Added
- Add support for Python 3.12 {pr}`2966`.
- Add support for categorial covariates in scArches in `scvi.model.archesmixin` {pr}`2936`.
- Add assertion error in cellAssign for checking duplicates in celltype markers {pr}`2951`.
- Add `scvi.external.poissonvi.get_region_factors` {pr}`2940`.
- {attr}`scvi.settings.dl_persistent_workers` allows using persistent workers in
{class}`scvi.dataloaders.AnnDataLoader` {pr}`2924`.
- Add option for using external indexes in data splitting classes that are under `scvi.dataloaders`
by passing `external_indexing=list[train_idx,valid_idx,test_idx]` as well as in all models
available {pr}`2902`.
- Add warning if creating data splits in `scvi.dataloaders` that create last batch with less than 3
cells {pr}`2916`.
- Add new experimental functional API for hyperparameter tuning with
{func}`scvi.autotune.run_autotune` and {class}`scvi.autotune.AutotuneExperiment` to replace
{class}`scvi.autotune.ModelTuner`, {class}`scvi.autotune.TunerManager`, and
{class}`scvi.autotune.TuneAnalysis` {pr}`2561`.
- Add experimental class {class}`scvi.nn.Embedding` implementing methods for extending embeddings
{pr}`2574`.
- Add experimental support for representing batches with continuously-valued embeddings by passing
in `batch_representation="embedding"` to {class}`scvi.model.SCVI` {pr}`2576`.
- Add experimental mixin classes {class}`scvi.model.base.EmbeddingMixin` and
{class}`scvi.module.base.EmbeddingModuleMixin` {pr}`2576`.
- Add option to generate synthetic spatial coordinates in {func}`scvi.data.synthetic_iid` with
argument `generate_coordinates` {pr}`2603`.
- Add experimental support for using custom {class}`lightning.pytorch.core.LightningDataModule`s
in {func}`scvi.autotune.run_autotune` {pr}`2605`.
- Add {class}`scvi.external.VELOVI` for RNA velocity estimation using variational inference
{pr}`2611`.
- Add `unsigned` argument to {meth}`scvi.hub.HubModel.pull_from_s3` to allow for unsigned
downloads of models from AWS S3 {pr}`2615`.
- Add support for `batch_key` in {meth}`scvi.model.CondSCVI.setup_anndata` {pr}`2626`.
- Add support for {meth}`scvi.model.base.RNASeqMixin` in {class}`scvi.model.CondSCVI` {pr}`2915`.
- Add `load_best_on_end` argument to {class}`scvi.train.SaveCheckpoint` to load the best model
state at the end of training {pr}`2672`.
- Add experimental class {class}`scvi.distributions.BetaBinomial` implementing the Beta-Binomial
distribution with mean-dispersion parameterization for modeling scBS-seq methylation data
{pr}`2692`.
- Add support for custom dataloaders in {class}`scvi.model.base.VAEMixin` methods by specifying
the `dataloader` argument {pr}`2748`.
- Add option to use a normal distribution in the generative model of {class}`scvi.model.SCVI` by
passing in `gene_likelihood="normal"` {pr}`2780`.
- Add {class}`scvi.external.MRVI` for modeling sample-level heterogeneity in single-cell RNA-seq
data {pr}`2756`.
- Add support for reference mapping with {class}`mudata.MuData` models to
{class}`scvi.model.base.ArchesMixin` {pr}`2578`.
- Add argument `return_mean` to {meth}`scvi.model.base.VAEMixin.get_reconstruction_error`
and {meth}`scvi.model.base.VAEMixin.get_elbo` to allow computation
without averaging across cells {pr}`2362`.
- Add support for setting `weights="importance"` in
{meth}`scvi.model.SCANVI.differential_expression` {pr}`2362`.
Changed
- Deprecate {func}`scvi.data.cellxgene`, to be removed in v1.3. Please directly use the
[cellxgene-census](https://chanzuckerberg.github.io/cellxgene-census/) instead {pr}`2542`.
