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CHANGELOG.md

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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

  • Add progress_bar argument to {class}scib_metrics.benchmark.Benchmarker {pr}152.
  • Add ability of {class}scib_metrics.benchmark.Benchmarker plotting code to handle missing sets of metrics {pr}181.

Changed

  • Changed Leiden clustering now has a seed argument for reproducibility {pr}173.
  • Changed passing None to bio_conservation_metrics or batch_correction_metrics in {class}scib_metrics.benchmark.Benchmarker now implies to skip this set of metrics {pr}181.

Fixed

  • Fix neighbors connectivities in test to use new scanpy fn {pr}170.
  • Fix Kmeans test {pr}172.
  • Fix deprecation and future warnings {pr}171.
  • Fix lisi return type and docstring {pr}182.

0.5.1 (2024-02-23)

Changed

  • Replace removed {class}jax.random.KeyArray with {class}jax.Array {pr}135.

0.5.0 (2024-01-04)

Changed

  • Refactor all relevant metrics to use NeighborsResults as input instead of sparse distance/connectivity matrices {pr}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 {pr}115.

0.4.0 (2023-09-19)

Added

  • Update isolated labels to use newest scib methodology {pr}108.

Fixed

  • Fix jax one-hot error {pr}107.

Removed

  • Drop Python 3.8 {pr}107.

0.3.3 (2023-03-29)

Fixed

  • Large scale tutorial now properly uses gpu index {pr}92

0.3.2 (2023-03-13)

Changed

  • Switch to Ruff for linting/formatting {pr}87
  • Update cookiecutter template {pr}88

0.3.1 (2023-02-16)

Changed

  • Expose chunk size for silhouette {pr}82

0.3.0 (2023-02-16)

Changed

  • Rename KmeansJax to Kmeans and fix ++ initialization, use Kmeans as default in benchmarker instead of Leiden {pr}81.
  • Warn about joblib, add progress bar postfix str {pr}80

0.2.0 (2023-02-02)

Added

  • Allow custom nearest neighbors methods in Benchmarker {pr}78.

0.1.1 (2023-01-04)

Added

  • Add new tutorial and fix scalability of lisi {pr}71.

0.1.0 (2023-01-03)

Added

  • Add benchmarking pipeline with plotting {pr}52 {pr}69.

Fixed

  • Fix diffusion distance computation, affecting kbet {pr}70.

0.0.9 (2022-12-16)

Added

  • Add kbet {pr}60.
  • Add graph connectivty metric {pr}61.

0.0.8 (2022-11-18)

Changed

  • Switch to random kmeans initialization due to kmeans++ complexity issues {pr}54.

Fixed

  • Begin fixes to make kmeans++ initialization faster {pr}49.

0.0.7 (2022-10-31)

Changed

  • Move PCR to utils module in favor of PCR comparison {pr}46.

Fixed

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

0.0.6 (2022-10-25)

Changed

  • Reimplement silhouette in a memory constant way, pdist using lax scan {pr}42.

0.0.5 (2022-10-24)

Added

  • Standardize language of docstring {pr}30.
  • Use K-means++ initialization {pr}23.
  • Add pc regression and pc comparsion {pr}16 {pr}38.
  • Lax'd silhouette {pr}33.
  • Cookicutter template sync {pr}35.

0.0.4 (2022-10-10)

Added

  • NMI/ARI metric with Leiden clustering resolution optimization {pr}24.
  • iLISI/cLISI metrics {pr}20.

0.0.1 - 0.0.3

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