CHANGELOG.md
LICENSE
MANIFEST.in
MODELS.md
QUICKSTART.md
README.md
pyproject.toml
requirements.txt
examples/tiny_db.fasta
examples/tiny_test.fasta
taxonova/__init__.py
taxonova/main.py
taxonova.egg-info/PKG-INFO
taxonova.egg-info/SOURCES.txt
taxonova.egg-info/dependency_links.txt
taxonova.egg-info/entry_points.txt
taxonova.egg-info/requires.txt
taxonova.egg-info/top_level.txt
taxonova/calibration/__init__.py
taxonova/calibration/ood.py
taxonova/calibration/tau_norm.py
taxonova/calibration/temperature.py
taxonova/cli/__init__.py
taxonova/cli/argument_parser.py
taxonova/cli/calibration_handler.py
taxonova/cli/classification_handler.py
taxonova/cli/config_builder.py
taxonova/cli/data_loader.py
taxonova/cli/download_models_handler.py
taxonova/cli/fit_ood_handler.py
taxonova/cli/logging_setup.py
taxonova/cli/species_safe_split.py
taxonova/cli/stratified_split.py
taxonova/cli/training_handler.py
taxonova/core/__init__.py
taxonova/core/factory.py
taxonova/core/loss.py
taxonova/data/__init__.py
taxonova/data/dataset.py
taxonova/data/fasta.py
taxonova/model/__init__.py
taxonova/model/model_config.py
taxonova/model/model_saver.py
taxonova/prediction/__init__.py
taxonova/prediction/attention.py
taxonova/prediction/confidence_predictor.py
taxonova/prediction/device_manager.py
taxonova/prediction/hierarchical_model.py
taxonova/prediction/model_utils.py
taxonova/prediction/output_processing.py
taxonova/prediction/predictor.py
taxonova/preprocessing/__init__.py
taxonova/preprocessing/sequence_processor.py
taxonova/training/__init__.py
taxonova/training/checkpoint_manager.py
taxonova/training/device_manager.py
taxonova/training/ema_manager.py
taxonova/training/hierarchical_trainer.py
taxonova/training/optimizer_manager.py
taxonova/training/phase2_decoupled.py
taxonova/training/smart_trainer.py
taxonova/training/stopping_criteria.py
taxonova/training/training_loop.py
taxonova/training/validation_manager.py
taxonova/utils/__init__.py
taxonova/utils/config.py
taxonova/utils/lineage_filter.py
taxonova/utils/model_downloader.py
taxonova/utils/resource_tracking.py
taxonova/utils/taxonomy_hierarchy.py
tests/test_filtering.py
tests/test_taxonova.py