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.

[Unreleased]#

[0.3.1]#

  • Fix documentation of cond() return type and handle pd.Series in model.predict() (#5, thanks Mark Keller)

[0.3.0]#

  • Depend on formulaic_contrast package

  • Refactor cond() implementation to use formulaic_contrast implementation.

[0.2.2]#

  • Sync with cookiecutter-template update (version 0.4)

  • Bump required Python version to 3.10

  • Allow data frames as design matrices

  • Allow matrices as input to LEMUR()

[0.2.1]#

  • Change example gene to one with clearer differential expression pattern

  • Remove error output in `align_harmony

[0.2.0]#

Major rewrite of the API. Instead of adding coefficients as custom fields to the input AnnData object, the API now follows an object-oriented style similar to scikit-learn or SCVI. This change was motivated by the feedback during the submission to the scverse ecosystem. (Thanks Gregor).

Changed#

  • Instead of calling fit = pylemur.tl.lemur(adata, ...), you now create a LEMUR model (model = pylemur.tl.LEMUR(adata, ...)) and subsequently call model.fit(), model.align_with_harmony(), and model.predict().

[0.1.0] - 2024-03-21#

  • Initial beta release of pyLemur