react-cheminfo 0.69.0 → 0.71.0

package/README.md

@@ -47,6 +47,7 @@ only when it drags a heavy dependency behind it.
 | `react-cheminfo/spectra`           | the spectra processing settings editors               | React; types only from spectra-processor, ml-pca |
 | `react-cheminfo/ir`                | the infrared chart, band table and editor             | React, ir-spectrum, convert-to-jcamp             |
 | `react-cheminfo/raman`             | the Raman editor: the infrared one, read for Raman    | the same as `react-cheminfo/ir`                  |
+| `react-cheminfo/mass`              | the mass spectrum chart, peak table and editor        | React, ms-spectrum, jcampconverter, xy-parser    |
 | `react-cheminfo/xtb`               | GFN2-xTB as a geometry relaxer                        | nothing on import; xtb-wasm on the first call    |
 | `react-cheminfo/host`              | data handed over by a page that frames the tool       | nothing on import; ajv once the page is framed   |
 | `react-cheminfo/host-testing`      | a stand-in host and SciPeaks' messages, for e2e tests | nothing; Node only                               |
@@ -79,6 +80,17 @@ because a spectrum of any kind is drawn with them and the next viewer built on
 them should find them already there rather than reach through an infrared
 package for them.
 
+`react-cheminfo/mass` is the infrared viewer's sibling for mass spectra: the
+same shell, the same three buckets of state, the same chart underneath, and
+neither imports the other. It reads JCAMP-DX through `jcampconverter` — the
+same release `ir-spectrum` reads through — and two columns of text through
+`xy-parser`, each reader fetched only once the bytes turn out to need it. A profile is peak picked by `ms-spectrum` as it is read, and every spectrum
+is judged high or low resolution on the strongest evidence it carries: the
+resolving power measured on its peak widths, else the instrument its file
+names, else the decimals its masses were written with — which then decides
+how many decimals every mass is written with. The peaks of the selected
+spectrum are labelled as the chart is zoomed.
+
 `react-cheminfo/xtb` is the door a page opens only when a visitor asks for a
 better number. `refineConformers` in
 `react-cheminfo/conformers` orchestrates a refinement against the
@@ -122,7 +134,8 @@ through a wildcard subpath exactly as `react-science` serves its own.
 | **Chemistry**              | `atomicOrbitalsOf`, `configurationOf`, `classifyMolfile`, `readStructure`, `toMolfileExport`                                                                                                                                                                                                                                           | `AtomicOrbitalViewer` (`/orbital`), `StructureEditor`, `Structure` (`/structure`)                                                                                                                                                                                                                   |
 | **Conformers**             | `generateConformers`, `continueConformers`, `refineConformers`, `conformerShape`, `isSameMinimum`, `rankByEnergy`, `minimiseConformer`, `DEFAULT_CONFORMER_OPTIONS`, `CONFORMER_STRATEGIES` (all `/conformers`); `GeometryRelaxer`, `readRelaxableGeometry`, `centredRmsd`                                                             | —                                                                                                                                                                                                                                                                                                   |
 | **Spectrum charts**        | `chartScale`, `chartAxisScale`, `plotRect`, `zoomDomain`, `zoomSelection`, `labelStackBaselines`, `layoutAnnotationBoxes`, `profilePath`, `stickPath`, `guidePlacement`, `readoutPlacement`, `stackCapacity`, `nextSpectrumColor`, `panelStyles`, `statusBar`                                                                          | `Axes`, `AxisGuide`, `ChartTracker`, `ChartStack`, `SelectionRect`, `TraceLegend`, `PlotCaption`, `useChartZoom`, `useChartPointer`, `useChartSize`, `SidePanelStack`, `PanelRail`, `Section`, `FilterInput`, `AboutDialogFrame`, `DocumentationDialogFrame`, `FigureDownload`, `useFigureDownload` |
-| **Infrared and Raman**     | `loadIrSpectra`, `toIrSpectrum`, `pickBands`, `assignBands`, `BAND_ASSIGNMENTS`, `irSpectrumToJcamp`, `IR_MODE_RULES`, `IR_TECHNIQUE_RULES`, `nearestBandAt`, `planBandLabels`, `irReducer` (all `/ir`)                                                                                                                                | `IrEditor`, `IrChart`, `BandsPanel`, `SpectraPanel`, `MetadataPanel`, `useIrEditor` (all `/ir`); `RamanEditor` (`/raman`)                                                                                                                                                                           |
+| **Infrared and Raman**     | `loadIrSpectra`, `toIrSpectrum`, `pickBands`, `pickBandAt`, `editBandsAt`, `bandsFromPeaks`, `peaksFromBands`, `assignBands`, `BAND_ASSIGNMENTS`, `irSpectrumToJcamp`, `IR_MODE_RULES`, `IR_TECHNIQUE_RULES`, `nearestBandAt`, `planBandLabels`, `irReducer` (all `/ir`)                                                               | `IrEditor`, `IrChart`, `BandsPanel`, `SpectraPanel`, `MetadataPanel`, `useIrEditor` (all `/ir`); `RamanEditor` (`/raman`)                                                                                                                                                                           |
+| **Mass spectra**           | `loadMassSpectra`, `toMassSpectra`, `analyseSpectrum`, `decideResolution`, `resolutionOf`, `mzDecimalsOf`, `planPeakLabels`, `peakTableRows`, `massSpectrumToJcamp`, `massReducer` (all `/mass`)                                                                                                                                       | `MassEditor`, `MassChart`, `SpectraPanel`, `PeaksPanel`, `MetadataPanel`, `useMassEditor` (all `/mass`)                                                                                                                                                                                             |
 | **Spectra**                | `FILTER_CATALOG`, `filterMenu`, `settingsProblems`, `normalizationFilters`, `addFilter`, `moveFilter`, `setFilterOption`, `principalComponentChoices`, `clampPrincipalComponents`, `EMPTY_SETTINGS` (all `/spectra`)                                                                                                                   | `SpectraSettingsEditor`, `FilterChainEditor`, `PrincipalComponentSelect` (all `/spectra`)                                                                                                                                                                                                           |
 | **About**                  | `resolveAbout`, `aboutProblems`                                                                                                                                                                                                                                                                                                        | `AboutPage`                                                                                                                                                                                                                                                                                         |
 | **Which build is running** | `formatBuiltAt`, `shortCommit`, `BuildInfo`                                                                                                                                                                                                                                                                                            | `AboutVersion`, `cheminfoBuildInfo` (`/vite`)                                                                                                                                                                                                                                                       |
@@ -133,7 +146,7 @@ through a wildcard subpath exactly as `react-science` serves its own.
