Commit Graph
639 Commits
Author SHA1 Message Date
osobhandClaude Opus 5.5 d3d8d7ded3 docs: README — szip is a clawhdf5-format feature
CI / test-arm64 (pull_request) Successful in 1m35s
CI / test (pull_request) Successful in 15m45s
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:25:03 -05:00
osobhandClaude Opus 5.5 c27a478e44 docs: fact-check the refreshed documentation against its sources
Numbers, API names, feature defaults and PR references checked against
CONFORMANCE.md, BENCHMARKS.md, CHANGELOG.md, the code and git history.

- int8 index figures (1.74x memory, 1.63x QPS) carry the dates git gives
  them (2026-09-19/20, machine not recorded, not re-run) instead of none;
  the Pi 5 1.18x carries 2026-09-21.
- BENCHMARKS headline: the libhdf5 chunked-write figure is the newest
  measurement (35x, 2026-09-23), not 45.3x (2026-08-03).
- Conformance counts follow the 2026-09-28 run (1 our-error, 2 ref-bug)
  in conformance/README.md, ROADMAP.md and CLAUDE.md, with a pointer to
  the bad_nbit_parms_walk.h5 flip.
- README: LZ4 is opt-in; the browser refuses reference/opaque/bitfield/
  time datasets too; zlib-rs byte-identity scoped to what was measured;
  macOS default links the system libz for inflate.
- Crate READMEs: system-zlib-decompress does something (macOS), SweepDetector
  lives in prefetch, checkpoint after more than 500 WAL entries, NetCDF-4
  unlimited-dimension size warning.
- agent-memory.md: string-dataset compression threshold, agents-md prints
  Markdown, float16 file sizes linked to their study.
- known-issues.md: contiguous selection reads, 1.21x vs h5py threads.
- docs/README.md, USE_CASES.md, ROADMAP.md, CLAUDE.md: range-read
  milestones M0-M5 and PRs #17-#19, missing README rows, CLI keygen/verify,
  dated figures, fast-math is not BLAS.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:23:51 -05:00
osobhandClaude Opus 5.5 a48cb9f1a4 docs: known issue — NetCDF-4 unlimited dimensions report size 0
Found while checking the README refresh: clawhdf5-netcdf4 reads an
unlimited dimension's size from its dimension-scale dataset, which
netCDF-C never extends, so a dimension with 2 records reports 0.
Variable shapes and values are right. To be fixed separately.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:15:51 -05:00
osobhandClaude Opus 5.5 3100f0143b docs: fix cross-links after the refresh; remove the stale benchmark script
- docs/README.md links the improvement logs and June plans where the
  refresh archived them (docs/archive/).
- clawhdf5-py README: 'r+' creates and replaces attributes (compact or
  dense); only deleting them is unsupported.
- scripts/run-benchmarks.sh benchmarked the pre-rename rustyhdf5-format
  and overwrote BENCHMARKS.md; nothing referenced it. Removed.
- Cargo.toml descriptions no longer name rustyhdf5/edgehdf5; clawhdf5-gpu
  says it is not HDF5 I/O.
- benchmarks/cross_platform.sh pointed at a ROADMAP section that no longer
  exists.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:15:18 -05:00
osobh 2bffd6b622 Merge branch 'docs/refresh-readme' into docs/readme-refresh 2026-09-28 11:14:06 -05:00
osobh c53c43b14f Merge branch 'docs/refresh-crates' into docs/readme-refresh 2026-09-28 11:14:06 -05:00
osobh 14790487a7 Merge branch 'docs/refresh-reference' into docs/readme-refresh 2026-09-28 11:14:06 -05:00
osobhandClaude Opus 5.5 3c557c9f0a docs: archive the improvement log/scan and the June superpowers plans
Moved to docs/archive/ (kept for their history, not deleted), each with a
one-line header saying it is historical and what supersedes it:

- IMPROVEMENT_LOG.md: three automated-loop PRs from April-May 2026, on
  the earlier quantumclaw PR numbering, which now collides with this
  repo's #12-#15. Superseded by CHANGELOG.md and git log.
- IMPROVEMENT_SCAN.md: one scan's notes (2026-05-04) of changes merged
  long ago. Superseded by CHANGELOG.md and git log.
- docs/superpowers/plans/*.md -> docs/archive/plans/: agent pre-work
  plans for d6c4d4f (2026-06-30), already marked implemented. The MPI plan
  promised collective MPI-IO, which is not what shipped (MpiVol is
  root-read + broadcast); its header says so and points at ROADMAP.md,
  where collective I/O is an open item.

