(chore): add tests

anndata/tests/helpers.py

@@ -12,6 +12,7 @@
 import numpy as np
 import pandas as pd
 import pytest
+import zarr
 from pandas.api.types import is_numeric_dtype
 from scipy import sparse
 
@@ -743,3 +744,22 @@ def shares_memory_sparse(x, y):
         marks=pytest.mark.gpu,
     ),
 ]
+
+
+class AccessTrackingStore(zarr.DirectoryStore):
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._access_count = {}
+
+    def __getitem__(self, key):
+        for tracked in self._access_count:
+            if tracked in key:
+                self._access_count[tracked] += 1
+        return super().__getitem__(key)
+
+    def get_access_count(self, key):
+        return self._access_count[key]
+
+    def set_key_trackers(self, keys_to_track):
+        for k in keys_to_track:
+            self._access_count[k] = 0

anndata/tests/test_backed_sparse.py

@@ -13,7 +13,7 @@
 from anndata._core.anndata import AnnData
 from anndata._core.sparse_dataset import sparse_dataset
 from anndata.experimental import read_dispatched
-from anndata.tests.helpers import assert_equal, subset_func
+from anndata.tests.helpers import AccessTrackingStore, assert_equal, subset_func
 
 if TYPE_CHECKING:
     from pathlib import Path
@@ -164,6 +164,34 @@ def test_dataset_append_disk(
     assert_equal(fromdisk, frommem)
 
 
+@pytest.mark.parametrize(
+    ["sparse_format"],
+    [
+        pytest.param(sparse.csr_matrix),
+        pytest.param(sparse.csc_matrix),
+    ],
+)
+def test_indptr_cache(
+    tmp_path: Path,
+    sparse_format: Callable[[ArrayLike], sparse.spmatrix],
+):
+    path = tmp_path / "test.zarr"  # diskfmt is either h5ad or zarr
+    a = sparse_format(sparse.random(10, 10))
+    store = AccessTrackingStore(path)
+    store.set_key_trackers("indptr")
+    f = zarr.open_group(store, "a")
+    ad._io.specs.write_elem(f, "a", a)
+    a_disk = sparse_dataset(f["a"])
+    a_disk[:1]
+    a_disk[3:5]
+    a_disk[6:7]
+    a_disk[8:9]
+    a_disk[...]
+    assert (
+        store.get_access_count("indptr") == 3
+    )  # one each for .zarray, .zattrs, and actual access
+
+
 @pytest.mark.parametrize(
     ["sparse_format", "a_shape", "b_shape"],
     [
@@ -198,6 +226,21 @@ def test_wrong_shape(
         a_disk.append(b_disk)
 
 
+def test_reset_group(tmp_path: Path):
+    path = tmp_path / "test.zarr"  # diskfmt is either h5ad or zarr
+    base = sparse.random(100, 100, format="csr")
+
+    if diskfmt == "zarr":
+        f = zarr.open_group(path, "a")
+    else:
+        f = h5py.File(path, "a")
+
+    ad._io.specs.write_elem(f, "base", base)
+    disk_mtx = sparse_dataset(f["base"])
+    with pytest.raises(TypeError):
+        disk_mtx.group = f
+
+
 def test_wrong_formats(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]):
     path = (
         tmp_path / f"test.{diskfmt.replace('ad', '')}"