Merge branch 'v3' into ryan/legacy-vlen

Author: d-v-b

.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"]

docs/_static/custom.css

@@ -74,7 +74,6 @@ Nat Methods 8, 441 (2011). https://doi.org/10.1038/nmeth.1618
 .sd-card .sd-card-header {
   border: none;
   background-color: white;
-  color: #150458 !important;
   font-size: var(--pst-font-size-h5);
   font-weight: bold;
   padding: 2.5rem 0rem 0.5rem 0rem;
@@ -107,7 +106,6 @@ html[data-theme=dark] .sd-shadow-sm {
 
 html[data-theme=dark] .sd-card .sd-card-header {
   background-color:var(--pst-color-background);
-  color: #150458 !important;
 }
 
 html[data-theme=dark] .sd-card .sd-card-footer {

docs/_static/custom.js

@@ -6,7 +6,6 @@
         "highlights": "getting_started.html#highlights",
         "contributing": "contributing.html",
         "projects-using-zarr": "getting_started.html#projects-using-zarr",
-        "acknowledgments": "acknowledgments.html",
         "contents": "getting_started.html#contents",
         "indices-and-tables": "api.html#indices-and-tables"
     }

docs/acknowledgments.rst

@@ -255,6 +255,8 @@ def setup(app: sphinx.application.Sphinx) -> None:
 # Output file base name for HTML help builder.
 htmlhelp_basename = "zarrdoc"
 
+maximum_signature_line_length = 80
+
 # -- Options for LaTeX output ---------------------------------------------
 
 latex_elements = {

docs/conf.py

@@ -14,7 +14,6 @@ Zarr-Python
     spec
     release
     license
-    acknowledgments
     contributing
 
 **Version**: |version|

docs/index.rst

@@ -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',

pyproject.toml

@@ -7,14 +7,16 @@
 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.common import JSON, AccessModeLiteral, ChunkCoords, MemoryOrder, ZarrFormat
 from zarr.core.config import config
 from zarr.core.group import AsyncGroup
 from zarr.core.metadata.v2 import ArrayV2Metadata
 from zarr.core.metadata.v3 import ArrayV3Metadata
-from zarr.store import (
+from zarr.storage import (
     StoreLike,
+    StorePath,
     make_store_path,
 )
 
@@ -225,6 +227,7 @@ 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:
@@ -243,9 +246,9 @@ 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, **kwargs: Any) -> AsyncGroup:
@@ -319,7 +322,8 @@ 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(
@@ -496,7 +500,9 @@ 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
 
@@ -769,7 +775,11 @@ 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
@@ -945,7 +955,8 @@ 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/asynchronous.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/api/synchronous.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):
@@ -222,15 +223,14 @@ 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:
@@ -253,7 +253,7 @@ 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,
@@ -276,7 +276,7 @@ async def create(
                 store_path,
                 shape=shape,
                 dtype=dtype,
-                chunks=chunk_shape,
+                chunks=_chunks,
                 dimension_separator=dimension_separator,
                 fill_value=fill_value,
                 order=order,
@@ -404,6 +404,10 @@ 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)
@@ -831,6 +835,10 @@ 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
@@ -2380,15 +2388,26 @@ 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),
             )
         )