Nothing links to the old paths (research/*.md mention IMPROVEMENT_LOG.md
and ROADMAP.md in prose only).

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:13:40 -05:00
osobhandClaude Opus 5.5 419cb52287 docs: ROADMAP rewritten from CHANGELOG, git log and known-issues
The old file was a tracker for the mid-2026 agent-memory tracks, last
updated 2026-08-05, with an OpenClaw track and "what's next" items that
have since shipped (CI, fuzz target, WAL checksums, HNSW parallel build).

Now: releases v2.0.0-v2.7.0 and every PR merged since (#3-#21, merge
dates from git log), range-read milestones M0-M5, a one-paragraph summary
of the agent-memory work, and what is genuinely next: crates.io and PyPI
publishing (plus the broken Node package), SWMR writing, MPI collective
I/O, paged-metadata single-request reads, Blosc2/ZFP encoders, and the
open items of docs/known-issues.md. OpenClaw and ZeroClaw are listed only
as withdrawn. No dates are given for future work.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:13:40 -05:00
osobhandClaude Opus 5.5 cab952bb00 docs(conformance): file classes, ref-bug and ref_fix, latest result
Explains each class compare.py assigns, how ref_bugs.py confirms a
ref-bug in every run and how ref.py corrects h5py's big-endian VL values
(ref_fix), and records the latest result (602 of 697 ok, 3 ref-bug,
2026-09-27) with a link to CONFORMANCE.md. Mentions --no-fetch.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:13:30 -05:00
osobhandClaude Opus 5.5 999cb86071 docs(wasm-viewer): package size re-measured after openUrl; round-trip costs
The size table predated openUrl (it said so). Re-measured on tank at
9b5803f with `bash examples/wasm-viewer/build.sh`, then `wc -c` and
`gzip -9 -n -c`: the wasm is 1,384,607 B (378,485 gzipped), was 627,501
(191,639); the glue 40,711 (8,181), was 21,826 (4,487); remote.js 9,326
(3,448). 476,062 B of the wasm is the function-name section. opt-level z
(CARGO_PROFILE_WASM_RELEASE_OPT_LEVEL=z) is now 1% smaller gzipped than
the profile's s; 3 is larger. h5wasm rows unchanged.

Also adds the measured cost of listing a large group and reading one
dataset by URL (passes / requests / bytes, from CHANGELOG, 2026-09-27).

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:13:30 -05:00
osobhandClaude Opus 5.5 b55b24b7ba docs: crate READMEs describe each crate as it is today
Every crate under crates/ now has a README (android, bench, cli, napi and
wasm had none), each saying what the crate is, its main types and
functions (names checked against the code), its cargo features with
defaults and which ones build C (checked with `cargo tree`), and links to
the top-level docs.

Corrections to the old stubs:
- clawhdf5-derive: the derive is `H5Type`, not `HDF5Type`, and it needs
  clawhdf5-format as a dependency.
- clawhdf5-filters: deflate backends only, and no library crate depends
  on it; the filter pipeline and every other codec are in -format.
- clawhdf5-gpu: vector distance compute, not I/O; not used by
  HDF5Memory::search.
- clawhdf5-io: MpiVol is root-read + broadcast, not collective MPI-IO.
- clawhdf5-ann: from_hdf5/search(q, k) did not exist; load_from_hdf5 and
  search(q, k, ef).
- clawhdf5-accel: checksum::crc32_simd did not exist; the SSE4 and wasm
  backends are reported but run the scalar kernels.
- clawhdf5-gpu: the old example called l2_distances, which does not
  exist (l2_search).
- clawhdf5-agent: it described a "vector store" with "GPU acceleration";
  it now covers HDF5Memory, search options, WAL, signing, the graph.
- crates.io/docs.rs badges removed and `cargo install <crate>` replaced:
  nothing is published; depend on git.
- fuzz: the opt-in CLAWHDF5_FUZZ_SECONDS smoke run in ci-test.sh.
- tools: the FileEditor interop tests that live in this crate.
- remote, py: license, other front ends, limits, File.mode/flush/chunks.

