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actually make CSRDataset and CSCDataset usable #1891

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flying-sheep wants to merge 3 commits into from
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actually make CSRDataset and CSCDataset usable #1891

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931e3a8
actually make CSRDataset and CSCDataset usable
flying-sheep Mar 6, 2025
748d1c7
test
flying-sheep Mar 6, 2025
50122b0
fix tests
flying-sheep Mar 6, 2025
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4 changes: 4 additions & 0 deletions src/anndata/_core/sparse_dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -639,6 +639,10 @@ class _CSCDataset(BaseCompressedSparseDataset, abc.CSCDataset):
"""Internal concrete version of :class:`anndata.abc.CSRDataset`."""


abc.CSRDataset.register(_CSRDataset)
abc.CSCDataset.register(_CSCDataset)
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@ilan-gold ilan-gold Mar 6, 2025

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This is a deep cut for me - don't these both already inherit from the ABC? I'd like to understand this one. Does it have to do with the multiple inheritance?

from anndata._core.sparse_dataset import _CSRDataset
from anndata.abc import CSRDataset
assert issubclass(_CSRDataset, CSRDataset)

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@flying-sheep flying-sheep Mar 6, 2025

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huh, you’re right.

I must have run into something else then, no idea why I thought that check wasn’t already right.



def sparse_dataset(group: GroupStorageType) -> abc.CSRDataset | abc.CSCDataset:
"""Generates a backed mode-compatible sparse dataset class.

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2 changes: 1 addition & 1 deletion src/anndata/compat/__init__.py
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Expand Up @@ -12,7 +12,7 @@
import h5py
import numpy as np
import pandas as pd
import scipy
import scipy.sparse
from packaging.version import Version

if TYPE_CHECKING:
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5 changes: 3 additions & 2 deletions tests/test_backed_sparse.py
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Expand Up @@ -14,6 +14,7 @@
from anndata._core.anndata import AnnData
from anndata._core.sparse_dataset import sparse_dataset
from anndata._io.specs.registry import read_elem_as_dask
from anndata.abc import CSCDataset, CSRDataset
from anndata.compat import CSArray, CSMatrix, DaskArray
from anndata.experimental import read_dispatched
from anndata.tests.helpers import AccessTrackingStore, assert_equal, subset_func
Expand All @@ -27,7 +28,6 @@
from numpy.typing import ArrayLike, NDArray
from pytest_mock import MockerFixture

from anndata.abc import CSCDataset, CSRDataset
from anndata.compat import ZarrGroup

Idx = slice | int | NDArray[np.integer] | NDArray[np.bool_]
Expand Down Expand Up @@ -319,7 +319,7 @@ def test_append_array_cache_bust(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"
)
def test_read_array(
tmp_path: Path,
sparse_format: Callable[[ArrayLike], CSMatrix],
sparse_format: type[CSMatrix],
diskfmt: Literal["h5ad", "zarr"],
subset_func,
subset_func2,
Expand All @@ -334,6 +334,7 @@ def test_read_array(
f = h5py.File(path, "a")
ad.io.write_elem(f, "mtx", a)
diskmtx = sparse_dataset(f["mtx"])
assert isinstance(diskmtx, CSCDataset if a.format == "csc" else CSRDataset)
ad.settings.use_sparse_array_on_read = True
assert issubclass(type(diskmtx[obs_idx, var_idx]), CSArray)
ad.settings.use_sparse_array_on_read = False
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