osobhandClaude Opus 5.5
e5d6f59e12
Read a file's metadata the way netCDF-C 4.9.3 does (libhdf5/hdf5open.c), for the whole file on first use (src/model.rs, replacing src/scope.rs): - links in creation order when the group tracks it, else name order; a group's datasets before its subgroups; dimension ids file-wide; - variables' dimensions from _Netcdf4Coordinates (file-wide ids), else the scales DIMENSION_LIST attaches when the first axis has one, else netCDF-C's phony dimensions phony_dim_<id> (create_phony_dims: shared by length and unlimitedness within a group, not between two axes of one variable, numbered subgroups first, a zero length unlimited); - datasets of types netCDF-C cannot represent are not variables (references, bit fields, time, arrays, compounds/enums/VLENs over them), replaying netCDF-C's file-wide type list, failed types included; - unlimited lengths as nc4_find_dim_len (its group and below). NcType gains Enum, Compound, VLen, Opaque and is #[non_exhaustive]; Variable::nc_type is netCDF-C's type (1-byte strings NC_CHAR). New clawhdf5_format::group_v2::links_in_creation_order_in. Tests compare with netCDF-C itself (tests/netcdf_c_view.py calls the libnetcdf netCDF4-python bundles through ctypes): new interop cases for h5py files without dimension scales, every type class, link order; and the gated corpus_vs_netcdf_c (CLAWHDF5_NETCDF_CORPUS): 420 of the 429 conformance-corpus files netCDF-C opens match (main: 68); the other 9 are explained in tests/corpus_known_differences.txt and known-issues. Co-Authored-By: Claude Opus 5.5 (1M context) <[email protected]>
27 lines
1.7 KiB
Plaintext
27 lines
1.7 KiB
Plaintext
# Files of the conformance corpus (conformance/.cache/corpus) that netCDF-C
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# opens and clawhdf5-netcdf4 reads differently, with the reason.
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# <path relative to the corpus root><TAB><reason>
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# Read by tests/corpus_vs_netcdf_c.rs; see docs/known-issues.md
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# ("NetCDF-4: differences from netCDF-C").
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#
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# External links: libhdf5 follows them into the other file (present in the
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# corpus); clawhdf5 does not follow external links (known-issues: "External
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# links and external raw data are not followed"), so the linked groups and
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# datasets are missing and, in files without dimension scales, the phony
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# dimension numbers after them shift.
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hdf5/test/testfiles/be_extlink1.h5 external link not followed
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hdf5/test/testfiles/le_extlink1.h5 external link not followed
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hdf5/tools/test/testfiles/h5diff_ext2softlink_src.h5 external link not followed
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hdf5/tools/test/testfiles/h5diff_grp_recurse_ext2-1.h5 external link not followed
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hdf5/tools/test/testfiles/h5diff_grp_recurse_ext2-2.h5 external link not followed
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#
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# Values the HDF5 reader refuses and libhdf5 1.14.6 (the netCDF4-python
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# wheel's) returns; metadata matches. The first three are the scale-offset
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# and N-Bit ref-bug / our-error files of CONFORMANCE.md (libhdf5 reads past
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# the stored data); bad_nbit_decompress.h5 is not in the conformance run and
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# is not investigated yet.
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cve_hdf5/cvefiles/cve-2025-2308.h5 values: scale-offset chunk shorter than its values (libhdf5 over-read)
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cve_hdf5/cvefiles/cve-2025-44904.h5 values: unfiltered chunks shorter than a chunk (libhdf5 over-read)
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hdf5/test/testfiles/bad_nbit_parms_walk.h5 values: N-Bit parameters too short (conformance our-error/ref-bug)
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hdf5/test/testfiles/bad_nbit_decompress.h5 values: N-Bit chunk refused ("element count exceeds chunk size"); not investigated
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