From 2bac6cf7435731c527fdb82f06a50c443149b322 Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Tue, 29 Jul 2025 11:55:23 +0200
Subject: [PATCH 1/3] fix: allow categorical index in `read_lazy`

---
 src/anndata/_io/specs/lazy_methods.py | 10 +++++++++-
 tests/lazy/test_read.py               | 11 +++++++++++
 2 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/src/anndata/_io/specs/lazy_methods.py b/src/anndata/_io/specs/lazy_methods.py
index b6ad2e591..d10116252 100644
--- a/src/anndata/_io/specs/lazy_methods.py
+++ b/src/anndata/_io/specs/lazy_methods.py
@@ -304,7 +304,15 @@ def read_dataframe(
     if not use_range_index:
         dim_name = elem.attrs["_index"]
         # no sense in reading this in multiple times
-        index = elem_dict[dim_name].compute()
+        if isinstance(elem_dict[dim_name], DaskArray):
+            index = elem_dict[dim_name].compute()
+        else:
+            import xarray
+
+            index = elem_dict[dim_name][
+                xarray.core.indexing.BasicIndexer((slice(None),))
+            ].array
+        index = pd.Index(index)
     else:
         dim_name = DUMMY_RANGE_INDEX_KEY
         index = pd.RangeIndex(len(elem_dict[elem.attrs["_index"]])).astype("str")
diff --git a/tests/lazy/test_read.py b/tests/lazy/test_read.py
index 9624668d6..c4aa4f113 100644
--- a/tests/lazy/test_read.py
+++ b/tests/lazy/test_read.py
@@ -211,3 +211,14 @@ def test_chunks_df(
     for k in ds:
         if isinstance(arr := ds[k].data, DaskArray):
             assert arr.chunksize == expected_chunks
+
+
+@pytest.mark.zarr_io
+def test_categorical_idx(tmp_path: Path):
+    adata = AnnData(shape=[10, 20])
+    adata.obs.index = adata.obs.index.astype("category")
+    orig_pth = tmp_path / "categorical_id.zarr"
+    adata.write_zarr(orig_pth)
+    remote = read_lazy(orig_pth)
+    remote_to_memory = remote.to_memory()
+    assert_equal(adata, remote_to_memory)

From 4a1c49e68b7025d65fabbb8b365409aa5648aaef Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Tue, 29 Jul 2025 12:16:45 +0200
Subject: [PATCH 2/3] chore: add warning

---
 src/anndata/_io/specs/lazy_methods.py | 3 +++
 tests/lazy/test_read.py               | 3 ++-
 2 files changed, 5 insertions(+), 1 deletion(-)

diff --git a/src/anndata/_io/specs/lazy_methods.py b/src/anndata/_io/specs/lazy_methods.py
index d10116252..bc51ee004 100644
--- a/src/anndata/_io/specs/lazy_methods.py
+++ b/src/anndata/_io/specs/lazy_methods.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+import warnings
 from contextlib import contextmanager
 from functools import partial, singledispatch
 from pathlib import Path
@@ -312,6 +313,8 @@ def read_dataframe(
             index = elem_dict[dim_name][
                 xarray.core.indexing.BasicIndexer((slice(None),))
             ].array
+            msg = f"Found non-string indices {index} in on-disk {elem} store"
+            warnings.warn(msg, stacklevel=2)
         index = pd.Index(index)
     else:
         dim_name = DUMMY_RANGE_INDEX_KEY
diff --git a/tests/lazy/test_read.py b/tests/lazy/test_read.py
index c4aa4f113..81d8c9780 100644
--- a/tests/lazy/test_read.py
+++ b/tests/lazy/test_read.py
@@ -219,6 +219,7 @@ def test_categorical_idx(tmp_path: Path):
     adata.obs.index = adata.obs.index.astype("category")
     orig_pth = tmp_path / "categorical_id.zarr"
     adata.write_zarr(orig_pth)
-    remote = read_lazy(orig_pth)
+    with pytest.warns(UserWarning, match=r"non-string indices"):
+        remote = read_lazy(orig_pth)
     remote_to_memory = remote.to_memory()
     assert_equal(adata, remote_to_memory)

From 2d77e899430d5409c4ce555607a9506634f99e54 Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Tue, 29 Jul 2025 12:18:40 +0200
Subject: [PATCH 3/3] chore: relnote

---
 docs/release-notes/2062.bugfix.md | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 docs/release-notes/2062.bugfix.md

diff --git a/docs/release-notes/2062.bugfix.md b/docs/release-notes/2062.bugfix.md
new file mode 100644
index 000000000..d72a295b5
--- /dev/null
+++ b/docs/release-notes/2062.bugfix.md
@@ -0,0 +1 @@
+Allow reading of non-string index in {func}`anndata.experimental.read_lazy` and {func}`anndata.experimental.read_elem_lazy` for {class}`anndata.experimental.backed.Dataset2D` {user}`ilan-gold`