The Rust examples of the facade, format, filters, accel, ann, derive and
agent READMEs were compiled and run as tests (netcdf4, gpu and remote
compiled only) in a scratch crate; the CLI example was run.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:13:30 -05:00
osobhandClaude Opus 5.5 b660952421 docs: docs/README.md indexes every document
One line per document: user guides, evidence (CONFORMANCE, BENCHMARKS,
the conformance README), design docs, crate and package READMEs, and the
historical notes (roadmap, improvement logs, June plans, research briefs).

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:10:22 -05:00
osobhandClaude Opus 5.5 b0b4018919 docs: QUICKSTART and USE_CASES on the current APIs
QUICKSTART used APIs that do not exist (file.dataset_names(),
File::attr, AttrValue::Str, memory.search(&q, 5), MemoryConfig::new with
a &str, consolidation without timestamps), `clawhdf5 = "2.0"` from
crates.io, and "3-45x faster than libhdf5". It now covers HDF5 in Rust
(write, read, strings, in-place append, remote, SWMR), Python (read, r+,
w, URLs), NetCDF-4, h5rs, agent memory and the CLI, every snippet
compiled and run (Python against a wheel built from the tree).

USE_CASES dropped claims with no source (the agent crate adds ~2MB,
IVF-PQ under 1.2 ms on modest hardware, an OpenClaw scenario, a .brain
layout and `clawhub publish` commands) and now covers the HDF5 cases
(no-C builds, threads, remote data, untrusted files, SWMR, in-place
edits), the agent cases with measured numbers, and when to use
something else.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:10:22 -05:00
osobhandClaude Opus 5.5 a90373ca84 docs: README rewritten around the HDF5 library and its evidence
Leads with what clawhdf5 is today for an HDF5 reader: the conformance
result (602 of 697, 0 mismatches, no panic/hang/crash; CONFORMANCE.md of
2026-09-28), the CVE corpus against h5dump and h5py, concurrent reads
against h5py threads and processes (BENCHMARKS.md, 2026-09-26, c5334b1)
and the libhdf5 comparison with its date and caveat; then a feature matrix
(supported / read only / not supported), install from git and maturin,
Rust and Python quick starts, remote files, the browser, SWMR, h5rs, a
short agent-memory section, the crate map and a documentation table.

