Merge remott e-tracking branch 'refs/remotes/origin/tom/fix/cm-nested-getitem' into tom/fix/cm-nested-getitem

Author: TomAugspurger

.github/workflows/gpu_test.yml

@@ -1,13 +1,13 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: GPU Test V3
+name: GPU Test
 
 on:
   push:
-    branches: [ v3 ]
+    branches: [ main ]
   pull_request:
-    branches: [ v3 ]
+    branches: [ main ]
   workflow_dispatch:
 
 env:

.github/workflows/hypothesis.yaml

@@ -3,11 +3,9 @@ on:
   push:
     branches:
       - "main"
-      - "v3"
   pull_request:
     branches:
       - "main"
-      - "v3"
     types: [opened, reopened, synchronize, labeled]
   schedule:
     - cron: "0 0 * * *" # Daily “At 00:00” UTC

.github/workflows/test.yml

@@ -1,13 +1,13 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Test V3
+name: Test
 
 on:
   push:
-    branches: [ v3 ]
+    branches: [ main ]
   pull_request:
-    branches: [ v3 ]
+    branches: [ main ]
   workflow_dispatch:
 
 concurrency:

docs/conf.py

@@ -21,7 +21,6 @@
 
 from importlib.metadata import version as get_version
 
-import zarr
 import sphinx
 
 # If extensions (or modules to document with autodoc) are in another directory,

docs/index.rst

@@ -16,6 +16,7 @@ Zarr-Python
     release
     license
     contributing
+    roadmap
 
 **Version**: |version|
 

docs/roadmap.rst

@@ -211,6 +211,7 @@ extend-select = [
     "B",   # flake8-bugbear
     "C4",  # flake8-comprehensions
     "FLY", # flynt
+    "G",   # flake8-logging-format
     "I",   # isort
     "ISC", # flake8-implicit-str-concat
     "PGH", # pygrep-hooks
@@ -222,20 +223,24 @@ extend-select = [
     "TCH", # flake8-type-checking
     "TRY", # tryceratops
     "UP",  # pyupgrade
+    "W",   # pycodestyle warnings
 ]
 ignore = [
     "ANN003",
     "ANN101",
     "ANN102",
     "ANN401",
     "PT004",  # deprecated
+    "PT005",  # deprecated
     "PT011",  # TODO: apply this rule
     "PT012",  # TODO: apply this rule
     "PYI013",
     "RET505",
     "RET506",
     "RUF005",
     "TRY003",
+    "UP027",  # deprecated
+    "UP038",  # https://github.com/astral-sh/ruff/issues/7871
     # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
     "W191",
     "E111",

pyproject.toml

@@ -2,7 +2,6 @@
 
 from abc import ABC, abstractmethod
 from asyncio import gather
-from types import TracebackType
 from typing import TYPE_CHECKING, NamedTuple, Protocol, runtime_checkable
 
 if TYPE_CHECKING:

src/zarr/abc/store.py

@@ -981,7 +981,11 @@ async def create_array(
 
     @deprecated("Use AsyncGroup.create_array instead.")
     async def create_dataset(
-        self, name: str, **kwargs: Any
+        self,
+        name: str,
+        *,
+        shape: ShapeLike,
+        **kwargs: Any,
     ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
         """Create an array.
 
@@ -992,6 +996,8 @@ async def create_dataset(
         ----------
         name : str
             Array name.
+        shape : int or tuple of ints
+            Array shape.
         kwargs : dict
             Additional arguments passed to :func:`zarr.AsyncGroup.create_array`.
 
@@ -1002,7 +1008,7 @@ async def create_dataset(
         .. deprecated:: 3.0.0
             The h5py compatibility methods will be removed in 3.1.0. Use `AsyncGroup.create_array` instead.
         """
-        return await self.create_array(name, **kwargs)
+        return await self.create_array(name, shape=shape, **kwargs)
 
     @deprecated("Use AsyncGroup.require_array instead.")
     async def require_dataset(
@@ -1705,7 +1711,13 @@ def create_dataset(self, name: str, **kwargs: Any) -> Array:
         return Array(self._sync(self._async_group.create_dataset(name, **kwargs)))
 
     @deprecated("Use Group.require_array instead.")
-    def require_dataset(self, name: str, **kwargs: Any) -> Array:
+    def require_dataset(
+        self,
+        name: str,
+        *,
+        shape: ShapeLike,
+        **kwargs: Any,
+    ) -> Array:
         """Obtain an array, creating if it doesn't exist.
 
         Arrays are known as "datasets" in HDF5 terminology. For compatibility
@@ -1732,9 +1744,15 @@ def require_dataset(self, name: str, **kwargs: Any) -> Array:
         .. deprecated:: 3.0.0
             The h5py compatibility methods will be removed in 3.1.0. Use `Group.require_array` instead.
         """
-        return Array(self._sync(self._async_group.require_array(name, **kwargs)))
+        return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs)))
 
-    def require_array(self, name: str, **kwargs: Any) -> Array:
+    def require_array(
+        self,
+        name: str,
+        *,
+        shape: ShapeLike,
+        **kwargs: Any,
+    ) -> Array:
         """Obtain an array, creating if it doesn't exist.
 
 
@@ -1756,7 +1774,7 @@ def require_array(self, name: str, **kwargs: Any) -> Array:
         -------
         a : Array
         """
-        return Array(self._sync(self._async_group.require_array(name, **kwargs)))
+        return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs)))
 
     def empty(self, *, name: str, shape: ChunkCoords, **kwargs: Any) -> Array:
         return Array(self._sync(self._async_group.empty(name=name, shape=shape, **kwargs)))

src/zarr/core/group.py

@@ -133,7 +133,7 @@ def sync(
 
     finished, unfinished = wait([future], return_when=asyncio.ALL_COMPLETED, timeout=timeout)
     if len(unfinished) > 0:
-        raise TimeoutError(f"Coroutine {coro} failed to finish in within {timeout}s")
+        raise TimeoutError(f"Coroutine {coro} failed to finish within {timeout} s")
     assert len(finished) == 1
     return_result = next(iter(finished)).result()