 | **Parallel coordinates**   | `parallelAxisOf`, `parallelAxisLayouts`, `parallelIncludedMask`, `parallelKeptCount`, `parallelNearestRow`, `parallelSegmentAt`, `parallelBandAt`, `parallelRangeOf`, `parallelPalette`, `parallelColorSteps`, `paintParallelLines`                                                                                                    | `ParallelCoordinates`                                                                                                                                                                                                                                                                               |
 | **Periodic table**         | `PERIODIC_ELEMENTS`, `elementBySymbol`, `elementByAtomicNumber`, `cellOf`, `placedElements`, `elementByArrowKey`, `EMPTY_BLOCK`, `categorySwatch`, `CATEGORY_LABELS`                                                                                                                                                                   | `PeriodicTable`, `ElementCell`, `CategoryLegend`                                                                                                                                                                                                                                                    |
 | **Taxonomy**               | `TAXON_RANKS`, `PRINCIPAL_RANKS`, `rankOrder`, `isPrincipalRank`, `isGenusOrBelow`, `isAboveGenus`, `principalLineage`, `lineageFromNodes`, `lineageFromRanks`, `genusOrBelow`, `ncbiTaxonomyUrl`, `splitOrganismName`                                                                                                                 | `TaxonLineage`, `OrganismName`, `useRankLabel`                                                                                                                                                                                                                                                      |
-| **Framed by a host**       | `hostStructureLoader`, `readHostMolecule`, `STRUCTURE_KINDS`, `connectHost`, `selectInputs`, `checkValue`, `kindAccepts`, `parseRequest` (all `/host`); `startStandInHost`, `SCIPEAKS_ETHYLBENZENE_LOAD` (`/host-testing`)                                                                                                             | `useHostConnection` (`/host`)                                                                                                                                                                                                                                                                       |
+| **Framed by a host**       | `hostStructureLoader`, `readHostMolecule`, `STRUCTURE_KINDS`, `IR_JDX_SCHEMA`, `IR_PEAKS_SCHEMA`, `connectHost`, `selectInputs`, `checkValue`, `kindAccepts`, `parseRequest`, `OUTPUT_DELAY` (all `/host`); `startStandInHost`, `sendStandInHostRequest`, `SCIPEAKS_ETHYLBENZENE_LOAD`, `sciPeaksEthylbenzeneIrLoad` (`/host-testing`) | `useHostConnection` (`/host`)                                                                                                                                                                                                                                                                       |
 | **Answer cards**           | `CARD_PARAM`, `isCardAddress`, `sitePageUrl`, `cardPageUrl`, `framedPageUrl`, `roomForPanels`; `answerAddresses`, `joinAddress`, `viewOrigins`, `cardMeta`, `pageAnswer`, `siteView` (all `/server`)                                                                                                                                   | `CardFrame`, `CardDetailsButton`, `CardFigure`, `CopyTableButton`, `fitCardToFrame`, `useFitCardToFrame`, `useOverlayRoom`, `holdRoomForPanels` (all `/card`); `StructureExportButton`, `useStructureDraft` (`/structure`)                                                                          |
 
 Everything in that table is exported from `./core`, `./ui`, `./slides`,
@@ -308,6 +321,9 @@ import { AccountButton } from 'react-cheminfo/ui';
 - `items` are the account's own pages, listed in the menu above Sign out.
 - `signInHref` keeps the invitation a real link, so a middle click opens a tab;
   a site with no page for it passes `onSignIn` alone and opens a dialog.
+- A site on the shared accounts draws the `AccountMenu` of
+  [service-accounts-frontend](https://github.com/cheminfo/service-monitor/tree/main/accounts-frontend),
+  which feeds this button from the session.
 
 ### `AtomicOrbitalViewer`
 
@@ -972,6 +988,54 @@ useHostConnection(TOOL, { load: loadFromHost, build: BUILD_INFO });
 - **The same document twice is applied once**, so a host re-sending a sample
   never overwrites what the visitor did with it.
