leonarski_fandFilip Leonarski
19b135186d
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* Rugnux: Processes a collection live while jfjoch_broker writes it (`rugnux <master.h5> <broker URL>`). * Rugnux: Processing starts on the first images and confirms its choices once all are in, so analysis can begin during collection. * Rugnux: Faster processing, especially on servers with several GPUs and CPU sockets and on computers without a GPU (`--no-gpu`, macOS). * Rugnux: Uses much less GPU memory, so large data sets stay on the GPU of smaller cards, and a data set too large for the card is processed on the CPU instead. * Rugnux: On macOS, Bragg integration runs on the Apple GPU. * Rugnux: Better handling of twinning and pseudo-symmetry, with the twin hypothesis written as `<prefix>_twin_<SG>.mtz`, and a wrong `--model` no longer confirms the data or decides the hand. * Rugnux: `--model` accepts predicted (AlphaFold) models and falls back to molecular replacement when the model is not placed as a rigid body (experimental `--mr` forces it), settling space group, hand and twinning and writing a different answer as `<prefix>_mr.mtz`. * Rugnux: Molecular replacement is faster and settles the space group in more cases with several copies in the asymmetric unit. * Rugnux: Deposition-ready mmCIF, a richer report, and numbered steps on the terminal with the full log in `<prefix>_log.txt`; `_P1.mtz`, `--estimate-beam-center` and `--beam-center-search` are removed. * Rugnux: The beam-stop shadow is found correctly on tilted detectors. * Rugnux: Stills files that record a stationary goniometer axis get the default stills geometry refinement. * jfjoch_viewer: "Analyze dataset" uses the same defaults as a bare `rugnux <file>`, and shows the results of processed CBF, marCCD and SMV sweeps. * jfjoch_viewer: The Files panel refreshes on F5 and every few seconds, and the plot type and other selections stay put during live collection. * jfjoch_writer: Memory stays bounded and old data files are closed efficiently on long runs, any failure ends the run in an error state the broker is told about, and the master file appears only after its data files; the ZeroMQ pusher logs when a stalled writer makes it drop images. * Fixes: The TCP image pusher no longer blocks the broker's receiver, GPU out-of-memory failures stop with a clear message, and the XDS plugin masks module and chip edges. --------- Co-authored-by: Filip Leonarski <jungfrau@filips-mac-mini.home> Reviewed-on: #85 Co-authored-by: Filip Leonarski <filip.leonarski@psi.ch>
51 lines
1.8 KiB
Plaintext
51 lines
1.8 KiB
Plaintext
cmake-build-debug/
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cmake-build-release/
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build*/
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python-client/
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openapi-generator-cli.jar
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# make_doc.sh: rendered HTML (default output dir) and the throw-away venv it builds in. The venv is
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# normally deleted at the end, but stays behind when the build fails.
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public/
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tmp_venv/
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# gen_python_client.sh: the built sdist/wheel.
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/dist/
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# output dirs of the retired rugnux_vs_xds.py, still lying around in older working trees
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rugnux_cmp*/
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# rugnux_anomalous.py ANODE work dir, when the config does not point it at the data
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rugnux_anomalous*/
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!rugnux_anomalous.py
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# Processing output and the data it came from. These are USER DATA: a merged .mtz/.cif or a model
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# carries a sample's measured unit cell, and its filename usually carries the sample's name - neither
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# of which may enter this repository (see CLAUDE.md). They accumulate in the working tree while
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# testing, so keep them un-addable rather than relying on everyone typing the right paths.
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*.mtz
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*.cif
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*.pdb
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*.hkl
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*_plot.txt
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*_detector.jpg
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# Test fixtures are checked in deliberately; add them with an explicit path.
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!tests/**
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# The timing benchmark's start models: public AlphaFold DB predictions (no measured cell, no sample)
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!tools/battery/models/AF-*-model_v*.cif
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# CMake configures GitInfo.cpp.in into the BINARY dir; a copy here is only ever the residue of an
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# in-source configure, and a stale one shipped a wrong version string once already.
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common/GitInfo.cpp
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# Review reports, work plans and investigation notes. They are working material for one task, they
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# go stale the moment the code moves, and Sphinx would publish anything left under docs/.
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docs/review/
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# Python bytecode (tools/battery and the root scripts)
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__pycache__/
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# tools/battery: the local site config (paths of this machine, private manifest); site.example.json is the template
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tools/battery/site.json
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