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leonarski_f 8edd0e5f3e docs: rugnux options, model and export pages brought in line with the usage text

RUGNUX_ADVANCED: --simulate-live/--fast-live rows, -e exclusive, stills
behaviour of --beam-center-check, -S, --min-partiality (0.5),
--capture-uncertainty, --adaptive-integration-radius (on for stills too),
--detector-distance/--rot1/--rot2/--no-refine-tilt; --background-radial
auto as it decides now; --refine-modules syntax; _cell.*_esd.
MODEL_AND_REFERENCE: the default refinement of a placed model in the
summary, the decision table and the step list; --mode scale does not refine.
INTEGRATION: the .ins written beside every .hkl (ZERR on rotation).
VIEWER: rugnux writes _process.h5 only with --no-merge/--write-process-h5.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 51d2564356ba46bda8730c855ff8d3ee7c23d605)

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.gitea/workflows

CI: the documentation also pushed to the gitea-pages branch of rugnux/gitea-pages, on every push for now (token test)

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acquisition_device

v1.0.0.rc-161 (#71 )

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broker

Refinement cut by the run's cancel; the hero shows the refined R-work / R-free

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common

Stills: the run's rocking curve goes to _process.h5 and --mode scale merges with it; MeasureRunWidth takes the window at each reflection's resolution

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compression

v1.0.0-rc.175 (#85 )

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detector_control

v1.0.0-rc.175 (#85 )

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docker

1.0.0-rc.174 (#84 )

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docs

docs: rugnux options, model and export pages brought in line with the usage text

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etc

v1.0.0-rc.166 (#76 )

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fpga

v1.0.0-rc.180: VERSION and update_version.sh

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frame_serialize

v1.0.0-rc.179 (#90 )

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frontend

Refinement cut by the run's cancel; the hero shows the refined R-work / R-free

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gemmi_gph

Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib

2026-10-25 07:20:32 +01:00

image_analysis

rugnux: unit-cell e.s.d.s - ZERR in a new SHELX .ins beside the .hkl, _cell.*_esd in the mmCIF, CELL_ESD_* in the report

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image_puller

v1.0.0-rc.178 (#88 )

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image_pusher

v1.0.0-rc.178 (#88 )

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include

v1.0.0-rc.133

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jungfrau

v1.0.0-rc.153 (#63 )

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licenses

fast-feedback-indexer vendored in image_analysis/indexing/fast-feedback-indexer instead of fetched

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preview

v1.0.0-rc.179 (#90 )

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reader

Stills: the run's rocking curve goes to _process.h5 and --mode scale merges with it; MeasureRunWidth takes the window at each reflection's resolution

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receiver

Refinement cut by the run's cancel; the hero shows the refined R-work / R-free

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rugnux

rugnux: unit-cell e.s.d.s - ZERR in a new SHELX .ins beside the .hkl, _cell.*_esd in the mmCIF, CELL_ESD_* in the report

2026-10-26 14:33:38 +01:00

tests

rugnux: unit-cell e.s.d.s - ZERR in a new SHELX .ins beside the .hkl, _cell.*_esd in the mmCIF, CELL_ESD_* in the report

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tools

rugnux: a placed model is refined by default - giving a model is the opt-in

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viewer

rugnux: a placed model is refined by default - giving a model is the opt-in

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writer

Stills: the run's rocking curve goes to _process.h5 and --mode scale merges with it; MeasureRunWidth takes the window at each reflection's resolution

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xds-plugin

v1.0.0-rc.175 (#85 )

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.gitattributes

v1.0.0-rc.153 (#63 )

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.gitignore

Refinement restraints: the CCP4 Monomer Library subset embedded in rugnux, read through gemmi's MonLib

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.readthedocs.yaml

version 1.0.0-rc.25

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CLAUDE.md

fast-feedback-indexer vendored in image_analysis/indexing/fast-feedback-indexer instead of fetched

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CMakeLists.txt

fast-feedback-indexer vendored in image_analysis/indexing/fast-feedback-indexer instead of fetched

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CONTRIBUTING.md

version 1.0.0-rc.27

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gen_python_client.sh

v1.0.0.rc-161 (#71 )

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gitea_create_release.py

v1.0.0-rc.94

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gitea_upload_file.py

v1.0.0-rc.156 (#66 )

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LICENSE

v1.0.0-rc.175 (#85 )

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make_doc.sh

v1.0.0.rc-161 (#71 )

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README.md

1.0.0-rc.174 (#84 )

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THIRD_PARTY_NOTICES.md

Refinement restraints: metal ions bound to their donors by the model's LINK records

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update_version.sh

v1.0.0-rc.175 (#85 )

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VERSION

v1.0.0-rc.180: VERSION and update_version.sh

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README.md

Jungfraujoch

Application to receive and analyse data from the PSI JUNGFRAU and EIGER detectors, together with rugnux, its program for processing stored diffraction data - rotation and serial, macromolecular and small-molecule - from images to merged reflections.

All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.