From 64ad5252ae3a0484628b0a743b8701cba2dbe0a2 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Sat, 19 Oct 2024 13:44:25 -0700
Subject: [PATCH 01/14] fix(array): thread order parameter through to array
 __init__

---
 src/zarr/api/asynchronous.py | 10 +++-------
 src/zarr/core/array.py       | 12 +++++-------
 tests/test_api.py            | 16 ++++++++++++++++
 tests/test_array.py          | 17 +++++++++++++++++
 4 files changed, 41 insertions(+), 14 deletions(-)

diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py
index 2c423ff59..680433565 100644
--- a/src/zarr/api/asynchronous.py
+++ b/src/zarr/api/asynchronous.py
@@ -712,7 +712,7 @@ async def create(
     dtype: npt.DTypeLike | None = None,
     compressor: dict[str, JSON] | None = None,  # TODO: default and type change
     fill_value: Any | None = 0,  # TODO: need type
-    order: MemoryOrder | None = None,  # TODO: default change
+    order: MemoryOrder | None = None,
     store: str | StoreLike | None = None,
     synchronizer: Any | None = None,
     overwrite: bool = False,
@@ -761,6 +761,7 @@ async def create(
         Default value to use for uninitialized portions of the array.
     order : {'C', 'F'}, optional
         Memory layout to be used within each chunk.
+        Default is set in Zarr's config (`array.order`).
     store : Store or str
         Store or path to directory in file system or name of zip file.
     synchronizer : object, optional
@@ -834,12 +835,6 @@ async def create(
         else:
             chunk_shape = shape
 
-    if order is not None:
-        warnings.warn(
-            "order is deprecated, use config `array.order` instead",
-            DeprecationWarning,
-            stacklevel=2,
-        )
     if synchronizer is not None:
         warnings.warn("synchronizer is not yet implemented", RuntimeWarning, stacklevel=2)
     if chunk_store is not None:
@@ -889,6 +884,7 @@ async def create(
         codecs=codecs,
         dimension_names=dimension_names,
         attributes=attributes,
+        order=order,
         **kwargs,
     )
 
diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py
index 6e3430c41..304cef016 100644
--- a/src/zarr/core/array.py
+++ b/src/zarr/core/array.py
@@ -471,10 +471,6 @@ async def create(
                 raise ValueError(
                     "dimension_separator cannot be used for arrays with version 3. Use chunk_key_encoding instead."
                 )
-            if order is not None:
-                raise ValueError(
-                    "order cannot be used for arrays with version 3. Use a transpose codec instead."
-                )
             if filters is not None:
                 raise ValueError(
                     "filters cannot be used for arrays with version 3. Use array-to-array codecs instead."
@@ -494,6 +490,7 @@ async def create(
                 dimension_names=dimension_names,
                 attributes=attributes,
                 exists_ok=exists_ok,
+                order=order,
             )
         elif zarr_format == 2:
             if dtype is str or dtype == "str":
@@ -545,6 +542,7 @@ async def _create_v3(
         dtype: npt.DTypeLike,
         chunk_shape: ChunkCoords,
         fill_value: Any | None = None,
+        order: Literal["C", "F"] | None = None,
         chunk_key_encoding: (
             ChunkKeyEncoding
             | tuple[Literal["default"], Literal[".", "/"]]
@@ -588,7 +586,7 @@ async def _create_v3(
             attributes=attributes or {},
         )
 
-        array = cls(metadata=metadata, store_path=store_path)
+        array = cls(metadata=metadata, store_path=store_path, order=order)
         await array._save_metadata(metadata, ensure_parents=True)
         return array
 
@@ -611,7 +609,7 @@ async def _create_v2(
         if not exists_ok:
             await ensure_no_existing_node(store_path, zarr_format=2)
         if order is None:
-            order = "C"
+            order = config.get("array.order", "C")
 
         if dimension_separator is None:
             dimension_separator = "."
@@ -627,7 +625,7 @@ async def _create_v2(
             filters=filters,
             attributes=attributes,
         )
-        array = cls(metadata=metadata, store_path=store_path)
+        array = cls(metadata=metadata, store_path=store_path, order=order)
         await array._save_metadata(metadata, ensure_parents=True)
         return array
 
diff --git a/tests/test_api.py b/tests/test_api.py
index 9b7b4f8b9..ddd7051b1 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -206,6 +206,22 @@ def test_open_with_mode_w_minus(tmp_path: pathlib.Path) -> None:
         zarr.open(store=tmp_path, mode="w-")
 
 
+@pytest.mark.parametrize("order", ["C", "F", None])
+@pytest.mark.parametrize("zarr_format", [2, 3])
+def test_array_order(order: str | None, zarr_format: int) -> None:
+    arr = zarr.ones(shape=(2, 2), order=order, zarr_format=zarr_format)
+    expected = order or zarr.config.get("array.order")
+    assert arr.order == expected
+
+    vals = np.asarray(arr)
+    if expected == "C":
+        assert vals.flags.c_contiguous
+    elif expected == "F":
+        assert vals.flags.f_contiguous
+    else:
+        raise AssertionError
+
+
 # def test_lazy_loader():
 #     foo = np.arange(100)
 #     bar = np.arange(100, 0, -1)
diff --git a/tests/test_array.py b/tests/test_array.py
index 829a04d30..1f79b8879 100644
--- a/tests/test_array.py
+++ b/tests/test_array.py
@@ -417,3 +417,20 @@ def test_update_attrs(zarr_format: int) -> None:
 
     arr2 = zarr.open_array(store=store, zarr_format=zarr_format)
     assert arr2.attrs["foo"] == "bar"
+
+
+@pytest.mark.parametrize("order", ["C", "F", None])
+@pytest.mark.parametrize("zarr_format", [2, 3])
+@pytest.mark.parametrize("store", ["memory"], indirect=True)
+def test_array_create_order(order: str | None, zarr_format: int, store: MemoryStore) -> None:
+    arr = Array.create(store=store, shape=(2, 2), order=order, zarr_format=zarr_format, dtype="i4")
+    expected = order or zarr.config.get("array.order")
+    assert arr.order == expected
+
+    vals = np.asarray(arr)
+    if expected == "C":
+        assert vals.flags.c_contiguous
+    elif expected == "F":
+        assert vals.flags.f_contiguous
+    else:
+        raise AssertionError

