Scikit-fingerprints

New features

* For each already existing distance and similarity function, bulk versions were added

Fixes and internal changes

* Added dependency on numba for distance calculation speedup

**Full Changelog**: https://github.com/scikit-fingerprints/scikit-fingerprints/compare/v1.14.0...v1.15.0

Breaking changes

* dropped support for Python 3.9

New features

* Python 3.13 support
* many new similarities and distances: Simpson, Braun-Blanquet, Fraggle, Harris-Lahey, Kulczynski, McConnaughey, CT4, Rogot-Goldberg, Russell, Sokal-Sneath
* much faster distances
* PubChem split
* expanded `run_in_parallel` function to run on single element functions

Fixes and internal changes

* Add more explicit Pandoc information
* Updated tests badge in README

**Full Changelog**: https://github.com/scikit-fingerprints/scikit-fingerprints/compare/v1.13.1...v1.14.0

What's Changed

Patch release that fixes feature names, requested in https://github.com/scikit-fingerprints/scikit-fingerprints/issues/389.

**Full Changelog**: https://github.com/scikit-fingerprints/scikit-fingerprints/compare/v1.13.0...v1.13.1

Breaking changes

* Removed one redundant feature from count MACCS, duplicate of another feature
* This is **the last** release supporting Python 3.9, future versions will work for Python 3.10 or newer

New features

* More interpretable feature names for many fingerprints with `.get_feature_names_out()`
* `descriptors` module with some commonly used descriptors, currently topological, constitutional, kappa, and charge
* BCUT2D fingerprint
* First 4 tutorials, also included in the documentation
* More documentation, typo fixes

Fixes and internal changes

* Updated Poetry to 2.0.1
* Migrated from black, isort etc. to ruff

New Contributors
* chmurzak made their first contribution in https://github.com/scikit-fingerprints/scikit-fingerprints/pull/330
* franciszekjob made their first contribution in https://github.com/scikit-fingerprints/scikit-fingerprints/pull/344
* iedylag made their first contribution in https://github.com/scikit-fingerprints/scikit-fingerprints/pull/347

**Full Changelog**: https://github.com/scikit-fingerprints/scikit-fingerprints/compare/v1.12.0...v1.13.0

Breaking changes

* MAP4 implementation has been fixed, and new results in molecular classification are much higher than before

New features

* Feature names for Mordred and RDKit2DDescriptors available via standard scikit-learn `.get_feature_names_out()` API
* Exposed full TQDM kwargs
* Updated E3FP version
* Added `valid_only` option to MolFromAminoseqTransformer
* Added examples for dataset loading functions
* Added more comprehensive User Guide

**Full Changelog**: https://github.com/scikit-fingerprints/scikit-fingerprints/compare/v1.11.0...v1.12.0

Breaking changes

* Changed a few filter names to always have `Filter` at the end of class name
* `extract_multioutput_pos_proba` is now `extract_pos_proba` and works for both single-task and multitask cases

New features

* scikit-fingerprints paper has been published at SoftwareX! Added paper link
* virtual screening metrics: EF, RIE, BEDROC

Fixes and internal changes

* Docs fixes for splitters
* README example fix

**Full Changelog**: https://github.com/scikit-fingerprints/scikit-fingerprints/compare/v1.10.1...v1.11.0