From a07e1f0a6057f0b126a932f5ecdc6a4955035ab0 Mon Sep 17 00:00:00 2001
From: ilan-gold <ilanbassgold@gmail.com>
Date: Wed, 20 Nov 2024 15:09:16 +0100
Subject: [PATCH] (fix): python debugger dask h5 meta array

---
 src/anndata/_io/specs/lazy_methods.py |  6 ++++--
 tests/test_io_elementwise.py          | 14 ++++++++++++--
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/anndata/_io/specs/lazy_methods.py b/src/anndata/_io/specs/lazy_methods.py
index a34f627e7..0b35c34da 100644
--- a/src/anndata/_io/specs/lazy_methods.py
+++ b/src/anndata/_io/specs/lazy_methods.py
@@ -150,7 +150,7 @@ def read_h5_array(
             c if c not in {None, -1} else s for c, s in zip(chunks, shape, strict=True)
         )
         if chunks is not None
-        else (_DEFAULT_STRIDE,) * len(shape)
+        else tuple(min(_DEFAULT_STRIDE, s) for s in shape)
     )
 
     chunk_layout = tuple(
@@ -159,7 +159,9 @@ def read_h5_array(
     )
 
     make_chunk = partial(make_dask_chunk, path, elem_name)
-    return da.map_blocks(make_chunk, dtype=dtype, chunks=chunk_layout)
+    return da.map_blocks(
+        make_chunk, dtype=dtype, chunks=chunk_layout, meta=np.array([])
+    )
 
 
 @_LAZY_REGISTRY.register_read(ZarrArray, IOSpec("array", "0.2.0"))
diff --git a/tests/test_io_elementwise.py b/tests/test_io_elementwise.py
index 3ca5324b8..5647bcfeb 100644
--- a/tests/test_io_elementwise.py
+++ b/tests/test_io_elementwise.py
@@ -73,8 +73,10 @@ def sparse_format(request):
     return request.param
 
 
-def create_dense_store(store, n_dims: int = 2):
-    X = np.random.randn(*[SIZE * (i + 1) for i in range(n_dims)])
+def create_dense_store(
+    store: str, n_dims: int = 2, shape=(SIZE, SIZE * 2)
+) -> H5Group | ZarrGroup:
+    X = np.random.randn(*shape)
 
     write_elem(store, "X", X)
     return store
@@ -317,6 +319,14 @@ def test_read_lazy_h5_cluster(sparse_format, tmp_path):
         assert_equal(X_from_disk, X_dask_from_disk)
 
 
+def test_undersized_shape_to_default(store):
+    shape = (3000, 50)
+    arr_store = create_dense_store(store, shape=shape)
+    X_dask_from_disk = read_elem_as_dask(arr_store["X"])
+    assert (c < s for c, s in zip(X_dask_from_disk.chunksize, shape))
+    assert X_dask_from_disk.shape == shape
+
+
 @pytest.mark.parametrize(
     ("arr_type", "chunks", "expected_chunksize"),
     [