Backport PR #2271: Add support for AnnData 0.10.0 (#2278)

scverse · Oct 9, 2023 · 68f8863 · 68f8863
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diff --git a/docs/release_notes/index.md b/docs/release_notes/index.md
@@ -17,6 +17,12 @@ is available in the [commit logs](https://github.com/YosefLab/scvi-tools/commits
 
 ## Version 1.0
 
+### 1.0.4 (2023-10-xx)
+
+### Added
+
+-   Add support for AnnData 0.10.0 {pr}`2271`.
+
 ### 1.0.3 (2023-08-13)
 
 ### Changed

diff --git a/scvi/data/_anntorchdataset.py b/scvi/data/_anntorchdataset.py
@@ -4,7 +4,15 @@
 import h5py
 import numpy as np
 import pandas as pd
-from anndata._core.sparse_dataset import SparseDataset
+
+try:
+    from anndata._core.sparse_dataset import SparseDataset
+except ImportError:
+    # anndata >= 0.10.0
+    from anndata._core.sparse_dataset import (
+        BaseCompressedSparseDataset as SparseDataset,
+    )
+
 from scipy.sparse import issparse
 from torch.utils.data import Dataset
 

diff --git a/scvi/data/_built_in_data/_synthetic.py b/scvi/data/_built_in_data/_synthetic.py
@@ -54,16 +54,16 @@ def _generate_synthetic(
         labels = np.random.randint(0, n_labels, size=(n_obs,))
         labels = np.array([f"label_{i}" for i in labels])
 
-    adata = AnnData(rna, dtype=np.float32)
+    adata = AnnData(rna)
     if return_mudata:
         mod_dict = {rna_key: adata}
 
         if n_proteins > 0:
-            protein_adata = AnnData(protein, dtype=np.float32)
+            protein_adata = AnnData(protein)
             protein_adata.var_names = protein_names
             mod_dict[protein_expression_key] = protein_adata
         if n_regions > 0:
-            mod_dict[accessibility_key] = AnnData(accessibility, dtype=np.float32)
+            mod_dict[accessibility_key] = AnnData(accessibility)
 
         adata = MuData(mod_dict)
     else:

diff --git a/scvi/data/_utils.py b/scvi/data/_utils.py
@@ -10,7 +10,14 @@
 import pandas as pd
 import scipy.sparse as sp_sparse
 from anndata import AnnData
-from anndata._core.sparse_dataset import SparseDataset
+
+try:
+    from anndata._core.sparse_dataset import SparseDataset
+except ImportError:
+    # anndata >= 0.10.0
+    from anndata._core.sparse_dataset import (
+        BaseCompressedSparseDataset as SparseDataset,
+    )
 
 # TODO use the experimental api once we lower bound to anndata 0.8
 try:

diff --git a/scvi/model/base/_archesmixin.py b/scvi/model/base/_archesmixin.py
@@ -245,7 +245,7 @@ def prepare_query_anndata(
 
         if inplace:
             if adata_out is not adata:
-                adata._init_as_actual(adata_out, dtype=adata._X.dtype)
+                adata._init_as_actual(adata_out)
         else:
             return adata_out