Removed: the unverifiable "1850+ tests" badge and "~86K lines" footer,
the "What's new v2.2 -> v2.7" list (it is CHANGELOG.md), the agent
comparison table with other products, the Phase 1/2 roadmap checklist,
and the long agent sections (now docs/agent-memory.md). Fixed: crates
listed as C-free, SZIP / N-Bit / scale-offset as read-only, virtual
datasets as written too, Python 'r+' can create attributes (it cannot
create or delete objects). Every code snippet was compiled and run
against the workspace, the Python ones against a wheel built from it.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:10:22 -05:00
osobhandClaude Opus 5.5 4d1a43fd7a docs: agent memory guide in docs/agent-memory.md
The agent-memory detail that lived only in README.md (architecture,
modules, performance and footprint tables, LongMemEval, feature flags and
settings, file schema, SQLite migration, research foundation) moves to its
own page, so the README can lead with the HDF5 library. Code examples are
updated to the current API (MemoryConfig::new takes a PathBuf,
HDF5Memory::search with SearchOptions, consolidation with timestamps) and
were compiled and run against the workspace; the CLI section was run
against the built `clawhdf5` binary. New: the CLI's search defaults to
0.7/0.3, not the library's 0.4/0.6; the /integrity group of signed stores.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:10:22 -05:00
osobhandClaude Opus 5.5 38107b90ed docs: CLAUDE.md regrouped into rules, invariants and workflows
Standing rules (no C by default, h5py must read what we write, one
float16 implementation, claims need evidence, OpenClaw/ZeroClaw
withdrawn, the known-issues rule) are gathered in one place; library and
agent-memory invariants are split; the CI section lists what
ci-test.sh and the conformance workflow run now instead of a dated
"two jobs, green" line. Adds the conformance, remote, wasm, Python and
benchmark workflows (idle load below 2, dated records), and warns that
scripts/run-benchmarks.sh is stale and overwrites BENCHMARKS.md. Crate
roles corrected (clawhdf5-io is I/O adapters; codecs live in
clawhdf5-format). Benchmark figures now live in BENCHMARKS.md only.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:08:53 -05:00
osobhandClaude Opus 5.5 24cc9d14d8 docs: known issue for the flapping bad_nbit_parms_walk classification
The committed CONFORMANCE.md counts bad_nbit_parms_walk.h5 as an
our-error because its six h5py reads agreed in that run; a rerun the
same day confirmed the over-read and counted it ref-bug. The ok count
(602 of 697) is the same either way.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:07:20 -05:00
osobhandClaude Opus 5.5 ac0020594b docs: design status notes reflect what is merged
range-reads.md opens with a table of milestones M0-M5 and the PRs that
merged them (#17-#21), replacing a header left garbled by earlier
merges, and each milestone's status names its PR. swmr.md says the
reader is merged (PR #19) and the writer does not exist. openclaw.md
links the Node package's known-issues entry.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:05:38 -05:00
osobhandClaude Opus 5.5 06d8e2ee45 docs: benchmark headline numbers, superseded sections labelled
A "Current headline numbers" table gives each figure's newest dated
measurement with its machine, command and section. Sections a later run
replaced are marked superseded with a link to the newer one; stale
"still open" notes and cross-references now point at the fixes. No
measured value changed.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:04:38 -05:00
osobhandClaude Opus 5.5 798331ddbc docs: known issues split into open issues and a condensed fixed history
An "Open issues" table at the top links each open entry; fixed entries
move to "Fixed (history)", newest first, keeping the date, PR, affected
releases and what users must do. Open entries re-checked against main
(9b5803f): the remaining audit gaps are gathered into one entry, the
range-read and remote limits no longer contradict themselves (Python and
the browser open URLs; SWMR reading is File::open_swmr), and the
nondeterministic damaged-chunk error, fixed in PR #19, has its own
history entry.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-28 11:04:38 -05:00
osobh 9b5803f587 Merge pull request 'Remote files open in a few requests; ObjectHeader::parse back to speed; last conformance mismatches resolved (602/697)' (#21) from feat/listing-header-last-files into main
CI / test-arm64 (push) Successful in 1m39s
CI / test (push) Successful in 15m37s
Reviewed-on: #21
2026-09-28 11:57:03 +00:00
osobhandClaude Opus 5.5 694ee0a090 docs: conformance report after the last non-ok files were classified (602 of 697 ok)
CI / test-arm64 (pull_request) Successful in 1m22s
CI / test (pull_request) Successful in 15m34s
Regenerated on tank: ok 600 -> 602 (attr_datatypes.hdf5 and
tcomplex_be.h5, compared against h5py's big-endian VL values corrected),
mismatch 2 -> 0; cve-2025-2308.h5 and cve-2025-44904.h5 are ref-bug
(h5py's values varied across six heaps in this run);
bad_nbit_parms_walk.h5 read the same in all six this run, so it stays
our-error, as the classification rule requires. Baseline raised.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 23:39:41 -05:00
osobh bf5a163dcf Merge branch 'perf/wasm-listing-passes' into feat/listing-header-last-files
# Conflicts:
#	CHANGELOG.md
2026-09-27 23:16:27 -05:00
osobh 4f90ce02a7 Merge branch 'perf/header-parse-and-last-files' into feat/listing-header-last-files 2026-09-27 23:16:23 -05:00
osobhandClaude Opus 5.5 5b45c60c9c docs: ObjectHeader::parse A/B after inlining the v1 message loop (at or below 8f59b2e)
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 23:15:09 -05:00
osobhandClaude Opus 5.5 2e5b059530 docs: fewer round trips for remote files in the browser, counted
CHANGELOG (Unreleased): the v1 B-tree lookup, `Storage::hint`, the walks
that go on past a missing node, and the counts before and after on an
h5py file like the reviewer's (3000 datasets, 198 MB, earliest and
latest libver, 1 MiB and 64 KiB blocks), the corpus read lazily at
512 B and 64 KiB blocks, and the Node/Chromium suite.
known-issues (browser limits, round trips): the new counts, why the
passes cannot go lower (the chain of addresses), why merging nearby
requests does not help such a file, and that a second listing refetches
at 1 MiB blocks when the file's metadata blocks exceed `cacheSize`.
range-reads.md M4 status and the viewer README follow.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:48:47 -05:00
osobhandClaude Opus 5.5 761bdbf24f format: look a name up in a v1 group down its B-tree, as libhdf5 does
Opening one dataset of a v1 (symbol table) group read every symbol
table node and every name of the group to find it: over openUrl, 74
requests and 193 MB to read one 64 KiB dataset of the reviewer's
3000-dataset h5py file (libver earliest) at 1 MiB blocks, 515 requests
and 34 MB at 64 KiB. Locally it made a lookup O(entries).

