Major changes
- Model hyperparameter tuning is available through {class}`~scvi.autotune.ModelTuner` (beta)
{pr}`1785`,{pr}`1802`,{pr}`1831`.
- Pre-trained models can now be uploaded to and downloaded from [Hugging Face models] using the
{mod}`~scvi.hub` module {pr}`1779`,{pr}`1812`,{pr}`1828`,{pr}`1841`, {pr}`1851`,{pr}`1862`.
- {class}`~anndata.AnnData` `.var` and `.varm` attributes can now be registered through new fields
in {mod}`~scvi.data.fields` {pr}`1830`,{pr}`1839`.
- {class}`~scvi.external.SCBASSET`, a reimplementation of the [original scBasset model], is
available for representation learning of scATAC-seq data (experimental) {pr}`1839`,{pr}`1844`,
{pr}`1867`,{pr}`1874`,{pr}`1882`.
- {class}`~scvi.train.LowLevelPyroTrainingPlan` and {class}`~scvi.model.base.PyroModelGuideWarmup`
added to allow the use of vanilla PyTorch optimization on Pyro models {pr}`1845`,{pr}`1847`.
- Add {meth}`scvi.data.cellxgene` function to download cellxgene datasets {pr}`1880`.
Minor changes
- Latent mode support changed so that user data is no longer edited in-place {pr}`1756`.
- Minimum supported PyTorch Lightning version is now 1.9 {pr}`1795`,{pr}`1833`,{pr}`1863`.
- Minimum supported Python version is now 3.8 {pr}`1819`.
- [Poetry] removed in favor of [Hatch] for builds and publishing {pr}`1823`.
- `setup_anndata` docstrings fixed, `setup_mudata` docstrings added {pr}`1834`,{pr}`1837`.
- {meth}`~scvi.data.add_dna_sequence` adds DNA sequences to {class}`~anndata.AnnData` objects using
[genomepy] {pr}`1839`,{pr}`1842`.
- Update tutorial formatting with pre-commit {pr}`1850`
- Expose `accelerators` and `devices` arguments in {class}`~scvi.train.Trainer` {pr}`1864`.
- Development in GitHub Codespaces is now supported {pr}`1836`.
Breaking changes
- {class}`~scvi.module.base.LossRecorder` has been removed in favor of
{class}`~scvi.module.base.LossOutput` {pr}`1869`.
Bug Fixes
- {class}`~scvi.train.JaxTrainingPlan` now correctly updates `global_step` through PyTorch
Lightning by using a dummy optimizer. {pr}`1791`.
- CUDA compatibility issue fixed in {meth}`~scvi.distributions.ZeroInflatedNegativeBinomial.sample`
{pr}`1813`.
- Device-backed {class}`~scvi.dataloaders.AnnTorchDataset` fixed to work with sparse data {pr}`1824`.
- Fix bug {meth}`~scvi.model.base._log_likelihood.compute_reconstruction_error` causing the first
batch to be ignored, see more details in {issue}`1854` {pr}`1857`.
Contributors
- {ghuser}`adamgayoso`
- {ghuser}`eroell`
- {ghuser}`gokceneraslan`
- {ghuser}`macwiatrak`
- {ghuser}`martinkim0`
- {ghuser}`saroudant`
- {ghuser}`vitkl`
- {ghuser}`watiss`