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.

0.3.3 (2023-03-29)

Fixed

Large scale tutorial now properly uses gpu index (#92)

0.3.2 (2023-03-13)

Changed

Switch to Ruff for linting/formatting (#87)
Update cookiecutter template (#88)

0.3.1 (2023-02-16)

Changed

Expose chunk size for silhouette (#82)

0.3.0 (2023-02-16)

Changed

Rename KmeansJax to Kmeans and fix ++ initialization, use Kmeans as default in benchmarker instead of Leiden (#81)
Warn about joblib, add progress bar postfix str (#80)

0.2.0 (2023-02-02)

Added

Allow custom nearest neighbors methods in Benchmarker (#78)

0.1.1 (2023-01-04)

Added

Add new tutorial and fix scalability of lisi (#71)

0.1.0 (2023-01-03)

Added

Add benchmarking pipeline with plotting (#52 and #69)

Fixed

Fix diffusion distance computation, affecting kbet (#70)

0.0.9 (2022-12-16)

Added

Add kbet (#60)
Add graph connectivty metric (#61)

0.0.8 (2022-11-18)

Switch to random kmeans initialization due to kmeans++ complexity issues (#54)
Begin fixes to make kmeans++ initialization faster (#49)

0.0.7 (2022-10-31)

Fix memory issue in KMeansJax by using _kmeans_full_run with map instead of vmap (#45)
Move PCR to utils module in favor of PCR comparison (#46)

0.0.6 (2022-10-25)

Reimplement silhouette in a memory constant way, pdist using lax scan (#42)

0.0.5 (2022-10-24)

Added

Standardize language of docstring (#30)
Use K-means++ initialization (#23)
Add pc regression and pc comparsion (#16 and #38)
Lax'd silhouette (#33)
Cookicutter template sync (#35)

0.0.4 (2022-10-10)

Added

NMI/ARI metric with Leiden clustering resolution optimization (#24)
iLISI/cLISI metrics (#20)

0.0.1 - 0.0.3

See the [GitHub releases][https://github.com/yoseflab/scib-metrics/releases] for details.