`group_v1::find_v1_entry` looks the name up as libhdf5's
`H5G__stab_lookup` does: `H5B_find`'s binary search at each B-tree node
with `H5G__node_cmp3` (left key < name <= right key, keys being names in
the local heap, compared bytewise like strcmp), then the one symbol
table node, after the heap's free list is checked as the listing does.
The heap's data segment (up to 1 MiB) is hinted, since the keys are read
one after another. Path resolution uses it for a v1 group; only when it
does not find a hard link of that name (a soft link, or a B-tree out of
name order, damaged or hand-made, where libhdf5 would report the name
missing) does it read every entry as before. A storage error is returned
as is (over the lazy reader, a miss: reading every entry would not get
further). The result differs from before only in a group holding two
entries of one name, where the B-tree's is now the one found, as in
libhdf5.

Measured with tests/lazy.rs listing_cost_of_a_given_file, open + read
one 64 KiB dataset of the reviewer-like file, passes/requests/bytes,
before -> after (open included):
  earliest, 1 MiB:  7/74/193.6 MB -> 6/5/5.2 MB
  earliest, 64 KiB: 9/515/34.1 MB -> 8/7/524 KB
  latest (dense groups, already a name-index lookup): 1 MiB 8/7/6.7 MB
  -> 7/7/6.7 MB, 64 KiB 9/8/581 KB -> 8/8/581 KB (the previous
  commit's hints: the name index header with the heap header)
New tests, failing before: every child of v1_groups_400.h5 resolves
to its listed address reading under 1/8 of the listing's bytes, and
missing names are not found; a name moved out of B-tree order is still
found (by the fallback); reading one of 2000 datasets lazily at 512-byte
blocks takes at most 7 passes and 6 requests (earliest; 529 requests,
333 kB before) and 8 passes, 9 requests (latest).
Conformance 600 of 697 (baseline 600), no file's class or detail
changed against a run of main.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:47:47 -05:00
osobhandClaude Opus 5.5 6f5d14fd62 format: group walks go on past a failed node and hint what they read next
Listing a large group over openUrl still took 6-11 passes (network round
trips) for the reviewer's 3000-dataset h5py file: each pass only found
the structures the walk reached before its first miss.

- The v1 and v2 B-tree collectors descend into every child of a node
  after one fails (they only read the siblings before, so a sibling's
  subtree came a pass later), then return the first error: results and
  errors unchanged. The v2 walk stops once its record budget is spent,
  so a shared-subtree tree still cannot multiply the work.
- Hints (`Storage::hint`, a no-op for every backend but the lazy one):
  a group B-tree node's and a symbol table node's body (read once their
  header gives a length, a round trip later when the body is in the
  next block), an object header's first chunk and its continuation
  chunks, the symbol table nodes a B-tree leaf names, a dense group's
  name index header and the heap's root block (both read right after
  the heap header). A listing also hints every child's object header as
  its entry is read, even after a failure, and every direct block of a
  dense group's heap (reading the indirect blocks, at most 4096 entries
  and 4 levels deep); a lookup does not.
- The fractal heap's indirect-block layout (entry sizes, where the first
  n entries end) is one helper used by the object reads and the hints.

Measured with tests/lazy.rs listing_cost_of_a_given_file on an h5py file
like the reviewer's (3000 datasets of 64 KiB, 198 MB), list('/'),
passes/requests/bytes, before -> after:
  earliest, 1 MiB:  6/73/192.5 MB -> 4/68/192.5 MB
  earliest, 64 KiB: 8/531/35.2 MB -> 5/530/35.3 MB
  latest,   1 MiB:  9/98/196.5 MB -> 5/86/196.5 MB
  latest,   64 KiB: 11/452/29.6 MB -> 6/454/30.5 MB
listing_a_large_group_takes_a_few_passes (512-byte blocks), budgets
tightened to the new counts: FileBuilder 600 children 5 -> 4 passes,
h5py 2000 children earliest 8 -> 5, latest 11 -> 6.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:47:44 -05:00
osobhandClaude Opus 5.5 ca81c3ebfa format, wasm: Storage::hint, fetched by the lazy reader with a pass's misses
A parser often learns where the next structures are (a node's children,
a structure's body once its prefix gives its length) before it reads
them one at a time. Over openUrl's restartable reader a structure only
reached after a miss costs a pass, and a round trip, of its own.

