feat: TOTALVI & MULTIVI Mudata Minification

CHANGELOG.md

@@ -4,7 +4,7 @@ Starting from version 0.20.1, this format is based on [Keep a Changelog], and th
 to [Semantic Versioning]. Full commit history is available in the
 [commit logs](https://github.com/scverse/scvi-tools/commits/).
 
-## Version 1.2
+## Version 1.3
 
 ### 1.3.0 (2024-XX-XX)
 
@@ -19,10 +19,15 @@ to [Semantic Versioning]. Full commit history is available in the
 - Add {class}`scvi.external.Decipher` for dimensionality reduction and interpretable
     representation learning in single-cell RNA sequencing data {pr}`3015`.
 
+## Version 1.2
+
 ### 1.2.1 (2024-XX-XX)
 
 #### Added
 
+- MuData support for {class}`~scvi.model.MULTIVI` via the method
+- Add MuData Minification option to {class}`~scvi.model.MULTIVI` and {class}`~scvi.model.TOTALVI` {pr}`3039`.
+
 #### Fixed
 
 - Breaking Change: Fix `get_outlier_cell_sample_pairs` function in {class}`scvi.external.MRVI`

pyproject.toml

@@ -93,7 +93,7 @@ regseq = ["biopython>=1.81", "genomepy"]
 # read loom
 loompy = ["loompy>=3.0.6"]
 # scvi.criticism and read 10x
-scanpy = ["scanpy>=1.6"]
+scanpy = ["scanpy>=1.6","scikit-misc"]
 
 optional = [
     "scvi-tools[autotune,aws,hub,loompy,pymde,regseq,scanpy]"
@@ -107,7 +107,6 @@ tutorials = [
     "pooch",
     "pynndescent",
     "igraph",
-    "scikit-misc",
     "scrublet",
     "scib-metrics",
     "scvi-tools[optional]",

src/scvi/data/_utils.py

@@ -311,10 +311,12 @@ def _get_adata_minify_type(adata: AnnData) -> MinifiedDataType | None:
     return adata.uns.get(_constants._ADATA_MINIFY_TYPE_UNS_KEY, None)
 
 
-def _is_minified(adata: AnnData | str) -> bool:
+def _is_minified(adata: AnnOrMuData | str) -> bool:
     uns_key = _constants._ADATA_MINIFY_TYPE_UNS_KEY
     if isinstance(adata, AnnData):
         return adata.uns.get(uns_key, None) is not None
+    elif isinstance(adata, MuData):
+        return adata.uns.get(uns_key, None) is not None
     elif isinstance(adata, str):
         with h5py.File(adata) as fp:
             return uns_key in read_elem(fp["uns"]).keys()