fix: honor use_consolidated_for_children, merge async attribute updates, cancel timed-out sync coroutines

[d-v-b]

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Summary

Five small, independent, backwards-compatible bugfixes in Group, sync, storage and the GPU buffer, each with a regression test where CI can run one. Originally prototyped as d-v-b#190 and rebased onto current main.

members ignored use_consolidated_for_children when the root has consolidated metadata

AsyncGroup._members short-circuited to _members_consolidated() whenever self.metadata.consolidated_metadata is not None, so the flag had no effect. Group.members (sync) also did not forward the flag, and _iter_members_deep did not pass it on recursive calls. All three now honor and forward it. The docstrings previously stated that root consolidated metadata is "always used"; they now describe the new behaviour.

• src/zarr/core/group.py

Group.update_attributes_async replaced attributes instead of merging

It called replace(self.metadata, attributes=new_attributes) while AsyncGroup.update_attributes and Group.update_attributes both merge. It now merges. An existing test that asserted the replace behaviour was updated.

• src/zarr/core/group.py

sync() timeout left the coroutine running

On timeout, wait() returned the future in unfinished but nothing cancelled it, so the coroutine kept running on the IO thread. future.cancel() is now called before raising TimeoutError.

• src/zarr/core/sync.py

Deprecation warning for zarr.storage.default_compressor pointed at a removed config key

The message recommended array.v2_default_compressor.numeric, which was removed in 3.1.0. It now points at the compressors= argument to zarr.create_array().

• src/zarr/storage/__init__.py

GPU NDBuffer.create(fill_value=None) diverged from CPU

The GPU buffer used cp.empty (uninitialised) when no fill value was given, while the CPU buffer uses np.zeros. It now zero-fills to match. cupy is not available in standard CI; GPU CI should validate this.

• src/zarr/core/buffer/gpu.py

Dropped from the original prototype

The require_array(dtype=None) change was dropped: #4189 deliberately kept the float64 default and tests it.

Test results

uv run pytest tests/test_group.py tests/test_sync.py tests/test_metadata/test_consolidated.py -q
914 passed, 207 skipped in 4.89s

Pre-commit (ruff, mypy, numpydoc-validation, codespell) passes.

TODO

• Add unit tests and/or doctests in docstrings
• Add docstrings and API docs for any new/modified user-facing classes and functions
• New/modified features documented in docs/user-guide/*.md (not applicable, bugfixes only)
• Changes documented as a new file in changes/
• GitHub Actions have all passed
• Test coverage is 100% (Codecov passes)

🤖 Generated with Claude Code

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.34%. Comparing base (ba883a5) to head (dfd2a2d).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #4343   +/-   ##
=======================================
  Coverage   94.34%   94.34%           
=======================================
  Files          92       92           
  Lines       12935    12941    +6     
=======================================
+ Hits        12203    12209    +6     
  Misses        732      732           

Files with missing lines	Coverage Δ
src/zarr/core/buffer/gpu.py	90.47% <100.00%> (+0.11%)	⬆️
src/zarr/core/group.py	95.54% <100.00%> (+0.01%)	⬆️
src/zarr/core/sync.py	94.28% <100.00%> (+0.05%)	⬆️
src/zarr/storage/__init__.py	95.00% <ø> (ø)

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