react-cheminfo 0.9.0 → 0.11.0

package/lib/spectra/core/filterEntries.js

@@ -0,0 +1,139 @@
+import { enumField, formulaField, integerField, numberField, zonesField, } from "./filterFields.js";
+const SG_FIELDS = [
+    integerField('windowSize', 'Window size', '9', 'An odd number of points, 5 or more.'),
+    integerField('polynomial', 'Polynomial degree', '3', 'Below the window size; 6 and above oscillates.'),
+];
+/** The x bounds every cropping and resampling step asks for. */
+export const RANGE_FIELDS = [
+    numberField('from', 'From (x)', 'the first x'),
+    numberField('to', 'To (x)', 'the last x'),
+];
+/** The two zone lists a step offers when it can keep or drop stretches of x. */
+export const ZONE_FIELDS = [
+    zonesField('zones', 'Zones to keep'),
+    zonesField('exclusions', 'Zones to drop', 'Dropping wins: name zones or exclusions, not both.'),
+];
+/** The five baseline estimates, none of which forwards a parameter. */
+export const BASELINE_ENTRIES = {
+    airPLSBaseline: {
+        label: 'airPLS baseline',
+        group: 'baseline',
+        summary: 'Subtracts an asymmetrically weighted penalized least-squares baseline — the general-purpose choice for a broad drift.',
+        fields: [],
+        fixed: 'Fitted against the point index, 100 iterations, tolerance 0.001.',
+    },
+    iterativePolynomialBaseline: {
+        label: 'Iterative polynomial baseline',
+        group: 'baseline',
+        summary: 'Fits a polynomial to the signal, iterating until the peaks stop pulling it up.',
+        fields: [],
+        fixed: 'Fitted against the point index, 100 iterations, tolerance 0.001.',
+    },
+    rollingAverageBaseline: {
+        label: 'Rolling-average baseline',
+        group: 'baseline',
+        summary: 'Subtracts a rolling mean. Cheap, and it eats into a broad peak.',
+        fields: [],
+        fixed: 'Window of a tenth of the points, duplicated at the edges.',
+    },
+    rollingBallBaseline: {
+        label: 'Rolling-ball baseline',
+        group: 'baseline',
+        summary: 'Rolls a ball under the signal — the robust choice when peaks overlap.',
+        fields: [],
+        fixed: 'Windows of 4 % and 8 % of the points.',
+    },
+    rollingMedianBaseline: {
+        label: 'Rolling-median baseline',
+        group: 'baseline',
+        summary: 'Subtracts a rolling median, which a peak pulls on far less than a mean.',
+        fields: [],
+        fixed: 'Window of a tenth of the points, duplicated at the edges.',
+    },
+};
+/** Smoothing, the derivatives, and everything that changes the y scale. */
+export const SIGNAL_ENTRIES = {
+    savitzkyGolay: {
+        label: 'Savitzky–Golay smoothing',
+        group: 'smoothing',
+        summary: 'Fits a polynomial over a sliding window; with a derivative above zero it is the general form of the three below.',
+        fields: [
+            ...SG_FIELDS,
+            integerField('derivative', 'Derivative', '0', 'Zero smooths; one, two and three differentiate.'),
+        ],
+    },
+    firstDerivative: {
+        label: 'First derivative',
+        group: 'smoothing',
+        summary: 'dy/dx by Savitzky–Golay. Removes an additive baseline and turns every peak into a zero crossing.',
+        fields: SG_FIELDS,
+    },
+    secondDerivative: {
+        label: 'Second derivative',
+        group: 'smoothing',
+        summary: 'd²y/dx² by Savitzky–Golay — the classic way to pull apart overlapping infrared bands.',
+        fields: SG_FIELDS,
+    },
+    thirdDerivative: {
+        label: 'Third derivative',
+        group: 'smoothing',
+        summary: 'd³y/dx³ by Savitzky–Golay. Rarely worth it: noise dominates.',
+        fields: SG_FIELDS,
+    },
+    centerMean: {
+        label: 'Centre on the mean',
+        group: 'scaling',
+        summary: 'Subtracts the mean of y, so the spectrum sits about zero.',
+        fields: [],
+    },
+    centerMedian: {
+        label: 'Centre on the median',
+        group: 'scaling',
+        summary: 'Subtracts the median of y — the same idea, unmoved by a few large peaks.',
+        fields: [],
+    },
+    divideBySD: {
+        label: 'Divide by the standard deviation',
+        group: 'scaling',
+        summary: 'Divides y by its standard deviation; after centring on the mean this is autoscaling.',
+        fields: [],
+    },
+    paretoNormalization: {
+        label: 'Pareto scaling',
+        group: 'scaling',
+        summary: 'Divides y by the square root of its standard deviation, so magnitude survives and noise is amplified less than by autoscaling.',
+        fields: [],
+    },
+    normed: {
+        label: 'Normalize',
+        group: 'scaling',
+        summary: 'Divides y so that a chosen aggregate reaches the value asked for.',
+        fields: [
+            enumField('algorithm', 'Divide by', [
+                { value: 'absolute', label: 'Sum of absolute values' },
+                { value: 'max', label: 'Largest value' },
+                { value: 'sum', label: 'Signed sum' },
+            ], 'Largest value with 100 is the familiar “normalize to 100 %”.'),
+            numberField('value', 'Target', '1'),
+        ],
+    },
+    rescale: {
+        label: 'Rescale between two values',
+        group: 'scaling',
+        summary: 'Maps y linearly onto the range given.',
+        fields: [
+            numberField('min', 'Minimum', '0'),
+            numberField('max', 'Maximum', '1'),
+        ],
+    },
+    yFunction: {
+        label: 'Apply a formula to y',
+        group: 'y-axis',
+        summary: 'Rewrites every y through an expression. A run of lowercase letters is read as a Math function, so `log10(y)` works as typed.',
+        fields: [
+            formulaField('function', 'Expression in y', 'For instance -log10(y), which reads transmittance as absorbance.'),
+        ],
+    },
+};
+/** Everything that moves, crops or resamples the x axis, and the two housekeeping steps. */
+//# sourceMappingURL=filterEntries.js.map

