Merge remote-tracking branch 'upstream/v3' into user/tom/feature/cons…

…olidated-metadata

.pre-commit-config.yaml

@@ -7,7 +7,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.7
+    rev: v0.6.8
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]

pyproject.toml

@@ -78,9 +78,9 @@ gpu = [
     "cupy-cuda12x",
 ]
 docs = [
-    'sphinx==7.4.7',
+    'sphinx==8.0.2',
     'sphinx-autobuild>=2021.3.14',
-    'sphinx-autoapi==3.3.1',
+    'sphinx-autoapi==3.3.2',
     'sphinx_design',
     'sphinx-issues',
     'sphinx-copybutton',

src/zarr/api/asynchronous.py

@@ -8,6 +8,7 @@
 import numpy as np
 import numpy.typing as npt
 
+from zarr.abc.store import Store
 from zarr.core.array import Array, AsyncArray, get_array_metadata
 from zarr.core.buffer import NDArrayLike
 from zarr.core.chunk_key_encodings import ChunkKeyEncoding
@@ -21,8 +22,9 @@
 from zarr.core.config import config
 from zarr.core.group import AsyncGroup, ConsolidatedMetadata, GroupMetadata
 from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata
-from zarr.store import (
+from zarr.storage import (
     StoreLike,
+    StorePath,
     make_store_path,
 )
 
@@ -286,6 +288,7 @@ async def open(
         Return type depends on what exists in the given store.
     """
     zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
+
     store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
 
     if path is not None:
@@ -304,9 +307,9 @@ async def open(
         return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
 
     try:
-        return await open_array(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
+        return await open_array(store=store_path, zarr_format=zarr_format, **kwargs)
     except KeyError:
-        return await open_group(store=store_path, zarr_format=zarr_format, mode=mode, **kwargs)
+        return await open_group(store=store_path, zarr_format=zarr_format, **kwargs)
 
 
 async def open_consolidated(*args: Any, use_consolidated: bool = True, **kwargs: Any) -> AsyncGroup:
@@ -383,7 +386,8 @@ async def save_array(
         or _default_zarr_version()
     )
 
-    store_path = await make_store_path(store, mode="w", storage_options=storage_options)
+    mode = kwargs.pop("mode", None)
+    store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
     if path is not None:
         store_path = store_path / path
     new = await AsyncArray.create(
@@ -560,7 +564,9 @@ async def group(
 
     zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
 
-    store_path = await make_store_path(store, storage_options=storage_options)
+    mode = None if isinstance(store, Store) else cast(AccessModeLiteral, "a")
+
+    store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
     if path is not None:
         store_path = store_path / path
 
@@ -854,7 +860,11 @@ async def create(
     if meta_array is not None:
         warnings.warn("meta_array is not yet implemented", RuntimeWarning, stacklevel=2)
 
-    mode = kwargs.pop("mode", cast(AccessModeLiteral, "r" if read_only else "w"))
+    mode = kwargs.pop("mode", None)
+    if mode is None:
+        if not isinstance(store, Store | StorePath):
+            mode = "a"
+
     store_path = await make_store_path(store, mode=mode, storage_options=storage_options)
     if path is not None:
         store_path = store_path / path
@@ -1030,7 +1040,8 @@ async def open_array(
         The opened array.
     """
 
-    store_path = await make_store_path(store, storage_options=storage_options)
+    mode = kwargs.pop("mode", None)
+    store_path = await make_store_path(store, mode=mode)
     if path is not None:
         store_path = store_path / path
 

src/zarr/api/synchronous.py

@@ -11,7 +11,7 @@
 if TYPE_CHECKING:
     from zarr.core.buffer import NDArrayLike
     from zarr.core.common import JSON, AccessModeLiteral, ChunkCoords, ZarrFormat
-    from zarr.store import StoreLike
+    from zarr.storage import StoreLike
 
 __all__ = [
     "array",

src/zarr/core/array.py

@@ -3,13 +3,14 @@
 import json
 from asyncio import gather
 from dataclasses import dataclass, field, replace
+from logging import getLogger
 from typing import TYPE_CHECKING, Any, Literal, cast
 
 import numpy as np
 import numpy.typing as npt
 
 from zarr._compat import _deprecate_positional_args
-from zarr.abc.store import set_or_delete
+from zarr.abc.store import Store, set_or_delete
 from zarr.codecs import BytesCodec
 from zarr.codecs._v2 import V2Compressor, V2Filters
 from zarr.core.attributes import Attributes
@@ -19,7 +20,7 @@
     NDBuffer,
     default_buffer_prototype,
 )
-from zarr.core.chunk_grids import RegularChunkGrid, _guess_chunks
+from zarr.core.chunk_grids import RegularChunkGrid, normalize_chunks
 from zarr.core.chunk_key_encodings import (
     ChunkKeyEncoding,
     DefaultChunkKeyEncoding,
@@ -67,10 +68,8 @@
 from zarr.core.metadata.v3 import ArrayV3Metadata
 from zarr.core.sync import collect_aiterator, sync
 from zarr.registry import get_pipeline_class
-from zarr.store import StoreLike, StorePath, make_store_path
-from zarr.store.common import (
-    ensure_no_existing_node,
-)
+from zarr.storage import StoreLike, make_store_path
+from zarr.storage.common import StorePath, ensure_no_existing_node
 
