# Release notes

Starting from version 0.20.1, this format is based on [Keep a Changelog][],
and this project adheres to [Semantic Versioning][]. Full commit history
is available in the [commit logs](https://github.com/YosefLab/scvi-tools/commits/).

[keep a changelog]: https://keepachangelog.com/en/1.0.0/
[semantic versioning]: https://semver.org/spec/v2.0.0.html

## [Unreleased]

### 1.1.0 (2023-MM-DD)

#### Removed

-   Remove deprecated `use_gpu` in favor of PyTorch Lightning arguments `accelerator` and `devices` {pr}`xxxx`.

## Version 1.0

### 1.0.0 (2023-06-02)

#### Added

-   Add {class}`scvi.criticism.PosteriorPredictiveCheck` for model evaluation {pr}`2058`.
-   Add {func}`scvi.data.reads_to_fragments` for scATAC data {pr}`1946`
-   Add default `stacklevel` for `warnings` in `scvi.settings` {pr}`1971`.
-   Add scBasset motif injection procedure {pr}`2010`.
-   Add importance sampling based differential expression procedure {pr}`1872`.
-   Raise clearer error when initializing {class}`scvi.external.SOLO` from {class}`scvi.model.SCVI` with extra categorical or continuous covariates {pr}`2027`.
-   Add option to generate {class}`mudata.MuData` in {meth}`scvi.data.synthetic_iid` {pr}`2028`.
-   Add option for disabling shuffling prior to splitting data in {class}`scvi.dataloaders.DataSplitter` {pr}`2037`.
-   Add {meth}`scvi.data.AnnDataManager.create_torch_dataset` and expose custom sampler ability {pr}`2036`.
-   Log training loss through Lightning's progress bar {pr}`2043`.
-   Filter Jax undetected GPU warnings {pr}`2044`.
-   Raise warning if MPS backend is selected for PyTorch, see https://github.com/pytorch/pytorch/issues/77764 {pr}`2045`.
-   Add `deregister_manager` function to {class}`scvi.model.base.BaseModelClass`, allowing to clear
    {class}`scvi.data.AnnDataManager` instances from memory {pr}`2060`.
-   Add option to use a linear classifier in {class}`scvi.model.SCANVI` {pr}`2063`.
-   Add lower bound 0.12.1 for Numpyro dependency {pr}`2078`.
-   Add new section in scBasset tutorial for motif scoring {pr}`2079`.

#### Fixed

-   Fix creation of minified adata by copying original uns dict {pr}`2000`. This issue arises with anndata>=0.9.0.
-   Fix {class}`scvi.model.TOTALVI` {class}`scvi.model.MULTIVI` handling of missing protein values {pr}`2009`.
-   Fix bug in {meth}`scvi.distributions.NegativeBinomialMixture.sample` where `theta` and `mu` arguments were switched around {pr}`2024`.
-   Fix bug in {meth}`scvi.dataloaders.SemiSupervisedDataLoader.resample_labels` where the labeled dataloader was not being reinitialized on subsample {pr}`2032`.
-   Fix typo in {class}`scvi.model.JaxSCVI` example snippet {pr}`2075`.

#### Changed

-   Use sphinx book theme for documentation {pr}`1673`.
-   {meth}`scvi.model.base.RNASeqMixin.posterior_predictive_sample` now outputs 3-d {class}`sparse.GCXS` matrices {pr}`1902`.
-   Add an option to specify `dropout_ratio` in {meth}`scvi.data.synthetic_iid` {pr}`1920`.
-   Update to lightning 2.0 {pr}`1961`
-   Hyperopt is new default searcher for tuner {pr}`1961`
-   {class}`scvi.train.AdversarialTrainingPlan` no longer encodes data twice during a training step, instead uses same latent for both optimizers {pr}`1961`, {pr}`1980`
-   Switch back to using sphinx autodoc typehints {pr}`1970`.
-   Disable default seed, run `scvi.settings.seed` after import for reproducibility {pr}`1976`.
-   Deprecate `use_gpu` in favor of PyTorch Lightning arguments `accelerator` and `devices`, to be removed in v1.1 {pr}`1978`.
-   Docs organization {pr}`1983`.
-   Validate training data and code URLs for {class}`scvi.hub.HubMetadata` and {class}`scvi.hub.HubModelCardHelper` {pr}`1985`.
-   Keyword arguments for encoders and decoders can now be passed in from the model level {pr}`1986`.
-   Expose `local_dir` as a public property in {class}`scvi.hub.HubModel` {pr}`1994`.
-   Use {func}`anndata.concat` internally inside {meth}`scvi.external.SOLO.from_scvi_model` {pr}`2013`.
-   {class}`scvi.train.SemiSupervisedTrainingPlan` and {class}`scvi.train.ClassifierTrainingPlan` now log accuracy,
    F1 score, and AUROC metrics {pr}`2023`.
-   Switch to cellxgene census for backend for cellxgene data function {pr}`2030`.
-   Change default `max_cells` and `truncation` in {meth}`scvi.model.base.RNASeqMixin._get_importance_weights` {pr}`2064`.
-   Refactor heuristic for default `max_epochs` as a separate function {meth}`scvi.model._utils.get_max_epochs_heuristic` {pr}`2083`.

#### Removed

-   Remove ability to set up ST data in {class}`~scvi.external.SpatialStereoscope.from_rna_model`, which was deprecated. ST data should be set up using {class}`~scvi.external.SpatialStereoscope.setup_anndata` {pr}`1949`.
-   Remove custom reusable doc decorator which was used for de docs {pr}`1970`.
-   Remove `drop_last` as an integer from {class}`~scvi.dataloaders.AnnDataLoader`, add typing and code cleanup {pr}`1975`.
-   Remove seqfish and seqfish plus datasets {pr}`2017`.
-   Remove support for Python 3.8 (NEP 29) {pr}`2021`.

## Version 0.20

### 0.20.3 (2023-03-21)

#### Fixed

-   Fix totalVI differential expression when integer sequential protein names are automatically used {pr}`1951`.
-   Fix peakVI scArches test case {pr}`1962`.

#### Changed

-   Allow passing in `map_location` into {meth}`~scvi.hub.HubMetadata.from_dir` and {meth}`~scvi.hub.HubModelCardHelper.from_dir` and set default to `"cpu"` {pr}`1960`.
-   Updated tutorials {pr}`1966`.

### 0.20.2 (2023-03-10)

#### Fixed

-   Fix `return_dist` docstring of {meth}`scvi.model.base.VAEMixin.get_latent_representation` {pr}`1932`.
-   Fix hyperlink to pymde docs {pr}`1944`

#### Changed

-   Use ruff for fixing and linting {pr}`1921`, {pr}`1941`.
-   Use sphinx autodoc instead of sphinx-autodoc-typehints {pr}`1941`.
-   Remove .flake8 and .prospector files {pr}`1923`.
-   Log individual loss terms in {meth}`scvi.module.MULTIVAE.loss` {pr}`1936`.
-   Setting up ST data in {class}`~scvi.external.SpatialStereoscope.from_rna_model` is deprecated. ST data should be set up using {class}`~scvi.external.SpatialStereoscope.setup_anndata` {pr}`1803`.

### 0.20.1 (2023-02-21)

#### Fixed

-   Fixed computation of ELBO during training plan logging when using global kl terms. [{pr}`1895`]
-   Fixed usage of {class}`scvi.train.SaveBestState` callback, which affected {class}`scvi.model.PEAKVI` training. If using {class}`~scvi.model.PEAKVI`, please upgrade. [{pr}`1913`]
-   Fixed original seed for jax-based models to work with jax 0.4.4. [{pr}`1907`, {pr}`1909`]

### New in 0.20.0 (2023-02-01)

#### 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`

[original scbasset model]: https://github.com/calico/scBasset
[poetry]: https://python-poetry.org/
[hatch]: https://hatch.pypa.io/latest/
[genomepy]: https://github.com/vanheeringen-lab/genomepy
[hugging face models]: https://huggingface.co/models

## Version 0.19

### New in 0.19.0 (2022-10-31)

#### Major Changes

-   {class}`~scvi.train.TrainingPlan` allows custom PyTorch optimizers [#1747].
-   Improvements to {class}`~scvi.train.JaxTrainingPlan` [#1747] [#1749].
-   {class}`~scvi.module.base.LossRecorder` is deprecated. Please substitute with {class}`~scvi.module.base.LossOutput` [#1749]
-   All training plans require keyword args after the first positional argument [#1749]
-   {class}`~scvi.module.base.JaxBaseModuleClass` absorbed features from the `JaxModuleWrapper`, rendering the `JaxModuleWrapper` obsolote, so it was removed. [#1751]
-   Add {class}`scvi.external.Tangram` and {class}`scvi.external.tangram.TangramMapper` that implement Tangram for mapping scRNA-seq data to spatial data [#1743].

#### Minor changes

-   Remove confusing warning about kl warmup, log kl weight instead [#1773]

#### Breaking changes

-   {class}`~scvi.module.base.LossRecorder` no longer allows access to dictionaries of values if provided during initialization [#1749].
-   `JaxModuleWrapper` removed. [#1751]

#### Bug Fixes

-   Fix `n_proteins` usage in {class}`~scvi.model.MULTIVI` [#1737].
-   Remove unused param in {class}`~scvi.model.MULTIVI` [#1741].
-   Fix random seed handling for Jax models [#1751].

