v0.10.0

Added

• Support for changing the CLI argument defaults from a call to the gecco.cli.main function.

Changed

• Allow training with sequences only containing negative samples (with a warning).
• Add an error in gecco convert when given input is not a folder.
• Update numpy, polars, pyhmmer and psutil to latest versions.
• Replace docopt with argparse parser for CLI argument parsing.
• Make embedded_hmms generic over the module name.
• Make ClusterCRF.trained accept any traversable.
• Allow changing the default ClusterCRF and TypeClassifier classes used in gecco.cli.

Fixed

• gecco.cli and gecco.crf submodules not being included in wheel distribution.
• gecco convert issue when given a relative path.
• Unused tqdm import in gecco.crf module.
• Unused build dependencies from setup.cfg and pyproject.toml.
• rich optional import logic in setup.py.