 if TYPE_CHECKING:
     from collections.abc import Iterable, Iterator, Sequence
@@ -82,6 +81,8 @@
 # Array and AsyncArray are defined in the base ``zarr`` namespace
 __all__ = ["create_codec_pipeline", "parse_array_metadata"]
 
+logger = getLogger(__name__)
+
 
 def parse_array_metadata(data: Any) -> ArrayV2Metadata | ArrayV3Metadata:
     if isinstance(data, ArrayV2Metadata | ArrayV3Metadata):
@@ -228,15 +229,14 @@ async def create(
 
         shape = parse_shapelike(shape)
 
-        if chunk_shape is None:
-            if chunks is None:
-                chunk_shape = chunks = _guess_chunks(shape=shape, typesize=np.dtype(dtype).itemsize)
-            else:
-                chunks = parse_shapelike(chunks)
+        if chunks is not None and chunk_shape is not None:
+            raise ValueError("Only one of chunk_shape or chunks can be provided.")
 
-            chunk_shape = chunks
-        elif chunks is not None:
-            raise ValueError("Only one of chunk_shape or chunks must be provided.")
+        dtype = np.dtype(dtype)
+        if chunks:
+            _chunks = normalize_chunks(chunks, shape, dtype.itemsize)
+        else:
+            _chunks = normalize_chunks(chunk_shape, shape, dtype.itemsize)
 
         if zarr_format == 3:
             if dimension_separator is not None:
@@ -259,7 +259,7 @@ async def create(
                 store_path,
                 shape=shape,
                 dtype=dtype,
-                chunk_shape=chunk_shape,
+                chunk_shape=_chunks,
                 fill_value=fill_value,
                 chunk_key_encoding=chunk_key_encoding,
                 codecs=codecs,
@@ -282,7 +282,7 @@ async def create(
                 store_path,
                 shape=shape,
                 dtype=dtype,
-                chunks=chunk_shape,
+                chunks=_chunks,
                 dimension_separator=dimension_separator,
                 fill_value=fill_value,
                 order=order,
@@ -410,6 +410,10 @@ async def open(
         metadata_dict = await get_array_metadata(store_path, zarr_format=zarr_format)
         return cls(store_path=store_path, metadata=metadata_dict)
 
+    @property
+    def store(self) -> Store:
+        return self.store_path.store
+
     @property
     def ndim(self) -> int:
         return len(self.metadata.shape)
@@ -837,6 +841,10 @@ def open(
         async_array = sync(AsyncArray.open(store))
         return cls(async_array)
 
+    @property
+    def store(self) -> Store:
+        return self._async_array.store
+
     @property
     def ndim(self) -> int:
         return self._async_array.ndim
@@ -2386,15 +2394,26 @@ def chunks_initialized(array: Array | AsyncArray) -> tuple[str, ...]:
 def _build_parents(node: AsyncArray | AsyncGroup) -> list[AsyncGroup]:
     from zarr.core.group import AsyncGroup, GroupMetadata
 
-    required_parts = node.store_path.path.split("/")[:-1]
-    parents = []
+    store = node.store_path.store
+    path = node.store_path.path
+    if not path:
+        return []
+
+    required_parts = path.split("/")[:-1]
+    parents = [
+        # the root group
+        AsyncGroup(
+            metadata=GroupMetadata(zarr_format=node.metadata.zarr_format),
+            store_path=StorePath(store=store, path=""),
+        )
+    ]
 
     for i, part in enumerate(required_parts):
-        path = "/".join(required_parts[:i] + [part])
+        p = "/".join(required_parts[:i] + [part])
         parents.append(
             AsyncGroup(
                 metadata=GroupMetadata(zarr_format=node.metadata.zarr_format),
-                store_path=StorePath(store=node.store_path.store, path=path),
+                store_path=StorePath(store=store, path=p),
             )
         )
 

src/zarr/core/chunk_grids.py

@@ -2,11 +2,12 @@
 
 import itertools
 import math
+import numbers
 import operator
 from abc import abstractmethod
 from dataclasses import dataclass
 from functools import reduce
-from typing import TYPE_CHECKING
+from typing import TYPE_CHECKING, Any
 
 import numpy as np
 
@@ -97,6 +98,49 @@ def _guess_chunks(
     return tuple(int(x) for x in chunks)
 