#### Contributors

-   [@watiss]
-   [@adamgayoso]
-   [@martinkim0]
-   [@marianogabitto]

[#1737]: https://github.com/YosefLab/scvi-tools/pull/1737
[#1741]: https://github.com/YosefLab/scvi-tools/pull/1741
[#1743]: https://github.com/YosefLab/scvi-tools/pull/1743
[#1747]: https://github.com/YosefLab/scvi-tools/pull/1747
[#1749]: https://github.com/YosefLab/scvi-tools/pull/1749
[#1751]: https://github.com/YosefLab/scvi-tools/pull/1751
[#1773]: https://github.com/YosefLab/scvi-tools/pull/1773
[@watiss]: https://github.com/watiss
[@adamgayoso]: https://github.com/adamgayoso
[@martinkim0]: https://github.com/martinkim0
[@marianogabitto]: https://github.com/marianogabitto

## Version 0.18

### New in 0.18.0 (2022-10-12)

#### Major Changes

-   Add latent mode support in {class}`~scvi.model.SCVI` [#1672]. This allows for loading a model using latent representations only (i.e. without the full counts). Not only does this speed up inference by using the cached latent distribution parameters (thus skipping the encoding step), but this also helps in scenarios where the full counts are not available but cached latent parameters are. We provide utility functions and methods to dynamically convert a model to latent mode.
-   Added {class}`~scvi.external.SCAR` as an external model for ambient RNA removal [#1683].
-   Add weight support to {class}`~scvi.model.MULTIVI` [#1697].

#### Minor changes

-   Faster inference in PyTorch with `torch.inference_mode` [#1695].
-   Upgrade to Lightning 1.6 [#1719].
-   Update CI workflow to separate static code checking from pytest [#1710].
-   Add Python 3.10 to CI workflow [#1711].
-   Add {meth}`~scvi.data.AnnDataManager.register_new_fields` [#1689].
-   Use sphinxcontrib-bibtex for references [#1731].
-   {meth}`~scvi.model.base.VAEMixin.get_latent_representation`: more explicit and better docstring [#1732].
-   Replace custom attrdict with {class}`~ml_collections` implementation [#1696].

#### Breaking changes

None

#### Bug Fixes

-   Fix links for breast cancer and mouse datasets [#1709].
-   fix quick start notebooks not showing [#1733].

#### Contributors

-   [@watiss]
-   [@adamgayoso]
-   [@martinkim0]
-   [@ricomnl]
-   [@marianogabitto]

[#1695]: https://github.com/YosefLab/scvi-tools/pull/1695
[#1696]: https://github.com/YosefLab/scvi-tools/pull/1696
[#1719]: https://github.com/YosefLab/scvi-tools/pull/1719
[#1710]: https://github.com/YosefLab/scvi-tools/pull/1710
[#1672]: https://github.com/YosefLab/scvi-tools/pull/1672
[#1709]: https://github.com/YosefLab/scvi-tools/pull/1709
[#1711]: https://github.com/YosefLab/scvi-tools/pull/1711
[#1683]: https://github.com/YosefLab/scvi-tools/pull/1683
[#1689]: https://github.com/YosefLab/scvi-tools/pull/1689
[#1697]: https://github.com/YosefLab/scvi-tools/pull/1697
[#1731]: https://github.com/YosefLab/scvi-tools/pull/1731
[#1732]: https://github.com/YosefLab/scvi-tools/pull/1732
[#1733]: https://github.com/YosefLab/scvi-tools/pull/1733
[@watiss]: https://github.com/watiss
[@adamgayoso]: https://github.com/adamgayoso
[@martinkim0]: https://github.com/martinkim0
[@ricomnl]: https://github.com/ricomnl
[@marianogabitto]: https://github.com/marianogabitto

## Version 0.17

### New in 0.17.4 (2021-09-20)

#### Changes

-   Support for PyTorch Lightning 1.7 [#1622].
-   Allow `flax` to use any mutable states used by a model generically with {class}`~scvi.module.base.TrainStateWithState` [#1665], [#1700].
-   Update publication links in `README` [#1667].
-   Docs now include floating window cross references with `hoverxref`, external links with `linkcode`, and `grid` [#1678].

#### Bug Fixes

-   Fix `get_likelihood_parameters()` failure when `gene_likelihood != "zinb"` in {class}`~scvi.model.base.RNASeqMixin` [#1618].
-   Fix exception logic when not using the observed library size in {class}`~scvi.module.VAE` initialization [#1660].
-   Replace instances of `super().__init__()` with an argument in `super()`, causing `autoreload` extension to throw errors [#1671].
-   Change cell2location tutorial causing docs build to fail [#1674].
-   Replace instances of `max_epochs` as `int`s for new PyTorch Lightning [#1686].
-   Catch case when `torch.backends.mps` is not implemented [#1692].
-   Fix Poisson sampling in {meth}`~scvi.module.VAE.sample` [#1702].

#### Contributors

-   [@adamgayoso]
-   [@watiss]
-   [@mkarikom]
-   [@tommycelsius]
-   [@ricomnl]

[#1618]: https://github.com/scverse/scvi-tools/pull/1618
[#1622]: https://github.com/scverse/scvi-tools/pull/1622
[#1660]: https://github.com/scverse/scvi-tools/pull/1660
[#1665]: https://github.com/scverse/scvi-tools/pull/1665
[#1667]: https://github.com/scverse/scvi-tools/pull/1667
[#1671]: https://github.com/scverse/scvi-tools/pull/1671
[#1674]: https://github.com/scverse/scvi-tools/pull/1674
[#1678]: https://github.com/scverse/scvi-tools/pull/1678
[#1686]: https://github.com/scverse/scvi-tools/pull/1686
[#1692]: https://github.com/scverse/scvi-tools/pull/1692
[#1700]: https://github.com/scverse/scvi-tools/pull/1700
[#1702]: https://github.com/scverse/scvi-tools/pull/1702
[@adamgayoso]: https://github.com/adamgayoso
[@watiss]: https://github.com/watiss
[@tommycelsius]: https://github.com/tommycelsius
[@mkarikom]: https://github.com/mkarikom
[@ricomnl]: https://github.com/ricomnl

### New in 0.17.3 (2022-08-26)

#### Changes

-   Pin sphinx_gallery to fix tutorial cards on docs [#1657]
-   Use latest tutorials in release [#1657]

#### Contributors

-   [@watiss]
-   [@adamgayoso]

[#1657]: https://github.com/scverse/scvi-tools/pull/1657
[@watiss]: https://github.com/watiss
[@adamgayoso]: https://github.com/adamgayoso

### New in 0.17.2 (2022-08-26)

#### Changes

-   Move `training` argument in {class}`~scvi.module.JaxVAE` constructor to a keyword argument into the call method. This simplifies the {class}`~scvi.module.base.JaxModuleWrapper` logic and avoids the reinstantiation of {class}`~scvi.module.JaxVAE` during evaluation [#1580].
-   Add a static method on the BaseModelClass to return the AnnDataManger's full registry [#1617].
-   Clarify docstrings for continuous and categorical covariate keys [#1637].
-   Remove poetry lock, use newer build system [#1645].

#### Bug Fixes

-   Fix CellAssign to accept extra categorical covariates [#1629].
-   Fix an issue where `max_epochs` is never determined heuristically for totalvi, instead it would always default to 400 [#1639].

#### Breaking Changes

-   Fix an issue where `max_epochs` is never determined heuristically for totalvi, instead it would always default to 400 [#1639].

#### Contributors

-   [@watiss]
-   [@RK900]
-   [@adamgayoso]
-   [@jjhong922]

[#1580]: https://github.com/scverse/scvi-tools/pull/1580
[#1617]: https://github.com/scverse/scvi-tools/pull/1617
[#1629]: https://github.com/scverse/scvi-tools/pull/1629
[#1637]: https://github.com/scverse/scvi-tools/pull/1637
[#1639]: https://github.com/scverse/scvi-tools/pull/1639
[#1645]: https://github.com/scverse/scvi-tools/pull/1645
[@watiss]: https://github.com/watiss
[@rk900]: https://github.com/RK900
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.17.1 (2022-07-14)

Make sure notebooks are up to date for real this time :).

