Merge branch 'main' into rm-spec-docs

Author: joshmoore

.github/workflows/releases.yml

@@ -55,7 +55,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/[email protected].2
+      - uses: pypa/[email protected].3
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

docs/contributing.rst

@@ -1,5 +1,5 @@
-Contributing to Zarr
-====================
+Contributing
+============
 
 Zarr is a community maintained project. We welcome contributions in the form of bug
 reports, bug fixes, documentation, enhancement proposals and more. This page provides

docs/guide/index.rst

@@ -4,5 +4,6 @@ Guide
 .. toctree::
     :maxdepth: 1
 
+    whatsnew_v3
     storage
     consolidated_metadata

docs/guide/whatsnew_v3.rst

@@ -0,0 +1,14 @@
+What's new in v3
+================
+
+This page gives an overview of major changes and additions in version 3.
+
+
+Dependencies
+------------
+- The new ``remote`` dependency group can be used to install a supported version of
+  ``fsspec``, required for remote data access.
+- The new ``gpu`` dependency group can be used to install a supported version of
+  ``cuda``, required for GPU functionality.
+- The ``jupyter`` optional dependency group has been removed, since v3 contains no
+  jupyter specific functionality.

docs/release.rst

@@ -39,6 +39,8 @@ Dependency Changes
   fsspec and any relevant implementations (e.g. s3fs) before using the ``RemoteStore``.
   By :user:`Joe Hamman <jhamman>` :issue:`2391`.
 
+* ``RemoteStore`` was renamed to ``FsspecStore``.
+  By :user:`Joe Hamman <jhamman>` :issue:`2557`.
 
 .. release_3.0.0-alpha:
 

pyproject.toml

@@ -53,9 +53,14 @@ license = {text = "MIT License"}
 keywords = ["Python", "compressed", "ndimensional-arrays", "zarr"]
 
 [project.optional-dependencies]
-fsspec = [
+# User extras
+remote = [
     "fsspec>=2023.10.0",
 ]
+gpu = [
+    "cupy-cuda12x",
+]
+# Development extras
 test = [
     "coverage",
     "pytest",
@@ -68,15 +73,7 @@ test = [
     "hypothesis",
     "universal-pathlib",
 ]
-
-jupyter = [
-    'notebook',
-    'ipytree>=0.2.2',
-    'ipywidgets>=8.0.0',
-]
-gpu = [
-    "cupy-cuda12x",
-]
+optional = ["rich", "universal-pathlib"]
 docs = [
     'sphinx==8.1.3',
     'sphinx-autobuild>=2021.3.14',
@@ -88,19 +85,9 @@ docs = [
     'pydata-sphinx-theme',
     'numpydoc',
     'numcodecs[msgpack]',
-    'msgpack',
-]
-extra = [
-    'msgpack',
-]
-optional = [
-    'universal-pathlib>=0.0.22',
-    'rich'
-]
-tree = [
-    'rich',
 ]
 
+
 [project.urls]
 "Bug Tracker" = "https://github.com/zarr-developers/zarr-python/issues"
 Changelog = "https://zarr.readthedocs.io/en/stable/release.html"
@@ -130,7 +117,7 @@ dependencies = [
     "numpy~={matrix:numpy}",
     "universal_pathlib",
 ]
-features = ["test", "extra"]
+features = ["test"]
 
 [[tool.hatch.envs.test.matrix]]
 python = ["3.11", "3.12", "3.13"]
@@ -161,7 +148,7 @@ dependencies = [
     "numpy~={matrix:numpy}",
     "universal_pathlib",
 ]
-features = ["test", "extra", "gpu"]
+features = ["test", "gpu"]
 
 [[tool.hatch.envs.gputest.matrix]]
 python = ["3.11", "3.12", "3.13"]
@@ -377,6 +364,7 @@ filterwarnings = [
     "ignore:The loop argument is deprecated since Python 3.8.*:DeprecationWarning",
     "ignore:Creating a zarr.buffer.gpu.*:UserWarning",
     "ignore:Duplicate name:UserWarning",  # from ZipFile
+    "ignore:.*is currently not part in the Zarr version 3 specification.*:UserWarning",
 ]
 markers = [
     "gpu: mark a test as requiring CuPy and GPU"

src/zarr/api/asynchronous.py

@@ -195,6 +195,14 @@ async def consolidate_metadata(
             v = dataclasses.replace(v, consolidated_metadata=ConsolidatedMetadata(metadata={}))
             members_metadata[k] = v
 