- Deprecate {func}`scvi.nn.one_hot`, to be removed in v1.3. Please directly use the
`one_hot` function in PyTorch instead {pr}`2608`.
- Deprecate {class}`scvi.train.SaveBestState`, to be removed in v1.3. Please use
{class}`scvi.train.SaveCheckpoint` instead {pr}`2673`.
- Deprecate `save_best` argument in {meth}`scvi.model.PEAKVI.train` and
{meth}`scvi.model.MULTIVI.train`, to be removed in v1.3. Please pass in `enable_checkpointing`
or specify a custom checkpointing procedure with {class}`scvi.train.SaveCheckpoint` instead
{pr}`2673`.
- Move {func}`scvi.model.base._utils._load_legacy_saved_files` to
{func}`scvi.model.base._save_load._load_legacy_saved_files` {pr}`2731`.
- Move {func}`scvi.model.base._utils._load_saved_files` to
{func}`scvi.model.base._save_load._load_saved_files` {pr}`2731`.
- Move {func}`scvi.model.base._utils._initialize_model` to
{func}`scvi.model.base._save_load._initialize_model` {pr}`2731`.
- Move {func}`scvi.model.base._utils._validate_var_names` to
{func}`scvi.model.base._save_load._validate_var_names` {pr}`2731`.
- Move {func}`scvi.model.base._utils._prepare_obs` to
{func}`scvi.model.base._de_core._prepare_obs` {pr}`2731`.
- Move {func}`scvi.model.base._utils._de_core` to
{func}`scvi.model.base._de_core._de_core` {pr}`2731`.
- Move {func}`scvi.model.base._utils._fdr_de_prediction` to
{func}`scvi.model.base._de_core_._fdr_de_prediction` {pr}`2731`.
- {func}`scvi.data.synthetic_iid` now generates unique variable names for protein and
accessibility data {pr}`2739`.
- The `data_module` argument in {meth}`scvi.model.base.UnsupervisedTrainingMixin.train` has been
renamed to `datamodule` for consistency {pr}`2749`.
- Change the default saving method of variable names for {class}`mudata.MuData` based models
(_e.g._ {class}`scvi.model.TOTALVI`) to a dictionary of per-mod variable names instead of a
concatenated array of all variable names. Users may replicate the previous behavior by
passing in `legacy_mudata_format=True` to {meth}`scvi.model.base.BaseModelClass.save`
{pr}`2769`.
- Changed internal activation function in {class}`scvi.nn.DecoderTOTALVI` to Softplus to
increase numerical stability. This is the new default for new models. Previously trained models
will be loaded with exponential activation function {pr}`2913`.
Fixed
- Fix logging of accuracy for cases with 1 sample per class in scANVI {pr}`2938`.
- Disable adversarial classifier if training with a single batch.
Previously this raised a None error {pr}`2914`.
- {meth}`~scvi.model.SCVI.get_normalized_expression` fixed for Poisson distribution and
Negative Binomial with latent_library_size {pr}`2915`.
- Fix {meth}`scvi.module.VAE.marginal_ll` when `n_mc_samples_per_pass=1` {pr}`2362`.
- {meth}`scvi.module.VAE.marginal_ll` when `n_mc_samples_per_pass=1` {pr}`2362`.
- Enable option to drop_last minibatch during training by `datasplitter_kwargs={"drop_last": True}`
{pr}`2926`.
- Fix JAX to be deterministic on CUDA when seed is manually set {pr}`2923`.
Removed
- Remove {class}`scvi.autotune.ModelTuner`, {class}`scvi.autotune.TunerManager`, and
{class}`scvi.autotune.TuneAnalysis` in favor of new experimental functional API with
{func}`scvi.autotune.run_autotune` and {class}`scvi.autotune.AutotuneExperiment` {pr}`2561`.
- Remove `feed_labels` argument and corresponding code paths in {meth}`scvi.module.SCANVAE.loss`
{pr}`2644`.
- Remove {class}`scvi.train._callbacks.MetricsCallback` and argument `additional_val_metrics` in
{class}`scvi.train.Trainer` {pr}`2646`.