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[@jjhong922]: https://github.com/jjhong922
[@adamgayoso]: https://github.com/adamgayoso

### New in 0.17.0 (2022-07-14)

#### Major Changes

-   Experimental MuData support for {class}`~scvi.model.TOTALVI` via the method {meth}`~scvi.model.TOTALVI.setup_mudata`. For several of the existing `AnnDataField` classes, there is now a MuData counterpart with an additional `mod_key` argument used to indicate the modality where the data lives (e.g. {class}`~scvi.data.fields.LayerField` to {class}`~scvi.data.fields.MuDataLayerField`). These modified classes are simply wrapped versions of the original `AnnDataField` code via the new {class}`scvi.data.fields.MuDataWrapper` method [#1474].
-   Modification of the {meth}`~scvi.module.VAE.generative` method's outputs to return prior and likelihood properties as {class}`~torch.distributions.distribution.Distribution` objects. Concerned modules are {class}`~scvi.module.AmortizedLDAPyroModule`, {class}`AutoZIVAE`, {class}`~scvi.module.MULTIVAE`, {class}`~scvi.module.PEAKVAE`, {class}`~scvi.module.TOTALVAE`, {class}`~scvi.module.SCANVAE`, {class}`~scvi.module.VAE`, and {class}`~scvi.module.VAEC`. This allows facilitating the manipulation of these distributions for model training and inference [#1356].
-   Major changes to Jax support for scvi-tools models to generalize beyond {class}`~scvi.model.JaxSCVI`. Support for Jax remains experimental and is subject to breaking changes:
    -   Consistent module interface for Flax modules (Jax-backed) via {class}`~scvi.module.base.JaxModuleWrapper`, such that they are compatible with the existing {class}`~scvi.model.base.BaseModelClass` [#1506].
    -   {class}`~scvi.train.JaxTrainingPlan` now leverages Pytorch Lightning to factor out Jax-specific training loop implementation [#1506].
    -   Enable basic device management in Jax-backed modules [#1585].

#### Minor changes

-   Add {meth}`~scvi.module.base.PyroBaseModuleClass.on_load` callback which is called on {meth}`~scvi.model.base.BaseModuleClass.load` prior to loading the module state dict [#1542].
-   Refactor metrics code and use {class}`~torchmetrics.MetricCollection` to update metrics in bulk [#1529].
-   Add `max_kl_weight` and `min_kl_weight` to {class}`~scvi.train.TrainingPlan` [#1595].
-   Add a warning to {class}`~scvi.model.base.UnsupervisedTrainingMixin` that is raised if `max_kl_weight` is not reached during training [#1595].

#### Breaking changes

-   Any methods relying on the output of `inference` and `generative` from existing scvi-tools models (e.g. {class}`~scvi.model.SCVI`, {class}`~scvi.model.SCANVI`) will need to be modified to accept `torch.Distribution` objects rather than tensors for each parameter (e.g. `px_m`, `px_v`) [#1356].
-   The signature of {meth}`~scvi.train.TrainingPlan.compute_and_log_metrics` has changed to support the use of {class}`~torchmetrics.MetricCollection`. The typical modification required will look like changing `self.compute_and_log_metrics(scvi_loss, self.elbo_train)` to `self.compute_and_log_metrics(scvi_loss, self.train_metrics, "train")`. The same is necessary for validation metrics except with `self.val_metrics` and the mode `"validation"` [#1529].

#### Bug Fixes

-   Fix issue with {meth}`~scvi.model.SCVI.get_normalized_expression` with multiple samples and additional continuous covariates. This bug originated from {meth}`~scvi.module.VAE.generative` failing to match the dimensions of the continuous covariates with the input when `n_samples>1` in {meth}`~scvi.module.VAE.inference` in multiple module classes [#1548].
-   Add support for padding layers in {meth}`~scvi.model.SCVI.prepare_query_anndata` which is necessary to run {meth}`~scvi.model.SCVI.load_query_data` for a model setup with a layer instead of X [#1575].

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]
-   [@PierreBoyeau]
-   [@RK900]
-   [@FlorianBarkmann]

[#1356]: https://github.com/YosefLab/scvi-tools/pull/1356
[#1474]: https://github.com/YosefLab/scvi-tools/pull/1474
[#1506]: https://github.com/YosefLab/scvi-tools/pull/1506
[#1529]: https://github.com/YosefLab/scvi-tools/pull/1529
[#1542]: https://github.com/YosefLab/scvi-tools/pull/1542
[#1548]: https://github.com/YosefLab/scvi-tools/pull/1548
[#1575]: https://github.com/YosefLab/scvi-tools/pull/1575
[#1585]: https://github.com/YosefLab/scvi-tools/pull/1585
[#1595]: https://github.com/scverse/scvi-tools/pull/1595
[@jjhong922]: https://github.com/jjhong922
[@adamgayoso]: https://github.com/adamgayoso
[@pierreboyeau]: https://github.com/PierreBoyeau
[@rk900]: https://github.com/RK900
[@florianbarkmann]: https://github.com/FlorianBarkmann

## Version 0.16

### New in 0.16.4 (2022-06-14)

Note: When applying any model using the {class}`~scvi.train.AdversarialTrainingPlan` (e.g. {class}`~scvi.model.TOTALVI`, {class}`~scvi.model.MULTIVI`), you should make sure to use v0.16.4 instead of v0.16.3 or v0.16.2. This release fixes a critical bug in the training plan.

#### Changes

#### Breaking changes

#### Bug Fixes

-   Fix critical issue in {class}`~scvi.train.AdversarialTrainingPlan` where `kl_weight` was overwritten to 0 at each step ([#1566]). Users should avoid using v0.16.2 and v0.16.3 which both include this bug.

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[#1566]: https://github.com/scverse/scvi-tools/issues/1566
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.16.3 (2022-06-04)

#### Changes

-   Removes sphinx max version and removes jinja dependency ([#1555]).

#### Breaking changes

#### Bug Fixes

-   Upper bounds protobuf due to pytorch lightning incompatibilities ([#1556]). Note that [#1556] has unique changes as PyTorch Lightning >=1.6.4 adds the upper bound in their requirements.

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[#1551]: https://github.com/scverse/scvi-tools/issues/1551
[#1555]: https://github.com/YosefLab/scvi-tools/pull/1555
[#1556]: https://github.com/YosefLab/scvi-tools/pull/1556
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.16.2 (2022-05-10)

#### Changes

#### Breaking changes

#### Bug Fixes

-   Raise appropriate error when `backup_url` is not provided and file is missing on {meth}`~scvi.model.base.BaseModelClass.load` ([#1527]).
-   Pipe `loss_kwargs` properly in {class}`~scvi.train.AdversarialTrainingPlan`, and fix incorrectly piped kwargs in {class}`~scvi.model.TOTALVI` and {class}`~scvi.model.MULTIVI` ([#1532]).

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[#1527]: https://github.com/YosefLab/scvi-tools/pull/1527
[#1532]: https://github.com/YosefLab/scvi-tools/pull/1532
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.16.1 (2022-04-22)

#### Changes

-   Update scArches Pancreas tutorial, DestVI tutorial ([#1520]).

#### Breaking changes

-   {class}`~scvi.dataloaders.SemiSupervisedDataLoader` and {class}`~scvi.dataloaders.SemiSupervisedDataSplitter` no longer take `unlabeled_category` as an initial argument. Instead, the `unlabeled_category` is fetched from the labels state registry, assuming that the {class}`~scvi.data.AnnDataManager` object is registered with a {class}`~scvi.data.fields.LabelsWithUnlabeledObsField` ([#1515]).

#### Bug Fixes

-   Bug fixed in {class}`~scvi.model.SCANVI` where `self._labeled_indices` was being improperly set ([#1515]).
-   Fix issue where {class}`~scvi.model.SCANVI.load_query_data` would not properly add an obs column with the unlabeled category when the `labels_key` was not present in the query data.
-   Disable extension of categories for labels in {class}`~scvi.model.SCANVI.load_query_data` ([#1519]).
-   Fix an issue with {meth}`~scvi.model.SCANVI.prepare_query_data` to ensure it does nothing when genes are completely matched ([#1520]).

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[#1515]: https://github.com/YosefLab/scvi-tools/pull/1515
[#1519]: https://github.com/YosefLab/scvi-tools/pull/1519
[#1520]: https://github.com/YosefLab/scvi-tools/pull/1520
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.16.0 (2022-04-12)

This release features a refactor of {class}`~scvi.model.DestVI` ([#1457]):

1. Bug fix in cell type amortization, which leads to on par performance of cell type amortization `V_encoder` with free parameter for cell type proportions `V`.
2. Bug fix in library size in {class}`~scvi.model.CondSCVI`, that lead to downstream dependency between sum over cell type proportions `v_ind` and library size
   `library` in {class}`~scvi.model.DestVI`.
3. `neg_log_likelihood_prior` is not computed anymore on random subset of single cells but cell type specific subclustering using cluster variance `var_vprior`,
   cluster mean `mean_vprior` and cluster mixture proportion `mp_vprior` for computation. This leads to more stable results and faster computation time.
   Setting `vamp_prior_p` in {func}`~scvi.model.DestVI.from_rna_model` to the expected resolution is critical in this algorithm.
4. The new default is to also use dropout `dropout` during the decoder of {class}`~scvi.model.CondSCVI` and subsequently `dropout_decoder` in {class}`~scvi.model.DestVI`,
   we found this to be beneficial after bug fixes listed above.
5. We changed the weighting of the loss on the variances of beta and the prior of eta.

:::{note}
Due to bug fixes listed above this version of {class}`~scvi.model.DestVI` is not backwards compatible. Despite instability in training in the
outdated version, we were able to reproduce results generated with this code. We therefore do not strictly encourage to rerun old experiments.
:::

We published a new tutorial. This new tutorial incorporates a new utility package [destvi_utils](https://github.com/YosefLab/destvi_utils) that generates exploratory plots of the results of {class}`~scvi.model.DestVI`. We refer to the manual of this package for further documentation.

