Zarr Python v3 updates

Remove workaround for zarr-developers/zarr-python#1978

Author: tomwhite

cubed/storage/backends/zarr_python_v3.py

@@ -3,7 +3,6 @@
 import zarr
 
 from cubed.types import T_DType, T_RegularChunks, T_Shape, T_Store
-from cubed.utils import join_path
 
 
 class ZarrV3ArrayGroup(dict):
@@ -40,41 +39,29 @@ def open_zarr_v3_array(
     if isinstance(chunks, int):
         chunks = (chunks,)
 
-    if mode in ("r", "r+"):
-        # TODO: remove when https://github.com/zarr-developers/zarr-python/issues/1978 is fixed
-        if mode == "r+":
-            mode = "w"
-        if dtype is None or not hasattr(dtype, "fields") or dtype.fields is None:
-            return zarr.open(store=store, mode=mode, path=path)
+    if dtype is None or not hasattr(dtype, "fields") or dtype.fields is None:
+        return zarr.open(
+            store=store,
+            mode=mode,
+            shape=shape,
+            dtype=dtype,
+            chunks=chunks,
+            path=path,
+        )
+
+    group = zarr.open_group(store=store, mode=mode, path=path)
+
+    # create/open all the arrays in the group
+    ret = ZarrV3ArrayGroup(shape=shape, dtype=dtype, chunks=chunks)
+    for field in dtype.fields:
+        field_dtype, _ = dtype.fields[field]
+        if mode in ("r", "r+"):
+            ret[field] = group[field]
         else:
-            ret = ZarrV3ArrayGroup(shape=shape, dtype=dtype, chunks=chunks)
-            for field in dtype.fields:
-                field_dtype, _ = dtype.fields[field]
-                field_path = field if path is None else join_path(path, field)
-                ret[field] = zarr.open(store=store, mode=mode, path=field_path)
-            return ret
-    else:
-        overwrite = True if mode == "a" else False
-        if dtype is None or not hasattr(dtype, "fields") or dtype.fields is None:
-            return zarr.create(
+            ret[field] = group.create_array(
+                field,
                 shape=shape,
-                dtype=dtype,
+                dtype=field_dtype,
                 chunk_shape=chunks,
-                store=store,
-                overwrite=overwrite,
-                path=path,
             )
-        else:
-            ret = ZarrV3ArrayGroup(shape=shape, dtype=dtype, chunks=chunks)
-            for field in dtype.fields:
-                field_dtype, _ = dtype.fields[field]
-                field_path = field if path is None else join_path(path, field)
-                ret[field] = zarr.create(
-                    shape=shape,
-                    dtype=field_dtype,
-                    chunk_shape=chunks,
-                    store=store,
-                    overwrite=overwrite,
-                    path=field_path,
-                )
-            return ret
+    return ret

cubed/tests/storage/test_zarr.py

@@ -8,7 +8,7 @@ def test_lazy_zarr_array(tmp_path):
     arr = lazy_zarr_array(zarr_path, shape=(3, 3), dtype=int, chunks=(2, 2))
 
     assert not zarr_path.exists()
-    with pytest.raises((TypeError, ValueError)):
+    with pytest.raises((FileNotFoundError, TypeError, ValueError)):
         arr.open()
 
     arr.create()