New in 0.7.0 (2020-10-14)#

scvi is now scvi-tools. Version 0.7 introduces many breaking changes. The best way to learn how to use scvi-tools is with our documentation and tutorials.

  • New high-level API and data loading, please see tutorials and examples for usage.

  • GeneExpressionDataset and associated classes have been removed.

  • Built-in datasets now return AnnData objects.

  • scvi-tools now relies entirely on the [AnnData] format.

  • scvi.models has been moved to scvi.core.module.

  • Posterior classes have been reduced to wrappers on DataLoaders

  • scvi.inference has been split to scvi.core.data_loaders for AnnDataLoader classes and scvi.core.trainers for trainer classes.

  • Usage of classes like Trainer and AnnDataLoader now require the AnnData data object as input.