Refactor [WIP]: Removed the spatial models from scvi-tools in v1.6 and move them to scVIVA-Tools

CHANGELOG.md

@@ -26,6 +26,10 @@ to [Semantic Versioning]. The full commit history is available in the [commit lo
 #### Removed
 
 - Removed the `tests`, `test`, `editing`, `dev`, `docs` and `docsbuild` extras in favour of the `dev`, `test` and `doc` dependency groups, {pr}`3607`.
+- Remove {class}`scvi.external.DestVI`, {class}`scvi.external.GimVI`, {class}`scvi.external.ResolVI`,
+    {class}`scvi.external.SCVIVA`, {class}`scvi.external.DiagVI`, {class}`scvi.external.Stereoscope`,
+    and {class}`scvi.external.Tangram` spatial models, along with their associated tutorials and
+    documentation, {pr}`3908`.
 
 ### 1.5.0 (2026-07-08)
 

docs/api/developer.md

@@ -155,7 +155,6 @@ Existing module classes with respective generative and inference procedures.
    module.AutoZIVAE
    module.Classifier
    module.LDVAE
-   module.MRDeconv
    module.PEAKVAE
    module.MULTIVAE
    module.SCANVAE
@@ -179,19 +178,12 @@ Module classes in the external API with respective generative and inference proc
    :template: class_no_inherited.rst
    :nosignatures:
 
-   external.gimvi.JVAE
-   external.gimvi._task.GIMVITrainingPlan
-   external.gimvi._task.CyclicMultiDataLoader
    external.cytovi.CytoVAE
    external.cellassign.CellAssignModule
    external.contrastivevi.ContrastiveDataSplitter
-   external.contrastivevi.ContrastiveDataLoader
-   external.stereoscope.RNADeconv
-   external.stereoscope.SpatialDeconv
    external.scbasset.ScBassetModule
    external.contrastivevi.ContrastiveVAE
    external.velovi.VELOVAE
-   external.tangram.TangramMapper
    external.mrvi.MRVAE
    external.mrvi._types.MRVIReduction
    external.methylvi.METHYLVAE
@@ -201,13 +193,8 @@ Module classes in the external API with respective generative and inference proc
    external.methylvi.METHYLANVAE
    external.decipher.DecipherPyroModule
    external.decipher._trainingplan.DecipherTrainingPlan
-   external.resolvi.RESOLVAE
    external.totalanvi.TOTALANVAE
-   external.scviva.nicheVAE
-   external.scviva.NicheLossOutput
-   external.scviva.differential_expression.DifferentialExpressionResults
    external.sysvi.SysVAE
-   external.diagvi.DIAGVAE
    external.drvi.DRVIModule
    external.drvi.DecoderDRVI
    external.drvi.SplitFCLayers

docs/api/user.md

@@ -25,7 +25,6 @@ import scvi
 
    model.AUTOZI
    model.CondSCVI
-   model.DestVI
    model.LinearSCVI
    model.PEAKVI
    model.SCANVI
@@ -49,9 +48,6 @@ import scvi
 
    external.CellAssign
    external.CYTOVI
-   external.GIMVI
-   external.RNAStereoscope
-   external.SpatialStereoscope
    external.SOLO
    external.SCAR
    external.SCBASSET
@@ -63,13 +59,9 @@ import scvi
    external.METHYLANVI
    external.Decipher
    external.TOTALANVI
-   external.RESOLVI
    external.SysVI
-   external.SCVIVA
-   external.DIAGVI
    external.DRVI
    external.JointEmbeddingSCVI
-   external.Tangram
 ```
 
 ## Data loading

docs/conf.py

@@ -61,6 +61,28 @@
     ("py:class", "optional"),
     ("py:class", "return"),
     ("py:meth", "save_hyperparameters"),
+    # Type hint resolves to the private defining module instead of the public re-export.
+    ("py:class", "scvi.external.contrastivevi._contrastive_dataloader.ContrastiveDataLoader"),
+    # Spatial models and DiagVI were removed from the public API in v1.6; CHANGELOG.md
+    # keeps historical references to them that can no longer resolve.
+    ("py:class", "scvi.external.DestVI"),
+    ("py:class", "scvi.external.GimVI"),
+    ("py:class", "scvi.external.GIMVI"),
+    ("py:class", "scvi.external.GIMVI.save"),
+    ("py:class", "scvi.external.ResolVI"),
+    ("py:class", "scvi.external.RESOLVI"),
+    ("py:meth", "scvi.external.RESOLVI.differential_expression"),
+    ("py:class", "scvi.external.SCVIVA"),
+    ("py:class", "scvi.external.DiagVI"),
+    ("py:class", "scvi.external.DIAGVI"),
+    ("py:class", "scvi.external.Stereoscope"),
+    ("py:class", "scvi.external.RNAStereoscope"),
+    ("py:class", "scvi.external.SpatialStereoscope"),
+    ("py:class", "scvi.external.SpatialStereoscope.from_rna_model"),
+    ("py:class", "scvi.external.SpatialStereoscope.setup_anndata"),
+    ("py:class", "scvi.external.Tangram"),
+    ("py:class", "scvi.model.DestVI"),
+    ("py:func", "scvi.model.DestVI.from_rna_model"),
 ]
 
 html_context = {
@@ -178,6 +200,9 @@ def _importable(name: str) -> bool:
     "**.ipynb_checkpoints",
     "tutorials/notebooks/.github/**",
     "tutorials/notebooks/README.md",
+    # Spatial models were removed from scvi-tools in v1.6; these tutorials no longer have
+    # a home in the docs nav (docs/tutorials/index_spatial.md was removed).
+    "tutorials/notebooks/spatial/**",
 ]
 
 # extlinks config

docs/installation.md

@@ -90,7 +90,6 @@ It has many optional dependencies which expand its capabilities:
 - _parallel_ - for parallelization engine
 - _interpretability_ - for supervised models interpretability
 - _dataloaders_ - for custom dataloaders use
-- _diagvi_ - for DiagVI model (requires torch_geometric and geomloss)
 - _mlflow_ - for MLflow support
 - _cuda_ - for Linux-based OS CUDA 12 GPU support
 - _cuda13_ - for Linux-based OS CUDA 13 GPU support

docs/tutorials/index.md

@@ -19,7 +19,6 @@ index_atac
 index_cytometry
 index_scbs
 index_multimodal
-index_spatial
 index_hub
 index_use_cases
 index_custom_dl

docs/tutorials/index_multimodal.md

@@ -9,8 +9,6 @@ notebooks/multimodal/totalVI_reference_mapping
 notebooks/multimodal/cite_scrna_integration_w_totalVI
 notebooks/multimodal/MultiVI_tutorial
 notebooks/multimodal/totalanvi
-notebooks/multimodal/DiagVI_spatial_proteomics
-notebooks/multimodal/DiagVI_spatial_transcriptomics
 ```
 
 ```{customcard}
@@ -22,7 +20,7 @@ Go through the totalVI workflow to analyze CITE-seq datasets
 
