Backport PR #1185 on branch 0.10.x (Backwards compat for SparseDataset usage)

anndata/_core/sparse_dataset.py

@@ -508,3 +508,30 @@ def sparse_dataset(group: ZarrGroup | H5Group) -> CSRDataset | CSCDataset:
 @_subset.register(BaseCompressedSparseDataset)
 def subset_sparsedataset(d, subset_idx):
     return d[subset_idx]
+
+
+## Backwards compat
+
+_sparsedataset_depr_msg = """\
+SparseDataset is deprecated and will be removed in late 2024. It has been replaced by the public classes CSRDataset and CSCDataset.
+
+For instance checks, use `isinstance(X, (anndata.experimental.CSRDataset, anndata.experimental.CSCDataset))` instead.
+
+For creation, use `anndata.experimental.sparse_dataset(X)` instead.
+"""
+
+
+class SparseDataset(ABC):
+    """DEPRECATED.
+
+    Use CSRDataset, CSCDataset, and sparse_dataset from anndata.experimental instead.
+    """
+
+    def __new__(cls, group):
+        warnings.warn(FutureWarning(_sparsedataset_depr_msg), stacklevel=2)
+        return sparse_dataset(group)
+
+    @classmethod
+    def __subclasshook__(cls, C):
+        warnings.warn(FutureWarning(_sparsedataset_depr_msg), stacklevel=3)
+        return issubclass(C, (CSRDataset, CSCDataset))

anndata/tests/test_deprecations.py

@@ -10,10 +10,12 @@
 import h5py
 import numpy as np
 import pytest
+import zarr
 from scipy import sparse
 
 import anndata as ad
 from anndata import AnnData
+from anndata.experimental import CSRDataset, write_elem
 from anndata.tests.helpers import assert_equal
 
 
@@ -144,3 +146,18 @@ def test_deprecated_sparse_dataset_values():
 
     with pytest.warns(FutureWarning, match="Please use .format"):
         mtx_backed.format_str
+
+
+def test_deprecated_sparse_dataset():
+    from anndata._core.sparse_dataset import SparseDataset
+
+    mem_X = sparse.random(50, 50, format="csr")
+    g = zarr.group()
+    write_elem(g, "X", mem_X)
+    with pytest.warns(FutureWarning, match="SparseDataset is deprecated"):
+        X = SparseDataset(g["X"])
+
+    assert isinstance(X, CSRDataset)
+
+    with pytest.warns(FutureWarning, match="SparseDataset is deprecated"):
+        assert isinstance(X, SparseDataset)

docs/release-notes/0.10.2.md

@@ -3,6 +3,10 @@
 ```{rubric} Bugfix
 ```
 
+* Added compatibility layer for packages relying on `anndata._core.sparse_dataset.SparseDataset`.
+  Note that this API is *deprecated* and new code should use {class}`~anndata.experimental.CSRDataset`, {class}`~anndata.experimental.CSCDataset`, and {func}`~anndata.experimental.sparse_dataset` instead.
+  {pr}`1185` {user}`ivirshup`
+
 ```{rubric} Documentation
 ```