From 8b706f2863aa427d1b3cf3ec8392c4759a0d2d4e Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Mon, 21 Oct 2024 10:08:29 -0700
Subject: [PATCH 02/14] type fixes

---
 tests/test_api.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_api.py b/tests/test_api.py
index ddd7051b1..7917c1ab5 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -208,7 +208,7 @@ def test_open_with_mode_w_minus(tmp_path: pathlib.Path) -> None:
 
 @pytest.mark.parametrize("order", ["C", "F", None])
 @pytest.mark.parametrize("zarr_format", [2, 3])
-def test_array_order(order: str | None, zarr_format: int) -> None:
+def test_array_order(order: Literal["C", "F"] | None, zarr_format: ZarrFormat) -> None:
     arr = zarr.ones(shape=(2, 2), order=order, zarr_format=zarr_format)
     expected = order or zarr.config.get("array.order")
     assert arr.order == expected

From 59d7f7910765a14cdbd0bc56e310312069e0bdda Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Mon, 21 Oct 2024 10:46:32 -0700
Subject: [PATCH 03/14] move defaults

---
 src/zarr/core/array.py | 27 ++++++++++++++-------------
 1 file changed, 14 insertions(+), 13 deletions(-)

diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py
index 304cef016..bdafa33f6 100644
--- a/src/zarr/core/array.py
+++ b/src/zarr/core/array.py
@@ -33,6 +33,7 @@
     ZARRAY_JSON,
     ZATTRS_JSON,
     ChunkCoords,
+    MemoryOrder,
     ShapeLike,
     ZarrFormat,
     concurrent_map,
@@ -203,14 +204,14 @@ class AsyncArray(Generic[T_ArrayMetadata]):
     metadata: T_ArrayMetadata
     store_path: StorePath
     codec_pipeline: CodecPipeline = field(init=False)
-    order: Literal["C", "F"]
+    order: MemoryOrder
 
     @overload
     def __init__(
         self: AsyncArray[ArrayV2Metadata],
         metadata: ArrayV2Metadata | ArrayV2MetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None: ...
 
     @overload
@@ -218,14 +219,14 @@ def __init__(
         self: AsyncArray[ArrayV3Metadata],
         metadata: ArrayV3Metadata | ArrayV3MetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None: ...
 
     def __init__(
         self,
         metadata: ArrayMetadata | ArrayMetadataDict,
         store_path: StorePath,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
     ) -> None:
         if isinstance(metadata, dict):
             zarr_format = metadata["zarr_format"]
@@ -261,7 +262,7 @@ async def create(
         attributes: dict[str, JSON] | None = None,
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -350,7 +351,7 @@ async def create(
         # v2 only
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -382,7 +383,7 @@ async def create(
         # v2 only
         chunks: ShapeLike | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -422,7 +423,6 @@ async def create(
             V2 only. V3 arrays cannot have a dimension separator.
         order : Literal["C", "F"], optional
             The order of the array (default is None).
-            V2 only. V3 arrays should not have 'order' parameter.
         filters : list[dict[str, JSON]], optional
             The filters used to compress the data (default is None).
             V2 only. V3 arrays should not have 'filters' parameter.
@@ -542,7 +542,7 @@ async def _create_v3(
         dtype: npt.DTypeLike,
         chunk_shape: ChunkCoords,
         fill_value: Any | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         chunk_key_encoding: (
             ChunkKeyEncoding
             | tuple[Literal["default"], Literal[".", "/"]]
@@ -600,7 +600,7 @@ async def _create_v2(
         chunks: ChunkCoords,
         dimension_separator: Literal[".", "/"] | None = None,
         fill_value: None | float = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         attributes: dict[str, JSON] | None = None,
@@ -608,8 +608,9 @@ async def _create_v2(
     ) -> AsyncArray[ArrayV2Metadata]:
         if not exists_ok:
             await ensure_no_existing_node(store_path, zarr_format=2)
+
         if order is None:
-            order = config.get("array.order", "C")
+            order = parse_indexing_order(config.get("array.order"))
 
         if dimension_separator is None:
             dimension_separator = "."
@@ -1177,7 +1178,7 @@ def create(
         # v2 only
         chunks: ChunkCoords | None = None,
         dimension_separator: Literal[".", "/"] | None = None,
-        order: Literal["C", "F"] | None = None,
+        order: MemoryOrder | None = None,
         filters: list[dict[str, JSON]] | None = None,
         compressor: dict[str, JSON] | None = None,
         # runtime
@@ -1368,7 +1369,7 @@ def store_path(self) -> StorePath:
         return self._async_array.store_path
 
     @property
-    def order(self) -> Literal["C", "F"]:
+    def order(self) -> MemoryOrder:
         return self._async_array.order
 
     @property

From 075b92987d07cc399b2023ea61d327572edc3d85 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Mon, 21 Oct 2024 10:49:16 -0700
Subject: [PATCH 04/14] apply MemoryOrder type to ArrayV2Metadata

---
 src/zarr/core/metadata/v2.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/zarr/core/metadata/v2.py b/src/zarr/core/metadata/v2.py
index 2e1833605..f18f2e4e8 100644
--- a/src/zarr/core/metadata/v2.py
+++ b/src/zarr/core/metadata/v2.py
@@ -25,7 +25,7 @@
 from zarr.core.array_spec import ArraySpec
 from zarr.core.chunk_grids import RegularChunkGrid
 from zarr.core.chunk_key_encodings import parse_separator
-from zarr.core.common import ZARRAY_JSON, ZATTRS_JSON, parse_shapelike
+from zarr.core.common import ZARRAY_JSON, ZATTRS_JSON, MemoryOrder, parse_shapelike
 from zarr.core.config import config, parse_indexing_order
 from zarr.core.metadata.common import parse_attributes
 
@@ -45,7 +45,7 @@ class ArrayV2Metadata(Metadata):
     chunks: tuple[int, ...]
     dtype: np.dtype[Any]
     fill_value: None | int | float | str | bytes = 0
-    order: Literal["C", "F"] = "C"
+    order: MemoryOrder = "C"
     filters: tuple[numcodecs.abc.Codec, ...] | None = None
     dimension_separator: Literal[".", "/"] = "."
     compressor: numcodecs.abc.Codec | None = None
@@ -59,7 +59,7 @@ def __init__(
         dtype: npt.DTypeLike,
         chunks: ChunkCoords,
         fill_value: Any,
-        order: Literal["C", "F"],
+        order: MemoryOrder,
         dimension_separator: Literal[".", "/"] = ".",
         compressor: numcodecs.abc.Codec | dict[str, JSON] | None = None,
         filters: Iterable[numcodecs.abc.Codec | dict[str, JSON]] | None = None,
@@ -185,7 +185,7 @@ def to_dict(self) -> dict[str, JSON]:
         return zarray_dict
 
     def get_chunk_spec(
-        self, _chunk_coords: ChunkCoords, order: Literal["C", "F"], prototype: BufferPrototype
+        self, _chunk_coords: ChunkCoords, order: MemoryOrder, prototype: BufferPrototype
     ) -> ArraySpec:
         return ArraySpec(
             shape=self.chunks,

From b072545ef06ef27c060b204e94be6aac44451d93 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Mon, 21 Oct 2024 10:51:12 -0700
Subject: [PATCH 05/14] more more

---
 src/zarr/core/array_spec.py  | 8 ++++----
 src/zarr/core/metadata/v3.py | 3 ++-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/src/zarr/core/array_spec.py b/src/zarr/core/array_spec.py
index e84a81cb0..c4d9c363f 100644
--- a/src/zarr/core/array_spec.py
+++ b/src/zarr/core/array_spec.py
@@ -1,11 +1,11 @@
 from __future__ import annotations
 
 from dataclasses import dataclass
-from typing import TYPE_CHECKING, Any, Literal
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 
-from zarr.core.common import parse_fill_value, parse_order, parse_shapelike
+from zarr.core.common import MemoryOrder, parse_fill_value, parse_order, parse_shapelike
 
 if TYPE_CHECKING:
     from zarr.core.buffer import BufferPrototype
@@ -17,7 +17,7 @@ class ArraySpec:
     shape: ChunkCoords
     dtype: np.dtype[Any]
     fill_value: Any
-    order: Literal["C", "F"]
+    order: MemoryOrder
     prototype: BufferPrototype
 
     def __init__(
@@ -25,7 +25,7 @@ def __init__(
         shape: ChunkCoords,
         dtype: np.dtype[Any],
         fill_value: Any,
-        order: Literal["C", "F"],
+        order: MemoryOrder,
         prototype: BufferPrototype,
     ) -> None:
         shape_parsed = parse_shapelike(shape)
diff --git a/src/zarr/core/metadata/v3.py b/src/zarr/core/metadata/v3.py
index e9d2f92d8..6b6f28dd9 100644
--- a/src/zarr/core/metadata/v3.py
+++ b/src/zarr/core/metadata/v3.py
@@ -31,6 +31,7 @@
     JSON,
     ZARR_JSON,
     ChunkCoords,
+    MemoryOrder,
     parse_named_configuration,
     parse_shapelike,
 )
@@ -289,7 +290,7 @@ def ndim(self) -> int:
         return len(self.shape)
 
     def get_chunk_spec(
-        self, _chunk_coords: ChunkCoords, order: Literal["C", "F"], prototype: BufferPrototype
+        self, _chunk_coords: ChunkCoords, order: MemoryOrder, prototype: BufferPrototype
     ) -> ArraySpec:
         assert isinstance(
             self.chunk_grid, RegularChunkGrid

From 87267342f0bae40dbfd8ad30d237e7c3d6e92a10 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Mon, 21 Oct 2024 10:58:17 -0700
Subject: [PATCH 06/14] more more more

---
 tests/test_api.py   | 4 ++--
 tests/test_array.py | 6 ++++--
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/tests/test_api.py b/tests/test_api.py
index 7917c1ab5..5b62e3a2f 100644
--- a/tests/test_api.py
+++ b/tests/test_api.py
@@ -21,7 +21,7 @@
     save_array,
     save_group,
 )
-from zarr.core.common import ZarrFormat
+from zarr.core.common import MemoryOrder, ZarrFormat
 from zarr.errors import MetadataValidationError
 from zarr.storage._utils import normalize_path
 from zarr.storage.memory import MemoryStore
@@ -208,7 +208,7 @@ def test_open_with_mode_w_minus(tmp_path: pathlib.Path) -> None:
 
 @pytest.mark.parametrize("order", ["C", "F", None])
 @pytest.mark.parametrize("zarr_format", [2, 3])
-def test_array_order(order: Literal["C", "F"] | None, zarr_format: ZarrFormat) -> None:
+def test_array_order(order: MemoryOrder | None, zarr_format: ZarrFormat) -> None:
     arr = zarr.ones(shape=(2, 2), order=order, zarr_format=zarr_format)
     expected = order or zarr.config.get("array.order")
     assert arr.order == expected
diff --git a/tests/test_array.py b/tests/test_array.py
index 1f79b8879..f182cb1a1 100644
--- a/tests/test_array.py
+++ b/tests/test_array.py
@@ -10,7 +10,7 @@
 from zarr.codecs import BytesCodec, VLenBytesCodec
 from zarr.core.array import chunks_initialized
 from zarr.core.buffer.cpu import NDBuffer
-from zarr.core.common import JSON, ZarrFormat
+from zarr.core.common import JSON, MemoryOrder, ZarrFormat
 from zarr.core.group import AsyncGroup
 from zarr.core.indexing import ceildiv
 from zarr.core.sync import sync
@@ -422,7 +422,9 @@ def test_update_attrs(zarr_format: int) -> None:
 @pytest.mark.parametrize("order", ["C", "F", None])
 @pytest.mark.parametrize("zarr_format", [2, 3])
 @pytest.mark.parametrize("store", ["memory"], indirect=True)
-def test_array_create_order(order: str | None, zarr_format: int, store: MemoryStore) -> None:
+def test_array_create_order(
+    order: MemoryOrder | None, zarr_format: int, store: MemoryStore
+) -> None:
     arr = Array.create(store=store, shape=(2, 2), order=order, zarr_format=zarr_format, dtype="i4")
     expected = order or zarr.config.get("array.order")
     assert arr.order == expected