+    if any(m.zarr_format == 3 for m in members_metadata.values()):
+        warnings.warn(
+            "Consolidated metadata is currently not part in the Zarr version 3 specification. It "
+            "may not be supported by other zarr implementations and may change in the future.",
+            category=UserWarning,
+            stacklevel=1,
+        )
+
     ConsolidatedMetadata._flat_to_nested(members_metadata)
 
     consolidated_metadata = ConsolidatedMetadata(metadata=members_metadata)
@@ -203,6 +211,7 @@ async def consolidate_metadata(
         group,
         metadata=metadata,
     )
+
     await group._save_metadata()
     return group
 

src/zarr/codecs/vlen_utf8.py

@@ -2,6 +2,7 @@
 
 from dataclasses import dataclass
 from typing import TYPE_CHECKING
+from warnings import warn
 
 import numpy as np
 from numcodecs.vlen import VLenBytes, VLenUTF8
@@ -25,6 +26,15 @@
 
 @dataclass(frozen=True)
 class VLenUTF8Codec(ArrayBytesCodec):
+    def __init__(self) -> None:
+        warn(
+            "The codec `vlen-utf8` is currently not part in the Zarr version 3 specification. It "
+            "may not be supported by other zarr implementations and may change in the future.",
+            category=UserWarning,
+            stacklevel=2,
+        )
+        super().__init__()
+
     @classmethod
     def from_dict(cls, data: dict[str, JSON]) -> Self:
         _, configuration_parsed = parse_named_configuration(
@@ -71,6 +81,15 @@ def compute_encoded_size(self, input_byte_length: int, _chunk_spec: ArraySpec) -
 
 @dataclass(frozen=True)
 class VLenBytesCodec(ArrayBytesCodec):
+    def __init__(self) -> None:
+        warn(
+            "The codec `vlen-bytes` is currently not part in the Zarr version 3 specification. It "
+            "may not be supported by other zarr implementations and may change in the future.",
+            category=UserWarning,
+            stacklevel=2,
+        )
+        super().__init__()
+
     @classmethod
     def from_dict(cls, data: dict[str, JSON]) -> Self:
         _, configuration_parsed = parse_named_configuration(

src/zarr/core/array.py

@@ -6,6 +6,7 @@
 from itertools import starmap
 from logging import getLogger
 from typing import TYPE_CHECKING, Any, Generic, Literal, cast, overload
+from warnings import warn
 
 import numpy as np
 import numpy.typing as npt
@@ -539,7 +540,7 @@ async def _create_v3(
         store_path: StorePath,
         *,
         shape: ShapeLike,
-        dtype: npt.DTypeLike,
+        dtype: np.dtype[Any],
         chunk_shape: ChunkCoords,
         fill_value: Any | None = None,
         order: MemoryOrder | None = None,
@@ -580,6 +581,14 @@ async def _create_v3(
                 else DefaultChunkKeyEncoding(separator=chunk_key_encoding[1])
             )
 
+        if dtype.kind in "UTS":
+            warn(
+                f"The dtype `{dtype}` is currently not part in the Zarr version 3 specification. It "
+                "may not be supported by other zarr implementations and may change in the future.",
+                category=UserWarning,
+                stacklevel=2,
+            )
+
         metadata = ArrayV3Metadata(
             shape=shape,
             data_type=dtype,
@@ -601,7 +610,7 @@ async def _create_v2(
         store_path: StorePath,
         *,
         shape: ChunkCoords,
-        dtype: npt.DTypeLike,
+        dtype: np.dtype[Any],
         chunks: ChunkCoords,
         dimension_separator: Literal[".", "/"] | None = None,
         fill_value: float | None = None,

src/zarr/core/metadata/v3.py

@@ -95,14 +95,14 @@ def validate_codecs(codecs: tuple[Codec, ...], dtype: DataType) -> None:
 
     # we need to have special codecs if we are decoding vlen strings or bytestrings
     # TODO: use codec ID instead of class name
-    codec_id = abc.__class__.__name__
-    if dtype == DataType.string and not codec_id == "VLenUTF8Codec":
+    codec_class_name = abc.__class__.__name__
+    if dtype == DataType.string and not codec_class_name == "VLenUTF8Codec":
         raise ValueError(
-            f"For string dtype, ArrayBytesCodec must be `VLenUTF8Codec`, got `{codec_id}`."
+            f"For string dtype, ArrayBytesCodec must be `VLenUTF8Codec`, got `{codec_class_name}`."
         )
-    if dtype == DataType.bytes and not codec_id == "VLenBytesCodec":
+    if dtype == DataType.bytes and not codec_class_name == "VLenBytesCodec":
         raise ValueError(
-            f"For bytes dtype, ArrayBytesCodec must be `VLenBytesCodec`, got `{codec_id}`."
+            f"For bytes dtype, ArrayBytesCodec must be `VLenBytesCodec`, got `{codec_class_name}`."
         )