leonarski_f
dd0bffb283
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This is an UNSTABLE release. It includes many experimental features, as well as many AI generated fixes. We recommend using rc.152 for production use. * rugnux: Add `--model model.pdb` - score the merged data against an atomic model and compute initial maps. It reports R-work/R-free (scaling the model to the observed amplitudes with an overall scale, an anisotropic B and a flat bulk solvent - the standard few-parameter model, so a batch of maps stays directly comparable) and writes 2Fo-Fc / Fo-Fc electron-density maps (CCP4) plus a map-coefficient MTZ. The structure itself is not refined; the model is only re-fractionalised into the data cell. * rugnux: The merged reflection output now carries French-Wilson amplitudes (|F| and its sigma) next to the intensities - MTZ `F`/`SIGF`, mmCIF `_refln.F_meas_au`, and the text HKL - computed with the correct centric/acentric Wilson prior and epsilon multiplicity, so a downstream program (e.g. phenix.refine) can refine against amplitudes. The intensity columns are unchanged. * rugnux: R-free test-set flags are now assigned deterministically and consistently across symmetry - a Bijvoet pair I(+)/I(-) is never split between the work and free sets, and the assignment is a reproducible per-hkl hash that depends only on the reflection index, so every dataset of one crystal form gets the same ~5% free set (what a multi-dataset campaign such as PanDDA needs). On small data the fraction is floored so the test set stays large enough for a stable R-free (~500 reflections, capped at 10%); it stays flat at 5% on ordinary data. When a reference MTZ carries a `FreeR_flag` column its test set is imported instead, letting a whole campaign inherit one shared free set. * rugnux: A reference MTZ (`--reference-mtz`) can now fix the space group and cell for rotation data too (previously rejected), without being used to scale - the rotation merge stays self-consistent. When the crystal has an indexing (merohedral) ambiguity - a lattice symmetry higher than its Laue symmetry, e.g. P3/P4/P6/C2 - the reference also resolves it: each candidate reindexing (identity plus the twin-law cosets of the metric symmetry) is scored by its intensity correlation against the reference and the data are re-merged in the best-correlating one. This is a metric-preserving relabelling of hkl (the cell is unchanged) and a no-op for a holohedral crystal such as lysozyme. * rugnux: `--model` validation now aligns the data to the model before scoring - the observed reflections are reindexed into the model's enantiomorph when the two differ only by hand (indistinguishable from merged intensities). A merohedral indexing ambiguity is resolved against the reference MTZ when one is given (so a whole campaign shares one indexing convention); only with a model and no reference does validation fall back to fitting each candidate reindexing and keeping the lowest R-free. * rugnux: De-novo symmetry - recover a genuine high-symmetry group whose data are imperfectly scaled. Such a merge's within-orbit chi² lands just past the self-consistency bound (each real symmetry step adds a little systematic scatter), right where a merohedral twin also lands, so the chi² ratio alone cannot separate them. The candidate is now rescued when the extra intensity-proportional systematic error it invokes stays small relative to the confirmed subgroup - a genuine symmetry step gains multiplicity without inflating the merge error model's b, whereas a twin forces non-equivalent reflections together and b balloons. Fixes cubic insulin (I23 instead of I222) with no change to any other crystal in the test battery, including the twins that must stay in their lower symmetry. * Docs: Document the French-Wilson amplitude estimation, R-free flagging, reference-based space-group/ambiguity resolution, and model-based validation/maps in CPU_DATA_ANALYSIS.md. * Frontend: The status-bar pill now shows a progress bar during detector calibration (previously only during measurement), and the calibration state and its button are labelled "Calibration"/"CALIBRATE" (the internal `Pedestal` state name is unchanged for back-compatibility).Reviewed-on: #69 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.