From 858d4fbde29b2e4697a49864187c47c8ec19bdd6 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Tue, 22 Oct 2024 06:34:21 -0700
Subject: [PATCH 07/14] feature(store,group,array): stores learn to delete
 prefixes when overwriting nodes

- add Store.delete_dir and Store.delete_prefix
- update array and group creation methods to call delete_dir
- change list_prefix to return absolue keys
---
 src/zarr/abc/store.py            | 30 ++++++++++++++++++++++++++++++
 src/zarr/core/array.py           | 14 ++++++++++++--
 src/zarr/core/group.py           | 21 ++++++++-------------
 src/zarr/storage/common.py       | 12 ++++++++++++
 src/zarr/storage/local.py        |  4 +++-
 src/zarr/storage/logging.py      |  3 +++
 src/zarr/storage/memory.py       | 11 ++++++++---
 src/zarr/storage/remote.py       |  7 ++++---
 src/zarr/storage/zip.py          |  2 +-
 src/zarr/testing/store.py        |  5 ++---
 tests/test_array.py              |  3 +++
 tests/test_group.py              | 23 ++++++++++++++++++++++-
 tests/test_store/test_logging.py |  8 ++++++--
 tests/test_store/test_zip.py     |  2 +-
 14 files changed, 115 insertions(+), 30 deletions(-)

diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py
index a995a6bf3..3927bfb9d 100644
--- a/src/zarr/abc/store.py
+++ b/src/zarr/abc/store.py
@@ -371,6 +371,36 @@ def list_dir(self, prefix: str) -> AsyncGenerator[str, None]:
         """
         ...
 
+    async def delete_dir(self, prefix: str, recursive: bool = True) -> None:
+        """
+        Remove all keys and prefixes in the store that begin with a given prefix.
+        """
+        if not self.supports_deletes:
+            raise NotImplementedError
+        if not self.supports_listing:
+            raise NotImplementedError
+        self._check_writable()
+        if recursive:
+            if not prefix.endswith("/"):
+                prefix += "/"
+            async for key in self.list_prefix(prefix):
+                await self.delete(f"{key}")
+        else:
+            async for key in self.list_dir(prefix):
+                await self.delete(f"{prefix}/{key}")
+
+    async def delete_prefix(self, prefix: str) -> None:
+        """
+        Remove all keys in the store that begin with a given prefix.
+        """
+        if not self.supports_deletes:
+            raise NotImplementedError
+        if not self.supports_listing:
+            raise NotImplementedError
+        self._check_writable()
+        async for key in self.list_prefix(prefix):
+            await self.delete(f"{key}")
+
     def close(self) -> None:
         """Close the store."""
         self._is_open = False
diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py
index bdafa33f6..4549cc3e7 100644
--- a/src/zarr/core/array.py
+++ b/src/zarr/core/array.py
@@ -554,7 +554,12 @@ async def _create_v3(
         attributes: dict[str, JSON] | None = None,
         exists_ok: bool = False,
     ) -> AsyncArray[ArrayV3Metadata]:
-        if not exists_ok:
+        if exists_ok:
+            if store_path.store.supports_deletes:
+                await store_path.delete_dir(recursive=True)
+            else:
+                await ensure_no_existing_node(store_path, zarr_format=3)
+        else:
             await ensure_no_existing_node(store_path, zarr_format=3)
 
         shape = parse_shapelike(shape)
@@ -606,7 +611,12 @@ async def _create_v2(
         attributes: dict[str, JSON] | None = None,
         exists_ok: bool = False,
     ) -> AsyncArray[ArrayV2Metadata]:
-        if not exists_ok:
+        if exists_ok:
+            if store_path.store.supports_deletes:
+                await store_path.delete_dir(recursive=True)
+            else:
+                await ensure_no_existing_node(store_path, zarr_format=2)
+        else:
             await ensure_no_existing_node(store_path, zarr_format=2)
 
         if order is None:
diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py
index 6e54b7ec9..914f001cc 100644
--- a/src/zarr/core/group.py
+++ b/src/zarr/core/group.py
@@ -404,7 +404,13 @@ async def from_store(
         zarr_format: ZarrFormat = 3,
     ) -> AsyncGroup:
         store_path = await make_store_path(store)
-        if not exists_ok:
+
+        if exists_ok:
+            if store_path.store.supports_deletes:
+                await store_path.delete_dir(recursive=True)
+            else:
+                await ensure_no_existing_node(store_path, zarr_format=zarr_format)
+        else:
             await ensure_no_existing_node(store_path, zarr_format=zarr_format)
         attributes = attributes or {}
         group = cls(
@@ -710,19 +716,8 @@ def _getitem_consolidated(
 
     async def delitem(self, key: str) -> None:
         store_path = self.store_path / key
-        if self.metadata.zarr_format == 3:
-            await (store_path / ZARR_JSON).delete()
-
-        elif self.metadata.zarr_format == 2:
-            await asyncio.gather(
-                (store_path / ZGROUP_JSON).delete(),  # TODO: missing_ok=False
-                (store_path / ZARRAY_JSON).delete(),  # TODO: missing_ok=False
-                (store_path / ZATTRS_JSON).delete(),  # TODO: missing_ok=True
-            )
-
-        else:
-            raise ValueError(f"unexpected zarr_format: {self.metadata.zarr_format}")
 
+        await store_path.delete_dir(recursive=True)
         if self.metadata.consolidated_metadata:
             self.metadata.consolidated_metadata.metadata.pop(key, None)
             await self._save_metadata()
diff --git a/src/zarr/storage/common.py b/src/zarr/storage/common.py
index 9ed8c274d..af434ecd3 100644
--- a/src/zarr/storage/common.py
+++ b/src/zarr/storage/common.py
@@ -101,6 +101,18 @@ async def delete(self) -> None:
         """
         await self.store.delete(self.path)
 
