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Fix silent wrong data and libhdf5 interop found by the HDF5 audit #11

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osobh merged 41 commits from fix/phase0-correctness into main 2026-09-26 02:42:54 +00:00
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+5 -3
2 changed files with 5 additions and 3 deletions
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.gitea/workflows/ci.yml
+2 -2
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@@ -33,10 +33,10 @@ jobs:
# build (pure-Rust zlib-rs) does not need it. # build (pure-Rust zlib-rs) does not need it.
apt-get install -y --no-install-recommends python3 python3-venv cmake apt-get install -y --no-install-recommends python3 python3-venv cmake
python3 -m venv /opt/interop python3 -m venv /opt/interop
/opt/interop/bin/pip install --no-cache-dir h5py numpy netCDF4 xarray /opt/interop/bin/pip install --no-cache-dir h5py numpy netCDF4 xarray hdf5plugin
echo "/opt/interop/bin" >> "$GITHUB_PATH" echo "/opt/interop/bin" >> "$GITHUB_PATH"
- name: Show interop library versions - name: Show interop library versions
run: /opt/interop/bin/python -c "import h5py, netCDF4; print('h5py', h5py.__version__, 'HDF5', h5py.version.hdf5_version, 'netCDF4', netCDF4.__version__)" run: /opt/interop/bin/python -c "import h5py, netCDF4, hdf5plugin; print('h5py', h5py.__version__, 'HDF5', h5py.version.hdf5_version, 'netCDF4', netCDF4.__version__, 'hdf5plugin', hdf5plugin.version)"
- name: Run CI script - name: Run CI script
env: env:
# Name the interpreter outright rather than relying on $GITHUB_PATH # Name the interpreter outright rather than relying on $GITHUB_PATH
scripts/ci-test.sh
+3 -1
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@@ -145,8 +145,10 @@ run_step "cargo test (fast-deflate / zlib-ng)" cargo test \
# skipping — the tests read the same variable. # skipping — the tests read the same variable.
PYTHON="${CLAWHDF5_PYTHON:-python3}" PYTHON="${CLAWHDF5_PYTHON:-python3}"
if "$PYTHON" -c "import h5py" >/dev/null 2>&1 || [ "${CLAWHDF5_REQUIRE_INTEROP:-0}" = "1" ]; then if "$PYTHON" -c "import h5py" >/dev/null 2>&1 || [ "${CLAWHDF5_REQUIRE_INTEROP:-0}" = "1" ]; then
# lz4/zstd so the hdf5plugin round-trips (our LZ4 and Zstd output read by
# libhdf5's registered plugins) compile and run too.
run_step "h5py interop (format, ignored tests)" cargo test \ run_step "h5py interop (format, ignored tests)" cargo test \
-p clawhdf5-format --test writer_h5py_tests -- --include-ignored -p clawhdf5-format --features lz4,zstd --test writer_h5py_tests -- --include-ignored
else else
echo "" echo ""
echo "==> [h5py interop] SKIPPED: no h5py in $PYTHON" echo "==> [h5py interop] SKIPPED: no h5py in $PYTHON"