 
+### Spectra in, bands back
+
+A measured infrared spectrum travels as `spectra.ir.jdx` — the JCAMP-DX text
+and the bands picked on it — and its bands alone as `spectra.ir.peaks`. A band
+is written the way SciPeaks stores one, so what comes back is saved as it
+arrives:
+
+```json
+{
+  "wavenumber": 1613.86,
+  "absorbance": 0.4737,
+  "transmittance": 0.336,
+  "kind": "m"
+}
+```
+
+`transmittance` is a fraction, not a percentage, and only `wavenumber` is
+required. Pipeline's own `spectra.ir` is a computed spectrum, not a measurement.
+
+An input with `many: true` takes every item of its kinds, and one with
+`optional: true` may go without; the request is refused only when no input got
+anything. `load` may return a promise, and requests are served in order.
+
+A tool hands values back through `outputs`, a store read synchronously — a
+`computed` signal does it:
+
+```ts
+// One item per value, with its `key` and the `id` of the item it came from.
+const peaks = computed(() => peakItems(measured.value, hostIds.value));
+
+useHostConnection(TOOL, {
+  load,
+  outputs: {
+    read: () => peaks.value,
+    subscribe: (heard) => peaks.subscribe(heard),
+  },
+  build: BUILD_INFO,
+});
+```
+
+- **`get`** is answered with the current values: `{ ok: true, items }`.
+- **`output`** is sent unasked when a value the host's load `accept`s, by
+  its key or its kind, changes: `{ type: 'output', document, items }`, 300 ms after the
+  last edit. It carries only the items that changed, each with the `id` of the
+  item it was made from, so a host knows which spectrum to save them on.
+- **Opening a document sends nothing back.** What the tool shows once `load`
+  returns is what the host already has, so `read` must reflect a load by then.
+
 `react-cheminfo/host-testing` serves a stand-in host for Playwright on
 `127.0.0.1`, and exports `SCIPEAKS_ETHYLBENZENE_LOAD`: the message SciPeaks'
 tool tab sends for a sample, byte for byte. visualizer-helper's tests pin the
@@ -985,6 +1049,10 @@ await page.goto(
 const { results } = await page.evaluate(readStandInHostLog);
 ```
 
+`sciPeaksEthylbenzeneIrLoad(jdx)` is the load SciPeaks' tool tab is to send
+for that sample's infrared spectrum, its bands as stored. Hand it the
+attachment's JCAMP-DX. `sendStandInHostRequest` sends a later `get`.
+
 ## Protecting a link
 
 The share dialog can hand out a **sealed link**: the whole query string moved

package/lib/about/core/providers.d.ts

@@ -27,5 +27,11 @@ export declare const PROVIDERS: readonly [{
     readonly fullName: "École polytechnique fédérale de Lausanne";
     readonly href: "https://www.epfl.ch";
     readonly location: "Lausanne, Switzerland";
+}, {
+    readonly id: "unil-esc";
+    readonly name: "ESC";
+    readonly fullName: "École des sciences criminelles, Université de Lausanne";
+    readonly href: "https://www.unil.ch/esc/";
+    readonly location: "Lausanne, Switzerland";
 }];
 //# sourceMappingURL=providers.d.ts.map

package/lib/about/core/providers.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"providers.d.ts","sourceRoot":"","sources":["../../../src/about/core/providers.ts"],"names":[],"mappings":"AAAA,yFAAyF;AACzF,MAAM,WAAW,aAAa;IAC5B,sDAAsD;IACtD,EAAE,EAAE,MAAM,CAAC;IACX,iEAAiE;IACjE,IAAI,EAAE,MAAM,CAAC;IACb,iEAAiE;IACjE,QAAQ,EAAE,MAAM,CAAC;IACjB,mCAAmC;IACnC,IAAI,EAAE,MAAM,CAAC;IACb,iEAAiE;IACjE,QAAQ,EAAE,MAAM,CAAC;CAClB;AAED,8CAA8C;AAC9C,MAAM,MAAM,UAAU,GAAG,CAAC,OAAO,SAAS,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC;AAE1D;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,SAAS,UAAU,EAAE,GAAG,aAAa,EAAE,CAUrE;AAED,uEAAuE;AACvE,eAAO,MAAM,SAAS;;;;;;;;;;;;EAeuB,CAAC"}

package/lib/about/core/providers.js

@@ -24,5 +24,12 @@ export const PROVIDERS = [
         href: 'https://www.epfl.ch',
         location: 'Lausanne, Switzerland',
     },
+    {
+        id: 'unil-esc',
+        name: 'ESC',
+        fullName: 'École des sciences criminelles, Université de Lausanne',
+        href: 'https://www.unil.ch/esc/',
+        location: 'Lausanne, Switzerland',
+    },
 ];
 //# sourceMappingURL=providers.js.map

package/lib/about/core/providers.js.map

@@ -1 +1 @@
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+{"version":3,"file":"providers.js","sourceRoot":"","sources":["../../../src/about/core/providers.ts"],"names":[],"mappings":"AAiBA;;;;;GAKG;AACH,MAAM,UAAU,SAAS,CAAC,GAA0B;IAClD,MAAM,MAAM,GAAoB,EAAE,CAAC;IACnC,KAAK,MAAM,EAAE,IAAI,GAAG,EAAE,CAAC;QACrB,MAAM,KAAK,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,EAAE,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,CAAC,CAAC;QACjE,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,qBAAqB,EAAE,EAAE,CAAC,CAAC;QAC7C,CAAC;QACD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;IACrB,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,uEAAuE;AACvE,MAAM,CAAC,MAAM,SAAS,GAAG;IACvB;QACE,EAAE,EAAE,MAAM;QACV,IAAI,EAAE,MAAM;QACZ,QAAQ,EAAE,0CAA0C;QACpD,IAAI,EAAE,qBAAqB;QAC3B,QAAQ,EAAE,uBAAuB;KAClC;IACD;QACE,EAAE,EAAE,UAAU;QACd,IAAI,EAAE,KAAK;QACX,QAAQ,EAAE,wDAAwD;QAClE,IAAI,EAAE,0BAA0B;QAChC,QAAQ,EAAE,uBAAuB;KAClC;CAC0C,CAAC"}

package/lib/about/ui/AboutProvidedBy.js

@@ -28,10 +28,18 @@ function ProviderLogo(props) {
     switch (provider.id) {
         case 'epfl':
             return _jsx(EpflLogo, { label: label });
+        case 'unil-esc':
+            return _jsx(UnilEscLockup, { label: label });
         default:
             return _jsx("span", { children: provider.name });
     }
 }
+// The school's name set in type beside its university's, in the black the
+// university writes its name in: no drawing of its emblem is kept here, and a
+// name nobody can misread credits it better than a guess at one.