- clawhdf5-format: `Storage::hint(offset, len)`, "about to be read by
  this operation". Default: nothing (every backend that reads when
  asked); `&T`, `Box`, `Arc` and the facade's `FileData` forward it
  (shifted past a user block, clamped to the file).
- clawhdf5-wasm `LazyStorage` records hinted blocks it lacks. A pass
  that misses nothing ignores them (a hint never adds a round trip); a
  pass that misses also asks for them, in file order, while the pass
  stays within what is left of the operation's `maxFetch` budget (a
  hint never makes a call fail). At most 1 MiB (or a block) per hint
  and 65536 blocks per pass are recorded, whatever a file makes a
  parser hint. `Operation::attempt` follows hints; the plain
  `LazyStorage::attempt` does not. `run_blocking` and the browser's
  driver use the former. `LazyStats::hinted_blocks` counts them.

No parser hints yet: results, passes and requests are unchanged.
Tests: hinted blocks come with a miss and never alone (cached ones
skipped, a plain attempt ignores them), and stay within the fetch
budget, a hint past the end or longer than the file harmless.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:41:09 -05:00
osobhandClaude Opus 5.5 05e1136027 docs: conformance report with the last non-ok files classified (602 of 697 ok, 0 our-error, 0 mismatch)
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:40:03 -05:00
osobhandClaude Opus 5.5 ff0b2f8a4e conformance: keep ref-bug files out of the root-cause tables, name the non-ok classes
A ref-bug file's refused objects were still listed as our-error root
causes. The summary line now names every non-ok class and its count, and
an empty root-cause table says None.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:33:42 -05:00
osobhandClaude Opus 5.5 96086add99 format: inline the version-1 message loop again (ObjectHeader::parse back to 8f59b2e's speed)
4313917 kept parse_v1_messages out of line (#[inline(never)]) so the
generic parser would not carry the loop; since ef428d7 the slice path is
compiled once in this crate, and the call itself was the remaining cost
of the chunk queue: A/B builds of object_header_parse_x401 with only this
attribute changed put #[inline(never)] and no attribute at 24.5-24.9 us
and #[inline] at 23.6-24.0 us, with 8f59b2e at 23.6-24.1 us. Lazily
creating the chunk list only when a continuation is found (tried too)
measured no faster and was not kept.

Same code otherwise: every chunk-queue check (65,536 chunks, cycles, file
size budget, one chunk buffer at a time, libhdf5 order, overlap allowed)
is unchanged.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:32:11 -05:00
osobhandClaude Opus 5.5 5c44630ea2 conformance: compare h5py's big-endian VL values corrected, confirm libhdf5 over-reads per run
The last 3 our-errors and 2 mismatches were documented as not ours but
still counted against us, on a heuristic (any big-endian VL mismatch) and
a fixed list.

- ref.py checks that the installed h5py returns big-endian VL elements
  with the file's bytes under a little-endian dtype (writing and reading
  a vlen('>f4') in memory) and, if so, relabels them with the file's byte
  order before hashing, marking the object `ref_fix`. The values are now
  compared: attr_datatypes.hdf5 /@vlen_uint64 and tcomplex_be.h5
  /VariableLengthDatasetFloatComplex are identical to ours (h5dump 1.14.6
  prints the same (1, 2), (3, 4, 5), (42)).
- ref_bugs.py re-reads each object h5py reads only through a libhdf5 bug
  in six processes with different heaps (import order, MALLOC_PERTURB_).
  Values the file determines are the same every time; these three change
  (6, 6 and 3 distinct results), so they are over-read memory, not data
  clawhdf5 could match. compare.py classifies a file `ref-bug` only when
  every difference is such an object confirmed in the same run.
- report.py: the ref-bug class, the evidence table, the corrected
  objects; test_ref.py covers both (run in the nightly job).

