Merge remote-tracking branch 'upstream/v3' into user/tom/fix/v2-no-fill-value

Author: TomAugspurger

.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 }}

.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

@@ -20,6 +20,7 @@
     from zarr.core.indexing import SelectorTuple
 
 __all__ = [
+    "BaseCodec",
     "ArrayArrayCodec",
     "ArrayBytesCodec",
     "ArrayBytesCodecPartialDecodeMixin",
@@ -34,11 +35,15 @@
 CodecOutput = TypeVar("CodecOutput", bound=NDBuffer | Buffer)
 
 
-class _Codec(Metadata, Generic[CodecInput, CodecOutput]):
+class BaseCodec(Metadata, Generic[CodecInput, CodecOutput]):
     """Generic base class for codecs.
-    Please use ArrayArrayCodec, ArrayBytesCodec or BytesBytesCodec for subclassing.
 
     Codecs can be registered via zarr.codecs.registry.
+
+    Warnings
+    --------
+    This class is not intended to be directly, please use
+    ArrayArrayCodec, ArrayBytesCodec or BytesBytesCodec for subclassing.
     """
 
     is_fixed_size: bool
@@ -148,19 +153,19 @@ async def encode(
         return await _batching_helper(self._encode_single, chunks_and_specs)
 
 
-class ArrayArrayCodec(_Codec[NDBuffer, NDBuffer]):
+class ArrayArrayCodec(BaseCodec[NDBuffer, NDBuffer]):
     """Base class for array-to-array codecs."""
 
     ...
 
 
-class ArrayBytesCodec(_Codec[NDBuffer, Buffer]):
+class ArrayBytesCodec(BaseCodec[NDBuffer, Buffer]):
     """Base class for array-to-bytes codecs."""
 
     ...
 
 
-class BytesBytesCodec(_Codec[Buffer, Buffer]):
+class BytesBytesCodec(BaseCodec[Buffer, Buffer]):
     """Base class for bytes-to-bytes codecs."""
 
     ...

src/zarr/abc/codec.py

@@ -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