+function UnilEscLockup(props) {
+    return (_jsxs("span", { role: "img", "aria-label": props.label, style: UNIL_LOCKUP_STYLE, children: [_jsx("span", { style: UNIL_NAME_STYLE, children: "UNIL" }), _jsx("span", { style: UNIL_RULE_STYLE }), _jsxs("span", { style: UNIL_SCHOOL_STYLE, children: ["\u00C9cole des", _jsx("br", {}), "sciences criminelles"] })] }));
+}
 function EpflLogo(props) {
     return (_jsx("svg", { width: 112, height: (112 * 53) / 182.4, viewBox: "0 0 182.4 53", role: "img", "aria-label": props.label, style: { display: 'block' }, children: _jsxs("g", { fill: "red", children: [_jsx("polygon", { points: "0 21.6 11.43 21.6 11.43 9.8 38.34 9.8 38.34 0 0 0 0 21.6" }), _jsx("polygon", { points: "0 53 38.34 53 38.34 43.2 11.43 43.2 11.43 31.4 0 31.4 0 53" }), _jsx("rect", { x: "11.43", y: "21.6", width: "24.61", height: "9.8" }), _jsx("path", { d: "M86,4.87a16.12,16.12,0,0,0-5.68-3.53A23.76,23.76,0,0,0,71.82,0H48.14V53H59.57V31.4H71.82a23.76,23.76,0,0,0,8.46-1.34A16.12,16.12,0,0,0,86,26.53a13.43,13.43,0,0,0,3.19-5,17.38,17.38,0,0,0,0-11.62A13.52,13.52,0,0,0,86,4.87ZM78,18.73a5.7,5.7,0,0,1-2.26,1.8,11.33,11.33,0,0,1-3.27.85,32,32,0,0,1-3.86.22H59.57V9.8h9.05a32,32,0,0,1,3.86.22,11,11,0,0,1,3.27.86A5.59,5.59,0,0,1,78,12.67a5,5,0,0,1,.86,3A5,5,0,0,1,78,18.73Z" }), _jsx("polygon", { points: "155.47 43.2 155.47 0 144.04 0 144.04 53 182.38 53 182.38 43.2 155.47 43.2" }), _jsx("polygon", { points: "97.42 21.6 108.85 21.6 108.85 9.8 135.76 9.8 135.76 0 97.42 0 97.42 21.6" }), _jsx("rect", { x: "97.42", y: "31.4", width: "11.43", height: "21.6" }), _jsx("rect", { x: "108.85", y: "21.6", width: "24.61", height: "9.8" })] }) }));
 }
@@ -83,4 +91,30 @@ const ROLES_STYLE = {
     paddingLeft: 20,
     borderTop: '1px solid var(--border)',
 };
+const UNIL_LOCKUP_STYLE = {
+    display: 'flex',
+    alignItems: 'center',
+    gap: 8,
+    height: 31,
+    // The institution's own colour, not a family token: the tile is white on
+    // every theme.
+    color: 'black',
+};
+const UNIL_NAME_STYLE = {
+    fontSize: 24,
+    fontWeight: 800,
+    letterSpacing: '0.02em',
+    lineHeight: 1,
+};
+const UNIL_RULE_STYLE = {
+    alignSelf: 'stretch',
+    width: 1,
+    background: 'black',
+};
+const UNIL_SCHOOL_STYLE = {
+    fontSize: 10.5,
+    fontWeight: 600,
+    lineHeight: 1.15,
+    whiteSpace: 'nowrap',
+};
 //# sourceMappingURL=AboutProvidedBy.js.map

package/lib/about/ui/AboutProvidedBy.js.map

@@ -1 +1 @@
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package/lib/chart/ui/useChartPointer.d.ts

@@ -36,7 +36,9 @@ export interface ChartPointerOptions<TReadout> {
     /**
      * What the chart reads at a point. Called on every move the pointer makes
      * inside the plot, and read live rather than closed over, so it may capture
-     * the scales as they are currently zoomed.
