New in 0.19.0 (2022-10-31)

Major Changes

• TrainingPlan allows custom PyTorch optimizers #1747.

• Improvements to JaxTrainingPlan #1747 #1749.

• LossRecorder is deprecated. Please substitute with LossOutput #1749

• All training plans require keyword args after the first positional argument #1749

• JaxBaseModuleClass absorbed features from the JaxModuleWrapper, rendering the JaxModuleWrapper obsolote, so it was removed. #1751

• Add scvi.external.Tangram and scvi.external.tangram.TangramMapper that implement Tangram for mapping scRNA-seq data to spatial data #1743.

Minor changes

• Remove confusing warning about kl warmup, log kl weight instead #1773

Breaking changes

• LossRecorder no longer allows access to dictionaries of values if provided during initialization #1749.

• JaxModuleWrapper removed. #1751

Bug Fixes

• Fix n_proteins usage in MULTIVI #1737.

• Remove unused param in MULTIVI #1741.

• Fix random seed handling for Jax models #1751.

Contributors

• @watiss

• @adamgayoso

• @martinkim0

• @marianogabitto