The READMEs said ds[...] reads only the selected elements, and the
facade's read_selection docs that only intersecting chunks are
decompressed. The bounding-box path runs only when the box covers at
most half the dataset; larger boxes (any strided slice across the
dataset), compact, virtual and unwritten datasets and chunked ones with
a non-default fill value decode the whole dataset. The READMEs, the
facade and format docs, the bindings' docstrings and known-issues now
say so, and how index lists are read.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Every ds[...] and g[k] resolved the path from the root again, two or
three times per open, and resolving a name in a large group scans its
links: visiting a group was O(n^2). 4000 scalar datasets in one group
took 39 s (v1 group) and 131 s (dense) to list, read and re-read; now
0.3 s each. A Dataset keeps its object address, a Group (and the file's
root) its address and, after the first lookup, its link table.
New facade API File::dataset_at(address), tested in integration_tests.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Each run of consecutive indices was its own uncached hyperslab read, so
a list over a compressed chunked dataset decoded the same chunk once per
run (d[range(0, 200000, 40)] over 20 gzip chunks: 8 s, h5py 0.014 s).
Plan::reads now groups the indices — a group ends only where a whole
chunk holds no selected index, or, unchunked, at a gap over 64 KiB — and
the selected rows are gathered from each group's block in Rust. Now
3.8 ms (h5py 4.1 ms, release, tank). The new test (1-D, 2-D and
contiguous, compared with h5py, 2 s bound) took 5.8 s before.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
np.concatenate copies structured dtypes field by field into np.empty, so
the padding of ds[[0, 3, 6]] held process memory. The runs' bytes are
joined in Rust, whole elements at a time, before anything becomes numpy:
the padding is the file's bytes (h5py's) and the result is still a view
of the Rust buffer. The h5py comparisons now compare every byte of
structured values; the new test failed on the padding before.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
PanicException derives from BaseException, so `except Exception` let a
library bug through. Every call from the bindings into the library now
runs under catch_unwind and a panic becomes InternalError (RuntimeError)
naming the object. Tests: a hidden hook panics inside the guard; and the
v4 chunk indexes are compared with h5py from Python — with the library
fix reverted, ds[0:30] of the implicit-index dataset now raises
InternalError instead of aborting the test run.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
ds[key] read the whole dataset and sliced it in numpy, and knew six
dtypes. Keys (ints, positive-step slices, Ellipsis, one increasing index
list, compound field names) now map onto hyperslab selections, and the
facade's read_selection bytes become the numpy buffer without a copy
(PyArray::from_vec viewed as the dtype). dtype mapping follows h5py for
all integer/IEEE float widths and byte orders, bool, enum, complex, fixed
and variable-length strings, vlen sequences, opaque, array types and
(nested, padded) compounds; anything it cannot describe exactly is a
TypeError. Attributes return what h5py returns; groups and files gain
the rest of the h5py mapping interface. Reads run under py.detach.
tests/test_read_vs_h5py.py compares >500 reads with h5py 3.16 on an
h5py-written file, checks errors match, that a damaged chunk outside the
selection is never touched, and 8 threads reading at once.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Resolves two gaps found in a project-state review:
1. Python build was broken: PyO3/numpy 0.23 caps at Python 3.13 but the
environment has 3.14. Bumped to 0.28 and updated the two breaking APIs
(PyObject -> Py<PyAny>, allow_threads -> detach). The extension module now
imports and round-trips under Python 3.14, unblocking cargo build --workspace.
2. The "HNSW vector search over agent memories" headline was unwired:
clawhdf5-ann had zero dependents and the agent used a linear cosine+BM25 scan.
- clawhdf5-ann is now a live index: insert, mark_deleted (soft delete with a
deleted bitset, traversed but never returned), compact, and a format
version tag (v2) with backward-compatible load of v1 files.
- clawhdf5-agent wires HNSW behind the `hnsw` feature (ON by default). The
index mirrors the cache (node id == cache index) and self-heals: it rebuilds
whenever hnsw_synced_len drifts from cache.len(), so unhooked pushes can't
desync it. Non-indexable stores (no/zero-dim/mixed embeddings) and queries
whose dim doesn't match fall back to the exact linear scan.
- hybrid.rs gains merge_vector_keyword, shared by the linear and HNSW paths.
- tests/hnsw_integration.rs validates recall vs a brute-force oracle plus
insert/delete/batch behaviour.
Disable HNSW for exact search with `--no-default-features --features float16`.
Co-Authored-By: Claude Opus 4.8 (1M context) <[email protected]>
