New in 0.10.0 (2021-04-20)

Changes

  • PeakVI minor enhancements to differential accessibility and fix scArches support (#1019)

  • Add DestVI to the codebase (#1011)

  • Versioned tutorial links (#1005)

  • Remove old VAEC (#1006)

  • Use .numpy() to convert torch tensors to numpy ndarrays (#1016)

  • Support backed AnnData (#1017), just load anndata with scvi.data.read_h5ad(path, backed='r+')

  • Solo interface enhancements (#1009)

  • Updated README (#1028)

  • Use Python warnings instead of logger warnings (#1021)

  • Change totalVI protein background default to False is fewer than 10 proteins used (#1034)

Bug fixes

  • Fix SaveBestState warning (#1024)

  • New default SCANVI max epochs if loaded with pretrained SCVI model (#1025), restores old <v0.9 behavior.

  • Fix marginal log likelihood computation, which was only being computed on final minibatch of a dataloader. This bug was introduced in the 0.9.X versions (#1033).

  • Fix bug where extra categoricals were not properly extended in transfer_anndata_setup() (#1030).