#### Changes

-   Docs changes (installation [#1498], {class}`~scvi.model.DestVI` user guide [#1501] and [#1508], dark mode code cells [#1499]).
-   Add `backup_url` to the {meth}`~scvi.model.base.BaseModelClass.load` method of each model class, enabling automatic downloading of model save file ([#1505]).

#### Breaking changes

-   Support for loading legacy loading is removed from {meth}`~scvi.model.base.BaseModelClass.load`. Utility to convert old files to the new file as been added {meth}`~scvi.model.base.BaseModelClass.convert_legacy_save` ([#1505]).
-   Breaking changes to {class}`~scvi.model.DestVI` as specified above ([#1457]).

#### Bug Fixes

-   {meth}`~scvi.model.base.RNASeqMixin.get_likelihood_parameters` fix for `n_samples > 1` and `dispersion="gene_cell"` [#1504].
-   Fix backwards compatibility for legacy TOTALVI models [#1502].

#### Contributors

-   [@cane11]
-   [@jjhong922]
-   [@adamgayoso]
-   [@romain-lopez]

[#1498]: https://github.com/YosefLab/scvi-tools/pull/1498
[#1499]: https://github.com/YosefLab/scvi-tools/pull/1499
[#1501]: https://github.com/YosefLab/scvi-tools/pull/1501
[#1508]: https://github.com/YosefLab/scvi-tools/pull/1508
[#1457]: https://github.com/YosefLab/scvi-tools/pull/1457
[#1502]: https://github.com/YosefLab/scvi-tools/pull/1502
[#1504]: https://github.com/YosefLab/scvi-tools/pull/1504
[#1505]: https://github.com/YosefLab/scvi-tools/pull/1505
[@cane11]: https://github.com/cane11
[@adamgayoso]: https://github.com/adamgayoso
[@romain-lopez]: https://github.com/romain-lopez
[@jjhong922]: https://github.com/jjhong922

## Version 0.15

### New in 0.15.5 (2022-04-06)

#### Changes

-   Add common types file [#1467].
-   New default is to not pin memory during training when using a GPU. This is much better for shared GPU environments without any performance regression [#1473].

#### Bug fixes

-   Fix LDA user guide bugs [#1479].
-   Fix unnecessary warnings, double logging [#1475].

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[#1479]: https://github.com/YosefLab/scvi-tools/pull/1479
[#1475]: https://github.com/YosefLab/scvi-tools/pull/1475
[#1467]: https://github.com/YosefLab/scvi-tools/pull/1467
[#1473]: https://github.com/YosefLab/scvi-tools/pull/1473
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.15.4 (2022-03-28)

#### Changes

-   Add peakVI publication reference [#1463].
-   Update notebooks with new install functionality for Colab [#1466].
-   Simplify changing the training plan for pyro [#1470].
-   Optionally scale ELBO by a scalar in {class}`~scvi.train.PyroTrainingPlan` [#1469].

#### Bug fixes

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]
-   [@vitkl]

[#1463]: https://github.com/YosefLab/scvi-tools/pull/1463
[#1466]: https://github.com/YosefLab/scvi-tools/pull/1466
[#1469]: https://github.com/YosefLab/scvi-tools/pull/1469
[#1470]: https://github.com/YosefLab/scvi-tools/pull/1470
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@vitkl]: https://github.com/vitkl

### New in 0.15.3 (2022-03-24)

#### Changes

#### Bug fixes

-   Raise `NotImplementedError` when `categorical_covariate_keys` are used with {meth}`scvi.model.SCANVI.load_query_data`. ([#1458]).
-   Fix behavior when `continuous_covariate_keys` are used with {meth}`scvi.model.SCANVI.classify`. ([#1458]).
-   Unlabeled category values are automatically populated when {meth}`scvi.model.SCANVI.load_query_data` run on `adata_target` missing labels column. ([#1458]).
-   Fix dataframe rendering in dark mode docs ([#1448])
-   Fix variance constraint in {class}`~scvi.model.AmortizedLDA` that set an artifical bound on latent topic variance ([#1445]).
-   Fix {meth}`scvi.model.base.ArchesMixin.prepare_query_data` to work cross device (e.g., model trained on cuda but method used on cpu; see [#1451]).

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[#1451]: https://github.com/YosefLab/scvi-tools/pull/1451
[#1445]: https://github.com/YosefLab/scvi-tools/pull/1445
[#1448]: https://github.com/YosefLab/scvi-tools/pull/1448
[#1458]: https://github.com/YosefLab/scvi-tools/pull/1458
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.15.2 (2022-03-15)

#### Changes

-   Remove setuptools pinned requirement due to new PyTorch 1.11 fix ([#1436]).
-   Switch to myst-parsed markdown for docs ([#1435]).
-   Add `prepare_query_data(adata, reference_model)` to {class}`~scvi.model.base.ArchesMixin` to enable query data cleaning prior to reference mapping ([#1441]).
-   Add Human Lung Cell Atlas tutorial ([#1442]).

#### Bug fixes

-   Errors when arbitrary kwargs are passed into `setup_anndata()` ([#1439]).
-   Fix {class}`scvi.external.SOLO` to use `train_size=0.9` by default, which enables early stopping to work properly ([#1438]).
-   Fix scArches version warning ([#1431]).
-   Fix backwards compat for {class}`~scvi.model.SCANVI` loading ([#1441]).

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]
-   [@grst]

[#1442]: https://github.com/YosefLab/scvi-tools/pull/1442
[#1441]: https://github.com/YosefLab/scvi-tools/pull/1441
[#1439]: https://github.com/YosefLab/scvi-tools/pull/1439
[#1438]: https://github.com/YosefLab/scvi-tools/pull/1438
[#1436]: https://github.com/YosefLab/scvi-tools/pull/1436
[#1435]: https://github.com/YosefLab/scvi-tools/pull/1435
[#1431]: https://github.com/YosefLab/scvi-tools/pull/1431
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@grst]: https://github.com/grst

### New in 0.15.1 (2022-03-11)

#### Changes

-   Remove `labels_key` from {class}`~scvi.model.MULTIVI` as it is not used in the model ([#1393]).
-   Use scvi-tools mean/inv_disp parameterization of negative binomial for {class}`~scvi.model.JaxSCVI` likelihood ([#1386]).
-   Use `setup` for Flax-based modules ([#1403]).
-   Reimplement {class}`~scvi.module.JaxVAE` using inference/generative paradigm with {class}`~scvi.module.base.JaxBaseModuleClass` ([#1406]).
-   Use multiple particles optionally in {class}`~scvi.model.JaxSCVI` ([#1385]).
-   {class}`~scvi.external.SOLO` no longer warns about count data ([#1411]).
-   Class docs are now one page on docs site ([#1415]).
-   Copied AnnData objects are assigned a new uuid and transfer is attempted ([#1416]).

#### Bug fixes

-   Fix an issue with using gene lists and proteins lists as well as `transform_batch` for {class}`~scvi.model.TOTALVI` ([#1413]).
-   Error gracefully when NaNs present in {class}`~scvi.data.fields.CategoricalJointObsmField` ([#1417]).

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]

[#1385]: https://github.com/YosefLab/scvi-tools/pull/1385
[#1386]: https://github.com/YosefLab/scvi-tools/pull/1386
[#1393]: https://github.com/YosefLab/scvi-tools/pull/1393
[#1403]: https://github.com/YosefLab/scvi-tools/pull/1403
[#1406]: https://github.com/YosefLab/scvi-tools/pull/1406
[#1411]: https://github.com/YosefLab/scvi-tools/pull/1411
[#1413]: https://github.com/YosefLab/scvi-tools/pull/1413
[#1415]: https://github.com/YosefLab/scvi-tools/pull/1415
[#1416]: https://github.com/YosefLab/scvi-tools/pull/1416
[#1417]: https://github.com/YosefLab/scvi-tools/pull/1417
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922

### New in 0.15.0 (2022-02-28)

In this release, we have completely refactored the logic behind our data handling strategy (i.e. `setup_anndata`) to allow for:

1. Readable data handling for existing models.
2. Modular code for easy addition of custom data fields to incorporate into models.
3. Avoidance of unexpected edge cases when more than one model is instantiated in one session.

**Important Note:** This change will not break pipelines for model users (with the exception of a small change to {class}`~scvi.model.SCANVI`).
However, there are several breaking changes for model developers. The data handling tutorial goes over these
changes in detail.

This refactor is centered around the new {class}`~scvi.data.AnnDataManager` class which orchestrates any data processing necessary
for scvi-tools and stores necessary information, rather than adding additional fields to the AnnData input.

:::{figure} figures/anndata_manager_schematic.svg
:align: center
:alt: Schematic of data handling strategy with AnnDataManager
:class: img-fluid

Schematic of data handling strategy with {class}`~scvi.data.AnnDataManager`
:::

We also have an exciting new experimental Jax-based scVI implementation via {class}`~scvi.model.JaxSCVI`. While this implementation has limited functionality, we have found it to be substantially faster than the PyTorch-based implementation. For example, on a 10-core Intel CPU, Jax on only a CPU can be as fast as PyTorch with a GPU (RTX3090). We will be planning further Jax integrations in the next releases.