package/lib/spectra/core/filterEntries.js.map

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package/lib/spectra/core/filterFields.d.ts

@@ -0,0 +1,94 @@
+/** What a chain step's option is edited with. */
+export type FilterFieldKind = 'boolean' | 'enum' | 'formula' | 'integer' | 'number' | 'zones';
+/** One choice of an `enum` field. */
+export interface FilterChoice {
+    /** What goes into the options object. */
+    value: string;
+    /** What the reader picks. */
+    label: string;
+}
+/** One editable option of a chain step. */
+export interface FilterField {
+    /**
+     * Where the value sits inside the step's `options`, dotted for a nested one
+     * such as `gsd.minMaxRatio`.
+     */
+    key: string;
+    /** What the field is called. */
+    label: string;
+    /** What it is edited with. */
+    kind: FilterFieldKind;
+    /**
+     * What upstream does when the field is left empty, shown in the control.
+     * @default undefined — the control carries no placeholder
+     */
+    placeholder?: string;
+    /**
+     * The choices, for an `enum` field.
+     * @default undefined — the field is not an enum
+     */
+    choices?: readonly FilterChoice[];
+    /**
+     * One line saying what the option changes, hung off the label.
+     * @default undefined — the label says enough
+     */
+    help?: string;
+}
+/** Which part of the signal a step works on, and so where it belongs in the menu. */
+export type FilterGroup = 'baseline' | 'scaling' | 'smoothing' | 'utility' | 'x-axis' | 'y-axis';
+/** The groups in the order a chain is usually built: shape, then scale, then axis. */
+export declare const FILTER_GROUPS: readonly FilterGroup[];
+/** What each group is called above its slice of the menu. */
+export declare const FILTER_GROUP_LABELS: Readonly<Record<FilterGroup, string>>;
+/**
+ * A whole number field.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param placeholder - What upstream does when it is empty.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export declare function integerField(key: string, label: string, placeholder?: string, help?: string): FilterField;
+/**
+ * A field taking any number.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param placeholder - What upstream does when it is empty.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export declare function numberField(key: string, label: string, placeholder?: string, help?: string): FilterField;
+/**
+ * A field taking one of a fixed set of values.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param choices - What may be picked.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export declare function enumField(key: string, label: string, choices: readonly FilterChoice[], help?: string): FilterField;
+/**
+ * A yes-or-no field.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export declare function booleanField(key: string, label: string, help?: string): FilterField;
+/**
+ * A field taking an expression over one variable.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export declare function formulaField(key: string, label: string, help?: string): FilterField;
+/**
+ * A field taking a list of `from` / `to` stretches.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export declare function zonesField(key: string, label: string, help?: string): FilterField;
+//# sourceMappingURL=filterFields.d.ts.map

package/lib/spectra/core/filterFields.d.ts.map

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package/lib/spectra/core/filterFields.js

