Backport PR #1421 on branch 0.10.x (Handle numcodecs bug for encoding…

… read-only string array) (#1422)

Co-authored-by: Isaac Virshup <[email protected]>

anndata/_io/specs/methods.py

@@ -427,6 +427,11 @@ def write_vlen_string_array_zarr(
 ):
     import numcodecs
 
+    # Workaround for https://github.com/zarr-developers/numcodecs/issues/514
+    # TODO: Warn to upgrade numcodecs if fixed
+    if not elem.flags.writeable:
+        elem = elem.copy()
+
     f.create_dataset(
         k,
         shape=elem.shape,

anndata/tests/test_io_elementwise.py

@@ -11,6 +11,7 @@
 import pandas as pd
 import pytest
 import zarr
+from packaging.version import Version
 from scipy import sparse
 
 import anndata as ad
@@ -333,3 +334,15 @@ def test_dataframe_column_uniqueness(store):
     result = read_elem(store["index_shared_okay"])
 
     assert_equal(result, index_shared_okay)
+
+
+@pytest.mark.parametrize("copy_on_write", [True, False])
+def test_io_pd_cow(store, copy_on_write):
+    if Version(pd.__version__) < Version("2"):
+        pytest.xfail("copy_on_write option is not available in pandas < 2")
+    # https://github.com/zarr-developers/numcodecs/issues/514
+    with pd.option_context("mode.copy_on_write", copy_on_write):
+        orig = gen_adata((3, 2))
+        write_elem(store, "adata", orig)
+        from_store = read_elem(store["adata"])
+        assert_equal(orig, from_store)

docs/release-notes/0.10.7.md

@@ -1,8 +1,10 @@
-### 0.10.6 {small}`the future`
+### 0.10.7 {small}`the future`
 
 ```{rubric} Bugfix
 ```
 
+* Handle upstream `numcodecs` bug where read-only string arrays cannot be encoded {user}`ivirshup` {pr}`1421`
+
 ```{rubric} Documentation
 ```