+    async def delete_dir(self, recursive: bool = False) -> None:
+        """
+        Delete all keys with the given prefix from the store.
+        """
+        await self.store.delete_dir(self.path, recursive=recursive)
+
+    async def delete_prefix(self) -> None:
+        """
+        Delete all keys with the given prefix from the store.
+        """
+        await self.store.delete_prefix(self.path)
+
     async def set_if_not_exists(self, default: Buffer) -> None:
         """
         Store a key to ``value`` if the key is not already present.
diff --git a/src/zarr/storage/local.py b/src/zarr/storage/local.py
index 5c03009a9..0ab2cc0be 100644
--- a/src/zarr/storage/local.py
+++ b/src/zarr/storage/local.py
@@ -226,7 +226,9 @@ async def list(self) -> AsyncGenerator[str, None]:
 
     async def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
-        to_strip = os.path.join(str(self.root / prefix))
+        to_strip = str(self.root)
+        if prefix.endswith("/"):
+            prefix = prefix[:-1]
         for p in (self.root / prefix).rglob("*"):
             if p.is_file():
                 yield str(p.relative_to(to_strip))
diff --git a/src/zarr/storage/logging.py b/src/zarr/storage/logging.py
index 66fd1687e..453a793cb 100644
--- a/src/zarr/storage/logging.py
+++ b/src/zarr/storage/logging.py
@@ -230,3 +230,6 @@ def with_mode(self, mode: AccessModeLiteral) -> Self:
                 log_level=self.log_level,
                 log_handler=self.log_handler,
             )
+
+
+# TODO: wrap delete methods here
diff --git a/src/zarr/storage/memory.py b/src/zarr/storage/memory.py
index f942d57b9..fa4ede2a8 100644
--- a/src/zarr/storage/memory.py
+++ b/src/zarr/storage/memory.py
@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from logging import getLogger
 from typing import TYPE_CHECKING, Self
 
 from zarr.abc.store import ByteRangeRequest, Store
@@ -14,6 +15,9 @@
     from zarr.core.common import AccessModeLiteral
 
 
+logger = getLogger(__name__)
+
+
 class MemoryStore(Store):
     """
     In-memory store for testing purposes.
@@ -137,7 +141,7 @@ async def delete(self, key: str) -> None:
         try:
             del self._store_dict[key]
         except KeyError:
-            pass
+            logger.debug("Key %s does not exist.", key)
 
     async def set_partial_values(self, key_start_values: Iterable[tuple[str, int, bytes]]) -> None:
         # docstring inherited
@@ -150,9 +154,10 @@ async def list(self) -> AsyncGenerator[str, None]:
 
     async def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
-        for key in self._store_dict:
+        # note: we materialize all dict keys into a list here so we can mutate the dict in-place (e.g. in delete_prefix)
+        for key in list(self._store_dict):
             if key.startswith(prefix):
-                yield key.removeprefix(prefix)
+                yield key
 
     async def list_dir(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
diff --git a/src/zarr/storage/remote.py b/src/zarr/storage/remote.py
index 0a0ec7f7c..0eb72eb34 100644
--- a/src/zarr/storage/remote.py
+++ b/src/zarr/storage/remote.py
@@ -298,6 +298,7 @@ async def list_dir(self, prefix: str) -> AsyncGenerator[str, None]:
 
     async def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
-        find_str = f"{self.path}/{prefix}"
-        for onefile in await self.fs._find(find_str, detail=False, maxdepth=None, withdirs=False):
-            yield onefile.removeprefix(find_str)
+        for onefile in await self.fs._find(
+            f"{self.path}/{prefix}", detail=False, maxdepth=None, withdirs=False
+        ):
+            yield onefile.removeprefix(f"{self.path}/")
diff --git a/src/zarr/storage/zip.py b/src/zarr/storage/zip.py
index 204a381bd..a7b8e1558 100644
--- a/src/zarr/storage/zip.py
+++ b/src/zarr/storage/zip.py
@@ -241,7 +241,7 @@ async def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
         async for key in self.list():
             if key.startswith(prefix):
-                yield key.removeprefix(prefix)
+                yield key
 
     async def list_dir(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py
index b4da75b06..fd9d6e691 100644
--- a/src/zarr/testing/store.py
+++ b/src/zarr/testing/store.py
@@ -249,8 +249,7 @@ async def test_list(self, store: S) -> None:
     async def test_list_prefix(self, store: S) -> None:
         """
         Test that the `list_prefix` method works as intended. Given a prefix, it should return
-        all the keys in storage that start with this prefix. Keys should be returned with the shared
-        prefix removed.
+        all the keys in storage that start with this prefix.
         """
         prefixes = ("", "a/", "a/b/", "a/b/c/")
         data = self.buffer_cls.from_bytes(b"")
@@ -264,7 +263,7 @@ async def test_list_prefix(self, store: S) -> None:
             expected: tuple[str, ...] = ()
             for key in store_dict:
                 if key.startswith(prefix):
-                    expected += (key.removeprefix(prefix),)
+                    expected += (key,)
             expected = tuple(sorted(expected))
             assert observed == expected
 
diff --git a/tests/test_array.py b/tests/test_array.py
index f182cb1a1..dac8ce859 100644
--- a/tests/test_array.py
+++ b/tests/test_array.py
@@ -48,6 +48,9 @@ def test_array_creation_existing_node(
     new_dtype = "float32"
 
     if exists_ok:
+        if not store.supports_deletes:
+            # TODO: confirm you get the expected error here
+            pytest.skip("store does not support deletes")
         arr_new = Array.create(
             spath / "extant",
             shape=new_shape,
diff --git a/tests/test_group.py b/tests/test_group.py
index 21e4ef4e5..13f412afa 100644
--- a/tests/test_group.py
+++ b/tests/test_group.py
@@ -290,6 +290,10 @@ def test_group_open(store: Store, zarr_format: ZarrFormat, exists_ok: bool) -> N
         with pytest.raises(ContainsGroupError):
             Group.from_store(store, attributes=attrs, zarr_format=zarr_format, exists_ok=exists_ok)
     else:
+        if not store.supports_deletes:
+            pytest.skip(
+                "Store does not support deletes but `exists_ok` is True, requiring deletes to override a group"
+            )
         group_created_again = Group.from_store(
             store, attributes=new_attrs, zarr_format=zarr_format, exists_ok=exists_ok
         )
@@ -703,6 +707,8 @@ def test_group_creation_existing_node(
     new_attributes = {"new": True}
 
     if exists_ok:
+        if not store.supports_deletes:
+            pytest.skip("store does not support deletes but exists_ok is True")
         node_new = Group.from_store(
             spath / "extant",
             attributes=new_attributes,
@@ -1075,7 +1081,9 @@ async def test_require_group(store: LocalStore | MemoryStore, zarr_format: ZarrF
     assert foo_group.attrs == {"foo": 100}
 
