Claude/storage codec bugfixes

[d-v-b]

I had claude do a comprehensive review of zarr-python and look for bugs, optimizations, etc. The tracking issue is over on my fork. I will be opening claude-authored PRs that fix the issues.

Summary

This PR addresses five pre-verified bugs (B1–B5 of #181):

B1 — MemoryStore SuffixByteRequest clamp (src/zarr/storage/_utils.py)
When SuffixByteRequest.suffix > len(data), the computed start index went
negative, causing numpy slicing to return too few bytes. Fixed by clamping:
start = max(0, len(data) - byte_range.suffix). This matches how ZipStore
and LocalStore already handle this case.

B2 — LoggingStore.get_partial_values generator exhaustion (src/zarr/storage/_logging.py)
The log-hint string was built by iterating over key_ranges with a list
comprehension, which exhausted a one-shot generator before passing it to
the wrapped store. Fixed by materialising key_ranges = list(key_ranges)
first.

B3 — getsize_prefix substring over-count (src/zarr/abc/store.py)
getsize_prefix("foo") called list_prefix("foo"), which matched both
"foo/a" and "foobar/b" in prefix-matching stores. Fixed by normalising
the prefix to end with "/" (matching delete_dir / is_empty), so only
keys under the exact directory are counted.

B4 — ZipStore.close() AttributeError when never opened (src/zarr/storage/_zip.py)
_lock is only created in _sync_open(). If close() was called on a
store that was never opened (e.g. with ZipStore(...): pass), it raised
AttributeError: _lock. Fixed by returning early from close() when
_is_open is False.

B5 — Missing raise in codecs_from_list (src/zarr/core/codec_pipeline.py)
In the BytesBytesCodec branch, when prev_codec is an ArrayArrayCodec,
the error message was assigned to msg but never raised. The sibling
branches (ArrayArrayCodec and ArrayBytesCodec cases) both do
raise TypeError(msg); this one was missing the raise. Fixed by adding
raise TypeError(msg).

Notes

• A towncrier changelog entry should be added before un-drafting this PR.
• Addresses B1–B5 of #181.

🤖 Generated with Claude Code

[d-v-b]

@dcherian do you have any ideas for better property-based tests that we could add, given these bugs?

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 93.53%. Comparing base (7bc3017) to head (d24c8ac).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4074      +/-   ##
==========================================
+ Coverage   93.52%   93.53%   +0.01%     
==========================================
  Files          90       90              
  Lines       11926    11932       +6     
==========================================
+ Hits        11154    11161       +7     
+ Misses        772      771       -1     

Files with missing lines	Coverage Δ
src/zarr/abc/store.py	96.17% <100.00%> (+0.04%)	⬆️
src/zarr/core/codec_pipeline.py	92.55% <100.00%> (+0.38%)	⬆️
src/zarr/storage/_logging.py	100.00% <100.00%> (ø)
src/zarr/storage/_utils.py	96.42% <100.00%> (ø)
src/zarr/storage/_zip.py	97.71% <100.00%> (+0.02%)	⬆️

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[dcherian]

Looks like a missing property test

[d-v-b]

👍 I will add one