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 22:26:32 -05:00
osobh 425585ee71 Merge pull request 'Benchmarks re-measured: LongMemEval with real embeddings, local reads on an idle machine' (#20) from docs/bench-refresh-2026-09-27 into main
CI / test-arm64 (push) Successful in 1m35s
CI / test (push) Successful in 16m51s
Reviewed-on: #20
2026-09-28 02:38:09 +00:00
osobhandClaude Opus 5.5 7179006aee docs: local read A/B re-run on an idle machine
CI / test-arm64 (pull_request) Successful in 1m25s
CI / test (pull_request) Successful in 15m57s
The first run of the day could not get an idle tank: two orphaned h5py
SWMR reader processes from earlier interop tests (since stopped) kept a
core each busy. Re-run with the load below 2 at every round:
ObjectHeader::parse is +4.2% (real: the ranges do not overlap; about 2.5
ns per header, not visible in the facade listing, which is -1.7%); full
deflate reads +1.7% (1 thread) to +36% (16 threads); the -5.6% single-
thread contiguous hyperslab result from the loaded run is noise (-1.7%,
overlapping ranges) and is withdrawn from known-issues.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 19:43:07 -05:00
osobhandClaude Opus 5.5 b39a705e77 docs: LongMemEval with real embeddings re-run on 2026-09-27
Oracle and full longmemeval_s haystack, f32 and --float16, plus --sweep
(both corpora) and --rerank-sweep, on tank at 7a8fae0 (MiniLM on the RTX
5060 Ti). Not idle: two orphaned h5py test processes kept the 1-minute load
at 2.1-2.7 (up to 8.4 during runs), so no latency figure was updated.

The headline (hybrid 0.4/0.6 turn Hit@5 81.4%) and the float16 claim
reproduce. Oracle hybrid is 86.8%, not 85.2%: the old figure was at the
0.7/0.3 default of the time (today's 0.7/0.3 gives 85.2%). The ablation's
0.7/0.3 row, vector-only MRR and seven sweep rows move in the last digit or
by one or two questions, most likely from the index tie-break of 3ed0489.
RRF turn MRR 0.5967 -> 0.5969 is not explained. Recency counts vary by one
question between identical runs, so the float16 "flips" note is corrected.
ROADMAP 8.2 no longer repeats the retracted session-level and MemX claims.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 19:25:36 -05:00
osobhandClaude Opus 5.5 d239292655 docs: local metadata and data reads after range-read M2/M3, rechecked
8f59b2e (main before PR #18) against 7a8fae0, separate binaries,
alternating rounds on tank (6 Criterion rounds of local_metadata_bench,
3 of concurrent_read --decode-threads 1). Still provisional: two orphaned
h5py test processes held the load at 2.1-2.6 and the load < 2 gate was
not met in 2 hours.

The facade listing regression is gone (-0.8%). ObjectHeader::parse x401
is +4.1% and one-thread contiguous hyperslab reads -5.6%; both listed as
open in known-issues. Full deflate reads are 7-23% faster.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 15:35:59 -05:00
osobh 7a8fae0357 Merge pull request 'Lazy remote files in the browser (M4), SWMR reader (M5), Python remote reads and editing' (#19) from feat/p3-wasm-swmr-python into main
CI / test-arm64 (push) Successful in 1m41s
CI / test (push) Failing after 20m45s
Reviewed-on: #19
2026-09-27 14:47:26 +00:00
osobhandClaude Opus 5.5 175d3a1f50 docs: chunk-cache order fix in the changelog and known issues
CI / test-arm64 (pull_request) Successful in 1m26s
CI / test (pull_request) Successful in 19m25s
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 08:03:24 -05:00
osobhandClaude Opus 5.5 4ad80736f4 format: the chunk cache keeps the index's chunk order
ChunkCache::chunks_for returned the chunk index's values in hash-map
order, which differs between File instances (a new HashMap per open).
Readers that stop at the first failing chunk therefore named different
chunks on different opens of the same damaged file: whole-dataset
selections here, and the indexed reader behind the storage harness's
intermittent cve-2025-2310.h5 failure. The cache now also keeps the
chunks in the order the index lists them (fetched or built under one
lock) and returns that order, as the uncached readers use.

Regression: several_damaged_chunks_report_the_same_chunk_every_time
(four chunks inflating to different short lengths; before the fix two
opens reported chunk [40, 0] and chunk [320, 0]).

