Changelog#

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased#

v0.2.0 - 2025-12-07#

Added#

  • Training option to ignore classes and features in less than N groups.

  • cvi command run independent cross-validation as done in the paper.

  • Support for training and evaluating random forest models.

  • Support for computing sample weights for observation groups in fit.

  • Report information content of the prediction in predict output.

Changed#

  • Relax anndata dependency to allow more recent releases.

  • Update MIBiG 3.1 dataset to filter out erroneous partial clusters.

  • Retrain CHAMOIS with filtered MIBIG 3.1 dataset and improved feature selection.

  • Make chamois.compositions.build_variables drop empty columns.

  • Rename screen command to compare.

  • Incorrect use of chemical groups in cross-validation commands.

  • Update Pfam to 38.0.

Fixed#

  • Issue with computation of probabilistic Jaccard distance in validate command.

  • Incorrect error message on non-existing class in explain command.

  • Incorrect merging of multiple feature tables in CLI.

  • Extraction of minimum class and features by groups for majority positive classes.

  • Incorrect error message in predict command.

  • Unsupported sample weighting in older scikit-learn releases.

v0.1.3 - 2025-03-30#

Fixed#

  • Build issue on missing rich package.

Added#

  • Jaccard index to reported metrics in chamois cv, chamois train and chamois validate commands.

v0.1.2 - 2025-03-26#

Fixed#

  • Make installation procedure not require extra packages in most cases.

  • Remove universal from bdist_wheel command in setup.cfg.

  • Seeds not being passed from the CLI to the actual ChemicalOntologyPredictor instances.

Documentation#

  • Add missing Javascript files for PyPI icons.

  • Update installation instructions for Docker and Singularity.

v0.1.1 - 2025-03-21#

Fixed#

  • Automated deployment and setup of filtered Pfam HMMs from GitHub.

v0.1.0 - 2025-03-21#

Initial release.