     # test that we can get the group using require_group and overwrite=True
-    foo_group = await root.require_group("foo", overwrite=True)
+    if store.supports_deletes:
+        foo_group = await root.require_group("foo", overwrite=True)
+        assert foo_group.attrs == {}
 
     _ = await foo_group.create_array(
         "bar", shape=(10,), dtype="uint8", chunk_shape=(2,), attributes={"foo": 100}
@@ -1354,3 +1362,16 @@ def test_group_deprecated_positional_args(method: str) -> None:
     with pytest.warns(FutureWarning, match=r"Pass name=.*, data=.* as keyword args."):
         arr = getattr(root, method)("foo_like", data, **kwargs)
         assert arr.shape == data.shape
+
+
+@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
+def test_delitem_removes_children(store: Store, zarr_format: ZarrFormat) -> None:
+    # https://github.com/zarr-developers/zarr-python/issues/2191
+    g1 = zarr.group(store=store)
+    g1.create_group("0")
+    g1.create_group("0/0")
+    arr = g1.create_array("0/0/0", shape=(1,))
+    arr[:] = 1
+    del g1["0"]
+    with pytest.raises(KeyError):
+        g1["0/0"]
diff --git a/tests/test_store/test_logging.py b/tests/test_store/test_logging.py
index 0258244c5..976da6818 100644
--- a/tests/test_store/test_logging.py
+++ b/tests/test_store/test_logging.py
@@ -45,10 +45,14 @@ async def test_logging_store_counter(store: Store) -> None:
     arr[:] = 1
 
     assert wrapped.counter["set"] == 2
-    assert wrapped.counter["get"] == 0  # 1 if overwrite=False
     assert wrapped.counter["list"] == 0
     assert wrapped.counter["list_dir"] == 0
-    assert wrapped.counter["list_prefix"] == 0
+    if store.supports_deletes:
+        assert wrapped.counter["get"] == 0  # 1 if overwrite=False
+        assert wrapped.counter["list_prefix"] == 1
+    else:
+        assert wrapped.counter["get"] == 1
+        assert wrapped.counter["list_prefix"] == 0
 
 
 async def test_with_mode():
diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py
index d05422ecd..eb129a1b2 100644
--- a/tests/test_store/test_zip.py
+++ b/tests/test_store/test_zip.py
@@ -103,4 +103,4 @@ async def test_with_mode(self, store: ZipStore) -> None:
 
     @pytest.mark.parametrize("mode", ["a", "w"])
     async def test_store_open_mode(self, store_kwargs: dict[str, Any], mode: str) -> None:
-        super().test_store_open_mode(store_kwargs, mode)
+        await super().test_store_open_mode(store_kwargs, mode)

From 9c173c1220866d4ecdb221cb22daee5d8e28ec8c Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Wed, 23 Oct 2024 06:14:42 -0700
Subject: [PATCH 08/14] fixup

---
 src/zarr/abc/store.py     | 2 +-
 src/zarr/storage/local.py | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py
index 1ed098910..76a71c5a9 100644
--- a/src/zarr/abc/store.py
+++ b/src/zarr/abc/store.py
@@ -399,7 +399,7 @@ async def delete_prefix(self, prefix: str) -> None:
             raise NotImplementedError
         self._check_writable()
         async for key in self.list_prefix(prefix):
-            await self.delete(f"{key}")
+            await self.delete(key)
 
     def close(self) -> None:
         """Close the store."""
diff --git a/src/zarr/storage/local.py b/src/zarr/storage/local.py
index 0ab2cc0be..c08b351b4 100644
--- a/src/zarr/storage/local.py
+++ b/src/zarr/storage/local.py
@@ -227,8 +227,7 @@ async def list(self) -> AsyncGenerator[str, None]:
     async def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         # docstring inherited
         to_strip = str(self.root)
-        if prefix.endswith("/"):
-            prefix = prefix[:-1]
+        prefix = prefix.rstrip("/")
         for p in (self.root / prefix).rglob("*"):
             if p.is_file():
                 yield str(p.relative_to(to_strip))

From d7a698284671df7c4de62e0ea3010328557cf86e Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Wed, 23 Oct 2024 16:13:24 -0700
Subject: [PATCH 09/14] fixup

---
 src/zarr/abc/store.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py
index 76a71c5a9..03f42584f 100644
--- a/src/zarr/abc/store.py
+++ b/src/zarr/abc/store.py
@@ -384,7 +384,7 @@ async def delete_dir(self, prefix: str, recursive: bool = True) -> None:
             if not prefix.endswith("/"):
                 prefix += "/"
             async for key in self.list_prefix(prefix):
-                await self.delete(f"{key}")
+                await self.delete(key)
         else:
             async for key in self.list_dir(prefix):
                 await self.delete(f"{prefix}/{key}")

From c38c2f7cd52dfa884e4f542de6aaed73a57835c7 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Thu, 24 Oct 2024 16:29:35 -0700
Subject: [PATCH 10/14] respond to review

---
 src/zarr/abc/store.py            | 26 +++++---------------------
 src/zarr/core/array.py           |  4 ++--
 src/zarr/core/group.py           |  4 ++--
 src/zarr/storage/common.py       | 13 +++++--------
 src/zarr/storage/logging.py      |  5 +++++
 src/zarr/testing/store.py        | 13 +++++++++++++
 tests/test_store/test_logging.py |  5 +++--
 tests/test_store/test_zip.py     |  4 ----
 8 files changed, 35 insertions(+), 39 deletions(-)

diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py
index 03f42584f..c7f21df50 100644
--- a/src/zarr/abc/store.py
+++ b/src/zarr/abc/store.py
@@ -342,8 +342,8 @@ def list(self) -> AsyncGenerator[str, None]:
     @abstractmethod
     def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         """
-        Retrieve all keys in the store that begin with a given prefix. Keys are returned with the
-        common leading prefix removed.
+        Retrieve all keys in the store that begin with a given prefix. Keys are returned as
+        absolute paths (i.e. including the prefix).
 
         Parameters
         ----------
@@ -371,7 +371,7 @@ def list_dir(self, prefix: str) -> AsyncGenerator[str, None]:
         """
         ...
 
