fix(format): parse HDF5 2.0 native complex datatypes (class 11)
Class 11 (datatype version 5) properties are a single base floating-point
datatype message, not a compound-style member list. The old parser read the
base type's bytes as member names, yielding a garbage datatype, and failed
with UnexpectedEof when a complex type was nested in a compound.
Parse the base type and surface the type as the equivalent {r, i} compound
(the shape h5py writes for numpy complex dtypes), with a size check against
the base type. Covered by byte-level tests taken from HDF5 2.0 output and an
h5py end-to-end test (writer_h5py_tests is now 27/27 against HDF5 2.0.0).
Found while validating a user report of InvalidDatatypeVersion
{ class: 6, version: 5 } against v2.1.0 (already fixed on main in a13ff51,
never released). Add docs/known-issues.md recording that report, this bug,
the open reference-v4 gap and a gpu_tests parallel-run hang; credit the
reporter in the changelog.
Co-Authored-By: Claude Fable 5.1 <[email protected]>
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osobh
co-authored by
Claude Fable 5.1
Claude Fable 5.1
parent
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# Known Issues
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Bugs found during development or downstream use, tracked here because this
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repository's issue tracker is disabled. One entry per bug; when an entry is
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fixed, record the fix in `CHANGELOG.md` and update its status here rather than
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deleting it.
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---
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## Compound datatype message version 5 is not parsed (HDF5 2.0)
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**Status:** fixed on `main` in `a13ff51` (2026-06-03); **not in the v2.1.0
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tag**, which was cut five commits earlier. Ships in the next release.
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**Reported by:** M. Scot Breitenfeld (The HDF Group), 2026-09-08, against v2.1.0.
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**Summary:** `clawhdf5-format` v2.1.0 rejects any dataset with a compound
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(struct) datatype written by an HDF5 2.0 library in `libver='latest'` mode:
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`InvalidDatatypeVersion { class: 6, version: 5 }`.
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**Reproduction** (h5py 3.16.0 / HDF5 2.0.0):
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```python
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import h5py, numpy as np
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dt = np.dtype([('x', 'f8'), ('y', 'f8'), ('id', 'i4')])
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data = np.array([(1.0, 2.0, 10), (3.0, 4.0, 20)], dtype=dt)
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f = h5py.File('compound.h5', 'w', libver='latest')
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f.create_dataset('particles', data=data)
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f.close()
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```
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Committed as `crates/clawhdf5-format/tests/writer_h5py_tests.rs::read_h5py_generated_compound`
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(`#[ignore]`d; needs `python3` with h5py on `PATH`). Run with
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`cargo test -p clawhdf5-format --test writer_h5py_tests -- --include-ignored`:
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v2.1.0 gives 25 passed / 1 failed; `main` passes everything.
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**Root cause:** the compound (class 6) branch of `Datatype::parse`
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(`crates/clawhdf5-format/src/datatype.rs`) accepted only versions 1–4. Datatype
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message versions 4 and 5 changed only the Reference and Complex classes, so a
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v5-tagged compound uses the unchanged v3 member-list layout.
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**Fix:** versions 3–5 are accepted for compound (class 6) and array (class 10)
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datatypes, and data layout message version 5 is accepted too (needed for every
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chunked dataset written by HDF5 2.0). Byte-level regression tests:
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`test_compound_v5_from_hdf5_2_0`, `test_array_v5_from_hdf5_2_0`.
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## Native complex datatype (class 11) is mis-parsed (HDF5 2.0)
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**Status:** fixed 2026-09-18. Found while validating the report above.
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**Summary:** HDF5 2.0 native complex types (`H5T_COMPLEX_IEEE_F64LE` etc.)
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were parsed as if they carried a compound-style member list. The properties are
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actually a single base floating-point datatype, so the parser produced a garbage
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datatype, or `UnexpectedEof` when the complex type was a compound member. h5py's
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default numpy-complex mapping is unaffected (it writes a `{r, i}` compound);
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only files using the native type through the C API / h5py low-level API hit this.
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**Fix:** class 11 parses its base type and is surfaced as the equivalent
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`{r, i}` compound. Tests: `test_complex_v5_from_hdf5_2_0`,
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`test_compound_with_complex_member_from_hdf5_2_0`,
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`writer_h5py_tests.rs::read_h5py_generated_native_complex`.
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## Revised reference datatype (class 7, version 4) is not parsed
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**Status:** open, unconfirmed against a real file.
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**Summary:** HDF5 1.12+ `H5T_STD_REF` references use datatype version 4 with
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reference types 2–4 (object2 / region2 / attribute), which `Datatype::parse`
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rejects with `InvalidReferenceType`. h5py still writes the legacy v1
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object/region references, which read correctly, so no reproducing file has been
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generated yet; one written with the C API (`H5T_STD_REF`) is needed.
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## `clawhdf5-gpu` `gpu_tests` can hang under the default parallel test runner
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**Status:** open. Observed 2026-09-18 (RTX 5060 Ti, Linux).
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**Summary:** during `cargo test --workspace`, the `gpu_tests` binary sat idle
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(~1% CPU) for 25+ minutes and had to be killed. Run single-threaded it passes
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in seconds (20/20): `cargo test -p clawhdf5-gpu --test gpu_tests -- --test-threads=1`.
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Suspected cause: several tests creating wgpu devices concurrently (possibly
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compounded by the rest of the workspace's tests loading the machine). Not yet
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root-caused; workaround is `--test-threads=1` for that crate.
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