harmonypy

• Stop excluding README.md from the build, because setup.py depends on this file.

• Replace scipy.cluster.vq.kmeans2 with the faster function sklearn.cluster.KMeans. Thanks to @johnarevalo for providing details about the running time with both functions in PR #20.

• Replace scipy.cluster.vq.kmeans with scipy.cluster.vq.kmeans2 to address
  issue #10 where we learned that kmeans does not always return k centroids,
  but kmeans2 does return k centroids. Thanks to @onionpork and @DennisPost10
  for reporting this.

Released on 2020-08-11

• Expose max_iter_harmony as a new top-level argument, in addition to the
  previously exposed max_iter_kmeans. This more closely resembles the
  original interface in the harmony R package. Thanks to @pinin4fjords
  for pull request #8

(This release was originally posted on 2020-08-11. Now, I am trying to re-post the same release again, in the hope that it gets automatically picked up by Zenodo).

Released on 2020-03-02

• Fix a bug in the LISI code that sometimes causes computation to break. Thanks
  to @tariqdaouda for reporting it in issue #1

• Fix a bug that prevents controlling the number of iterations. Thanks to
  @liboxun for reporting it in issue #3

• Fix a bug causing slightly different results than expected. Thanks to
  @bli25broad for pull request #2

• Add support for multiple categorical batch variables.