Files

T

osobhandClaude Opus 5.5 6a4707d791 format: add the Storage trait; make the error enums non-exhaustive

Range-read milestone M1, first step (docs/design/range-reads.md §3(a)):
a synchronous, no_std read interface with u64 offsets, read_at returning
Cow<[u8]>, read_ranges, len and an as_contiguous fast path. Implemented
for [u8], Vec<u8>, &T, Box<T> and Arc<T>; slices serve borrowed bytes.
read_exact_at reproduces the parsers' UnexpectedEof bounds error exactly,
so converted modules keep their error values.

FormatError gains Storage(String) and ContiguousStorageRequired; it and
the facade Error are now #[non_exhaustive] (breaking for exhaustive
matches, noted in the changelog; the Python bindings' match gets a
wildcard arm).

Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>

2026-09-26 12:44:36 -05:00

src

format: add the Storage trait; make the error enums non-exhaustive

2026-09-26 12:44:36 -05:00

tests

test(py): detect a held GIL, and errors h5py does not raise

2026-09-26 09:03:53 -05:00

build.rs

Merge pull request 'docs(clawhdf5): document DType variants, fix unresolved doc links' (#17 ) from sdlc-docs/clawhdf5-types-20260514-165210 into main

2026-05-14 23:54:48 +00:00

Cargo.toml

fix(py): one name, clawhdf5, for the Python distribution and module

2026-09-26 08:09:54 -05:00

pyproject.toml

fix(py): one name, clawhdf5, for the Python distribution and module

2026-09-26 08:09:54 -05:00

README.md

docs: say when a selection read decodes more than the selection

2026-09-26 09:04:48 -05:00

README.md

clawhdf5-py

Python bindings for clawhdf5 — a pure-Rust HDF5 library. The package is clawhdf5 (import clawhdf5); it needs numpy and no libhdf5.

Install

Not on PyPI yet. Build it into a virtualenv with maturin:

pip install maturin numpy
cd crates/clawhdf5-py
maturin develop --release
python -c "import clawhdf5; print(clawhdf5.__version__)"

Reading

The read API follows h5py:

import numpy as np
import clawhdf5

with clawhdf5.File("data.h5", "r") as f:
    f.keys(), f["group"].items(), "group/data" in f
    ds = f["group/data"]           # or f["/group/data"], f["group"]["data"]
    ds.shape, ds.dtype, ds.attrs["units"]
    ds[10:20, ::2]                 # a small selection reads only its chunks
    ds[-1], ds[..., 0], ds[[1, 4, 7]]
    np.asarray(ds)
    f["table"]["id"]               # a compound field

Dataset.dtype is the numpy dtype h5py reports: integers and IEEE floats of every width in either byte order, bool, enums (with dtype.metadata['enum']), complex, S<n> fixed strings, object for variable-length strings (bytes values) and sequences (array values), V<n> opaque, array types, and compounds as structured dtypes. Other types raise TypeError.
Keys are h5py's: integers, slices with a positive step, ..., one increasing list of integers, compound field names. Each maps onto a hyperslab selection. None, negative steps and boolean masks are refused with h5py's errors.
What is read from the file: a selection whose bounding box covers at most half the dataset decodes only the chunks (or contiguous rows) the box overlaps. The library decodes the whole dataset for a larger box (including a strided slice such as ds[::100] across a chunked dataset), and for compact, virtual and unwritten datasets and chunked ones with a non-default fill value. An index list is read one group of neighbouring chunks at a time (a new group only past a chunk with no selected index), so each chunk is decoded once. ds[()], ds[...] and np.asarray(ds) use the file's chunk cache; other selections do not.
The bytes the library reads become the numpy array's buffer without a copy, and the read runs with the GIL released, so threads read in parallel. A bug in the library (a Rust panic) raises clawhdf5.InternalError, a RuntimeError.
Attributes return what h5py returns; clawhdf5.Empty stands for a null dataspace (h5py's Empty).

Writing

clawhdf5.File(path, "w") with create_dataset(name, data=array, chunks=..., compression="gzip"), create_group and attrs[...] = ... writes float64, float32, int64, int32 and uint8 arrays; the file is written on close().

Tests

pip install pytest h5py
pytest crates/clawhdf5-py/tests

tests/test_read_vs_h5py.py compares every read with h5py on a file h5py writes. scripts/ci-test.sh builds the wheel and runs these in CI.

License

MIT