+     * the scales as they are currently zoomed — and called again at the held
+     * position whenever it changes, which is how a zoom made without moving the
+     * pointer is read under it.
      */
     read: (point: ChartPoint) => TReadout;
     /**
@@ -76,6 +78,12 @@ export interface ChartPointerOptions<TReadout> {
  * is under the pointer" **after** the row's "this trace is being read", and
  * wipes it. Heard as `pointerout`, the report lands first and the row has the
  * last word. The containment test is what `pointerleave` was giving for free.
+ *
+ * What is returned is read again at render whenever `read` changes, because a
+ * zoom by the wheel, a key or the end of a drag changes the scales without
+ * moving the pointer, and a crosshair still quoting the window before it would
+ * name a mass the line it is drawn on no longer stands at. `onReadout` is told
+ * on the next move, as it always is.
  * @param options - The chart, and how to read a point on it.
  * @returns Where the pointer is and what it reads, both `null` while it is
  * anywhere but over the plot.

package/lib/chart/ui/useChartPointer.d.ts.map

@@ -1 +1 @@
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package/lib/chart/ui/useChartPointer.js

@@ -14,7 +14,7 @@
  * that panel is a linked viewer that reports its own hovers back, would
  * ping-pong between the two until the tab stops answering.
  */
-import { useEffect, useLayoutEffect, useRef, useState } from 'react';
+import { useEffect, useLayoutEffect, useMemo, useRef, useState } from 'react';
 import { svgPointAt } from "../core/svgPoint.js";
 /**
  * Follow the pointer over a chart.
@@ -35,12 +35,18 @@ import { svgPointAt } from "../core/svgPoint.js";
  * is under the pointer" **after** the row's "this trace is being read", and
  * wipes it. Heard as `pointerout`, the report lands first and the row has the
  * last word. The containment test is what `pointerleave` was giving for free.
+ *
+ * What is returned is read again at render whenever `read` changes, because a
+ * zoom by the wheel, a key or the end of a drag changes the scales without
+ * moving the pointer, and a crosshair still quoting the window before it would
+ * name a mass the line it is drawn on no longer stands at. `onReadout` is told
+ * on the next move, as it always is.
  * @param options - The chart, and how to read a point on it.
  * @returns Where the pointer is and what it reads, both `null` while it is
  * anywhere but over the plot.
  */
 export function useChartPointer(options) {
-    const { svgRef } = options;
+    const { svgRef, read } = options;
     const [pointer, setPointer] = useState(POINTER_AWAY);
     const latest = useRef(options);
     const reported = useRef(null);
@@ -77,7 +83,9 @@ export function useChartPointer(options) {
             svg.removeEventListener('pointerout', out);
         };
     }, [svgRef]);
-    return pointer;
+    return useMemo(() => pointer.position === null
+        ? pointer
+        : { position: pointer.position, readout: read(pointer.position) }, [pointer, read]);
 }
 /**
  * Whether a `pointerout` means the pointer has left the chart.

package/lib/chart/ui/useChartPointer.js.map

@@ -1 +1 @@
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+{"version":3,"file":"useChartPointer.js","sourceRoot":"","sources":["../../../src/chart/ui/useChartPointer.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAGH,OAAO,EAAE,SAAS,EAAE,eAAe,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,OAAO,CAAC;AAI9E,OAAO,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAC;AA8CjD;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AACH,MAAM,UAAU,eAAe,CAC7B,OAAsC;IAEtC,MAAM,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,OAAO,CAAC;IACjC,MAAM,CAAC,OAAO,EAAE,UAAU,CAAC,GAAG,QAAQ,CAAyB,YAAY,CAAC,CAAC;IAC7E,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC;IAC/B,MAAM,QAAQ,GAAG,MAAM,CAAkB,IAAI,CAAC,CAAC;IAE/C,eAAe,CAAC,GAAG,EAAE;QACnB,MAAM,CAAC,OAAO,GAAG,OAAO,CAAC;IAC3B,CAAC,CAAC,CAAC;IAEH,SAAS,CAAC,GAAG,EAAE;QACb,MAAM,GAAG,GAAG,MAAM,CAAC,OAAO,CAAC;QAC3B,IAAI,GAAG,KAAK,IAAI;YAAE,OAAO;QAEzB,SAAS,IAAI,CAAC,IAA4B;YACxC,MAAM,EAAE,WAAW,EAAE,SAAS,EAAE,GAAG,MAAM,CAAC,OAAO,CAAC;YAClD,UAAU,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,gBAAgB,CAAC,OAAO,EAAE,IAAI,EAAE,WAAW,CAAC,CAAC,CAAC;YACtE,IAAI,WAAW,CAAC,QAAQ,CAAC,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,WAAW,CAAC;gBAAE,OAAO;YACrE,QAAQ,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,CAAC;YAChC,SAAS,EAAE,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;QAC5B,CAAC;QAED,SAAS,IAAI,CAAC,KAAmB;YAC/B,MAAM,EAAE,IAAI,EAAE,IAAI,EAAE,GAAG,MAAM,CAAC,OAAO,CAAC;YACtC,MAAM,KAAK,GAAG,UAAU,CAAC,GAAG,EAAE,KAAK,CAAC,OAAO,EAAE,KAAK,CAAC,OAAO,CAAC,CAAC;YAC5D,IAAI,CACF,KAAK,KAAK,IAAI,IAAI,CAAC,YAAY,CAAC,IAAI,EAAE,KAAK,CAAC;gBAC1C,CAAC,CAAC,YAAY;gBACd,CAAC,CAAC,EAAE,QAAQ,EAAE,KAAK,EAAE,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,EAAE,CAC9C,CAAC;QACJ,CAAC;QAED,SAAS,GAAG,CAAC,KAAmB;YAC9B,IAAI,SAAS,CAAC,GAAG,EAAE,KAAK,CAAC,aAAa,CAAC;gBAAE,IAAI,CAAC,YAAY,CAAC,CAAC;QAC9D,CAAC;QAED,GAAG,CAAC,gBAAgB,CAAC,aAAa,EAAE,IAAI,CAAC,CAAC;QAC1C,GAAG,CAAC,gBAAgB,CAAC,YAAY,EAAE,GAAG,CAAC,CAAC;QACxC,OAAO,GAAG,EAAE;YACV,GAAG,CAAC,mBAAmB,CAAC,aAAa,EAAE,IAAI,CAAC,CAAC;YAC7C,GAAG,CAAC,mBAAmB,CAAC,YAAY,EAAE,GAAG,CAAC,CAAC;QAC7C,CAAC,CAAC;IACJ,CAAC,EAAE,CAAC,MAAM,CAAC,CAAC,CAAC;IAEb,OAAO,OAAO,CACZ,GAAG,EAAE,CACH,OAAO,CAAC,QAAQ,KAAK,IAAI;QACvB,CAAC,CAAC,OAAO;QACT,CAAC,CAAC,EAAE,QAAQ,EAAE,OAAO,CAAC,QAAQ,EAAE,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,EACrE,CAAC,OAAO,EAAE,IAAI,CAAC,CAChB,CAAC;AACJ,CAAC;AAED;;;;;;;;;;GAUG;AACH,MAAM,UAAU,SAAS,CACvB,GAAmB,EACnB,OAA2B;IAE3B,IAAI,GAAG,KAAK,IAAI;QAAE,OAAO,IAAI,CAAC;IAC9B,OAAO,CAAC,CAAC,OAAO,YAAY,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC;AAC9D,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,WAAW,CACzB,OAAwB,EACxB,IAAqB,EACrB,WAA2D;IAE3D,IAAI,OAAO,KAAK,IAAI;QAAE,OAAO,IAAI,CAAC;IAClC,IAAI,OAAO,KAAK,IAAI,IAAI,IAAI,KAAK,IAAI;QAAE,OAAO,KAAK,CAAC;IACpD,OAAO,WAAW,CAAC,OAAO,EAAE,IAAI,CAAC,CAAC;AACpC,CAAC;AAED;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,gBAAgB,CAC9B,OAA+B,EAC/B,IAA4B,EAC5B,WAA2D;IAE3D,IAAI,OAAO,KAAK,IAAI;QAAE,OAAO,OAAO,CAAC;IACrC,IAAI,OAAO,CAAC,QAAQ,KAAK,IAAI,IAAI,IAAI,CAAC,QAAQ,KAAK,IAAI,EAAE,CAAC;QACxD,OAAO,OAAO,CAAC,QAAQ,KAAK,IAAI,CAAC,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC;IAC7D,CAAC;IACD,IACE,OAAO,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,QAAQ,CAAC,CAAC;QACtC,OAAO,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,QAAQ,CAAC,CAAC,EACtC,CAAC;QACD,OAAO,IAAI,CAAC;IACd,CAAC;IACD,OAAO,WAAW,CAAC,OAAO,CAAC,OAAO,EAAE,IAAI,CAAC,OAAO,EAAE,WAAW,CAAC;QAC5D,CAAC,CAAC,OAAO;QACT,CAAC,CAAC,IAAI,CAAC;AACX,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,YAAY,CAAC,IAAc,EAAE,KAAiB;IAC5D,OAAO,CACL,KAAK,CAAC,CAAC,IAAI,IAAI,CAAC,IAAI;QACpB,KAAK,CAAC,CAAC,IAAI,IAAI,CAAC,KAAK;QACrB,KAAK,CAAC,CAAC,IAAI,IAAI,CAAC,GAAG;QACnB,KAAK,CAAC,CAAC,IAAI,IAAI,CAAC,MAAM,CACvB,CAAC;AACJ,CAAC;AAED,oEAAoE;AACpE,MAAM,YAAY,GAAwB,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC"}

package/lib/credits/core/credits.d.ts

@@ -144,6 +144,36 @@ export declare const CREDITS: readonly [{
     readonly href: "https://github.com/cheminfo/spc-parser";
     readonly description: "reads the SPC files of Thermo Galactic GRAMS, Shimadzu and PerkinElmer.";
     readonly license: "MIT";
+}, {
+    readonly id: "ms-spectrum";
+    readonly name: "ms-spectrum";
+    readonly href: "https://github.com/cheminfo/mass-tools/tree/main/packages/ms-spectrum";
+    readonly description: "tells a profile from a peak table, picks the peaks and establishes their charges.";
+    readonly license: "MIT";
+}, {
+    readonly id: "ml-gsd";
+    readonly name: "ml-gsd";
+    readonly href: "https://github.com/mljs/global-spectral-deconvolution";
+    readonly description: "finds the peaks of a continuous spectrum, and their widths.";
+    readonly license: "MIT";
+}, {
+    readonly id: "jcampconverter";
+    readonly name: "jcampconverter";
+    readonly href: "https://www.npmjs.com/package/jcampconverter";
+    readonly description: "reads JCAMP-DX files.";
+    readonly license: "CC-BY-NC-SA-4.0";
+}, {
+    readonly id: "xy-parser";
+    readonly name: "xy-parser";
+    readonly href: "https://github.com/cheminfo/xy-parser";