@@ -0,0 +1,82 @@
+/** The groups in the order a chain is usually built: shape, then scale, then axis. */
+export const FILTER_GROUPS = [
+    'baseline',
+    'smoothing',
+    'scaling',
+    'y-axis',
+    'x-axis',
+    'utility',
+];
+/** What each group is called above its slice of the menu. */
+export const FILTER_GROUP_LABELS = {
+    baseline: 'Baseline',
+    smoothing: 'Smoothing and derivatives',
+    scaling: 'Scaling',
+    'y-axis': 'y axis',
+    'x-axis': 'x axis',
+    utility: 'Housekeeping',
+};
+/**
+ * A whole number field.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param placeholder - What upstream does when it is empty.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export function integerField(key, label, placeholder, help) {
+    return { key, label, kind: 'integer', placeholder, help };
+}
+/**
+ * A field taking any number.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param placeholder - What upstream does when it is empty.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export function numberField(key, label, placeholder, help) {
+    return { key, label, kind: 'number', placeholder, help };
+}
+/**
+ * A field taking one of a fixed set of values.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param choices - What may be picked.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export function enumField(key, label, choices, help) {
+    return { key, label, kind: 'enum', choices, help };
+}
+/**
+ * A yes-or-no field.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export function booleanField(key, label, help) {
+    return { key, label, kind: 'boolean', help };
+}
+/**
+ * A field taking an expression over one variable.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export function formulaField(key, label, help) {
+    return { key, label, kind: 'formula', help };
+}
+/**
+ * A field taking a list of `from` / `to` stretches.
+ * @param key - Where the value sits in the step's options.
+ * @param label - What the field is called.
+ * @param help - One line saying what it changes.
+ * @returns The descriptor.
+ */
+export function zonesField(key, label, help) {
+    return { key, label, kind: 'zones', help };
+}
+//# sourceMappingURL=filterFields.js.map

package/lib/spectra/core/filterFields.js.map

@@ -0,0 +1 @@
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package/lib/spectra/core/index.d.ts

@@ -0,0 +1,14 @@
+export type { ProblemSeverity, SettingsProblem } from './problems.ts';
+export { formulaProblem, isUsableLabel } from './problems.ts';
+export type { FilterCatalogEntry } from './filterEntries.ts';
+export type { FilterChoice, FilterField, FilterFieldKind, FilterGroup, } from './filterFields.ts';
+export { FILTER_GROUPS, FILTER_GROUP_LABELS } from './filterFields.ts';
+export { FILTER_CATALOG, FILTER_NAMES, filterEntry, filterMenu, filterNamesInGroup, } from './filterCatalog.ts';
+export { addFilter, defaultFilter, duplicateFilter, filterOptions, moveFilter, readFilterOption, removeFilter, setFilterOption, } from './filterChain.ts';
+export type { PrincipalComponentSelection, PrincipalComponentSettings, } from './principalComponents.ts';
+export { DEFAULT_PRINCIPAL_COMPONENTS, PCA_METHODS, clampPrincipalComponents, principalComponentChoices, principalComponentLabel, selectedExplainedVariance, } from './principalComponents.ts';
+export type { ExclusionZone, MatrixFilter, MatrixFilterName, NormalizationSettings, PostProcessingSettings, ScaleMethod, ScaleSettings, SpectraCalculation, SpectraProcessorSettings, SpectraRange, SpectraSettings, SpectrumFilter, SpectrumFilterName, } from './settings.ts';
+export { DEFAULT_MAX_MEMORY, DEFAULT_NUMBER_OF_POINTS, EMPTY_SETTINGS, normalizationFilters, withNormalizationFilters, } from './settings.ts';
+export { MATRIX_FILTER_NAMES, SCALE_METHODS, settingsProblems, } from './settingsProblems.ts';
+export { chainProblems } from './chainProblems.ts';
+//# sourceMappingURL=index.d.ts.map

package/lib/spectra/core/index.d.ts.map

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package/lib/spectra/core/index.js

