Variables got the first unused dimension of equal size, so a variable on
an unlimited dimension with fewer records got an anonymous dim_<n>, and
dimensions of one size could be swapped. Resolve them as netCDF-C does
(libhdf5/hdf5open.c): _Netcdf4Coordinates ids, else the scales
DIMENSION_LIST references (the last one attached to an axis), searched in
the variable's group and its parents; a coordinate variable is on its own
scale. Size matching remains only for axes the file names nothing for.
variables()/variable_names() leave out dimension scales that are only
dimensions, and _nc4_non_coord_<name> is the variable <name>.
Variable::shape is the netCDF shape (an unlimited dimension's length) and
the reads pad unwritten records with the fill value (_FillValue, else
NC_FILL_*; NaN from read_f64); Variable::stored_shape is the HDF5 extent.
New NetCDF4File::variable_names.
Tests compare with netCDF4-python variable by variable: the known-issues
reproducer, equal sizes, (p, p), scalars, inherited dimensions, unwritten
records, h5py dimension scales, h5netcdf and xarray files. CI installs
h5netcdf. known-issues entry moved to Fixed (history); stale open-table
row for the unlimited-size fix removed.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The last 3 our-errors and 2 mismatches were documented as not ours but
still counted against us, on a heuristic (any big-endian VL mismatch) and
a fixed list.
- ref.py checks that the installed h5py returns big-endian VL elements
with the file's bytes under a little-endian dtype (writing and reading
a vlen('>f4') in memory) and, if so, relabels them with the file's byte
order before hashing, marking the object `ref_fix`. The values are now
compared: attr_datatypes.hdf5 /@vlen_uint64 and tcomplex_be.h5
/VariableLengthDatasetFloatComplex are identical to ours (h5dump 1.14.6
prints the same (1, 2), (3, 4, 5), (42)).
- ref_bugs.py re-reads each object h5py reads only through a libhdf5 bug
in six processes with different heaps (import order, MALLOC_PERTURB_).
Values the file determines are the same every time; these three change
(6, 6 and 3 distinct results), so they are over-read memory, not data
clawhdf5 could match. compare.py classifies a file `ref-bug` only when
every difference is such an object confirmed in the same run.
- report.py: the ref-bug class, the evidence table, the corrected
objects; test_ref.py covers both (run in the nightly job).
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
ci-test.sh gains a step that lints clawhdf5-py, builds its wheel with
maturin, unpacks it under target/ (the interpreter's environment is not
touched) and runs the pytest suite, which compares reads with h5py. It
skips without maturin/pytest, and fails instead under
CLAWHDF5_REQUIRE_INTEROP=1. The CI interop venv installs maturin and
pytest, so CI runs it.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
dump_matches_h5dump requires byte identity with the h5dump on PATH, and
CI's rust:latest (Debian 13.7) installs hdf5-tools 1.14.5, not the 1.14.6
the test was written against. Ran the whole clawhdf5-tools suite in
rust:latest with Debian's hdf5-tools and pip h5py 3.16.0 (HDF5 2.0.0), as
CI sets it up, with CLAWHDF5_REQUIRE_INTEROP=1: 18 of 18 pass, so the
comparison needs no loosening. The version is now printed in the CI log
so a future Debian update that changes the output is easy to spot.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The clawhdf5-tools interop tests compare h5rs with h5ls, h5stat, h5dump and
h5diff, and CLAWHDF5_REQUIRE_INTEROP=1 turns a missing tool into a failure.
Also hold clawhdf5-tools to the no-C-in-the-default-build check.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The facade already builds for the browser target without mmap (and
with it: memmap2 compiles there and File::open just fails, as std::fs
does). Nothing needed gating; keep it that way with a ci-test.sh step,
and install the target in the CI container.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Runs conformance/run.sh in rust:latest on a schedule and on demand, with its
own venv (pinned h5py/numpy/hdf5plugin/netCDF4) and hdf5-tools. Fails on any
panic, hang, crash or OOM in clawhdf5 and on a drop against
conformance/baseline.json; prints CONFORMANCE.md into the job log and
uploads nothing. Plain git checkout, no JavaScript actions.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The interop step built writer_h5py_tests without the lz4/zstd features,
so the hdf5plugin round-trips added with the registered LZ4 framing and
the Zstd content-size fix never compiled in CI, and CI never installed
hdf5plugin.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
The core crates (clawhdf5, -agent, -format, -io, -filters, -ann, -accel,
-netcdf4, -cli) now build no C by default: deflate defaults to zlib-rs,
a pure-Rust port of zlib-ng, and zlib-ng becomes the opt-in
`fast-deflate`, which overrides zlib-rs wherever it is enabled. A default
build no longer needs cmake or a C compiler.
Measured on tank, both builds run alternately, three rounds, medians:
zlib-rs is within 6% of zlib-ng on every HDF5 read and write (512x512
deflate-6 chunked write 1.458 vs 1.484 ms; 64 MB compressed read 64.4
vs 65.2 ms), and compressed output is byte-identical. Details in
BENCHMARKS.md, "Deflate backend".
Getting there took two fixes the first measurement exposed:
- zlib-rs needs `std` to detect SIMD at runtime. flate2 enables it via
its default `runtime_detection`, which `default-features = false` had
switched off, leaving zlib-rs 3.5x slower on inflate. The `zlib-rs`
features now enable it.
