Release notes

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.modules.

  • Posterior classes have been reduced to wrappers on DataLoaders

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

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

0.6.7 (2020-8-05)

  • downgrade anndata>=0.7 and scanpy>=1.4.6 @galen

  • make loompy optional, raise sckmisc import error @adam

  • fix PBMCDataset download bug @galen

  • fix AnnDatasetFromAnnData _X in adata.obs bug @galen

0.6.6 (2020-7-08)

  • add tqdm to within cluster DE genes @adam

  • restore tqdm to use simple bar instead of ipywidget @adam

  • move to numpydoc for doctstrings @adam

  • update issues templates @adam

  • Poisson variable gene selection @valentine-svensson

  • BrainSmallDataset set defualt save_path_10X @gokcen-eraslan

  • train_size must be float between 0.0 and 1.0 @galen

  • bump dependency versions @galen

  • remove reproducibility notebook @galen

  • fix scanVI dataloading @pierre

0.6.5 (2020-5-10)

  • updates to totalVI posterior functions and notebooks @adam

  • update seurat v3 HVG selection now using skmisc loess @adam

0.6.4 (2020-4-14)

  • add back Python 3.6 support @adam

  • get_sample_scale() allows gene selection @valentine-svensson

  • bug fix to the dataset to anndata method with how cell measurements are stored @adam

  • fix requirements @adam

0.6.3 (2020-4-01)

  • bug in version for Louvian in @adam

0.6.2 (2020-4-01)

  • update highly variable gene selection to handle sparse matrices @adam

  • update DE docstrings @pierre

  • improve posterior save load to also handle subclasses @pierre

  • Create NB and ZINB distributions with torch and refactor code accordingly @pierre

  • typos in autozivae @achille

  • bug in csc sparse matrices in anndata data loader @adam

0.6.1 (2020-3-13)

  • handles gene and cell attributes with the same name @han-yuan

  • fixes anndata overwriting when loading @adam, @pierre

  • formatting in basic tutorial @adam

0.6.0 (2020-2-28)

  • updates on TotalVI and LDVAE @adam

  • fix documentation, compatibility and diverse bugs @adam, @pierre @romain

  • fix for external module on scanpy @galen

0.5.0 (2019-10-17)

0.4.1 (2019-08-03)

0.4.0 (2019-07-25)

  • gimVI @achille

  • synthetic correlated datasets, fixed bug in marginal log likelihood @oscar

  • autotune, dataset enhancements @gabriel

  • documentation @jeff

  • more consistent posterior API, docstring, validation set @adam

  • fix anndataset @michael-raevsky

  • linearly decoded VAE @valentine-svensson

  • support for scanpy, fixed bugs, dataset enhancements @achille

  • fix filtering bug, synthetic correlated datasets, docstring, differential expression @pierre

  • better docstring @jamie-morton

  • classifier based on library size for doublet detection @david-kelley

0.3.0 (2019-05-03)

0.2.4 (2018-12-20)

0.2.2 (2018-11-08)

  • added baselines and datasets for sMFISH imputation @jules

  • added harmonization content @chenling

  • fixing bugs on DE @romain

0.2.0 (2018-09-04)

0.1.6 (2018-08-08)

  • MMD and adversarial inference wrapper @eddie

  • Documentation @jeff

  • smFISH data imputation @max

0.1.5 (2018-07-24)

0.1.3 (2018-06-22)

0.1.2 (2018-06-13)

0.1.0 (2017-09-05)

  • First scVI TensorFlow version @romain