History

0.6.8 (2020-9-16)

• scvi is now deprecated, please uninstall and install scvi-tools (available shortly)

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 setup.py @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)

• do not automatically upper case genes @adam

• AutoZI @oscar

• Made the intro tutorial more user friendly @adam

• Tests for LDVAE notebook @adam

• black codebase @achille @gabriel @adam

• fix compatibility issues with sklearn and numba @romain

• fix Anndata @francesco-brundu

• docstring, totalVI, totalVI notebook and CITE-seq data @adam

• fix type @eduardo-beltrame

• fixing installation guide @jeff

• improved error message for dispersion @stephen-flemming

0.4.1 (2019-08-03)

• docstring @achille

• differential expression @oscar @pierre

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)

• corrected notebook @jules

• added UMAP and updated harmonization code @chenling @romain

• support for batch indices in csvdataset @primoz-godec

• speeding up likelihood computations @william-yang

• better anndata interop @casey-greene

• early stopping based on classifier accuracy @david-kelley

0.2.4 (2018-12-20)

• updated to torch v1 @jules

• added stress tests for harmonization @chenling

• fixed autograd breaking @romain

• make removal of empty cells more efficient @john-reid

• switch to os.path.join @casey-greene

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)

• annotation notebook @eddie

• Memory footprint management @jeff

• updated early stopping @max

• docstring @james-webber

0.1.6 (2018-08-08)

• MMD and adversarial inference wrapper @eddie

• Documentation @jeff

• smFISH data imputation @max

0.1.5 (2018-07-24)

• Dataset additions @eddie

• Documentation @yining

• updated early stopping @max

0.1.3 (2018-06-22)

• Notebook enhancement @yining

• Semi-supervision @eddie

0.1.2 (2018-06-13)

• First release on PyPi

• Skeleton code & dependencies @jeff

• Unit tests @max

• PyTorch implementation of scVI @eddie @max

• Dataset preprocessing @eddie @max @yining

0.1.0 (2017-09-05)

• First scVI TensorFlow version @romain