5 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5	bc500d1578	rugnux: report what --model found, and attribute GEMMI's bundled headers ... Two things left open by the previous commit. A model that was validated left nothing in the results report. R-work, R-free, the bulk-solvent parameters and the map filenames went to the log and nowhere else, so a run given --model was, in the file anyone reads afterwards, indistinguishable from one that was not - and the WARNING line added last commit was the only trace of a model that failed. Section 10. MODEL VALIDATION now carries it: MODEL_FILE, the space group the model is in, R_WORK / R_FREE with their reflection counts, the bulk-solvent k_sol / b_sol and overall scale, the mean 2Fo-Fc density at the atom centres, the hand and indexing operators the written reflections were brought into the model's frame with, and MAPS_PREFIX. A model that could not be used gets MODEL_VALIDATION= NOT_PERFORMED and the reason instead, in the shape the merging section already uses. A run that asked for no model has no section at all. That moves WARNINGS from 10 to 11, which is what REPORT_VERSION is for: it is now 4. No existing key was renamed and no table column moved, so a consumer that greps for what it needs is unaffected; one that keys on the section number of WARNINGS is not, hence the bump. The four third-party headers GEMMI has always bundled - fast_float, half, pocketfft and tinydir - were never listed in THIRD_PARTY_NOTICES.md, riding instead under GEMMI's single MPL-2.0 row. They are other authors' code under other licences (Apache-2.0 OR MIT OR BSL-1.0, MIT, BSD-3-Clause, BSD-2-Clause), and MPL-2.0 does not speak for them. Each now has its own row and its own licence text, alongside the PEGTL and sajson entries added with the CIF parser, and a note records why the six are listed separately from GEMMI. Their terms live in the headers rather than in LICENSE files, so five of the six texts are kept by hand; COLLECT.sh says so and copies the one - PEGTL - that ships a file. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:50:13 +02:00
leonarski_fandClaude Opus 5	e65cfdc675	rugnux: record in the report how the run was invoked, what it cost and what it ran on ... The results report said what the run determined but nothing about how it was produced, so a report read next to a lost shell history could not be reproduced or compared. Four keys in the header block, all new, none renamed - a consumer that greps for what it needs is unaffected, so REPORT_VERSION does not move: COMMAND_LINE= rugnux -o myrun --model model.pdb dataset_master.h5 WALL_TIME= 262.41 GPU_COUNT= 4 GPU= 4x NVIDIA A100-SXM4-80GB The command line is argv as one shell-ready line; an argument that would not survive being pasted back into a shell is single-quoted, so a file prefix with a space comes back as the one argument it was. It replaces the raw argv echo at the top of the run, which had no quoting at all. WALL_TIME is the whole invocation, timed from the top of the CLI. It is deliberately not result.total_time_s, which starts inside Rugnux::Run and so counts neither opening the file nor setting up the analysis - and which --mode scale never sets at all, having no ProcessResult of its own. It is printed on stdout as well, next to the processing time it is slightly larger than. The GPUs are the reason rugnux is fast, and until now nothing said whether any were being used. get_gpu_names() reports them per device and get_gpu_description() collapses repeats, so four identical cards read as one line rather than the same name four times and a mixed machine keeps one group per model. Both have a CPU-only implementation, so the JFJOCH_USE_CUDA=OFF build reports GPU_COUNT= 0 rather than failing to link. The same line is printed at startup, before the run rather than after it: a machine that turns out to have no GPU - a driver mismatch, a CUDA_VISIBLE_DEVICES left over from another job - is worth knowing about while there is still time to stop, not once the run has taken an order of magnitude longer than it should. GPU_COUNT= 0 is written with no GPU= line beside it, because the absence is the statement. The header comment claiming timing is deliberately absent from the report is now wrong and says so: rates and per-image costs stay on stdout, the total does not. Verified on the rotation test dataset in both build configurations, with and without CUDA_VISIBLE_DEVICES, in --mode mx and --mode scale. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_016WmryXe8ASbNi632sUMfsa	2026-08-27 13:09:54 +02:00
leonarski_fandClaude Opus 5	3175e65400	Space-group search: say what it tested, and what it could not ... Three reporting changes. None of them touches a decision: the merged .mtz, .hkl, .cif and _image.dat are byte-identical before and after on two test crystals, and the space group and cell are unchanged. REPORT_VERSION moves to 3 and one warning appears where the second change is working. The alternatives line was misleading. "Best space group: C2 or P21 or P2 (indistinguishable from these data)" sat forty lines below the run's single cell, which is C2's. P2 and P21 are primitive: their lattice is a sub-lattice of that one, their cell has half its volume, and their indices are not the ones in the written files. A user acting on "P21" got a group name with no cell, beside a cell belonging to a different group, with nothing saying so. The report now names the alternatives whose centring differs from the chosen group's, gives the volume ratio of the cell each implies, and says that adopting one means reindexing. It stays byte-identical when every alternative shares the chosen centring, which is every other case that occurs - the enantiomorphic and origin-ambiguous pairs, where one cell really