- Both deflate paths streamed through flate2's 32 KiB read/write
wrappers. They now hand the codec the whole chunk in one call, into a
buffer sized up front (~5% on chunked writes). This also fixes a
silent short read: the streaming reader returned a truncated stream's
bytes without an error; a truncated chunk is now DecompressionError.
In clawhdf5-filters, output longer than the stated size is now an
error rather than silently cut off.
CI: ci-test.sh lints and tests the zlib-ng path, and fails if a
C-building crate (*-sys, cc, cmake) enters a core crate's default
dependency tree. The arm64 job no longer installs cmake.
Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
Read from the job logs of the first run with the arm64 job, rather than
guessed:
- The x86 `test` job has been failing on every push, in about three
seconds. It runs in `rust:latest` and starts with actions/checkout, a
JavaScript action, and `rust:latest` has no `node`: exit 127 before a
line of code was built. It is replaced with a plain git checkout (the
image has git), and actions/cache, JavaScript for the same reason, is
dropped.
- `test-arm64` got through checkout, toolchain, the aarch64 check and
clippy, then failed building libz-ng-sys — pulled in by
clawhdf5-format's default `fast-deflate` — because the host runner had
no cmake. The x86 image lacks it too, so the x86 job would have hit the
same wall one step later.
Both jobs now install cmake where they can (the Docker job and the x86
container run as root) and say plainly when they cannot (a host runner),
instead of failing inside a build script. vision-01 now has cmake.
Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
The NEON kernels in clawhdf5-accel — `dot_i8` including its SDOT path,
and the f32 NEON kernels that predate it — are cfg'd out on x86, so the
existing job has never compiled, linted or tested a line of them. They
were verified once, by hand, on a Raspberry Pi 5.
`test-arm64` runs on `linux_arm64`, which two runners serve in different
ways: vision-01 executes steps on the host with Rust preinstalled, and
vision-02 executes them in docker.gitea.com/runner-images. The job is
written to work in both: no `container:`, no JavaScript actions (those
are fetched from GitHub, which not every runner reliably reaches), and
an explicit `+stable` toolchain so a host's default — vision-01's is a
January nightly — is neither relied on nor changed. Fetches retry, since
one runner's outbound network was seen failing intermittently.
It lints the accel crate and tests accel, ann and format. It reports
rather than requires the dot-product extension: on a core without it the
plain-NEON kernel is the one that runs, and the tests cover whichever is
present.
Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
The workflow already installed h5py into /opt/interop and set
CLAWHDF5_REQUIRE_INTEROP=1, but it reached the tests only by appending
that venv to $GITHUB_PATH, which Gitea's runner does not reliably
propagate into test subprocesses. If `python3` resolved to the system
interpreter instead, every interop suite would skip. Setting
CLAWHDF5_PYTHON outright removes the question: together with
REQUIRE_INTEROP the suites either run or the build goes red.
Verified both directions locally — with a venv the four suites run 94
tests green; with a bogus interpreter and REQUIRE_INTEROP=1 the facade
and netCDF4 suites fail 22 tests rather than skipping.
Also documents creating the local `.venv` that `ci-test.sh` detects.
Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
- clippy --all-targets plus a clawhdf5-format feature matrix (parallel, lz4,
zstd, pcodec, fast-checksum); fix the accumulated lint backlog in test,
bench and feature-gated code (no behaviour changes).
- Install python3 + h5py/numpy/netCDF4/xarray in the CI container and set
CLAWHDF5_REQUIRE_INTEROP=1, which makes a missing interop dependency a test
failure. Every h5py/netCDF4 interop test used to skip silently in CI. Run
the #[ignore]d writer_h5py_tests suite explicitly.
- cargo bench --no-run so benches can't rot; fix bench.rs and memory_bench.rs,
which no longer compiled against the current strategy/consolidation APIs.
- Optional fuzz smoke run via CLAWHDF5_FUZZ_SECONDS.
- CHANGELOG and docs/known-issues.md updated.
Co-Authored-By: Claude Fable 5.1 <[email protected]>
- Add .gitea/workflows/ci.yml running scripts/ci-test.sh (fmt, clippy,
test, no_std check) on push/PR to main.
- Fix stale rustyhdf5-py/rustyhdf5-format package names in
ci-test.sh/check-nostd.sh, which had been silently no-op'ing those
checks (cargo warns but doesn't fail on an unknown --exclude/-p
target).
- With those checks actually running, fix the real issues they surface:
- clippy: useless_conversion in chunked_write.rs, byte_char_slices in
global_heap.rs/object_header.rs.
- cargo fmt: apply formatting across the workspace (whitespace only).
- no_std (thumbv7em-none-eabihf) build errors in clawhdf5-format:
core::sync::atomic::AtomicU64 doesn't exist on that target (no
native 64-bit atomics) — switch profiling.rs's counters to
portable-atomic, which falls back to a CAS-based emulation there
and is a no-op wrapper elsewhere. Add missing alloc imports for
Box (filters.rs), Vec (filters_szip.rs), and format! (dict_encoding.rs)
on no_std paths. Replace f64::powi (std/libm-only) with a small
local exponentiation-by-squaring helper in the scale-offset filter.