#### Changes

-   Major refactor to data handling strategy with the introduction of {class}`~scvi.data.AnnDataManager` ([#1237]).
-   Prevent clobbering between models using the same AnnData object with model instance specific {class}`~scvi.data.AnnDataManager` mappings ([#1342]).
-   Add `size_factor_key` to {class}`~scvi.model.SCVI`, {class}`~scvi.model.MULTIVI`, {class}`~scvi.model.SCANVI`, and {class}`~scvi.model.TOTALVI` ([#1334]).
-   Add references to the scvi-tools journal publication to the README ([#1338], [#1339]).
-   Addition of {func}`scvi.model.utils.mde` ([#1372]) for accelerated visualization of scvi-tools embeddings.
-   Documentation and user guide fixes ([#1364], [#1361])
-   Fix for {class}`~scvi.external.SOLO` when {class}`~scvi.model.SCVI` was setup with a `labels_key` ([#1354])
-   Updates to tutorials ([#1369], [#1371])
-   Furo docs theme ([#1290])
-   Add {class}`scvi.model.JaxSCVI` and {class}`scvi.module.JaxVAE`, drop Numba dependency for checking if data is count data ([#1367]).

#### Breaking changes

-   The keyword argument `run_setup_anndata` has been removed from built-in datasets since there is no longer a model-agnostic `setup_anndata` method ([#1237]).

-   The function `scvi.model._metrics.clustering_scores` has been removed due to incompatbility with new data handling ([#1237]).

-   {class}`~scvi.model.SCANVI` now takes `unlabeled_category` as an argument to {meth}`~scvi.model.SCANVI.setup_anndata` rather than on initialization ([#1237]).

-   `setup_anndata` is now a class method on model classes and requires specific function calls to ensure proper {class}`~scvi.data.AnnDataManager` setup and model save/load.
    Any model inheriting from {class}`~scvi.model.base.BaseModelClass` will need to re-implement this method ([#1237]).

    > -   To adapt existing custom models to v0.15.0, one can references the guidelines below. For some examples of how this was done for the existing models in the codebase, please reference the following PRs: ([#1301], [#1302]).
    >     : 1. `scvi._CONSTANTS` has been changed to `scvi.REGISTRY_KEYS`. 2. `setup_anndata()` functions are now class functions and follow a specific structure. Please refer to {meth}`~scvi.model.SCVI.setup_anndata` for an example. 3. `scvi.data.get_from_registry()` has been removed. This method can be replaced by {meth}`scvi.data.AnnDataManager.get_from_registry`. 4. The setup dict stored directly on the AnnData object, `adata["_scvi"]`, has been deprecated. Instead, this information now lives in {attr}`scvi.data.AnnDataManager.registry`.
    >     : - The data registry can be accessed at {attr}`scvi.data.AnnDataManager.data_registry`. - Summary stats can be accessed at {attr}`scvi.data.AnnDataManager.summary_stats`. - Any field-specific information (e.g. `adata.obs["categorical_mappings"]`) now lives in field-specific state registries. These can be retrieved via the function {meth}`~scvi.data.AnnDataManager.get_state_registry`. 5. `register_tensor_from_anndata()` has been removed. To register tensors with no relevant `AnnDataField` subclass, create a new
    >     a new subclass of {class}`~scvi.data.fields.BaseAnnDataField` and add it to appropriate model's `setup_anndata()` function.

#### Contributors

-   [@jjhong922]
-   [@adamgayoso]
-   [@watiss]

[#1237]: https://github.com/YosefLab/scvi-tools/pull/1237
[#1290]: https://github.com/YosefLab/scvi-tools/pull/1290
[#1301]: https://github.com/YosefLab/scvi-tools/pull/1301
[#1302]: https://github.com/YosefLab/scvi-tools/pull/1302
[#1334]: https://github.com/YosefLab/scvi-tools/pull/1334
[#1338]: https://github.com/YosefLab/scvi-tools/pull/1338
[#1339]: https://github.com/YosefLab/scvi-tools/pull/1339
[#1342]: https://github.com/YosefLab/scvi-tools/pull/1342
[#1354]: https://github.com/YosefLab/scvi-tools/pull/1354
[#1361]: https://github.com/YosefLab/scvi-tools/pull/1361
[#1364]: https://github.com/YosefLab/scvi-tools/pull/1364
[#1367]: https://github.com/YosefLab/scvi-tools/pull/1367
[#1369]: https://github.com/YosefLab/scvi-tools/pull/1369
[#1371]: https://github.com/YosefLab/scvi-tools/pull/1371
[#1372]: https://github.com/YosefLab/scvi-tools/pull/1372
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@watiss]: https://github.com/watiss

## Version 0.14

### New in 0.14.6 (2021-02-05)

Bug fixes, minor improvements of docs, code formatting.

#### Changes

-   Update black formatting to stable release ([#1324])
-   Refresh readme, move tasks image to docs ([#1311]).
-   Add 0.14.5 release note to index ([#1296]).
-   Add test to ensure extra {class}`~scvi.model.SCANVI` training of a pre-trained {class}`~scvi.model.SCVI` model does not change original model weights ([#1284]).
-   Fix issue in {class}`~scvi.model.TOTALVI` protein background prior initialization to not include protein measurements that are known to be missing ([#1282]).
-   Upper bound setuptools due to PyTorch import bug ([#1309]).

#### Contributors

-   [@adamgayoso]
-   [@watiss]
-   [@jjhong922]

[#1282]: https://github.com/YosefLab/scvi-tools/pull/1282
[#1284]: https://github.com/YosefLab/scvi-tools/pull/1284
[#1296]: https://github.com/YosefLab/scvi-tools/pull/1296
[#1309]: https://github.com/YosefLab/scvi-tools/pull/1309
[#1311]: https://github.com/YosefLab/scvi-tools/pull/1311
[#1324]: https://github.com/YosefLab/scvi-tools/pull/1324
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@watiss]: https://github.com/watiss

### New in 0.14.5 (2021-11-22)

Bug fixes, new tutorials.

#### Changes

-   Fix `kl_weight` floor for Pytorch-based models ([#1269]).
-   Add support for more Pyro guides ([#1267]).
-   Update scArches, harmonization tutorials, add basic R tutorial, tabula muris label transfer tutorial ([#1274]).

#### Contributors

-   [@adamgayoso]
-   [@jjhong922]
-   [@watiss]
-   [@vitkl]

[#1267]: https://github.com/YosefLab/scvi-tools/pull/1267
[#1269]: https://github.com/YosefLab/scvi-tools/pull/1269
[#1274]: https://github.com/YosefLab/scvi-tools/pull/1274
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@vitkl]: https://github.com/vitkl
[@watiss]: https://github.com/watiss

### New in 0.14.4 (2021-11-16)

Bug fixes, some tutorial improvements.

#### Changes

-   `kl_weight` handling for Pyro-based models ([#1242]).
-   Allow override of missing protein inference in {class}`~scvi.model.TOTALVI` ([#1251]). This allows to treat all 0s in a particular batch for one protein as biologically valid.
-   Fix load documentation (e.g., {meth}`~scvi.model.SCVI.load`, {meth}`~scvi.model.TOTALVI.load`) ([#1253]).
-   Fix model history on load with Pyro-based models ([#1255]).
-   Model construction tutorial uses new static setup anndata ([#1257]).
-   Add codebase overview figure to docs ([#1231]).

#### Contributors

-   [@adamgayoso]
-   [@jjhong922]
-   [@watiss]

[#1231]: https://github.com/YosefLab/scvi-tools/pull/1231
[#1242]: https://github.com/YosefLab/scvi-tools/pull/1242
[#1251]: https://github.com/YosefLab/scvi-tools/pull/1251
[#1253]: https://github.com/YosefLab/scvi-tools/pull/1253
[#1255]: https://github.com/YosefLab/scvi-tools/pull/1255
[#1257]: https://github.com/YosefLab/scvi-tools/pull/1257
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@watiss]: https://github.com/watiss

### New in 0.14.3 (2021-10-19)

Bug fix.

#### Changes

-   Bug fix to {func}`~scvi.model.base.BaseModelClass` to retain tensors registered by `register_tensor_from_anndata` ([#1235]).
-   Expose an instance of our `DocstringProcessor` to aid in documenting derived implementations of `setup_anndata` method ([#1235]).

#### Contributors

-   [@adamgayoso]
-   [@jjhong922]
-   [@watiss]

[#1235]: https://github.com/YosefLab/scvi-tools/pull/1235
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@watiss]: https://github.com/watiss

### New in 0.14.2 (2021-10-18)

Bug fix and new tutorial.

#### Changes

-   Bug fix in {class}`~scvi.external.RNAStereoscope` where loss was computed with mean for a minibatch instead of sum. This ensures reproducibility with the original implementation ([#1228]).
-   New Cell2location contributed tutorial ([#1232]).

#### Contributors

-   [@adamgayoso]
-   [@jjhong922]
-   [@vitkl]
-   [@watiss]

[#1228]: https://github.com/YosefLab/scvi-tools/pull/1228
[#1232]: https://github.com/YosefLab/scvi-tools/pull/1232
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@vitkl]: https://github.com/vitkl
[@watiss]: https://github.com/watiss

### New in 0.14.1 (2021-10-11)

Minor hotfixes.