-    async def delete_dir(self, prefix: str, recursive: bool = True) -> None:
+    async def delete_dir(self, prefix: str) -> None:
         """
         Remove all keys and prefixes in the store that begin with a given prefix.
         """
@@ -380,24 +380,8 @@ async def delete_dir(self, prefix: str, recursive: bool = True) -> None:
         if not self.supports_listing:
             raise NotImplementedError
         self._check_writable()
-        if recursive:
-            if not prefix.endswith("/"):
-                prefix += "/"
-            async for key in self.list_prefix(prefix):
-                await self.delete(key)
-        else:
-            async for key in self.list_dir(prefix):
-                await self.delete(f"{prefix}/{key}")
-
-    async def delete_prefix(self, prefix: str) -> None:
-        """
-        Remove all keys in the store that begin with a given prefix.
-        """
-        if not self.supports_deletes:
-            raise NotImplementedError
-        if not self.supports_listing:
-            raise NotImplementedError
-        self._check_writable()
+        if not prefix.endswith("/"):
+            prefix += "/"
         async for key in self.list_prefix(prefix):
             await self.delete(key)
 
diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py
index 4549cc3e7..7b5733116 100644
--- a/src/zarr/core/array.py
+++ b/src/zarr/core/array.py
@@ -556,7 +556,7 @@ async def _create_v3(
     ) -> AsyncArray[ArrayV3Metadata]:
         if exists_ok:
             if store_path.store.supports_deletes:
-                await store_path.delete_dir(recursive=True)
+                await store_path.delete_dir()
             else:
                 await ensure_no_existing_node(store_path, zarr_format=3)
         else:
@@ -613,7 +613,7 @@ async def _create_v2(
     ) -> AsyncArray[ArrayV2Metadata]:
         if exists_ok:
             if store_path.store.supports_deletes:
-                await store_path.delete_dir(recursive=True)
+                await store_path.delete_dir()
             else:
                 await ensure_no_existing_node(store_path, zarr_format=2)
         else:
diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py
index 914f001cc..5e6803930 100644
--- a/src/zarr/core/group.py
+++ b/src/zarr/core/group.py
@@ -407,7 +407,7 @@ async def from_store(
 
         if exists_ok:
             if store_path.store.supports_deletes:
-                await store_path.delete_dir(recursive=True)
+                await store_path.delete_dir()
             else:
                 await ensure_no_existing_node(store_path, zarr_format=zarr_format)
         else:
@@ -717,7 +717,7 @@ def _getitem_consolidated(
     async def delitem(self, key: str) -> None:
         store_path = self.store_path / key
 
-        await store_path.delete_dir(recursive=True)
+        await store_path.delete_dir()
         if self.metadata.consolidated_metadata:
             self.metadata.consolidated_metadata.metadata.pop(key, None)
             await self._save_metadata()
diff --git a/src/zarr/storage/common.py b/src/zarr/storage/common.py
index af434ecd3..337fbc59a 100644
--- a/src/zarr/storage/common.py
+++ b/src/zarr/storage/common.py
@@ -101,17 +101,14 @@ async def delete(self) -> None:
         """
         await self.store.delete(self.path)
 
-    async def delete_dir(self, recursive: bool = False) -> None:
+    async def delete_dir(self) -> None:
         """
         Delete all keys with the given prefix from the store.
         """
-        await self.store.delete_dir(self.path, recursive=recursive)
-
-    async def delete_prefix(self) -> None:
-        """
-        Delete all keys with the given prefix from the store.
-        """
-        await self.store.delete_prefix(self.path)
+        path = self.path
+        if not path.endswith("/"):
+            path += "/"
+        await self.store.delete_dir(path)
 
     async def set_if_not_exists(self, default: Buffer) -> None:
         """
diff --git a/src/zarr/storage/logging.py b/src/zarr/storage/logging.py
index 453a793cb..755d7a58e 100644
--- a/src/zarr/storage/logging.py
+++ b/src/zarr/storage/logging.py
@@ -222,6 +222,11 @@ async def list_dir(self, prefix: str) -> AsyncGenerator[str, None]:
             async for key in self._store.list_dir(prefix=prefix):
                 yield key
 
+    async def delete_dir(self, prefix: str) -> None:
+        # docstring inherited
+        with self.log(prefix):
+            await self._store.delete_dir(prefix=prefix)
+
     def with_mode(self, mode: AccessModeLiteral) -> Self:
         # docstring inherited
         with self.log(mode):
diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py
index fd9d6e691..b39c548fb 100644
--- a/src/zarr/testing/store.py
+++ b/src/zarr/testing/store.py
@@ -213,11 +213,24 @@ async def test_exists(self, store: S) -> None:
         assert await store.exists("foo/zarr.json")
 
     async def test_delete(self, store: S) -> None:
+        if not store.supports_deletes:
+            pytest.skip("store does not support deletes")
         await store.set("foo/zarr.json", self.buffer_cls.from_bytes(b"bar"))
         assert await store.exists("foo/zarr.json")
         await store.delete("foo/zarr.json")
         assert not await store.exists("foo/zarr.json")
 
+    async def test_delete_dir(self, store: S) -> None:
+        if not store.supports_deletes:
+            pytest.skip("store does not support deletes")
+        await store.set("zarr.json", self.buffer_cls.from_bytes(b"root"))
+        await store.set("foo/zarr.json", self.buffer_cls.from_bytes(b"bar"))
+        await store.set("foo/c/0", self.buffer_cls.from_bytes(b"chunk"))
+        await store.delete_dir("foo")
+        assert await store.exists("zarr.json")
+        assert not await store.exists("foo/zarr.json")
+        assert not await store.exists("foo/c/0")
+
     async def test_empty(self, store: S) -> None:
         assert await store.empty()
         await self.set(
diff --git a/tests/test_store/test_logging.py b/tests/test_store/test_logging.py
index 976da6818..50db5c1c5 100644
--- a/tests/test_store/test_logging.py
+++ b/tests/test_store/test_logging.py
@@ -47,12 +47,13 @@ async def test_logging_store_counter(store: Store) -> None:
     assert wrapped.counter["set"] == 2
     assert wrapped.counter["list"] == 0
     assert wrapped.counter["list_dir"] == 0
+    assert wrapped.counter["list_prefix"] == 0
     if store.supports_deletes:
         assert wrapped.counter["get"] == 0  # 1 if overwrite=False
-        assert wrapped.counter["list_prefix"] == 1
+        assert wrapped.counter["delete_dir"] == 1
     else:
         assert wrapped.counter["get"] == 1
-        assert wrapped.counter["list_prefix"] == 0
+        assert wrapped.counter["delete_dir"] == 0
 
 
 async def test_with_mode():
diff --git a/tests/test_store/test_zip.py b/tests/test_store/test_zip.py
index eb129a1b2..8dee47449 100644
--- a/tests/test_store/test_zip.py
+++ b/tests/test_store/test_zip.py
@@ -14,7 +14,6 @@
 from zarr.testing.store import StoreTests
 
 if TYPE_CHECKING:
-    from collections.abc import Coroutine
     from typing import Any
 
