clawhdf5/CLAUDE.md

# clawhdf5

## Purpose
Pure-Rust HDF5 format implementation with HNSW vector search, WAL-backed persistence, agent memory storage, and GPU-accelerated I/O. Used by ZeroClaw as its persistent memory and knowledge graph backend.

## Architecture

Cargo workspace with 16 crates under `crates/` (plus `libaec-sys`, an internal FFI bindings crate for the optional `szip` feature):

| Crate | Role |
|-------|------|
| `clawhdf5-format` | HDF5 binary spec parser (superblock, B-tree, heap) — also holds shared type definitions and physical constants |
| `clawhdf5-io` | Read/write implementation |
| `clawhdf5-filters` | Compression filters (gzip, LZ4, Zstd, Blosc) |
| `clawhdf5-derive` | Proc-macro derive for HDF5-serializable structs |
| `clawhdf5` | Main facade crate |
| `clawhdf5-netcdf4` | NetCDF-4 compatibility layer |
| `clawhdf5-ann` | HNSW approximate nearest-neighbor vector index |
| `clawhdf5-agent` | Agent memory, session history, knowledge graph storage |
| `clawhdf5-gpu` | GPU-accelerated I/O via wgpu (hand-written WGSL compute shaders) |
| `clawhdf5-accel` | CPU SIMD acceleration path |
| `clawhdf5-migrate` | SQLite → HDF5 agent-memory migration |
| `clawhdf5-android` | Android JNI bindings |
| `clawhdf5-cli` | Command-line interface |
| `clawhdf5-napi` | Node.js native addon bindings |
| `clawhdf5-py` | PyO3 Python bindings |
| `clawhdf5-bench` | Benchmark suite |

## Key Features
- Zero-C-dependency HDF5 read/write: no libhdf5, and deflate defaults to
  pure-Rust zlib-rs (`fast-deflate` opts into zlib-ng, which needs cmake).
  `ci-test.sh` fails if a C-building crate enters the core crates' default
  tree. flate2 must keep `runtime_detection` with zlib-rs — without it zlib-rs
  loses SIMD and inflates 3.5x slower. MSRV is 1.92 (`rust-version`, checked
  in CI).
- HNSW vector index for semantic similarity search over agent memories — the
  `clawhdf5-agent` `hnsw` feature is **on by default**, so `hybrid_search` uses
  the approximate `clawhdf5-ann` index for the vector stage (the index mirrors
  the cache and self-heals on drift). Build the agent with
  `--no-default-features --features float16` to force the exact linear cosine scan.
  The agent's `parallel` feature (also default) builds the index on a thread
  pool; the graph is identical with or without it.
  The index uses the HNSW paper's diversity heuristic for neighbour selection
  (plain closest-M capped recall on clustered data: 0.31 recall@10 at 100K). Its
  graph is saved to `<store>.h5.ann` at each checkpoint and reloaded by `open()`
  (tied to the checkpoint by a generation id; stale/damaged sidecars are
  ignored and the index rebuilt). `MemoryConfig::quantized_index` (**on by
  default** for new stores, persisted; stores predating the setting load as
  `false` and keep their f32 index — guarded by
  `tests/fixtures/store_v2_5_0.h5`; CLI opt-out is `create --f32-index`)
  stores the index's own copy of the embeddings as `i8`,
  which roughly halves a loaded store's memory (2.72x -> 1.74x the raw vectors
  at 100K); because quantised distances are approximate and `ef` cannot
  compensate, the query path then re-scores the candidate pool against the
  exact embeddings, which holds recall at the f32 index's level. It is also
  faster at equal recall: 1.63x the QPS on x86-64 (AVX2) and 1.18x on a
  Raspberry Pi 5 (`clawhdf5_accel::dot_i8`, NEON `SDOT` via inline asm since
  the intrinsic is unstable; plain NEON on pre-dotprod cores). The aarch64
  code is `cfg`'d out on x86, so x86 CI never compiles or lints it — test it
  on real ARM (`rpivision02`, 10.0.2.3, is a Pi 5). `hybrid_search` keeps one incremental BM25
  index for the life of the store and never writes the store: Hebbian
  activation boosts are persisted by the next checkpoint (or on drop), not per
  query. Measure any search-path change with
  `cargo run --release -p clawhdf5-bench --bin search_harness` (baselines in
  `BENCHMARKS.md`).
- WAL (write-ahead log) for crash-safe persistence, with a chained CRC32
  trailer per entry (each entry's CRC folds in the previous entry's CRC) so a
  corrupted, reordered, duplicated, or spliced entry stops replay cleanly
  instead of loading bad or tampered data. The pre-chaining per-entry-CRC
  format (v2) is still fully readable; the oldest no-CRC format (v1) is only
  reachable through the one-time migration path in `HDF5Memory::open`, not
  through the public `WalFile::read_entries`.
  **What the WAL guarantees:** integrity, ordering, and recovery from a
  *process* crash at any point — including between a checkpoint and the WAL
  truncate (each checkpoint records a `WalMark` in `/meta`, and `open()` skips
  the WAL prefix the `.h5` already contains, so entries are never applied
  twice). Checkpoints and snapshots are made durable as a unit (temp file
  synced, renamed, directory synced). **What it does not guarantee:**
  individual WAL appends are *not* fsynced (a deliberate latency trade-off), so
  saves made since the last checkpoint can be lost on power failure or kernel
  panic. Current header version is 4 (adds the `Update` record used by
  `save_or_update`); v3 files are read and upgraded in place.
- A store has a **single writer**: `HDF5Memory::create`/`open` hold an exclusive
  advisory lock on `<store>.h5.lock` and a second opener gets
  `MemoryError::Locked`. Use `HDF5Memory::open_read_only` for a lock-free,
  never-writing point-in-time view (the CLI's `recall`/`stats`/`agents-md`/
  `export` do). An unreadable WAL (torn header, bad magic) is quarantined to
  `<store>.h5.wal.corrupt-<ts>` rather than blocking `open()`; a WAL with an
  unknown *newer* version still fails and is left untouched.
- `MemoryConfig::float16` (off by default, persisted; CLI `create --float16`)
  writes `/memory/embeddings` as IEEE half precision (48% smaller file at
  100K, same recall). `MemoryCache::half_precision` rounds each embedding as
  it enters the cache (push, update, WAL replay, and on load of a store still
  `f32` on disk), so memory and file agree bit for bit; the conversions live
  in `clawhdf5_format::float16` and must stay the single implementation.
  Values beyond ±65504 are `MemoryError::InvalidEntry`. Interop: every file
  must open in h5py — `f32` datasets and empty datasets did not until
  2026-09-23 (see `docs/known-issues.md`); the agent's `h5py_interop` test
  guards a whole store.
- `MemoryConfig::compression` is off by default; when on, embeddings are
  deflate-compressed, or Zstd with the agent's `zstd` feature (links libzstd).
- `Dataset::verify_provenance()` (clawhdf5 facade, `provenance` feature, on by
  default) recomputes a dataset's SHA-256 and compares it against the
  `_provenance_sha256` attribute written automatically on save when
  `DatasetBuilder::with_provenance` is used. It's opt-in per call, not run
  automatically on open — it decodes and hashes the whole dataset. The hash
  is unkeyed (tamper-*evident*, not tamper-*proof*): it detects accidental
  corruption, not a deliberate actor able to modify both the data and the
  stored hash.
- `clawhdf5-agent`'s `HDF5Memory::save`/`save_batch`/`save_or_update` run every
  write through an in-memory (session-scoped, not persisted to disk)
  provenance ledger and write-anomaly detector: a content hash per record
  (`provenance.rs`) for detecting accidental mid-session corruption, plus
  rate-limit/injection-pattern/source-distribution checks (`anomaly.rs`).
  Alerts never block a save — drain them with `HDF5Memory::take_anomaly_alerts`.
  `MemorySource` for this bookkeeping is inferred from the caller-supplied
  `source_channel` string (a heuristic, not an authenticated trust boundary).
- GPU-accelerated batch I/O for large dataset processing
- Python and Node.js bindings for cross-language use
- NetCDF-4 compatibility for scientific data interop