#### Changes

-   Filter out mitochrondrial genes as a preprocessing step in the Amortized LDA tutorial ([#1213])
-   Remove `verbose=True` argument from early stopping callback ([#1216])

#### Contributors

-   [@adamgayoso]
-   [@jjhong922]
-   [@watiss]

[#1213]: https://github.com/YosefLab/scvi-tools/pull/1213
[#1216]: https://github.com/YosefLab/scvi-tools/pull/1216
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@watiss]: https://github.com/watiss

### New in 0.14.0 (2021-10-07)

In this release, we have completely revamped the scvi-tools documentation website by creating a new set of user guides that provide:

1. The math behind each method (in a succinct, online methods-like way)
2. The relationship between the math and the functions associated with each model
3. The relationship between math variables and code variables

Our previous User Guide guide has been renamed to Tutorials and contains all of our existing tutorials (including tutorials for developers).

Another noteworthy addition in this release is the implementation of the (amortized) Latent Dirichlet Allocation (aka LDA) model applied to single-cell gene expression data. We have also prepared a tutorial that demonstrates how to use this model, using a PBMC 10K dataset from 10x Genomics as an example application.

Lastly, in this release we have made a change to reduce user and developer confusion by making the previously global `setup_anndata` method a static class-specific method instead. This provides more clarity on which parameters are applicable for this call, for each model class. Below is a before/after for the DESTVI and TOTALVI model classes:

:::{figure} figures/setup_anndata_before_after.svg
:align: center
:alt: setup_anndata before and after
:class: img-fluid

`setup_anndata` before and after
:::

#### Changes

-   Added fixes to support PyTorch Lightning 1.4 ([#1103])
-   Simplified data handling in R tutorials with sceasy and addressed bugs in package installation ([#1122]).
-   Moved library size distribution computation to model init ([#1123])
-   Updated Contribution docs to describe how we backport patches ([#1129])
-   Implemented Latent Dirichlet Allocation as a PyroModule ([#1132])
-   Made `setup_anndata` a static method on model classes rather than one global function ([#1150])
-   Used Pytorch Lightning's `seed_everything` method to set seed ([#1151])
-   Fixed a bug in {class}`~scvi.model.base.PyroSampleMixin` for posterior sampling ([#1158])
-   Added CITE-Seq datasets ([#1182])
-   Added user guides to our documentation ([#1127], [#1157], [#1180], [#1193], [#1183], [#1204])
-   Early stopping now prints the reason for stopping when applicable ([#1208])

#### Breaking changes

-   `setup_anndata` is now an abstract method on model classes. Any model inheriting from {class}`~scvi.model.base.BaseModelClass` will need to implement this method ([#1150])

#### Contributors

-   [@adamgayoso]
-   [@PierreBoyeau]
-   [@talashuach]
-   [@jjhong922]
-   [@watiss]
-   [@mjayasur]
-   [@vitkl]
-   [@galenxing]

[#1103]: https://github.com/YosefLab/scvi-tools/pull/1103
[#1122]: https://github.com/YosefLab/scvi-tools/pull/1122
[#1123]: https://github.com/YosefLab/scvi-tools/pull/1123
[#1127]: https://github.com/YosefLab/scvi-tools/pull/1127
[#1129]: https://github.com/YosefLab/scvi-tools/pull/1129
[#1132]: https://github.com/YosefLab/scvi-tools/pull/1132
[#1150]: https://github.com/YosefLab/scvi-tools/pull/1150
[#1151]: https://github.com/YosefLab/scvi-tools/pull/1151
[#1157]: https://github.com/YosefLab/scvi-tools/pull/1157
[#1158]: https://github.com/YosefLab/scvi-tools/pull/1158
[#1180]: https://github.com/YosefLab/scvi-tools/pull/1180
[#1182]: https://github.com/YosefLab/scvi-tools/pull/1182
[#1183]: https://github.com/YosefLab/scvi-tools/pull/1183
[#1193]: https://github.com/YosefLab/scvi-tools/pull/1193
[#1204]: https://github.com/YosefLab/scvi-tools/pull/1204
[#1208]: https://github.com/YosefLab/scvi-tools/pull/1208
[@adamgayoso]: https://github.com/adamgayoso
[@galenxing]: https://github.com/galenxing
[@jjhong922]: https://github.com/jjhong922
[@mjayasur]: https://github.com/mjayasur
[@pierreboyeau]: https://github.com/PierreBoyeau
[@talashuach]: https://github.com/talashuach
[@vitkl]: https://github.com/vitkl
[@watiss]: https://github.com/watiss

## Version 0.13

### New in 0.13.0 (2021-08-23)

#### Changes

-   Added {class}`~scvi.model.MULTIVI` ([#1115], [#1118]).
-   Documentation CSS tweaks ([#1116]).

#### Breaking changes

None!

#### Contributors

-   [@adamgayoso]
-   [@talashuach]
-   [@jjhong922]

[#1115]: https://github.com/YosefLab/scvi-tools/pull/1115
[#1116]: https://github.com/YosefLab/scvi-tools/pull/1116
[#1118]: https://github.com/YosefLab/scvi-tools/pull/1118
[@adamgayoso]: https://github.com/adamgayoso
[@jjhong922]: https://github.com/jjhong922
[@talashuach]: https://github.com/talashuach

## Version 0.12

### New in 0.12.2 (2021-08-11)

#### Changes

-   Updated `OrderedDict` typing import to support all Python 3.7 versions ([#1114]).

#### Breaking changes

None!

#### Contributors

-   [@adamgayoso]
-   [@galenxing]
-   [@jjhong922]

[#1114]: https://github.com/YosefLab/scvi-tools/pull/1114
[@adamgayoso]: https://github.com/adamgayoso
[@galenxing]: https://github.com/galenxing
[@jjhong922]: https://github.com/jjhong922

### New in 0.12.1 (2021-07-29)

#### Changes

-   Update Pytorch Lightning version dependency to `>=1.3,<1.4` ([#1104]).

#### Breaking changes

None!

#### Contributors

-   [@adamgayoso]
-   [@galenxing]

[#1104]: https://github.com/YosefLab/scvi-tools/pull/1104
[@adamgayoso]: https://github.com/adamgayoso
[@galenxing]: https://github.com/galenxing

### New in 0.12.0 (2021-07-15)

This release adds features for tighter integration with Pyro for model development, fixes for {class}`~scvi.external.SOLO`, and other enhancements. Users of {class}`~scvi.external.SOLO` are strongly encouraged to upgrade as previous bugs will affect performance.

#### Enchancements

-   Add {class}`scvi.model.base.PyroSampleMixin` for easier posterior sampling with Pyro ([#1059]).
-   Add {class}`scvi.model.base.PyroSviTrainMixin` for automated training of Pyro models ([#1059]).
-   Ability to pass kwargs to {class}`~scvi.module.Classifier` when using {class}`~scvi.external.SOLO` ([#1078]).
-   Ability to get doublet predictions for simulated doublets in {class}`~scvi.external.SOLO` ([#1076]).
-   Add "comparison" column to differential expression results ([#1074]).
-   Clarify {class}`~scvi.external.CellAssign` size factor usage. See class docstring.

#### Changes

-   Update minimum Python version to `3.7.2` ([#1082]).
-   Slight interface changes to {class}`~scvi.train.PyroTrainingPlan`. `"elbo_train"` and `"elbo_test"` are now the average over minibatches as ELBO should be on scale of full data and `optim_kwargs` can be set on initialization of training plan ([#1059], [#1101]).
-   Use pandas read pickle function for pbmc dataset metadata loading ([#1099]).
-   Adds `n_samples_overall` parameter to functions for denoised expression/accesibility/etc. This is used in during differential expression ([#1090]).
-   Ignore configure optimizers warning when training Pyro-based models ([#1064]).

#### Bug fixes

-   Fix scale of library size for simulated doublets and expression in {class}`~scvi.external.SOLO` when using observed library size to train original {class}`~scvi.model.SCVI` model ([#1078], [#1085]). Currently, library sizes in this case are not appropriately put on the log scale.
-   Fix issue where anndata setup with a layer led to errors in {class}`~scvi.external.SOLO` ([#1098]).
-   Fix `adata` parameter of {func}`scvi.external.SOLO.from_scvi_model`, which previously did nothing ([#1078]).
-   Fix default `max_epochs` of {class}`~scvi.model.SCANVI` when initializing using pre-trained model of {class}`~scvi.model.SCVI` ([#1079]).
-   Fix bug in `predict()` function of {class}`~scvi.model.SCANVI`, which only occurred for soft predictions ([#1100]).

#### Breaking changes

None!