+    readonly description: "reads two columns of numbers out of any text file.";
+    readonly license: "MIT";
+}, {
+    readonly id: "convert-to-jcamp";
+    readonly name: "convert-to-jcamp";
+    readonly href: "https://github.com/cheminfo/convert-to-jcamp";
+    readonly description: "writes spectra back out as JCAMP-DX.";
+    readonly license: "MIT";
 }, {
     readonly id: "occ";
     readonly name: "OCC";
@@ -180,6 +210,12 @@ export declare const CREDITS: readonly [{
     readonly href: "https://molstar.org/";
     readonly description: "the 3D viewer, its representations and its surfaces.";
     readonly license: "MIT";
+}, {
+    readonly id: "nmrium";
+    readonly name: "NMRium";
+    readonly href: "https://www.nmrium.org/";
+    readonly description: "displays and processes the NMR spectra, read from their original files.";
+    readonly license: "MIT AND CC-BY-NC-SA-4.0";
 }, {
     readonly id: "blueprint";
     readonly name: "Blueprint";
@@ -305,6 +341,11 @@ export declare const CREDITS: readonly [{
     readonly href: "https://www.wikidata.org/";
     readonly description: "the name of every compound in every language, and its article in each Wikipedia.";
     readonly license: "CC0-1.0";
+}, {
+    readonly id: "pubchem";
+    readonly name: "PubChem";
+    readonly href: "https://pubchem.ncbi.nlm.nih.gov/";
+    readonly description: "the identifier, the names and the synonyms each compound is linked to.";
 }, {
     readonly id: "country-flag-icons";
     readonly name: "country-flag-icons";

package/lib/credits/core/credits.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"credits.d.ts","sourceRoot":"","sources":["../../../src/credits/core/credits.ts"],"names":[],"mappings":"AAAA,wCAAwC;AACxC,MAAM,WAAW,WAAW;IAC1B,iDAAiD;IACjD,EAAE,EAAE,MAAM,CAAC;IACX,qEAAqE;IACrE,IAAI,EAAE,MAAM,CAAC;IACb,4BAA4B;IAC5B,IAAI,EAAE,MAAM,CAAC;IACb,8CAA8C;IAC9C,WAAW,EAAE,MAAM,CAAC;IACpB;;;OAGG;IACH,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,qCAAqC;AACrC,MAAM,MAAM,QAAQ,GAAG,CAAC,OAAO,OAAO,CAAC,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,CAAC;AAEtD;;;;;;;;;GASG;AACH,wBAAgB,OAAO,CAAC,GAAG,EAAE,SAAS,QAAQ,EAAE,GAAG,WAAW,EAAE,CAU/D;AAED;;;;GAIG;AACH,wBAAgB,QAAQ,CAAC,EAAE,EAAE,MAAM,GAAG,WAAW,GAAG,SAAS,CAE5D;AAED;;;GAGG;AACH,eAAO,MAAM,OAAO;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6ZuB,CAAC"}

package/lib/credits/core/credits.js

@@ -157,6 +157,41 @@ export const CREDITS = [
         description: 'reads the SPC files of Thermo Galactic GRAMS, Shimadzu and PerkinElmer.',
         license: 'MIT',
     },
+    {
+        id: 'ms-spectrum',
+        name: 'ms-spectrum',
+        href: 'https://github.com/cheminfo/mass-tools/tree/main/packages/ms-spectrum',
+        description: 'tells a profile from a peak table, picks the peaks and establishes their charges.',
+        license: 'MIT',
+    },
+    {
+        id: 'ml-gsd',
+        name: 'ml-gsd',
+        href: 'https://github.com/mljs/global-spectral-deconvolution',
+        description: 'finds the peaks of a continuous spectrum, and their widths.',
+        license: 'MIT',
+    },
+    {
+        id: 'jcampconverter',
+        name: 'jcampconverter',
+        href: 'https://www.npmjs.com/package/jcampconverter',
+        description: 'reads JCAMP-DX files.',
+        license: 'CC-BY-NC-SA-4.0',
+    },
+    {
+        id: 'xy-parser',
+        name: 'xy-parser',
+        href: 'https://github.com/cheminfo/xy-parser',
+        description: 'reads two columns of numbers out of any text file.',
+        license: 'MIT',
+    },
+    {
+        id: 'convert-to-jcamp',
+        name: 'convert-to-jcamp',
+        href: 'https://github.com/cheminfo/convert-to-jcamp',
+        description: 'writes spectra back out as JCAMP-DX.',
+        license: 'MIT',
+    },
     {
         id: 'occ',
         name: 'OCC',
@@ -199,6 +234,15 @@ export const CREDITS = [
         description: 'the 3D viewer, its representations and its surfaces.',
         license: 'MIT',
     },
+    {
+        // The viewer is MIT; the core and plugins that read and process the
+        // spectra (@zakodium/nmrium-core, -core-plugins) are CC-BY-NC-SA-4.0.
