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Changelog

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.

0.6.0 (unreleased)#

Added#

0.5.1 (2024-02-23)#

Changed#

0.5.0 (2024-01-04)#

Changed#

  • Refactor all relevant metrics to use NeighborsResults as input instead of sparse distance/connectivity matrices #129.

0.4.1 (2023-10-08)#

Fixed#

  • Fix KMeans. All previous versions had a bug with KMeans and ARI/NMI metrics are not reliable with this clustering #115.

0.4.0 (2023-09-19)#

Added#

  • Update isolated labels to use newest scib methodology #108.

Fixed#

  • Fix jax one-hot error #107.

Removed#

  • Drop Python 3.8 #107.

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 #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)#

Changed#

  • Switch to random kmeans initialization due to kmeans++ complexity issues #54.

Fixed#

  • Begin fixes to make kmeans++ initialization faster #49.

0.0.7 (2022-10-31)#

Changed#

  • Move PCR to utils module in favor of PCR comparison #46.

Fixed#

  • Fix memory issue in KMeansJax by using _kmeans_full_run with map instead of vmap #45.

0.0.6 (2022-10-25)#

Changed#

  • 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 #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.

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