 ```{customcard}
 :path: notebooks/multimodal/scarches_scvi_tools
-:tags: Integration, Transfer-learning, Dimensionality-reduction, Removal-of-variance, Analysis, Modality-imputation, Semi-supervised, Cell-type-annotation
+:tags: Integration, Transfer-learning, Dimensionality-reduction, Removal-of-variance, Analysis, Modality-imputation
 
 Map cells from a query dataset to the latent space of a reference dataset with the scArches method
 ```
@@ -54,17 +52,3 @@ Go through the MultiVI workflow to perform joint analysis of paired and unpaired
 
 Use TotalANVI to perform semi-supervised analysis of CITE-seq data, leveraging partial cell type annotations for label prediction, protein imputation, and differential abundance
 ```
-
-```{customcard}
-:path: notebooks/multimodal/DiagVI_spatial_proteomics
-:tags: Analysis, Integration, Modality-imputation, Dimensionality-reduction
-
-Perform integration of spatial proteomics and single-cell transcriptomics data with DiagVI
-```
-
-```{customcard}
-:path: notebooks/multimodal/DiagVI_spatial_transcriptomics
-:tags: Analysis, Integration, Modality-imputation, Dimensionality-reduction
-
-Perform integration of spatial and single-cell transcriptomics data with DiagVI
-```

docs/user_guide/index.md

@@ -149,42 +149,9 @@ scvi-tools is composed of models that can perform one or many analysis tasks. In
    * - :doc:`/user_guide/models/multivi`
      - Integration of paired/unpaired multiome data, missing modality imputation, normalization of other cell- and sample-level confounding factors
      - :cite:p:`AshuachGabitto21`
-   * - :doc:`/user_guide/models/diagvi`
-     - Diagonal integration of unpaired multiome data, dimensionality reduction, cross-modality imputation, cell label transfer
-     -
 
 ```
 
-## Spatial transcriptomics analysis
-
-```{eval-rst}
-.. list-table::
-   :widths: 15 100 25
-   :header-rows: 1
-
-   * - Model
-     - Tasks
-     - Reference
-   * - :doc:`/user_guide/models/destvi`
-     - Multi-resolution deconvolution, cell-type-specific gene expression imputation, comparative analysis
-     - :cite:p:`Lopez22`
-   * - :doc:`/user_guide/models/stereoscope`
-     - Deconvolution
-     - :cite:p:`Andersson20`
-   * - :doc:`/user_guide/models/gimvi`
-     - Imputation of missing spatial genes
-     - :cite:p:`Lopez19`
-   * - :doc:`/user_guide/models/tangram`
-     - Deconvolution, single cell spatial mapping
-     - :cite:p:`Biancalani21`
-   * - :doc:`/user_guide/models/resolvi`
-     - Generative model of single-cell resolved spatial transcriptomics
-     - :cite:p:`Ergen25`
-   * - :doc:`/user_guide/models/scviva`
-     - Representation of cells and their environments in spatial transcriptomics
-     - :cite:p:`Levy25`
-```
-
 ## General purpose analysis
 
 ```{eval-rst}