 
+def normalize_chunks(chunks: Any, shape: tuple[int, ...], typesize: int) -> tuple[int, ...]:
+    """Convenience function to normalize the `chunks` argument for an array
+    with the given `shape`."""
+
+    # N.B., expect shape already normalized
+
+    # handle auto-chunking
+    if chunks is None or chunks is True:
+        return _guess_chunks(shape, typesize)
+
+    # handle no chunking
+    if chunks is False:
+        return shape
+
+    # handle 1D convenience form
+    if isinstance(chunks, numbers.Integral):
+        chunks = tuple(int(chunks) for _ in shape)
+
+    # handle dask-style chunks (iterable of iterables)
+    if all(isinstance(c, (tuple | list)) for c in chunks):
+        # take first chunk size for each dimension
+        chunks = tuple(
+            c[0] for c in chunks
+        )  # TODO: check/error/warn for irregular chunks (e.g. if c[0] != c[1:-1])
+
+    # handle bad dimensionality
+    if len(chunks) > len(shape):
+        raise ValueError("too many dimensions in chunks")
+
+    # handle underspecified chunks
+    if len(chunks) < len(shape):
+        # assume chunks across remaining dimensions
+        chunks += shape[len(chunks) :]
+
+    # handle None or -1 in chunks
+    if -1 in chunks or None in chunks:
+        chunks = tuple(
+            s if c == -1 or c is None else int(c) for s, c in zip(shape, chunks, strict=False)
+        )
+
+    return tuple(int(c) for c in chunks)
+
+
 @dataclass(frozen=True)
 class ChunkGrid(Metadata):
     @classmethod

src/zarr/core/group.py

@@ -36,8 +36,8 @@
 from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata
 from zarr.core.metadata.common import ArrayMetadata
 from zarr.core.sync import SyncMixin, sync
-from zarr.store import StoreLike, StorePath, make_store_path
-from zarr.store.common import ensure_no_existing_node
+from zarr.storage import StoreLike, make_store_path
+from zarr.storage.common import StorePath, ensure_no_existing_node
 
 if TYPE_CHECKING:
     from collections.abc import AsyncGenerator, Generator, Iterable, Iterator
@@ -501,7 +501,9 @@ async def open(
                 # alternatively, we could warn and favor v3
                 raise ValueError("Both zarr.json and .zgroup objects exist")
             if zarr_json_bytes is None and zgroup_bytes is None:
-                raise FileNotFoundError(store_path)
+                raise FileNotFoundError(
+                    f"could not find zarr.json or .zgroup objects in {store_path}"
+                )
             # set zarr_format based on which keys were found
             if zarr_json_bytes is not None:
                 zarr_format = 3
@@ -1169,6 +1171,10 @@ def _members_consolidated(
                 ):
                     yield from obj._members_consolidated(max_depth, current_depth + 1, prefix=key)
 
+    async def keys(self) -> AsyncGenerator[str, None]:
+        async for key, _ in self.members():
+            yield key
+
     async def contains(self, member: str) -> bool:
         # TODO: this can be made more efficient.
         try:
@@ -1294,15 +1300,18 @@ def __delitem__(self, key: str) -> None:
         self._sync(self._async_group.delitem(key))
 
     def __iter__(self) -> Iterator[str]:
-        raise NotImplementedError
+        yield from self.keys()
 
     def __len__(self) -> int:
-        raise NotImplementedError
+        return self.nmembers()
 
     def __setitem__(self, key: str, value: Any) -> None:
         """__setitem__ is not supported in v3"""
         raise NotImplementedError
 
+    def __repr__(self) -> str:
+        return f"<Group {self.store_path}>"
+
     async def update_attributes_async(self, new_attributes: dict[str, Any]) -> Group:
         new_metadata = replace(self.metadata, attributes=new_attributes)
 
@@ -1377,6 +1386,9 @@ def members(self, max_depth: int | None = 0) -> tuple[tuple[str, Array | Group],
 
         return tuple((kv[0], _parse_async_node(kv[1])) for kv in _members)
 
+    def keys(self) -> Generator[str, None]:
+        yield from self._sync_iter(self._async_group.keys())
+
     def __contains__(self, member: str) -> bool:
         return self._sync(self._async_group.contains(member))
 

src/zarr/storage/__init__.py

@@ -0,0 +1,15 @@
+from zarr.storage.common import StoreLike, StorePath, make_store_path
+from zarr.storage.local import LocalStore
+from zarr.storage.memory import MemoryStore
+from zarr.storage.remote import RemoteStore
+from zarr.storage.zip import ZipStore
+
+__all__ = [
+    "LocalStore",
+    "MemoryStore",
+    "RemoteStore",
+    "StoreLike",
+    "StorePath",
+    "ZipStore",
+    "make_store_path",
+]