@@ -0,0 +1,9 @@
+export { formulaProblem, isUsableLabel } from "./problems.js";
+export { FILTER_GROUPS, FILTER_GROUP_LABELS } from "./filterFields.js";
+export { FILTER_CATALOG, FILTER_NAMES, filterEntry, filterMenu, filterNamesInGroup, } from "./filterCatalog.js";
+export { addFilter, defaultFilter, duplicateFilter, filterOptions, moveFilter, readFilterOption, removeFilter, setFilterOption, } from "./filterChain.js";
+export { DEFAULT_PRINCIPAL_COMPONENTS, PCA_METHODS, clampPrincipalComponents, principalComponentChoices, principalComponentLabel, selectedExplainedVariance, } from "./principalComponents.js";
+export { DEFAULT_MAX_MEMORY, DEFAULT_NUMBER_OF_POINTS, EMPTY_SETTINGS, normalizationFilters, withNormalizationFilters, } from "./settings.js";
+export { MATRIX_FILTER_NAMES, SCALE_METHODS, settingsProblems, } from "./settingsProblems.js";
+export { chainProblems } from "./chainProblems.js";
+//# sourceMappingURL=index.js.map

package/lib/spectra/core/index.js.map

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package/lib/spectra/core/principalComponents.d.ts

@@ -0,0 +1,70 @@
+import type { PCAOptions } from 'ml-pca';
+/**
+ * How the principal components are computed.
+ *
+ * `spectra-processor` hands out the normalized matrix and stops there, so the
+ * decomposition is the consumer's `new PCA(matrix, options)` call — these are
+ * that call's options, read off `ml-pca` rather than retyped.
+ */
+export type PrincipalComponentSettings = Omit<PCAOptions, 'isCovarianceMatrix'>;
+/**
+ * Which two components a score plot is drawn against.
+ *
+ * Both are columns of the score matrix, counting from zero: `PC1` is `0`. The
+ * labels say `PC1` because that is what a chemist writes; the numbers stay
+ * zero-based because that is what indexes the matrix.
+ */
+export interface PrincipalComponentSelection {
+    /** The component along x — `0` is `PC1`. */
+    x: number;
+    /** The component along y — `1` is `PC2`. */
+    y: number;
+}
+/** The first two components, which is what a score plot opens on. */
+export declare const DEFAULT_PRINCIPAL_COMPONENTS: PrincipalComponentSelection;
+/** How `ml-pca` may be asked to decompose the matrix. */
+export declare const PCA_METHODS: ReadonlyArray<{
+    value: NonNullable<PCAOptions['method']>;
+    label: string;
+}>;
+/**
+ * What one component is called, with the share of the variance it carries.
+ * @param index - The component, counting from zero.
+ * @param explainedVariance - What `pca.getExplainedVariance()` returned, as fractions.
+ * @returns For instance `PC1 — 74.2 %`, or just `PC1` when no variance is known.
+ */
+export declare function principalComponentLabel(index: number, explainedVariance?: readonly number[]): string;
+/**
+ * Every component that can be picked, in order.
+ *
+ * A component nobody can read is worse than none, so the share of the variance
+ * travels with the label: a reader picking `PC7 — 0.3 %` can see they are about
+ * to plot noise.
+ * @param count - How many components the decomposition produced.
+ * @param explainedVariance - What `pca.getExplainedVariance()` returned.
+ * @returns The choices, one per component.
+ */
+export declare function principalComponentChoices(count: number, explainedVariance?: readonly number[]): ReadonlyArray<{
+    index: number;
+    label: string;
+}>;
+/**
+ * The selection made safe against the decomposition that actually came back.
+ *
+ * A saved selection outlives the data it was made on: reload with fewer spectra
+ * and `PC8` no longer exists. Rather than let a plot ask for a column that is
+ * not there, the pair is pulled back inside what was computed, and the two axes
+ * are kept apart so the plot never collapses onto its diagonal.
+ * @param selection - What the reader picked, possibly on other data.
+ * @param count - How many components the decomposition produced.
+ * @returns A selection both of whose components exist.
+ */
+export declare function clampPrincipalComponents(selection: PrincipalComponentSelection, count: number): PrincipalComponentSelection;
+/**
+ * The share of the variance the two picked components carry together.
+ * @param selection - Which components are drawn.
+ * @param explainedVariance - What `pca.getExplainedVariance()` returned.
+ * @returns The sum as a fraction, or undefined when either share is unknown.
+ */
+export declare function selectedExplainedVariance(selection: PrincipalComponentSelection, explainedVariance: readonly number[]): number | undefined;
+//# sourceMappingURL=principalComponents.d.ts.map

package/lib/spectra/core/principalComponents.d.ts.map

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package/lib/spectra/core/principalComponents.js