 
@@ -65,9 +64,6 @@ def test_store_supports_partial_writes(self, store: ZipStore) -> None:
     def test_store_supports_listing(self, store: ZipStore) -> None:
         assert store.supports_listing
 
-    def test_delete(self, store: ZipStore) -> Coroutine[Any, Any, None]:
-        pass
-
     def test_api_integration(self, store: ZipStore) -> None:
         root = zarr.open_group(store=store)
 

From cafb46ad88335001e8180c39bb776c4f9310e8f5 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Thu, 24 Oct 2024 16:56:48 -0700
Subject: [PATCH 11/14] fixup

---
 src/zarr/storage/logging.py | 3 ---
 src/zarr/testing/store.py   | 2 ++
 tests/test_array.py         | 1 -
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/src/zarr/storage/logging.py b/src/zarr/storage/logging.py
index 755d7a58e..be259579e 100644
--- a/src/zarr/storage/logging.py
+++ b/src/zarr/storage/logging.py
@@ -235,6 +235,3 @@ def with_mode(self, mode: AccessModeLiteral) -> Self:
                 log_level=self.log_level,
                 log_handler=self.log_handler,
             )
-
-
-# TODO: wrap delete methods here
diff --git a/src/zarr/testing/store.py b/src/zarr/testing/store.py
index b39c548fb..3aece0f4a 100644
--- a/src/zarr/testing/store.py
+++ b/src/zarr/testing/store.py
@@ -224,10 +224,12 @@ async def test_delete_dir(self, store: S) -> None:
         if not store.supports_deletes:
             pytest.skip("store does not support deletes")
         await store.set("zarr.json", self.buffer_cls.from_bytes(b"root"))
+        await store.set("foo-bar/zarr.json", self.buffer_cls.from_bytes(b"root"))
         await store.set("foo/zarr.json", self.buffer_cls.from_bytes(b"bar"))
         await store.set("foo/c/0", self.buffer_cls.from_bytes(b"chunk"))
         await store.delete_dir("foo")
         assert await store.exists("zarr.json")
+        assert await store.exists("foo-bar/zarr.json")
         assert not await store.exists("foo/zarr.json")
         assert not await store.exists("foo/c/0")
 
diff --git a/tests/test_array.py b/tests/test_array.py
index e827b07b0..96475d43e 100644
--- a/tests/test_array.py
+++ b/tests/test_array.py
@@ -52,7 +52,6 @@ def test_array_creation_existing_node(
 
     if exists_ok:
         if not store.supports_deletes:
-            # TODO: confirm you get the expected error here
             pytest.skip("store does not support deletes")
         arr_new = Array.create(
             spath / "extant",

From a1e71f1ef723ceeb8640396f366c7888e2df8329 Mon Sep 17 00:00:00 2001
From: Joseph Hamman <joe@earthmover.io>
Date: Thu, 24 Oct 2024 17:03:23 -0700
Subject: [PATCH 12/14] fixup

---
 tests/test_group.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/test_group.py b/tests/test_group.py
index 7de5b629f..6bacca488 100644
--- a/tests/test_group.py
+++ b/tests/test_group.py
@@ -1384,7 +1384,7 @@ def test_group_deprecated_positional_args(method: str) -> None:
 @pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
 def test_delitem_removes_children(store: Store, zarr_format: ZarrFormat) -> None:
     # https://github.com/zarr-developers/zarr-python/issues/2191
-    g1 = zarr.group(store=store)
+    g1 = zarr.group(store=store, zarr_format=zarr_format)
     g1.create_group("0")
     g1.create_group("0/0")
     arr = g1.create_array("0/0/0", shape=(1,))

From 5677683736363a0fe8013e604d9ead22a49d2d17 Mon Sep 17 00:00:00 2001
From: Joe Hamman <jhamman1@gmail.com>
Date: Mon, 4 Nov 2024 20:52:17 -0800
Subject: [PATCH 13/14] Update src/zarr/abc/store.py

---
 src/zarr/abc/store.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py
index c7f21df50..2d26d7dcb 100644
--- a/src/zarr/abc/store.py
+++ b/src/zarr/abc/store.py
@@ -342,8 +342,8 @@ def list(self) -> AsyncGenerator[str, None]:
     @abstractmethod
     def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         """
-        Retrieve all keys in the store that begin with a given prefix. Keys are returned as
-        absolute paths (i.e. including the prefix).
+        Retrieve all keys in the store that begin with a given prefix. Keys are returned relative 
+        to the root of the store.
 
         Parameters
         ----------

From 7e9ec76ea9095bf854a8e74fcc0393396531bd67 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 5 Nov 2024 04:53:53 +0000
Subject: [PATCH 14/14] style: pre-commit fixes

---
 src/zarr/abc/store.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/zarr/abc/store.py b/src/zarr/abc/store.py
index 2d26d7dcb..eefe04d50 100644
--- a/src/zarr/abc/store.py
+++ b/src/zarr/abc/store.py
@@ -342,7 +342,7 @@ def list(self) -> AsyncGenerator[str, None]:
     @abstractmethod
     def list_prefix(self, prefix: str) -> AsyncGenerator[str, None]:
         """
-        Retrieve all keys in the store that begin with a given prefix. Keys are returned relative 
+        Retrieve all keys in the store that begin with a given prefix. Keys are returned relative
         to the root of the store.
 
         Parameters