docs: editor coverage — version-2 B-trees, shrinking, dense attributes, reuse
CHANGELOG (Unreleased): the new FileEditor operations, space reuse, and the two reader fixes (implicit index grid, object-header continuation chains). known-issues: the editor's remaining refusals (skipped heap blocks, heaps with filters or child indirect blocks, freeing a heap block, implicit-index insertions, ...) and the append-waste sizes before and after reuse (measure_append_waste, tank 2026-09-26; file sizes are deterministic). range-reads design: status note on the reader changes. README and CLAUDE.md: what the editor covers and how to test it. Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
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@@ -26,40 +26,49 @@ libhdf5 modify them.
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## In-place modification (`FileEditor`) limits
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**Status:** open (documented 2026-09-26). `clawhdf5::FileEditor` refuses,
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with `Error::Unsupported` and without writing anything:
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- new, moved or resized chunks in a **version-2 B-tree** chunk index (what
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libhdf5 uses for two or more unlimited dimensions) — existing unfiltered
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chunks, and filtered ones that re-encode to the same size and filter
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mask, are
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overwritten in place; `resize` works — and new chunks in an **implicit**
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index (it has all of its chunks from the start);
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- **shrinking** a dataset;
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**Status:** open (documented 2026-09-26, updated the same day when
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version-2 B-tree chunk indexes, shrinking, dense attributes and space
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reuse were added). `clawhdf5::FileEditor` refuses, with
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`Error::Unsupported` and without writing anything:
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- new chunks in an **implicit** index (it has all of its chunks from the
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start; they are written in place, and allocated/filled on growth under
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early allocation as libhdf5 does);
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- variable-length and reference data;
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- chunks through a filter this build cannot encode (scale-offset, N-Bit,
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SZIP, or a plugin filter it lacks), even an optional one: libhdf5 skips
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an optional filter only when its own build lacks it, which none does for
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these;
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- attributes of an object in **dense storage**, past its compact limit (8
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by default) or with tracked **creation order**;
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- attributes in dense storage when the heap cannot take them the way
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libhdf5 would: an attribute that needs a heap block larger than the next
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one (libhdf5 skips blocks and records them as free space — in practice an
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attribute of roughly 1 to 4 KiB going into a young heap), a heap with I/O
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filters or child indirect blocks (more than about 512 KiB of attributes),
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free space the heap tracks outside direct blocks, replacing the last
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attribute left in a heap block by one of another size (libhdf5 frees the
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block), directly addressed huge objects; and shared attribute messages;
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- version-1 object headers asked for an attribute larger than a header
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message (they have no dense storage);
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- partial edge chunks stored unfiltered (`H5Pset_chunk_opts`), external
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raw data files, virtual datasets;
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- files with a metadata cache image, paged or persistent free-space
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management, a driver info block, or version-3 consistency flags set.
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**Space is never reused.** There is no free-space manager: the old bytes of
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a filtered chunk that grows and has to move, and of an attribute that is
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replaced by a larger one, are leaked (`h5repack` reclaims them). A chunk
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that is the last thing in the file grows in place instead, which covers the
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usual append. Measured 2026-09-26 on tank with
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`cargo test --release -p clawhdf5-tools --test edit_interop -- --ignored
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--nocapture measure_append_waste` (file sizes are deterministic): 1000
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appends of 100 `f8` values to a 1-D dataset with 1024-element chunks give
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810 504 bytes unfiltered, as libhdf5's file, and 307 210 bytes with gzip
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(libhdf5: 306 058; `h5repack`: 306 104); 2000 appends of 10 values with
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4096-element gzip chunks give 119 684 bytes against libhdf5's 50 292
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(`h5repack`: 49 930), because the chunk being appended to is followed by
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new index blocks and moves each time it grows.
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**Space is reused only within one editor.** Space an edit frees (a filtered
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chunk that moves, chunks a shrink removes, B-tree nodes merged away, a
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heap's replaced blocks) is reused by later edits of the same `FileEditor`;
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what is left when it is dropped is leaked, as libhdf5 leaks it without a
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persistent free-space manager (`h5repack` reclaims it). A chunk that is the
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last thing in the file grows in place, which covers the usual append.
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Measured 2026-09-26 on tank with `cargo test -p clawhdf5-tools --test
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edit_interop -- --ignored --nocapture measure_append_waste` (one editor for
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the whole workload; file sizes are deterministic): 1000 appends of 100 `f8`
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values to a 1-D dataset with 1024-element chunks give 810 504 bytes
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unfiltered, as libhdf5's file, and 306 780 bytes with gzip (307 210 before
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reuse; libhdf5: 306 058; `h5repack`: 306 104); 2000 appends of 10 values
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with 4096-element gzip chunks give 79 829 bytes (119 684 before reuse)
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against libhdf5's 50 292 (`h5repack`: 49 930): the chunk being appended to
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is followed by new index blocks and moves each time it grows, and the
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space it leaves is too small for its next, larger version.
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**No journal.** A crash while an edit patches existing structures can leave
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the file inconsistent; see the `FileEditor` documentation.
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