Fix/memorystore buffer aliasing - #4157
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d-v-b merged 7 commits intoJul 17, 2026
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* fix: byte-order handling for structured dtypes in the bytes codec The bytes codec neither byte-swapped structured-dtype fields to its configured endian on encode (numpy reports byteorder '|' for void dtypes, so the top-level byteorder comparison never detected a mismatch) nor honored its endian when decoding, silently corrupting any structured data whose field byte order differed from the stored one (e.g. virtual references to external big-endian data). Encode now detects byte-order mismatches by comparing full dtypes via newbyteorder, and decode reinterprets raw bytes in the stored byte order before converting to the data type's declared byte order, so the stored layout (codec state) and the in-memory layout (array data type) are independent. Closes zarr-developers#4141 Assisted-by: ClaudeCode:claude-fable-5 * test: fold structured byte-order cases into existing bytes codec tests Extend test_endian's parametrization with structured dtypes and test_bytes_codec_sync_roundtrip with endian/dtype parametrization plus stored-layout and decoded-dtype assertions, instead of adding parallel test functions for the same properties. Assisted-by: ClaudeCode:claude-fable-5 * refactor: rename stored_dtype to view_dtype in BytesCodec decode The variable is the dtype used to view the raw chunk bytes (byte order from the codec's endian configuration), not a property of the stored data or of the returned buffer, which always carries the array's declared dtype. Assisted-by: ClaudeCode:claude-fable-5 * docs: note that the decode-side byte-order conversion copies the chunk Assisted-by: ClaudeCode:claude-fable-5
Encoding an uncompressed chunk hands the store a zero-copy view of the caller's array, and MemoryStore keeps whatever it is given alive in a dict rather than serializing it. Mutating the source array after a write therefore rewrote chunks already committed to the store, silently. Stores that serialize on write (LocalStore, ZipStore, remote stores) are unaffected, so they keep the full benefit of zarr-developers#3885. Only MemoryStore pays the copy, and only where it was aliasing to begin with: an uncompressed 34 MB write goes from ~23 ms to ~39 ms, while compressed writes are unchanged. Copying at the store boundary rather than narrowing the fast path in _merge_chunk_array also fixes the single-chunk case, which aliased in v3.2.1 too. Assisted-by: ClaudeCode:claude-opus-4.8
Assisted-by: ClaudeCode:claude-opus-4.8
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Codecov Report✅ All modified and coverable lines are covered by tests. @@ Coverage Diff @@
## main #4157 +/- ##
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Coverage 93.84% 93.84%
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Files 91 91
Lines 12570 12572 +2
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+ Hits 11796 11798 +2
Misses 774 774
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d-v-b
marked this pull request as ready for review
July 17, 2026 11:46
maxrjones
approved these changes
Jul 17, 2026
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@maxrjones ran a regression check on our pre-3.3.0 release state, and found a few regressions that need fixing. Here's the first fix, which ensures that memory storage always copies buffers, instead of hanging on to aliases of arrays owned by the caller.
this PR was written by claude code and opened by me; to view claude's original output, see d-v-b#224