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 08:03:11 -05:00
osobhandClaude Opus 5.5 fcf45b6845 clawhdf5: initialise swmr in File::from_std_file
The editor branch added File::from_std_file and the SWMR branch added the
swmr field to File; merged, the constructor did not set it.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 08:03:11 -05:00
osobh e80b12521e Merge branch 'feat/p3-m4-wasm-lazy' into feat/p3-wasm-swmr-python
# Conflicts:
#	CHANGELOG.md
#	docs/design/range-reads.md
#	docs/known-issues.md
2026-09-27 07:59:14 -05:00
osobh 5d42b4241c Merge branch 'feat/p3-python-remote-edit' into feat/p3-wasm-swmr-python
# Conflicts:
#	CHANGELOG.md
#	docs/design/range-reads.md
#	docs/known-issues.md
2026-09-27 07:59:14 -05:00
osobh 527a1a7ac6 Merge branch 'feat/p3-m5-swmr-reader' into feat/p3-wasm-swmr-python 2026-09-27 07:59:14 -05:00
osobhandClaude Opus 5.5 18e9be0af7 py: only well-formed masks are NotImplementedError; others stay TypeError
A boolean array of the axis's length, or of the dataset's whole shape, is
a mask h5py would apply (NotImplementedError here); one of any other shape
(np.array(True), a wrong length) is a key h5py itself refuses with
TypeError, which test_errors_match_h5py requires us to match.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 07:57:49 -05:00
osobhandClaude Opus 5.5 7a4acbce12 docs: openUrl hardening after review (limits, listing passes, CORS tests)
CHANGELOG (M4 section), known-issues (wasm limits: maxFetch, the 1 GiB
decode limit, the 4 GiB file limit on wasm32, bodies cut off at their
length, listing passes, the cross-origin tests, and a pre-existing
nondeterministic error choice on cve-2025-2310.h5 that can fail the
native corpus comparison), the viewer README (options, how listing
costs, tests) and the M4 status in docs/design/range-reads.md.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 07:54:29 -05:00
osobhandClaude Opus 5.5 2379e6163e wasm: openUrl takes Headers, aborts sibling requests on failure, checks parallel
- opts.headers is read as fetch reads it (a Headers, [name, value] pairs
  or a plain object); it was spread as an object, which silently dropped
  a Headers instance (a common way to pass Authorization). A caller's
  Range is not sent.
- When one range request of a batch fails, the others in flight are
  aborted (one AbortController per batch, its signal passed to fetch)
  and no new ones start; the first failure is the error. The workers
  used to go on issuing requests nobody waited for.
- parallel must be an integer from 1 to 1024 (openUrl) or a positive
  integer (fetchRanges): a non-number gave NaN workers, so none ran and
  fetchRanges returned nothing.

Tests (test.mjs): headers as object, Headers and pairs reach the fetch;
bad parallel values are option errors; fetchRanges with a 500 on the
third of 20 ranges at parallel 3 starts 3 requests and aborts the 2 in
flight. Before: the Headers case sent no header, 17 requests started
after the failure with none aborted, and parallel "x" returned.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 07:53:22 -05:00
osobhandClaude Opus 5.5 581c6ddef8 wasm-viewer tests: the cross-origin path without exposed headers
serve.py always exposed Content-Range and ETag, and Node has no CORS, so
openUrl's documented cross-origin path (length from a HEAD request,
answers checked by body length alone, no validator) was never run.

- serve.py /noexpose/ serves ranges without Content-Range, ETag,
  Last-Modified or Accept-Ranges (what a page sees of a server that
  does not expose them); /unexposed/ sends them but exposes none, for a
  real browser. HEAD requests are counted (0 bytes).
- test.mjs: every fixture check through /noexpose/ at 1 MiB and 512-byte
  blocks (one HEAD each, requests and bytes as the server counted them),
  concurrent reads with cacheSize 0, a short answer still caught, and a
  server without a HEAD length a clear error.
- browser.sh: the page on 127.0.0.1 opens the file from localhost, once
  with Content-Range exposed and once through /unexposed/, where the
  server's log must show the HEAD.

Checked by breaking the HEAD length in remote.js: the new checks fail.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 07:51:30 -05:00
osobhandClaude Opus 5.5 d09e55e229 edit: plan from a new description of the held file, not a clone (Linux)
Planning from a mapping of a clone of the locked descriptor shared its
flock: a process forked by another thread meanwhile (any Command) kept the
lock alive for a moment after the editor was dropped, and a test that
reopened the file at once saw Error::Locked (once in a full run). On Linux
plan through /proc/self/fd (a new open file description of the same
file, which still follows a rename); elsewhere keep the clone.

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
2026-09-27 07:51:22 -05:00