fix: zarr v2 compatability fixes

- port normalize_chunks from v2
- add array.store property
- default to append in create

Author: jhamman

src/zarr/api/asynchronous.py

@@ -724,7 +724,7 @@ 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", cast(AccessModeLiteral, "r" if read_only else "a"))
     store_path = await make_store_path(store, mode=mode)
     if path is not None:
         store_path = store_path / path

src/zarr/core/array.py

@@ -8,12 +8,12 @@
 import numpy as np
 import numpy.typing as npt
 
-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
 from zarr.core.buffer import BufferPrototype, NDArrayLike, 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,
@@ -129,7 +129,7 @@ async def create(
         fill_value: Any | None = None,
         attributes: dict[str, JSON] | None = None,
         # v3 only
-        chunk_shape: ChunkCoords | None = None,
+        chunk_shape: ChunkCoords | None = None,  # TODO: handle bool and iterable of iterable types
         chunk_key_encoding: (
             ChunkKeyEncoding
             | tuple[Literal["default"], Literal[".", "/"]]
@@ -139,7 +139,7 @@ async def create(
         codecs: Iterable[Codec | dict[str, JSON]] | None = None,
         dimension_names: Iterable[str] | None = None,
         # v2 only
-        chunks: ShapeLike | None = None,
+        chunks: ShapeLike | None = None,  # TODO: handle bool and iterable of iterable types
         dimension_separator: Literal[".", "/"] | None = None,
         order: Literal["C", "F"] | None = None,
         filters: list[dict[str, JSON]] | None = None,
@@ -152,15 +152,14 @@ 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)
+        if chunk_shape:
+            _chunks = normalize_chunks(chunk_shape, shape, dtype.itemsize)
 
         if zarr_format == 3:
             if dimension_separator is not None:
@@ -183,7 +182,7 @@ 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,
@@ -206,7 +205,7 @@ async def create(
                 store_path,
                 shape=shape,
                 dtype=dtype,
-                chunks=chunk_shape,
+                chunks=_chunks,
                 dimension_separator=dimension_separator,
                 fill_value=fill_value,
                 order=order,
@@ -393,6 +392,10 @@ async def open(
                 metadata=ArrayV3Metadata.from_dict(json.loads(zarr_json_bytes.to_bytes())),
             )
 
+    @property
+    def store(self) -> Store:
+        return self.store_path.store
+
     @property
     def ndim(self) -> int:
         return len(self.metadata.shape)
@@ -697,6 +700,10 @@ 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

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
 
@@ -98,6 +99,50 @@ 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 = (
+            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)
+        )
+
+    out = tuple(int(c) for c in chunks)
+    return out
+
+
 @dataclass(frozen=True)
 class ChunkGrid(Metadata):
     @classmethod

src/zarr/core/group.py

@@ -173,7 +173,9 @@ 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

src/zarr/store/common.py

@@ -78,12 +78,12 @@ async def make_store_path(
     store_like: StoreLike | None, *, mode: AccessModeLiteral | None = None
 ) -> StorePath:
     if isinstance(store_like, StorePath):
-        if mode is not None:
-            assert AccessMode.from_literal(mode) == store_like.store.mode
+        if (mode is not None) and (AccessMode.from_literal(mode) != store_like.store.mode):
+            raise ValueError(f"mode mismatch (mode={mode} != store.mode={store_like.store.mode})")
         return store_like
     elif isinstance(store_like, Store):
-        if mode is not None:
-            assert AccessMode.from_literal(mode) == store_like.mode
+        if (mode is not None) and (AccessMode.from_literal(mode) != store_like.mode):
+            raise ValueError(f"mode mismatch (mode={mode} != store.mode={store_like.mode})")
         await store_like._ensure_open()
         return StorePath(store_like)
     elif store_like is None: