Fixes for zarr-python 3.0.0

Author: tomwhite

sgkit/tests/io/test_dataset.py

@@ -58,7 +58,7 @@ def test_save_unequal_chunks_error():
     # Normal zarr errors shouldn't be caught
     with pytest.raises(
         (FileExistsError, ValueError),
-        match="(path '' contains an array|Store already exists)",
+        match="(path '' contains an array|is not empty)",
     ):
         save_dataset(ds, {".zarray": ""})
 

sgkit/tests/test_testing.py

@@ -7,6 +7,9 @@
 from sgkit.testing import simulate_genotype_call_dataset
 
 
+@pytest.mark.filterwarnings(
+    "ignore::UserWarning"
+)  # codec `vlen-utf8` not in Zarr v3 spec`
 def test_simulate_genotype_call_dataset__zarr(tmp_path):
     path = str(tmp_path / "ds.zarr")
     ds = simulate_genotype_call_dataset(n_variant=10, n_sample=10)