, and community members providing feedback to make bacpipe better for bioacoustic research!
Authors 8
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Leiden University · Naturalis Biodiversity Center · Tilburg University
Affiliation as printed
Naturalis Biodiversity Center
Leiden University
Tilburg University
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Muséum national d'Histoire naturelle
Affiliation as printed
Muséum national d'Histoire naturelle
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Affiliation as printed
Flanders Marine Institute
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Affiliation as printed
University College London
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Affiliation as printed
Tilburg University
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Institut de Recherche et Coordination Acoustique Musique
Affiliation as printed
Institut de Recherche et Coordination Acoustique Musique
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Muséum national d'Histoire naturelle
Affiliation as printed
Muséum national d'Histoire naturelle
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