docs: h5rs in the changelog and the crate table
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
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@@ -112,6 +112,50 @@
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`quantized_index = false`, or pass `create --f32-index` to the CLI, to opt
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out. The CLI's `--quantized-index` is still accepted but is now a no-op.
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### Tools
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- New crate **`clawhdf5-tools`** with the binary **`h5rs`**: HDF5
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command-line tools without libhdf5, built only on the `clawhdf5` facade
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and `clawhdf5-format` (no C, so it also builds as a static musl binary).
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- `h5rs ls [-r] [-v] FILE[/path]` lists objects like h5ls (its first two
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columns are h5ls's text on the test files) plus the datatype; `-v` adds
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address, link count, layout and chunk index, chunk size, storage,
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filters, datatype and attributes.
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- `h5rs dump [--json] [-A] [-p] [-d PATH] FILE` prints DDL text that is
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byte-identical to h5dump 1.14.6's on the test files (all layouts and
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chunk indexes, v1/v2 groups, compound, enum, strings, links, named
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types, attributes), or JSON in the HDF Group's hdf5-json layout (schema
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in the crate README).
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- `h5rs stat FILE` reports h5stat's object, link, rank, layout, filter,
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attribute, raw-data and file-size figures (equal to h5stat's on the test
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files); metadata space is one figure, not broken down.
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- `h5rs diff [-r] [-q] [-d D] [-p R] A B [OBJ1 [OBJ2]]` compares objects,
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kinds, datatypes, shapes, attributes, values and link targets; exit
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status 0/1/2 as h5diff's. Objects that cannot be compared count as a
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difference (h5diff exits 0 for them), and NaN equals NaN.
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- `h5rs check [--data] FILE` is a structural validator: it walks every
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object, parses every header message, verifies the checksums of every
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version 2+ structure it meets (superblock, object headers and
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continuation chunks, v2 B-tree nodes, fractal heap headers and — which
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the library's reads do not — every direct and indirect heap block, and
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extensible/fixed array chunk indexes), checks each chunk index against
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its dataset (aligned, in-extent, unique, plausibly sized chunks), and
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that raw data lies inside the file without overlaps. Every problem is
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printed with its address; exit 1 when there are any. libhdf5's h5check
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reads only the 1.8 format. On the conformance corpus it passes all 418
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files that both clawhdf5 and h5py read in full, and flags 149 of the
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180 CVE reproducers.
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- Values over `--max-bytes` (default 1 GiB) are reported instead of read;
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a panic is caught and reported as an internal error (exit 3).
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`scripts/h5rs-fuzz.sh` runs every subcommand over a corpus (default the
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CVE reproducers, optionally with byte-flipped copies) with overflow
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checks, a timeout and a memory limit, and fails on any panic, crash or
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hang; `scripts/h5rs-check-ok-files.sh` runs `check --data` over the
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fully-read conformance files.
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- Because the library does not verify fractal heap block checksums when
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it reads a dense group's links or dense attributes, `h5rs` verifies a
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heap's blocks before reading from it and refuses a damaged one, as
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libhdf5 does, instead of printing what the damaged block holds.
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### Signing
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- `clawhdf5-agent`: **Ed25519-signed checkpoints** — the README's
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"cryptographically verifiable memory", now true. With
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@@ -5,7 +5,7 @@ Pure-Rust HDF5 format implementation with HNSW vector search, WAL-backed persist
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## Architecture
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Cargo workspace with 16 crates under `crates/` (plus `libaec-sys`, an internal FFI bindings crate for the optional `szip` feature):
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Cargo workspace with 17 crates under `crates/` (plus `libaec-sys`, an internal FFI bindings crate for the optional `szip` feature):
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| Crate | Role |
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|-------|------|
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@@ -21,7 +21,8 @@ Cargo workspace with 16 crates under `crates/` (plus `libaec-sys`, an internal F
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| `clawhdf5-accel` | CPU SIMD acceleration path |
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| `clawhdf5-migrate` | SQLite → HDF5 agent-memory migration |
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| `clawhdf5-android` | Android JNI bindings |
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| `clawhdf5-cli` | Command-line interface |
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| `clawhdf5-cli` | Command-line interface (agent memory) |
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| `clawhdf5-tools` | `h5rs`: pure-Rust HDF5 tools — `ls`, `dump` (DDL / hdf5-json), `stat`, `diff`, `check` (structural + checksum validator) |
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| `clawhdf5-napi` | Node.js native addon bindings |
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| `clawhdf5-py` | PyO3 Python bindings |
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| `clawhdf5-bench` | Benchmark suite |
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@@ -188,6 +189,16 @@ cargo run -p clawhdf5-cli -- --help
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# create, save, search, recall, stats, flush-wal, agents-md, export, snapshot subcommands
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```
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### HDF5 tools (`h5rs`, crate `clawhdf5-tools`)
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```bash
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cargo run -p clawhdf5-tools -- ls -r file.h5 # also dump [--json], stat, diff, check
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bash scripts/h5rs-fuzz.sh # every subcommand over the CVE corpus: no panic/crash/hang
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bash scripts/h5rs-check-ok-files.sh --data # check passes every fully-read conformance file
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```
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Its interop tests compare against h5ls/h5stat/h5dump/h5diff (Debian
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`hdf5-tools`, installed in CI); `dump` must stay byte-identical to h5dump on
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the test files.
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### Python bindings
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```bash
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cd crates/clawhdf5-py
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