Merge branch 'main' into typing-test-store

Author: dstansby

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.7
+    rev: v0.12.11
     hooks:
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
@@ -17,7 +17,7 @@ repos:
       - id: codespell
         args: ["-L", "fo,ihs,kake,te", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: trailing-whitespace
@@ -53,6 +53,6 @@ repos:
     hooks:
       - id: numpydoc-validation
   - repo: https://github.com/twisted/towncrier
-    rev: 24.8.0
+    rev: 25.8.0
     hooks:
       - id: towncrier-check

changes/2859.removal.rst

@@ -0,0 +1,2 @@
+The ``Store.set_partial_writes`` method, which was not used by Zarr-Python, has been removed.
+``store.supports_partial_writes`` is now always ``False``.

changes/3403.misc.rst

@@ -0,0 +1,6 @@
+Moves some indexing-specific exceptions to ``zarr.errors``, and ensures that all Zarr-specific
+exception classes accept a pre-formatted string as a single argument. This is a breaking change to
+the following exceptions classes: :class:`zarr.errors.BoundsCheckError`, :class:`zarr.errors.NegativeStepError`
+:class:`zarr.errors.VindexInvalidSelectionError`. These classes previously generated internally
+formatted error messages when given a single argument. After this change, formatting of the error
+message is up to the routine invoking the error.

changes/3411.bugfix.rst

@@ -0,0 +1 @@
+LocalStore now uses atomic writes, which should prevent some cases of corrupted data.

changes/3425.bugfix.rst

@@ -0,0 +1 @@
+Fix ChunkGrid definition (broken in 3.1.2)

changes/3428.bugfix.rst

@@ -0,0 +1 @@
+Ensure syntax like ``root['/subgroup']`` works equivalently to ``root['subgroup']`` when using consolidated metadata.

pyproject.toml

@@ -379,6 +379,7 @@ testpaths = ["tests", "docs/user-guide"]
 log_cli_level = "INFO"
 xfail_strict = true
 asyncio_mode = "auto"
+asyncio_default_fixture_loop_scope = "function"
 doctest_optionflags = [
     "NORMALIZE_WHITESPACE",
     "ELLIPSIS",

src/zarr/abc/store.py

@@ -4,15 +4,14 @@
 from asyncio import gather
 from dataclasses import dataclass
 from itertools import starmap
-from typing import TYPE_CHECKING, Protocol, runtime_checkable
+from typing import TYPE_CHECKING, Literal, Protocol, runtime_checkable
 
 if TYPE_CHECKING:
     from collections.abc import AsyncGenerator, AsyncIterator, Iterable
     from types import TracebackType
     from typing import Any, Self, TypeAlias
 
     from zarr.core.buffer import Buffer, BufferPrototype
-    from zarr.core.common import BytesLike
 
 __all__ = ["ByteGetter", "ByteSetter", "Store", "set_or_delete"]
 
@@ -310,25 +309,12 @@ async def delete(self, key: str) -> None:
         ...
 
     @property
-    @abstractmethod
-    def supports_partial_writes(self) -> bool:
-        """Does the store support partial writes?"""
-        ...
-
-    @abstractmethod
-    async def set_partial_values(
-        self, key_start_values: Iterable[tuple[str, int, BytesLike]]
-    ) -> None:
-        """Store values at a given key, starting at byte range_start.
+    def supports_partial_writes(self) -> Literal[False]:
+        """Does the store support partial writes?
 
-        Parameters
-        ----------
-        key_start_values : list[tuple[str, int, BytesLike]]
-            set of key, range_start, values triples, a key may occur multiple times with different
-            range_starts, range_starts (considering the length of the respective values) must not
-            specify overlapping ranges for the same key
+        Partial writes are no longer used by Zarr, so this is always false.
         """
-        ...
+        return False
 
     @property
     @abstractmethod
@@ -499,7 +485,7 @@ async def get(
         self, prototype: BufferPrototype, byte_range: ByteRequest | None = None
     ) -> Buffer | None: ...
 
-    async def set(self, value: Buffer, byte_range: ByteRequest | None = None) -> None: ...
+    async def set(self, value: Buffer) -> None: ...
 
     async def delete(self) -> None: ...
 

src/zarr/api/asynchronous.py

@@ -862,7 +862,8 @@ async def open_group(
             overwrite=overwrite,
             attributes=attributes,
         )
-    raise GroupNotFoundError(store, store_path.path)
+    msg = f"No group found in store {store!r} at path {store_path.path!r}"
+    raise GroupNotFoundError(msg)
 
 
 async def create(
@@ -1268,7 +1269,8 @@ async def open_array(
                 overwrite=overwrite,
                 **kwargs,
             )
-        raise ArrayNotFoundError(store_path.store, store_path.path) from err
+        msg = f"No array found in store {store_path.store} at path {store_path.path}"
+        raise ArrayNotFoundError(msg) from err
 
 
 async def open_like(

src/zarr/core/array.py

@@ -257,7 +257,8 @@ async def get_array_metadata(
         else:
             zarr_format = 2
     else:
-        raise MetadataValidationError("zarr_format", "2, 3, or None", zarr_format)
+        msg = f"Invalid value for 'zarr_format'. Expected 2, 3, or None. Got '{zarr_format}'."  # type: ignore[unreachable]
+        raise MetadataValidationError(msg)
 
     metadata_dict: dict[str, JSON]
     if zarr_format == 2: