fix(typing): fix mypy errors in indexing with numpy 2.5.1 stubs - #231
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fix(typing): fix mypy errors in indexing with numpy 2.5.1 stubs#231d-v-b wants to merge 4 commits into
d-v-b wants to merge 4 commits into
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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
numpy 2.5.1's type stubs infer a float64 array for np.asarray on a narrowed list/int, breaking the declared selection types in replace_lists and CoordinateIndexer.__init__. Cast the asarray result in replace_lists (a plain list may hold ints or bools, so the stubs cannot infer ArrayOfIntOrBool), and pass dtype=np.intp explicitly in CoordinateIndexer, which also makes the runtime dtype deterministic. Assisted-by: ClaudeCode:claude-fable-5
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Fixes the two mypy errors reported on zarr-developers#4151 (the dependabot bump of numpy 2.5.0 → 2.5.1 and mypy 2.1.0 → 2.2.0), both in
src/zarr/core/indexing.py:replace_lists(line 514): numpy 2.5.1's stubs inferndarray[..., float64]fornp.asarray(dim_sel)on a narrowedlist. A plainlistmay hold ints or bools, so the stubs cannot inferArrayOfIntOrBool; the result is nowcastto that alias, matching the existing cast style in the file.CoordinateIndexer.__init__(line 1195):np.asarray([i])on anis_integer-narrowedilikewise infers float64. Passingdtype=np.intpexplicitly satisfiesCoordinateSelectionNormalizedand makes the runtime dtype deterministic across platforms as a bonus.Verified locally:
uv run mypy src testsclean with the current lock (numpy 2.5.0) and with numpy upgraded to 2.5.1uv run pytest tests/test_indexing.py: 427 passed, 1 skipped, 2 xfailed🤖 Generated with Claude Code