#### Contributors

-   [@vitkl]
-   [@adamgayoso]
-   [@galenxing]
-   [@PierreBoyeau]
-   [@Munfred]
-   [@njbernstein]
-   [@mjayasur]

[#1059]: https://github.com/YosefLab/scvi-tools/pull/1059
[#1064]: https://github.com/YosefLab/scvi-tools/pull/1064
[#1074]: https://github.com/YosefLab/scvi-tools/pull/1074
[#1076]: https://github.com/YosefLab/scvi-tools/pull/1076
[#1078]: https://github.com/YosefLab/scvi-tools/pull/1078
[#1079]: https://github.com/YosefLab/scvi-tools/pull/1079
[#1082]: https://github.com/YosefLab/scvi-tools/pull/1082
[#1085]: https://github.com/YosefLab/scvi-tools/pull/1085
[#1090]: https://github.com/YosefLab/scvi-tools/pull/1090
[#1098]: https://github.com/YosefLab/scvi-tools/pull/1098
[#1099]: https://github.com/YosefLab/scvi-tools/pull/1099
[#1100]: https://github.com/YosefLab/scvi-tools/pull/1100
[#1101]: https://github.com/YosefLab/scvi-tools/pull/1101
[@adamgayoso]: https://github.com/adamgayoso
[@galenxing]: https://github.com/galenxing
[@mjayasur]: https://github.com/mjayasur
[@munfred]: https://github.com/Munfred
[@njbernstein]: https://github.com/njbernstein
[@pierreboyeau]: https://github.com/PierreBoyeau
[@vitkl]: https://github.com/vitkl

## Version 0.11

### New in 0.11.0 (2021-05-23)

From the user perspective, this release features the new differential expression functionality (to be described in a manuscript). For now, it is accessible from {func}`~scvi.model.SCVI.differential_expression`. From the developer perspective, we made changes with respect to {class}`scvi.dataloaders.DataSplitter` and surrounding the Pyro backend. Finally, we also made changes to adapt our code to PyTorch Lightning version 1.3.

#### Changes

-   Pass `n_labels` to {class}`~scvi.module.VAE` from {class}`~scvi.model.SCVI` ([#1055]).
-   Require PyTorch lightning > 1.3, add relevant fixes ([#1054]).
-   Add DestVI reference ([#1060]).
-   Add PeakVI links to README ([#1046]).
-   Automatic delta and eps computation in differential expression ([#1043]).
-   Allow doublet ratio parameter to be changed for used in SOLO ([#1066]).

#### Bug fixes

-   Fix an issue where `transform_batch` options in {class}`~scvi.model.TOTALVI` was accidentally altering the batch encoding in the encoder, which leads to poor results ([#1072]). This bug was introduced in version 0.9.0.

#### Breaking changes

These breaking changes do not affect the user API; though will impact model developers.

-   Use PyTorch Lightning data modules for {class}`scvi.dataloaders.DataSplitter` ([#1061]). This induces a breaking change in the way the data splitter is used. It is no longer callable and now has a `setup` method. See {class}`~scvi.train.TrainRunner` and its source code, which is straightforward.
-   No longer require training plans to be initialized with `n_obs_training` argument ([#1061]). `n_obs_training` is now a property that can be set before actual training to rescale the loss.
-   Log Pyro loss as `train_elbo` and sum over steps ([#1071])

#### Contributors

-   [@adamgayoso]
-   [@romain-lopez]
-   [@PierreBoyeau]
-   [@talashuach]
-   [@cataclysmus]
-   [@njbernstein]

[#1043]: https://github.com/YosefLab/scvi-tools/pull/1043
[#1046]: https://github.com/YosefLab/scvi-tools/pull/1046
[#1054]: https://github.com/YosefLab/scvi-tools/pull/1054
[#1055]: https://github.com/YosefLab/scvi-tools/pull/1055
[#1060]: https://github.com/YosefLab/scvi-tools/pull/1060
[#1061]: https://github.com/YosefLab/scvi-tools/pull/1061
[#1066]: https://github.com/YosefLab/scvi-tools/pull/1066
[#1071]: https://github.com/YosefLab/scvi-tools/pull/1071
[#1072]: https://github.com/YosefLab/scvi-tools/pull/1072
[@adamgayoso]: https://github.com/adamgayoso
[@cataclysmus]: https://github.com/cataclysmus
[@njbernstein]: https://github.com/njbernstein
[@pierreboyeau]: https://github.com/PierreBoyeau
[@romain-lopez]: https://github.com/romain-lopez
[@talashuach]: https://github.com/talashuach

## Version 0.10

### New in 0.10.1 (2021-05-04)

#### Changes

-   Includes new optional variance parameterization for the `Encoder` module ([#1037]).
-   Provides new way to select subpopulations for DE using Pandas queries ([#1041]).
-   Update reference to peakVI ([#1046]).
-   Pin Pytorch Lightning version to \<1.3

#### Contributors

-   [@adamgayoso]
-   [@PierreBoyeau]
-   [@talashuach]

[#1037]: https://github.com/YosefLab/scvi-tools/pull/1037
[#1041]: https://github.com/YosefLab/scvi-tools/pull/1041
[#1046]: https://github.com/YosefLab/scvi-tools/pull/1046
[@adamgayoso]: https://github.com/adamgayoso
[@pierreboyeau]: https://github.com/PierreBoyeau
[@talashuach]: https://github.com/talashuach

### 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]).

#### Contributors

-   [@adamgayoso]
-   [@romain-lopez]
-   [@talashuach]
-   [@mjayasur]
-   [@wukathy]
-   [@PierreBoyeau]
-   [@morris-frank]

[#1005]: https://github.com/YosefLab/scvi-tools/pull/1005
[#1006]: https://github.com/YosefLab/scvi-tools/pull/1006
[#1009]: https://github.com/YosefLab/scvi-tools/pull/1009
[#1011]: https://github.com/YosefLab/scvi-tools/pull/1011
[#1016]: https://github.com/YosefLab/scvi-tools/pull/1016
[#1017]: https://github.com/YosefLab/scvi-tools/pull/1017
[#1019]: https://github.com/YosefLab/scvi-tools/pull/1019
[#1021]: https://github.com/YosefLab/scvi-tools/pull/1021
[#1024]: https://github.com/YosefLab/scvi-tools/pull/1025
[#1025]: https://github.com/YosefLab/scvi-tools/pull/1025
[#1028]: https://github.com/YosefLab/scvi-tools/pull/1028
[#1030]: https://github.com/YosefLab/scvi-tools/pull/1033
[#1033]: https://github.com/YosefLab/scvi-tools/pull/1033
[#1034]: https://github.com/YosefLab/scvi-tools/pull/1034
[@adamgayoso]: https://github.com/adamgayoso
[@mjayasur]: https://github.com/mjayasur
[@morris-frank]: https://github.com/morris-frank
[@pierreboyeau]: https://github.com/PierreBoyeau
[@romain-lopez]: https://github.com/romain-lopez
[@talashuach]: https://github.com/talashuach
[@wukathy]: https://github.com/wukathy

## Version 0.9

### New in 0.9.1 (2021-03-20)

#### Changes

-   Update Pyro module backend to better enfore usage of `model` and `guide`, automate passing of number of training examples to Pyro modules ([#990])
-   Minimum Pyro version bumped ([#988])
-   Improve docs clarity ([#989])
-   Add glossary to developer user guide ([#999])
-   Add num threads config option to `scvi.settings` ([#1001])
-   Add CellAssign tutorial ([#1004])

#### Contributors

-   [@adamgayoso]
-   [@galenxing]
-   [@mjayasur]
-   [@wukathy]

[#1001]: https://github.com/YosefLab/scvi-tools/pull/1001
[#1004]: https://github.com/YosefLab/scvi-tools/pull/1004
[#988]: https://github.com/YosefLab/scvi-tools/pull/988
[#989]: https://github.com/YosefLab/scvi-tools/pull/989
[#990]: https://github.com/YosefLab/scvi-tools/pull/990
[#999]: https://github.com/YosefLab/scvi-tools/pull/999
[@adamgayoso]: https://github.com/adamgayoso
[@galenxing]: https://github.com/galenxing
[@mjayasur]: https://github.com/mjayasur
[@wukathy]: https://github.com/wukathy

### New in 0.9.0 (2021-03-03)

This release features our new software development kit for building new probabilistic models. Our hope is that others will be able to develop new models by importing scvi-tools into their own packages.

#### Important changes

From the user perspective, there are two package-wide API breaking changes and one {class}`~scvi.model.SCANVI` specific breaking change enumerated below. From the method developer perspective, the entire model backend has been revamped using PyTorch Lightning, and no old code will be compatible with this and future versions. Also, we dropped support for Python 3.6.

##### Breaking change: The `train` method

-   `n_epochs` is now `max_epochs` for consistency with PytorchLightning and to better relect the functionality of the parameter.
-   `use_cuda` is now `use_gpu` for consistency with PytorchLightning.
-   `frequency` is now `check_val_every_n_epoch` for consistency with PytorchLightning.
-   `train_fun_kwargs` and `kwargs` throughout the `train()` methods in the codebase have been removed and various arguments have been reorganized into `plan_kwargs` and `trainer_kwargs`. Generally speaking, `plan_kwargs` deal with model optimization like kl warmup, while `trainer_kwargs` deal with the actual training loop like early stopping.

##### Breaking change: GPU handling

-   `use_cuda` was removed from the init of each model and was not replaced by `use_gpu`. By default every model is intialized on CPU but can be moved to a device via `model.to_device()`. If a model is trained with `use_gpu=True` the model will remain on the GPU after training.
-   When loading saved models, scvi-tools will always attempt to load the model on GPU unless otherwise specified.
-   We now support specifying which GPU device to use if there are multiple available GPUs.

##### Breaking change: {class}`~scvi.model.SCANVI`

-   {class}`~scvi.model.SCANVI` no longer pretrains an {class}`~scvi.model.SCVI` model by default. This functionality however is preserved via the new {func}`~scvi.model.SCANVI.from_scvi_model` method.
-   `n_epochs_unsupervised` and `n_epochs_semisupervised` have been removed from `train`. It has been replaced with `max_epochs` for semisupervised training.
-   `n_samples_per_label` is a new argument which will subsample the number of labelled training examples to train on per label each epoch.

