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leonarski_fandClaude Opus 5.5 f3bf945cca docs: rc176 - molecular replacement as a pipeline step, Metal and multi-GPU MR, header polarization, Rugnux live tab

- Pipeline figures: the structure/MR box carries the Metal badge.
- RUGNUX_OVERVIEW: a model/molecular-replacement step (triggers, outputs, GPUs).
- GPU_DATA_ANALYSIS: multi-card model validation and MR; the Apple GPU's model density and MR
  rotation function. Install/release/viewer/benchmarking/report/--no-gpu texts no longer say Bragg
  integration is the only Metal engine.
- --polarization default in RUGNUX_ADVANCED and the tutorial follows the usage text (miniCBF/d*TREK header).
- WEB_FRONTEND and JFJOCH_BROKER: the Rugnux live tab; the scan result's rotation lattice.
- battery README: a --model-check run records the REFMAC version.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01PXc1zD1yxHqaR1DGdCTHL4

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.gitea/workflows

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acquisition_device

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broker

broker rugnux live: the analysis is cut 60 s after the last image by default

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common

Readers: polarization from miniCBF and d*TREK headers (RESULT-CHANGING)

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compression

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docs

docs: rc176 - molecular replacement as a pipeline step, Metal and multi-GPU MR, header polarization, Rugnux live tab

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etc

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fpga

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frame_serialize

rugnux: the library returns its outputs in memory; the callers write the files

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frontend

frontend: rugnux live polish - failed run steps take the full row, Supercell tile not highlighted

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gemmi_gph

Model scale fit: no log ratio at |Fcalc| = 0, and no LM step once the model has underflowed

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image_analysis

ModelGrid: the model density on the Apple GPU (Metal), bit-identical to the CPU

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image_puller

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include

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jungfrau

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licenses

battery: a "standard" timing benchmark on open data, with every model committed

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preview

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reader

Merge mac-tiff-rm into rc176: marCCD TIFF frames read without memory-mapping (macOS page faults), output unchanged

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receiver

broker rugnux live: the scan result carries rugnux's rotation lattice

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rugnux

Merge failed-perimage into rc176: a rotation run that finds no lattice still reports every image (spots, resolution, background; not indexed), live and offline

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tests

ModelValidationTest: the CPU density is gemmi's to rounding, the same on any number of threads

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tools

docs: rc176 - molecular replacement as a pipeline step, Metal and multi-GPU MR, header polarization, Rugnux live tab

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viewer

rugnux: the library returns its outputs in memory; the callers write the files

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writer

broker rugnux live: no files, END built from the result in memory, and review fixes

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.gitattributes

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.gitignore

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.readthedocs.yaml

version 1.0.0-rc.25

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CLAUDE.md

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CMakeLists.txt

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CONTRIBUTING.md

version 1.0.0-rc.27

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gen_python_client.sh

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gitea_create_release.py

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gitea_upload_file.py

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LICENSE

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make_doc.sh

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README.md

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rugnux_anomalous.py

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rugnux_stills_ab.py

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stills_datasets.tsv

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THIRD_PARTY_NOTICES.md

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update_version.sh

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VERSION

1.0.0-rc.176

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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.