History

0.5

First published version.

0.6

More robust graph partition.
Allow forcing feature genes.
Rename "project" to "convey" to prepare for addition of atlas projection functionality.

0.7.0

Switch to new project template.
Fix some edge cases in the pipeline.
Switch to using psutil for detecting system resources.
Fix binary wheel issues.
Give up on using travis-ci.

0.8.0

Add inner fold factor computation for metacells quality control.
Add deviant fold factor computation for metacells quality control.
Add projection of query data onto an atlas.
Self-adjusting pile sizes.
Add convenience function for computing data for MCView.
Better control over filtering using absolute fold factors.
Fix edge case in computing noisy lonely genes.
Additional outliers certificates.
Stricter deviants detection policy

0.9.0

Improved and published projection algorithm.
Restrict number of rare gene candidates.
Tighter control over metacells size and internal quality.
Improved divide-and-conquer strategy.
Base deviants (outliers) on gaps between cells.
Terminology changes (see the README for details).
Projection!

0.9.1

Fix build for python 3.11.
More robust gene selection, KNN graph creation, and metacells partition.
More thorough binary wheels.

0.9.2

Fix numpy compatibility issue.
Fix K of UMAP skeleton KNN graph (broken in 0.9.1).

0.9.3

Allow specifying both target UMIs and target size (in cells) for the metacells, and adaptively try to satisfy both. This should produce better-sized metacells "out of the box" compared to 0.9.[0-2].

0.9.4

Fix minor bug in regularization of metacell fractions.
Fix issue with canonical sparse matrices after downsampling (probably due to scipy.sparse updates?)
Fix using deprecated AnnData APIs.

0.9.5

Improve recovery from unstable convex solvers.
Fix an edge case in computing deviant cells using the gaps policy.
Turns out the threadpoolctl is not thread-safe (the irony!), causing deadlocks. Work around this.