#### New Model Implementations

-   {class}`~scvi.model.PEAKVI` implementation ([#877], [#921])
-   {class}`~scvi.external.SOLO` implementation ([#923], [#933])
-   {class}`~scvi.external.CellAssign` implementation ([#940])
-   {class}`~scvi.external.RNAStereoscope` and {class}`~scvi.external.SpatialStereoscope` implementation ([#889], [#959])
-   Pyro integration via {class}`~scvi.module.base.PyroBaseModuleClass` ([#895] [#903], [#927], [#931])

#### Enhancements

-   {class}`~scvi.model.SCANVI` bug fixes ([#879])
-   {class}`~scvi.external.GIMVI` moved to external api ([#885])
-   {class}`~scvi.model.TOTALVI`, {class}`~scvi.model.SCVI`, and {class}`~scvi.model.SCANVI` now support multiple covariates ([#886])
-   Added callback for saving the best state of a model ([#887])
-   Option to disable progress bar ([#905])
-   load() documentation improvements ([#913])
-   updated tutorials, guides, documentation ([#924], [#925], [#929], [#934], [#947], [#971])
-   track is now public ([#938])
-   {class}`~scvi.model.SCANVI` now logs classficiation loss ([#966])
-   get_likelihood_parameter() bug ([#967])
-   model.history are now pandas DataFrames ([#949])

#### Contributors

-   [@adamgayoso]
-   [@galenxing]
-   [@romain-lopez]
-   [@wukathy]
-   [@giovp]
-   [@njbernstein]
-   [@saketkc]

[#877]: https://github.com/YosefLab/scvi-tools/pull/887
[#879]: https://github.com/YosefLab/scvi-tools/pull/879
[#885]: https://github.com/YosefLab/scvi-tools/pull/885
[#886]: https://github.com/YosefLab/scvi-tools/pull/886
[#887]: https://github.com/YosefLab/scvi-tools/pull/887
[#889]: https://github.com/YosefLab/scvi-tools/pull/889
[#895]: https://github.com/YosefLab/scvi-tools/pull/895
[#903]: https://github.com/YosefLab/scvi-tools/pull/903
[#905]: https://github.com/YosefLab/scvi-tools/pull/905
[#913]: https://github.com/YosefLab/scvi-tools/pull/913
[#921]: https://github.com/YosefLab/scvi-tools/pull/921
[#923]: https://github.com/YosefLab/scvi-tools/pull/923
[#924]: https://github.com/YosefLab/scvi-tools/pull/924
[#925]: https://github.com/YosefLab/scvi-tools/pull/925
[#927]: https://github.com/YosefLab/scvi-tools/pull/927
[#929]: https://github.com/YosefLab/scvi-tools/pull/929
[#931]: https://github.com/YosefLab/scvi-tools/pull/931
[#933]: https://github.com/YosefLab/scvi-tools/pull/933
[#934]: https://github.com/YosefLab/scvi-tools/pull/934
[#938]: https://github.com/YosefLab/scvi-tools/pull/938
[#940]: https://github.com/YosefLab/scvi-tools/pull/940
[#947]: https://github.com/YosefLab/scvi-tools/pull/947
[#949]: https://github.com/YosefLab/scvi-tools/pull/949
[#959]: https://github.com/YosefLab/scvi-tools/pull/959
[#966]: https://github.com/YosefLab/scvi-tools/pull/966
[#967]: https://github.com/YosefLab/scvi-tools/pull/967
[#971]: https://github.com/YosefLab/scvi-tools/pull/971
[@adamgayoso]: https://github.com/adamgayoso
[@galenxing]: https://github.com/galenxing
[@giovp]: https://github.com/giovp
[@njbernstein]: https://github.com/njbernstein
[@romain-lopez]: https://github.com/romain-lopez
[@saketkc]: https://github.com/saketkc
[@wukathy]: https://github.com/wukathy

## Version 0.8

### New in 0.8.1 (2020-12-23)

#### Enhancements

-   `freeze_classifier` option in {func}`~scvi.model.SCANVI.load_query_data` for the case when
-   `weight_decay` passed to {func}`~scvi.model.SCANVI.train` also passes to `ClassifierTrainer`

### New in 0.8.0 (2020-12-17)

#### Enhancements

##### Online updates of {class}`~scvi.model.SCVI`, {class}`~scvi.model.SCANVI`, and {class}`~scvi.model.TOTALVI` with the scArches method

It is now possible to iteratively update these models with new samples, without altering the model for the "reference" population.
Here we use the [scArches method](https://github.com/theislab/scarches). For usage, please see the tutorial in the user guide.

To enable scArches in our models, we added a few new options. The first is `encode_covariates`, which is an `SCVI` option to encode the one-hotted
batch covariate. We also allow users to exchange batch norm in the encoder and decoder with layer norm, which can be though of as batch norm but per cell.
As the layer norm we use has no parameters, it's a bit faster than models with batch norm. We don't find many differences between using batch norm or layer norm
in our models, though we have kept defaults the same in this case. To run scArches effectively, batch norm should be exhanged with layer norm.

##### Empirical initialization of protein background parameters with totalVI

The learned prior parameters for the protein background were randomly initialized. Now, they can be set with the `empirical_protein_background_prior`
option in {class}`~scvi.model.TOTALVI`. This option fits a two-component Gaussian mixture model per cell, separating those proteins that are background
for the cell and those that are foreground, and aggregates the learned mean and variance of the smaller component across cells. This computation is done
per batch, if the `batch_key` was registered. We emphasize this is just for the initialization of a learned parameter in the model.

##### Use observed library size option

Many of our models like `SCVI`, `SCANVI`, and {class}`~scvi.model.TOTALVI` learn a latent library size variable.
The option `use_observed_lib_size` may now be passed on model initialization. We have set this as `True` by default,
as we see no regression in performance, and training is a bit faster.

#### Important changes

-   To facilitate these enhancements, saved {class}`~scvi.model.TOTALVI` models from previous versions will not load properly. This is due to an architecture change of the totalVI encoder, related to latent library size handling.
-   The default latent distribtuion for {class}`~scvi.model.TOTALVI` is now `"normal"`.
-   Autotune was removed from this release. We could not maintain the code given the new API changes and we will soon have alternative ways to tune hyperparameters.
-   Protein names during `setup_anndata` are now stored in `adata.uns["_scvi"]["protein_names"]`, instead of `adata.uns["scvi_protein_names"]`.

#### Bug fixes

-   Fixed an issue where the unlabeled category affected the SCANVI architecture prior distribution. Unfortunately, by fixing this bug, loading previously trained (\<v0.8.0) {class}`~scvi.model.SCANVI` models will fail.

## Version 0.7

### New in 0.7.1 (2020-10-20)

This small update provides access to our new Discourse forum from the documentation.

### 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.

## Pre-Version 0.7

### scvi History

The scvi-tools package used to be scvi. This page commemorates all the hard work on the scvi package by our numerous contributors.

#### Contributors

-   [@romain]
-   [@adam]
-   [@eddie]
-   [@jeff]
-   [@pierre]
-   [@max]
-   [@yining]
-   [@gabriel]
-   [@achille]
-   [@chenling]
-   [@jules]
-   [@david-kelley]
-   [@william-yang]
-   [@oscar]
-   [@casey-greene]
-   [@jamie-morton]
-   [@valentine-svensson]
-   [@stephen-flemming]
-   [@michael-raevsky]
-   [@james-webber]
-   [@galen]
-   [@francesco-brundu]
-   [@primoz-godec]
-   [@eduardo-beltrame]
-   [@john-reid]
-   [@han-yuan]
-   [@gokcen-eraslan]

#### 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]

[@achille]: https://github.com/ANazaret
[@adam]: https://github.com/adamgayoso
[@casey-greene]: https://github.com/cgreene
[@chenling]: https://github.com/chenlingantelope
[@david-kelley]: https://github.com/davek44
[@eddie]: https://github.com/Edouard360
[@eduardo-beltrame]: https://github.com/Munfred
[@francesco-brundu]: https://github.com/fbrundu
[@gabriel]: https://github.com/gabmis
[@galen]: https://github.com/galenxing
[@gokcen-eraslan]: https://github.com/gokceneraslan
[@han-yuan]: https://github.com/hy395
[@james-webber]: https://github.com/jamestwebber
[@jamie-morton]: https://github.com/mortonjt
[@jeff]: https://github.com/jeff-regier
[@john-reid]: https://github.com/JohnReid
[@jules]: https://github.com/jules-samaran
[@max]: https://github.com/maxime1310
[@michael-raevsky]: https://github.com/raevskymichail
[@oscar]: https://github.com/oscarclivio
[@pierre]: https://github.com/PierreBoyeau
[@primoz-godec]: https://github.com/PrimozGodec
[@romain]: https://github.com/romain-lopez
[@stephen-flemming]: https://github.com/sjfleming
[@valentine-svensson]: https://github.com/vals
[@william-yang]: https://github.com/triyangle
[@yining]: https://github.com/imyiningliu