Add array storage helpers (#2065)

* implement store.list_prefix and store._set_dict

* simplify string handling

* add nchunks_initialized, and necessary additions for it

* rename _iter_chunks to _iter_chunk_coords

* fix test name

* bring in correct store list_dir implementations

* bump numcodecs to dodge zstd exception

* remove store._set_dict, and add _set_many and get_many instead

* update deprecation warning template

* add a type annotation

* refactor chunk iterators. they are not properties any more, just methods, and they can take an origin kwarg

* _get_many returns tuple[str, buffer]

* stricter store types

* fix types

* lint

* remove deprecation warnings

* fix zip list_prefix

* tests for nchunks_initialized, chunks_initialized; add selection_shape kwarg to grid iteration; make chunk grid iterators consistent for array and async array

* add nchunks test

* fix docstrings

* fix docstring

* revert unnecessary changes to project config

src/zarr/abc/store.py

@@ -1,16 +1,24 @@
+from __future__ import annotations
+
 from abc import ABC, abstractmethod
 from asyncio import gather
 from collections.abc import AsyncGenerator, Iterable
-from types import TracebackType
-from typing import Any, NamedTuple, Protocol, runtime_checkable
+from typing import TYPE_CHECKING, Any, NamedTuple, Protocol, runtime_checkable
+
+if TYPE_CHECKING:
+    from collections.abc import AsyncGenerator, Iterable
+    from types import TracebackType
+    from typing import Any, TypeAlias
 
-from typing_extensions import Self
+    from typing_extensions import Self
 
-from zarr.core.buffer import Buffer, BufferPrototype
-from zarr.core.common import AccessModeLiteral, BytesLike
+    from zarr.core.buffer import Buffer, BufferPrototype
+    from zarr.core.common import AccessModeLiteral, BytesLike
 
 __all__ = ["Store", "AccessMode", "ByteGetter", "ByteSetter", "set_or_delete"]
 
+ByteRangeRequest: TypeAlias = tuple[int | None, int | None]
+
 
 class AccessMode(NamedTuple):
     str: AccessModeLiteral
@@ -100,14 +108,14 @@ async def get(
         self,
         key: str,
         prototype: BufferPrototype,
-        byte_range: tuple[int | None, int | None] | None = None,
+        byte_range: ByteRangeRequest | None = None,
     ) -> Buffer | None:
         """Retrieve the value associated with a given key.
 
         Parameters
         ----------
         key : str
-        byte_range : tuple[int, Optional[int]], optional
+        byte_range : tuple[int | None, int | None], optional
 
         Returns
         -------
@@ -119,13 +127,13 @@ async def get(
     async def get_partial_values(
         self,
         prototype: BufferPrototype,
-        key_ranges: list[tuple[str, tuple[int | None, int | None]]],
+        key_ranges: Iterable[tuple[str, ByteRangeRequest]],
     ) -> list[Buffer | None]:
         """Retrieve possibly partial values from given key_ranges.
 
         Parameters
         ----------
-        key_ranges : list[tuple[str, tuple[int, int]]]
+        key_ranges : Iterable[tuple[str, tuple[int | None, int | None]]]
             Ordered set of key, range pairs, a key may occur multiple times with different ranges
 
         Returns
@@ -195,7 +203,9 @@ def supports_partial_writes(self) -> bool:
         ...
 
     @abstractmethod
-    async def set_partial_values(self, key_start_values: list[tuple[str, int, BytesLike]]) -> None:
+    async def set_partial_values(
+        self, key_start_values: Iterable[tuple[str, int, BytesLike]]
+    ) -> None:
         """Store values at a given key, starting at byte range_start.
 
         Parameters
@@ -259,21 +269,32 @@ def close(self) -> None:
         """Close the store."""
         self._is_open = False
 
+    async def _get_many(
+        self, requests: Iterable[tuple[str, BufferPrototype, ByteRangeRequest | None]]
+    ) -> AsyncGenerator[tuple[str, Buffer | None], None]:
+        """
+        Retrieve a collection of objects from storage. In general this method does not guarantee
+        that objects will be retrieved in the order in which they were requested, so this method
+        yields tuple[str, Buffer | None] instead of just Buffer | None
+        """
+        for req in requests:
+            yield (req[0], await self.get(*req))
+
 
 @runtime_checkable
 class ByteGetter(Protocol):
     async def get(
-        self, prototype: BufferPrototype, byte_range: tuple[int, int | None] | None = None
+        self, prototype: BufferPrototype, byte_range: ByteRangeRequest | None = None
     ) -> Buffer | None: ...
 
 
 @runtime_checkable
 class ByteSetter(Protocol):
     async def get(
-        self, prototype: BufferPrototype, byte_range: tuple[int, int | None] | None = None
+        self, prototype: BufferPrototype, byte_range: ByteRangeRequest | None = None
     ) -> Buffer | None: ...
 
-    async def set(self, value: Buffer, byte_range: tuple[int, int] | None = None) -> None: ...
+    async def set(self, value: Buffer, byte_range: ByteRangeRequest | None = None) -> None: ...
 
     async def delete(self) -> None: ...
 

src/zarr/codecs/sharding.py

@@ -17,7 +17,7 @@
     Codec,
     CodecPipeline,
 )
-from zarr.abc.store import ByteGetter, ByteSetter
+from zarr.abc.store import ByteGetter, ByteRangeRequest, ByteSetter
 from zarr.codecs.bytes import BytesCodec
 from zarr.codecs.crc32c_ import Crc32cCodec
 from zarr.core.array_spec import ArraySpec
@@ -78,7 +78,7 @@ class _ShardingByteGetter(ByteGetter):
     chunk_coords: ChunkCoords
 
     async def get(
-        self, prototype: BufferPrototype, byte_range: tuple[int, int | None] | None = None
+        self, prototype: BufferPrototype, byte_range: ByteRangeRequest | None = None
     ) -> Buffer | None:
         assert byte_range is None, "byte_range is not supported within shards"
         assert (
@@ -91,7 +91,7 @@ async def get(
 class _ShardingByteSetter(_ShardingByteGetter, ByteSetter):
     shard_dict: ShardMutableMapping
 
-    async def set(self, value: Buffer, byte_range: tuple[int, int] | None = None) -> None:
+    async def set(self, value: Buffer, byte_range: ByteRangeRequest | None = None) -> None:
         assert byte_range is None, "byte_range is not supported within shards"
         self.shard_dict[self.chunk_coords] = value