[willend]

McCode's NeXus output stops using libNeXus. The NeXus C API (napi.h) has been frozen and deprecated upstream. It is replaced by about 300 lines of native HDF5 code in the runtime, keeping the same NX* function names, so --format=NeXus needs only HDF5.

This is the full replacement that #2889 was the pre-study for. #2889 fixed the napi-based writer and added Test_NeXus_output. This PR keeps those fixes and passes the same test.

The libNeXus dependency is removed from packaging, devel tools, CI, toolchains and docs (commit 1318d48ff); the conda-forge recipes are the remaining follow-up.

What changes

• mccode-r.h.in no longer includes napi.h. It declares the napi subset McCode and the Monitor_nD libraries use: NXhandle, NXstatus, NXlink, NX_OK/NX_ERROR, NX_CHAR/NX_FLOAT64/NX_INT32, NX_UNLIMITED, NXACC_RDWR/NXACC_CREATE5, and NX_COMP_NONE/NX_COMP_LZW/NX_COMP_LZW_LVL0..9. Existing -DNX_COMPRESSION=NX_COMP_LZW_LVL1 flags keep working.

• mccode-r.c implements the 19 functions used, on HDF5:

  • files: NXopen, NXclose;
  • groups: NXmakegroup, NXopengroup, NXclosegroup;
  • data sets: NXmakedata, NXcompmakedata, NXcompmakedata64, NXopendata, NXclosedata, NXputdata, NXputslab64;
  • attributes and queries: NXputattr, NXgetinfo64, NXgetgroupinfo;
  • links: NXgetgroupID, NXmakelink;
  • error reporting: NXMDisableErrorReporting, NXMEnableErrorReporting.

  Components that use nxhandle/NX* directly keep compiling.

• Build: NEXUSFLAGS (in PlatformDefaults.cmake, the Debian toolchains, MCUtil.cmake and InstallMCCODE.cmake) link only HDF5. Debian packages depend on libhdf5-dev instead of libnexus-dev. An existing mccode_config.json that still passes -lNeXus keeps working: the runtime's own NX* take precedence.

Design

• Open groups are a stack of HDF5 handles, at most 32 deep. HDF5 resolves names relative to the current group, so no path buffers are needed: long component or monitor names are written, not skipped or overflowed. A failed open leaves the stack unchanged, and closing below the root is reported.
• The file layout follows libNeXus 4.4.3:
  • groups carry an NX_class attribute;
  • strings are fixed-length, scalar attributes replace existing ones, and one-element string data sets are kept;
  • compression uses chunked storage with shuffle and deflate, as NX_COMPRESSION sets it;
  • links are hard links with a target attribute;
  • the root attributes are unchanged, including NeXus_version = 4.4.2.
• Error suppression nests. In napi, one nested disable/enable pair silenced error reporting for the rest of the run.
• Chunks are kept below HDF5's 4 GiB limit inside NXcompmakedata64.
• HDF5's automatic error printing is turned off at file open, as napi did. The MPI per-node file/VDS code relied on that side effect.

Output differences against the libNeXus build

The new and old builds were compared with h5dump -p and h5diff, with timestamps masked. Covered: serial runs, list-buffer flushes (2.5M events), --IDF, MPI with 2 ranks (node files and the VDS), Test_NeXus_comp_par_runtime, and a McXtrace instrument. Group and data-set layout, chunking, filters and data were identical, down to byte-identical file sizes. The remaining differences:

• Long monitor paths (over about 1000 characters) are now written. Their group can't be linked from /entry1/data because NXlink keeps napi's 1024-character targetPath; this is reported.
• No root NX_class is written; the libNeXus 4.4.3 builds in use never wrote one.
• The file_time offset is now correct during daylight saving time; napi was one hour off.
• Errors napi hid are now printed as NeXus error: ….

Limitations for component authors

• Only the 19 functions listed above exist. Code calling another napi function, or including napi.h itself, will not build.
• NXopengroup doesn't check NX_class.
• NXgetgroupinfo fills name and class only at the root.
• NXputdata writes the whole data set; use NXputslab64 to append.

CI (willend/McCode, workflow_dispatch, merge commit 1e3c36752)

mcstas-basictest and mcxtrace-basictest are both green. The NeXus output regression test passed in all 12 classic jobs: Linux gcc-13, clang, Debian and conda; macOS clang; Windows MSVC. The antlr jobs skip it by design.

Follow-ups (not in this PR)

• Drop nexus/libnexus from environment.yml, meta-pkgs/windows/*.yml and mccode-create-conda-yml (now hdf5), remove 3rdparty/nexus-package
• conda-forge feedstock recipes (outside this repo): replace libnexus by hdf5
• Source-build CI jobs: install libhdf5-dev / Homebrew hdf5 instead of libnexus-dev / nexusformat, no nexus CMake dirs
• Code generator hints say -DUSE_NEXUS -lhdf5; manuals and examples updated
• Toolchains: unused nexus dirs removed (Debian), NEXUSINCLUDE points at the HDF5 headers (macOS, MinGW); mccode-build-conda no longer passes nexus dirs
• Not tested: ASan (it hangs at startup on macOS; Linux needed), GPU builds, macOS x86_64

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