## Workflows

### Build
```bash
cargo build --release
```

### Test
```bash
cargo test --workspace
```

### CI
`.gitea/workflows/ci.yml` has two jobs, both green as of 2026-09-22:
- **`test`** (`ubuntu-latest`, in `rust:latest`) runs `scripts/ci-test.sh` with
  the h5py/netCDF4 interop suites required (`CLAWHDF5_REQUIRE_INTEROP=1`).
  Served by the `tank` and `architect` runners.
- **`test-arm64`** (`linux_arm64`) lints and tests the aarch64 code — the NEON
  kernels are `cfg`'d out on x86, so this is the only place they are built.
  Served by `vision-01` (host mode) and `vision-02` (Docker), so steps must
  work in both.

Keep workflows free of JavaScript actions (`actions/checkout`, `actions/cache`,
…): `rust:latest` has no `node`, and not every runner reaches GitHub, where
they are fetched from. Check out with plain `git` instead. The `test` job
installs `cmake` for the opt-in `fast-deflate` (zlib-ng) steps; the default
build needs no C toolchain, so `test-arm64` does not.
All runners are on `gitea-runner` 3.5.0, from `docker.gitea.com/act_runner`
— `gitea/act_runner:latest` on Docker Hub is frozen at 0.6.1.

### CLI
```bash
cargo run -p clawhdf5-cli -- --help
# create, save, search, recall, stats, flush-wal, agents-md, export, snapshot subcommands
```

### Python bindings
```bash
cd crates/clawhdf5-py
maturin develop
python -c "import clawhdf5; print(clawhdf5.__version__)"
```

## Integration
ZeroClaw imports this as a Cargo feature (`clawhdf5` feature flag) to persist agent memory with HNSW vector search for context retrieval.