v0.10.3

Added

• --no-trim CLI flag to disable cluster trimming.

Changed

• Allow disabling predicted cluster trimming in ClusterRefiner.

v0.10.2

Changed

• Bump pyhmmer dependency to v0.12.0.
• Use SPDX license qualifier in pyproject.toml.

v0.10.1

Changed

• Remove unneeded psutil package dependency.

Fixed

• Missing --output flag in gecco convert command (#19).

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.

v0.10.0-alpha.3

Added

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

v0.10.0-alpha.2

Fixed

• gecco.cli and gecco.crf submodules not being included in wheel distribution.

v0.10.0-alpha.1

Changed

• 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 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.

v0.9.10

Fixed

• Progress reading display when reading from compressed files.
• Change labeling routine to use broad overlaps when annotating genes with cluster tables (#15).

Changed

• Bump supported polars dependency to v0.20.
• Bump supported statsmodels dependency to v0.14.
• Report identifier of sequences with uni-valued labels when training.

v0.9.9

Added

• Support for gzip, bzip2, lz4 and xz-compressed input files.

Fixed

• Outdated use of pandas API in gecco cv command.

Changed

• Bump pyhmmer dependency to v0.10.0.
• Bump pyrodigal dependency to v3.0.0.
• Make gecco cv output a gene table with a ground truth column.

v0.9.8

Fixed

• ClusterTable.from_clusters extracting cluster IDs in the wrong column.
• Deprecation warnings in polars.read_csv and polars.write_csv with recent polars versions.
• Deprecation warnings in importlib_resources with recent Python versions.