does describe them all. It does not print derived cell constants: the primitive cell of a C-centred monoclinic is not P2's conventional cell, and deriving that is a reduction plus a per-group setting choice, which is more than a report line should carry. A centring the data could not test now says so. Prediction runs in P so the search can confirm a centring from the reflections it extinguishes, but when the indexer returns the primitive sub-cell those reflections are never predicted, and an absent count of 0 reads as "predicts no absences" when it means "none was measured". The search abstains correctly and the centring is then taken from the metric, but none of that reached the user. The candidate table gains a three-valued centring column and the report raises a warning where the metric decides it. No decision logic changed - the flag is two counts the search had already made, and nothing reads it back. The twin-law H is now reported for every operator, and the adopted promotion's ratio against its bound. It was previously visible only inside a refusal message, which is why recalibrating that bound recently required rebuilding the statistic from reference data rather than reading it out of runs we already had. The ratio is reported at the Stage A promotion where it is computed, not in the Stage B table, whose rows all share one point group and would have printed the same number on every line. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 21:04:12 +02:00
leonarski_fandClaude Opus 5	a4228b9c1d	tests: follow REPORT_VERSION to 2 ... 80e10f51b added an anisotropy section to the result report and moved REPORT_VERSION from 1 to 2, but left ResultReportTest asserting 1, so the [Diagnostics] tag has been failing on this branch since that commit. The assertion is the point of the test - a consumer greps that key - so it follows the constant. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01CHMmeM1d489zvNFT7ZMN2P	2026-08-25 20:57:37 +02:00
leonarski_f	538f3504d3	v1.0.0.rc-161 (#71) ... This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * **rugnux: significantly better quality of results, and faster.** A large rework of integration, scaling, merging, geometry refinement and space-group determination, together with measurements the program previously made no attempt at - the direct beam before indexing, the beam stop, the goniometer rotation scale, and the stretches of a sweep the crystal did not deliver. A rotation dataset typically gains observations at better <I/sigma> and R_meas, and every `mx` and `scale` run writes a `<prefix>_report.txt` results report modelled on XDS's `CORRECT.LP`. Many defaults moved with it: spot detection is self-calibrating, beam-stop detection and rotation geometry post-refinement are on, resolution limits default to as far as the detector reaches, and ice-ring handling engages only where the crystal is measured to have ice. * **jfjoch_viewer:** the beam-stop shadow, the detector calibration and the beam-centre measurement are reachable from "Analyze dataset"; the settings panel reports how the sample moved and how polarized the beam was; image rendering and interaction are faster. * **Performance:** bitshuffle+LZ4 images are decoded on the GPU rather than on the host, with the bitshuffle inverse fused into preprocessing so the decompressed frame is never held in device memory. * **Broker, writer, packaging and build:** image-slot lifetime and locking fixes, per-image datasets sized by the images actually written, the Debian/Ubuntu broker package renamed to `jfjoch`, and `image_analysis` compiling under MSVC again. **Breaking change to the rugnux command line:** * `--azint-only` and `--scale` are **removed**, replaced by `--mode azint` and `--mode scale`; the full pipeline is `--mode mx` and remains the default. A script passing the old flags now fails with the list of valid modes rather than silently running the wrong one. * `-t`/`--stride` is **refused on rotation data**: skipping frames cuts every reflection's rocking curve, so the combined fulls and their partiality would be measured over frames the sweep never recorded. Select a contiguous range with `-s`/`-e` instead. `--mode azint` and `--force-still` still take a stride. **Breaking changes to OpenAPI** - regenerate the client (`jfjoch-client` 1.0.0-rc.161, `frontend/src/client`) or read the affected fields as optional: * `image_scale_b` is removed from the `plot_type` enum, so a client requesting that plot now gets an error rather than a curve. * `azim_int_settings.high_q_recipA`, `spot_finding_settings.high_resolution_limit` and `spot_finding_settings.low_resolution_limit` are no longer `required`. All three mean "no limit at that end" when unset and are omitted from the response instead of carrying a placeholder value, which raises in a client generated from an rc.160-or-earlier spec. A value of 0 is still accepted and means the same thing. **Breaking changes to the stored formats** - a consumer reading these fields must treat them as optional: * The per-image image-scale B factor is no longer computed, so `/entry/MX/imageScaleBFactor` is absent from newly written HDF5 files and the corresponding key is absent from the CBOR DataMessage and END blocks. Files written by rc.160 and earlier still contain it and still open; nothing in the pipeline reads it any more. * `_reflns.jfjoch_diffrn_ISa` now carries the whole-range `1/sqrt(a*b)` that XDS's ISa denotes, and the error-model `a` and `b` are reported in XDS's convention; the strong-reflection asymptote moves to `_reflns.jfjoch_diffrn_ISa_asymptotic`. **A file written by an earlier version carries the asymptote under the plain `ISa` name.** Reviewed-on: #71 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>	2026-08-13 17:03:10 +02:00