osobhandClaude Opus 5.5 d074385944 fix(format): read partial edge chunks stored unfiltered ...

Layout message v4 flag bit 0 (H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS, set
with H5Pset_chunk_opts) makes libhdf5 store every chunk that extends past
the dataset's extent without the filter pipeline, while its filter mask
still reads 0. The parser ignored the flag, so readers tried to inflate
raw bytes: libhdf5's own h5fc_edge_v3.h5 failed with "deflate: ...
unknown compression method".

DataLayout::Chunked gains dont_filter_partial_edge_chunks (always false
for v3), and list_chunks — the one place every read path gets its chunk
list from — marks such partial chunks as having skipped every filter, so
the full, cached, indexed, parallel and selection readers all copy them
as-is. chunked_write.rs gets `..` in one exhaustive test pattern for the
new field.

Regression: libhdf5_edge_chunk_fixture_reads (h5fc_edge_v3.h5 from the
HDF5 tools test files, committed as a 2.5 KB fixture), and
h5py_unfiltered_partial_edge_chunks_read (the flag set through h5py's
bundled libhdf5 via ctypes, as h5py has no binding for it: fixed array,
extensible array and B-tree v2 indexes, 1-D and 2-D, plus a hyperslab
of the last chunk), and v4_chunked_dont_filter_partial_edge_chunks_flag.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>

2026-09-25 21:08:36 -05:00

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