6 Commits

Include renames

Author	SHA1	Message	Date
leonarski_fandClaude Opus 5.5	1f27fba1f3	Model validation expands strict NCS; the written cell follows the model's indexing ... - ModelValidation reads the model and, where it carries non-given NCS operators (_struct_ncs_oper 'generate' / MTRIX without the given flag), expands them (gemmi expand_ncs, vendored assembly.cpp from GEMMI 0.7.5, MPL-2.0 as the rest of gemmi_gph). Same in the battery's model_check.py and depdata_check.py. An icosahedral-virus entry deposited as 3 of the 45 chains of its ASU was scored against a fifteenth of its atoms: R-free 0.545 -> 0.297. - The indexing the model chooses (AdoptModelFrame) now moves the cell with the indices (reseat_integrated in the main path; CellInBasis in the forecast, twin-file and stills/scale paths). A near-symmetry law (b within 2% of c, beta a degree off 90, a~b in P1) relabelled the reflections only, so the files were written with two axes swapped or beta flipped relative to the indices. Where the law moved the cell, the validation is remade on the moved cell. Measured on 18 open/in-house sets with models: p.hkl and MTZ reflection data bit-identical on all; cell and model R unchanged where the law is exact; the cell now matches the deposited one on the 6 pseudo-merohedral cases (orthorhombic a/c swap, three monoclinic beta flips, a P1 alpha/beta swap), R-free within +-0.001 there. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01EizBKhTqrAYago9KJG3dA3	2026-10-10 13:35:49 +02:00
leonarski_f	fc68a9baed	v1.0.0-rc.146 (#56) ... This is an UNSTABLE release. The release has significant modifications for data processing - in case of troubles go back to 1.0.0-rc.144. jfjoch_process: Generate a dedicated file (_process.h5), which can be used as a replacement for the _master.h5 file for a reanalyzed dataset. jfjoch_process: Improve the performance of scaling and merging, implement on the fly scaling. jfjoch_writer: All final data analysis results are repopulated in the _master.h5 file. jfjoch_scale: Dedicated tool for rescaling/merging existing data. jfjoch_viewer: Fix bugs where pixel labels where displayed on a wrong pixel. WARNING! Scaling and merging are experimental at the moment, and may not provide reasonable results for the time being. Reviewed-on: #56	2026-05-28 18:48:35 +02:00
leonarski_f	061152279c	v1.0.0-rc.91	2025-10-20 20:43:44 +02:00
leonarski_f	28d224afab	version 1.0.0-rc.25	2024-11-22 21:25:20 +01:00
leonarski_f	16bbf54f2a	Remove open source license (for now)	2023-09-15 10:47:21 +02:00
leonarski_f	1757d42182	Initial commit ... Signed-off-by: Filip Leonarski <filip.leonarski@psi.ch>	2023-04-06 11:17:59 +02:00