+        id: 'nmrium',
+        name: 'NMRium',
+        href: 'https://www.nmrium.org/',
+        description: 'displays and processes the NMR spectra, read from their original files.',
+        license: 'MIT AND CC-BY-NC-SA-4.0',
+    },
     {
         id: 'blueprint',
         name: 'Blueprint',
@@ -345,6 +389,12 @@ export const CREDITS = [
         description: 'the name of every compound in every language, and its article in each Wikipedia.',
         license: 'CC0-1.0',
     },
+    {
+        id: 'pubchem',
+        name: 'PubChem',
+        href: 'https://pubchem.ncbi.nlm.nih.gov/',
+        description: 'the identifier, the names and the synonyms each compound is linked to.',
+    },
     {
         id: 'country-flag-icons',
         name: 'country-flag-icons',

package/lib/credits/core/credits.js.map

@@ -1 +1 @@
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package/lib/download/core/drawingMarkup.d.ts

@@ -1,11 +1,18 @@
+import type { SvgBox } from './svgBounds.ts';
 /**
  * One drawing, serialized with every token it names written out.
  *
  * The copy is taken first and read from the original, because the values are a
  * property of where the figure sits on the page: a detached clone inherits
  * nothing and would resolve every token to an empty string.
+ *
+ * Given a crop, the copy shows that rectangle of the drawing rather than its
+ * window on the page, at one pixel per drawing unit — so a canvas left zoomed
+ * in is saved at the same size as one left zoomed out.
  * @param drawing - The drawing, as it sits on the page.
+ * @param crop - The rectangle to show, in drawing units. Defaults to `null`,
+ *   the drawing as it is on screen.
  * @returns Its markup.
  */
-export declare function drawingMarkup(drawing: SVGSVGElement): string;
+export declare function drawingMarkup(drawing: SVGSVGElement, crop?: SvgBox | null): string;
 //# sourceMappingURL=drawingMarkup.d.ts.map

package/lib/download/core/drawingMarkup.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"drawingMarkup.d.ts","sourceRoot":"","sources":["../../../src/download/core/drawingMarkup.ts"],"names":[],"mappings":"AAEA;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAI5D"}
+{"version":3,"file":"drawingMarkup.d.ts","sourceRoot":"","sources":["../../../src/download/core/drawingMarkup.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAC;AAE7C;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,aAAa,CAC3B,OAAO,EAAE,aAAa,EACtB,IAAI,GAAE,MAAM,GAAG,IAAW,GACzB,MAAM,CASR"}

package/lib/download/core/drawingMarkup.js

@@ -1,3 +1,4 @@
+import { viewBoxAttribute } from "../../chart/core/viewTransform.js";
 import { cssTokenNames, resolveCssTokens } from "./cssTokens.js";
 /**
  * One drawing, serialized with every token it names written out.
@@ -5,11 +6,22 @@ import { cssTokenNames, resolveCssTokens } from "./cssTokens.js";
  * The copy is taken first and read from the original, because the values are a
  * property of where the figure sits on the page: a detached clone inherits
  * nothing and would resolve every token to an empty string.
+ *
+ * Given a crop, the copy shows that rectangle of the drawing rather than its
+ * window on the page, at one pixel per drawing unit — so a canvas left zoomed
+ * in is saved at the same size as one left zoomed out.
  * @param drawing - The drawing, as it sits on the page.
+ * @param crop - The rectangle to show, in drawing units. Defaults to `null`,
+ *   the drawing as it is on screen.
  * @returns Its markup.
  */
-export function drawingMarkup(drawing) {
+export function drawingMarkup(drawing, crop = null) {
     const clone = drawing.cloneNode(true);
+    if (crop !== null) {
+        clone.setAttribute('viewBox', viewBoxAttribute(crop));
+        clone.setAttribute('width', String(Math.round(crop.width)));
+        clone.setAttribute('height', String(Math.round(crop.height)));
+    }
     const markup = new XMLSerializer().serializeToString(clone);
     return resolveCssTokens(markup, tokenValues(drawing, cssTokenNames(markup)));
 }

package/lib/download/core/drawingMarkup.js.map

@@ -1 +1 @@
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package/lib/download/core/figurePng.d.ts

@@ -18,4 +18,18 @@ export declare const FIGURE_PNG_TYPE = "image/png";
  * @throws {Error} When the browser cannot paint or encode it.
  */
 export declare function figurePng(figure: FigureSvg, scale?: number): Promise<Blob>;
+/**
+ * Where the browser reads an SVG document back from, to paint it.
+ *
+ * An object URL rather than a `data:` one, because a figure of a few thousand
+ * dots runs to hundreds of kilobytes and a `data:` URL that long is refused
+ * outright by some browsers — except for a document holding a
+ * `<foreignObject>`, which is how native MathML sits in a chart. Chromium
+ * taints any canvas that paints such a document read from an object URL, and
+ * the figure then cannot be saved at all; read from a `data:` URL it paints
+ * clean. Such a figure carries a handful of labels, far short of that length.
+ * @param markup - The SVG document.
+ * @returns The URL; one starting with `blob:` is revoked once read.
+ */
+export declare function svgImageUrl(markup: string): string;
 //# sourceMappingURL=figurePng.d.ts.map

package/lib/download/core/figurePng.d.ts.map

@@ -1 +1 @@
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