leonarski_fandFilip Leonarski
19b135186d
Build Packages / Create release (push) Successful in 7s
Build Packages / build:portable:macos-arm64:nocuda (push) Successful in 4m56s
Build Packages / build:rugnux:linux-aarch64:cuda (push) Successful in 9m10s
Build Packages / build:portable:linux-x86_64:nocuda (push) Successful in 13m51s
Build Packages / build:portable:linux-x86_64:cuda (push) Successful in 16m56s
Build Packages / build:jfjoch:rocky8:nocuda (push) Successful in 20m59s
Build Packages / build:portable:windows-x86_64:nocuda (push) Successful in 21m25s
Build Packages / build:jfjoch:rocky9:nocuda (push) Successful in 21m17s
Build Packages / build:jfjoch:ubuntu2204:nocuda (push) Successful in 14m14s
Build Packages / HDF5 consumer tests (DIALS, XDS) (push) Successful in 25m59s
Build Packages / build:portable:windows-x86_64:cuda (push) Successful in 25m48s
Build Packages / build:jfjoch:ubuntu2404:nocuda (push) Successful in 15m52s
Build Packages / build:jfjoch:rocky8:cuda-sls9 (push) Successful in 19m33s
Build Packages / Generate python client (push) Successful in 29s
Build Packages / Build documentation (push) Successful in 1m19s
Build Packages / build:jfjoch:ubuntu2204:cuda (push) Successful in 20m49s
Build Packages / build:jfjoch:rocky9:cuda-sls9 (push) Successful in 25m31s
Build Packages / build:jfjoch:rocky8:cuda (push) Successful in 25m24s
Build Packages / build:jfjoch:rocky9:cuda (push) Successful in 26m5s
Build Packages / build:jfjoch:ubuntu2404:cuda (push) Successful in 22m19s
Build Packages / Unit tests (push) Failing after 2h28m24s
Build Packages / Validation Battery (push) Successful in 40m33s
* 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>
Jungfraujoch Frontend
Building
To build web interface:
cd frontend_ui
npm install
npm run openapi
npm run build
Available Scripts
In the project directory, you can run:
npm start
Runs the app in the development mode.
The page will reload if you make edits.
You will also see any lint errors in the console.
npm test
Launches the test runner in the interactive watch mode.
See the section about running tests for more information.
npm run build
Builds the app for production to the dist folder.
It correctly bundles React in production mode and optimizes the build for the best performance.
The build is minified and the filenames include the hashes.
Your app is ready to be deployed!
npm run openapi
npm audit findings
npm audit currently reports 17 advisories (3 high, 13 moderate, 1 low). All of
them live in build-time tooling and never reach the production bundle
shipped to the browser. Summary of the chains:
| Source dep | Vulnerable transitives | When it runs |
|---|---|---|
@redocly/cli |
@opentelemetry/*, dompurify (via redoc), ws (via simple-websocket), js-yaml, protobufjs, @babel/core |
npm run redocly / redocly4broker — static OpenAPI HTML generation |
vite |
esbuild@0.27.x |
Dev server and dep pre-bundling. Production build uses Rollup. |
vite-plugin-svgr |
@babel/core, js-yaml (via cosmiconfig) |
Vite build plugin |
openapi-typescript-codegen |
js-yaml |
npm run openapi — TS client generation |
Notes on the high-severity items:
esbuildGHSA-gv7w-rqvm-qjhr is a Deno-specific RCE viaNPM_CONFIG_REGISTRY; GHSA-g7r4-m6w7-qqqr is an arbitrary-file-read in the dev server on Windows. Neither applies to a Linux build of the production bundle.wsGHSA-96hv-2xvq-fx4p only matters whensimple-websocketopens a socket, which happens during docs generation, not at runtime.
npm audit fix cannot resolve any of these without downgrading
@redocly/cli (no real fix) or jumping vite to a major that switches the
bundler to Rolldown.