A Catch2 executable that builds in the portable configurations (JFJOCH_VIEWER_ONLY /
JFJOCH_RUGNUX_ONLY) and links only what those build - JFJochRugnux, JFJochReader,
JFJochImageAnalysis, JFJochWriter, JFJochCommon - so it can run on the macOS arm64 and
Windows x64 jobs, where the receiver/broker/FPGA/HLS sources are not built and there is no GPU.
EXCLUDE_FROM_ALL, so a product build does not pay for it; catch2 is now made available in the
portable configure as well (it is EXCLUDE_FROM_ALL too).
The cases tagged [portable] cover what depends on the architecture, the compiler or the
standard library: bitshuffle/LZ4/zstd, HDF5 read-back (legacy/VDS/integrated, the direct-chunk
path), miniCBF/marCCD/SMV header parsing, CBOR, CPU spot finding, azimuthal mapping, Bragg
prediction/integration, gemmi MTZ/mmCIF. New in tests/PortableTest.cpp:
- a golden FNV-1a hash of two frames of compression_benchmark.h5, decoded from the raw chunk by
the hperf and the classic bitshuffle and through the HDF5 filter (x86 hashes
affea29c511b6ec2 / e46913009c95a1f1);
- a golden hash of a bitshuffle/LZ4 encode (the writer must produce the same bytes everywhere);
- the shipped bitshuffle block selector against the classic reference over elem 1/2/4/8 and
block tails;
- the FFTW indexer, named explicitly, on a synthetic orthorhombic lattice (the existing FFT
indexer lattice tests run only under CUDA);
- a 4-frame end-to-end rugnux run on the git-LFS rotation dataset (HDF5 via external links, CPU
spot finding, indexing, integration); SKIPs when LFS was not pulled.
All 45 take ~4 s on Linux (~2 s without the LFS case), CPU-only build.
M_PI replaced by PI (common/JFJochMath.h) in the two tagged files that used it, as MSVC does not
define M_PI. The CBF gzip test shells out to gzip and is left untagged.
CI: build and run jfjoch_portable_test "[portable]" in build-windows (both variants),
build-rugnux-windows, build-macos-viewer and build-rugnux-macos, after the build and before
packaging.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
-z (now also --reference; --reference-mtz still works) takes an SF-mmCIF
(e.g. a deposited -sf.cif, gzipped or not) as well as an MTZ. The format is
recognised by content: a file starting with "MTZ " is an MTZ, anything else
is parsed as CIF. The first merged reflection block with the requested
column (or, by default, one the auto choice accepts) is converted to a
gemmi::Mtz in memory with GEMMI's CifToMtz and then read by the unchanged
MTZ loader, so the in-memory reference is exactly what the MTZ path yields.
Unmerged (_diffrn_refln) and anomalous-only blocks are passed over; the log
names the block used.
The R-free set comes from _refln.status (f -> FreeR_flag 0, o -> 1: the
CCP4 convention the loader already reads) and is preferred to
_refln.pdbx_r_free_flag, whose convention varies by program; a status
column with no 'f' is ignored and pdbx_r_free_flag is used instead.
Checked on two open-arm sets in the deposited setting (one with F_meas_au
only, one with intensity_meas): reference loaded with the deposited cell and
group, the inherited free set agrees with the deposited status 'f' on every
common reflection, and the merge correlates at CC 0.99 with the deposition.
Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01D1G8gJVAy6gp1K5Dz3NE5C
leonarski_fandClaude Opus 5.5