@@ -0,0 +1,90 @@
+/** The first two components, which is what a score plot opens on. */
+export const DEFAULT_PRINCIPAL_COMPONENTS = {
+    x: 0,
+    y: 1,
+};
+/** How `ml-pca` may be asked to decompose the matrix. */
+export const PCA_METHODS = [
+    { value: 'SVD', label: 'Singular value decomposition' },
+    { value: 'NIPALS', label: 'NIPALS' },
+    { value: 'covarianceMatrix', label: 'Covariance matrix' },
+];
+/**
+ * What one component is called, with the share of the variance it carries.
+ * @param index - The component, counting from zero.
+ * @param explainedVariance - What `pca.getExplainedVariance()` returned, as fractions.
+ * @returns For instance `PC1 — 74.2 %`, or just `PC1` when no variance is known.
+ */
+export function principalComponentLabel(index, explainedVariance) {
+    const name = `PC${String(index + 1)}`;
+    const share = explainedVariance?.[index];
+    if (share === undefined || !Number.isFinite(share))
+        return name;
+    return `${name} — ${(share * 100).toFixed(1)} %`;
+}
+/**
+ * Every component that can be picked, in order.
+ *
+ * A component nobody can read is worse than none, so the share of the variance
+ * travels with the label: a reader picking `PC7 — 0.3 %` can see they are about
+ * to plot noise.
+ * @param count - How many components the decomposition produced.
+ * @param explainedVariance - What `pca.getExplainedVariance()` returned.
+ * @returns The choices, one per component.
+ */
+export function principalComponentChoices(count, explainedVariance) {
+    const choices = [];
+    for (let index = 0; index < count; index++) {
+        choices.push({
+            index,
+            label: principalComponentLabel(index, explainedVariance),
+        });
+    }
+    return choices;
+}
+/**
+ * The selection made safe against the decomposition that actually came back.
+ *
+ * A saved selection outlives the data it was made on: reload with fewer spectra
+ * and `PC8` no longer exists. Rather than let a plot ask for a column that is
+ * not there, the pair is pulled back inside what was computed, and the two axes
+ * are kept apart so the plot never collapses onto its diagonal.
+ * @param selection - What the reader picked, possibly on other data.
+ * @param count - How many components the decomposition produced.
+ * @returns A selection both of whose components exist.
+ */
+export function clampPrincipalComponents(selection, count) {
+    if (count < 1)
+        return { x: 0, y: 0 };
+    const last = count - 1;
+    const x = clamp(selection.x, last);
+    let y = clamp(selection.y, last);
+    if (y === x && count > 1)
+        y = x === 0 ? 1 : x - 1;
+    return { x, y };
+}
+/**
+ * The share of the variance the two picked components carry together.
+ * @param selection - Which components are drawn.
+ * @param explainedVariance - What `pca.getExplainedVariance()` returned.
+ * @returns The sum as a fraction, or undefined when either share is unknown.
+ */
+export function selectedExplainedVariance(selection, explainedVariance) {
+    const along = explainedVariance[selection.x];
+    const up = explainedVariance[selection.y];
+    if (along === undefined || up === undefined)
+        return undefined;
+    return along + up;
+}
+/**
+ * A component index brought inside the components that exist.
+ * @param index - What was asked for.
+ * @param last - The highest component there is.
+ * @returns A whole number between zero and `last`.
+ */
+function clamp(index, last) {
+    if (!Number.isFinite(index))
+        return 0;
+    return Math.min(Math.max(Math.round(index), 0), last);
+}
+//# sourceMappingURL=principalComponents.js.map

package/lib/spectra/core/principalComponents.js.map

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package/lib/spectra/core/problems.d.ts

@@ -0,0 +1,57 @@
+/** How much a problem matters. */
+export type ProblemSeverity = 'error' | 'warning';
+/** Something the settings get wrong, or probably get wrong. */
+export interface SettingsProblem {
+    /**
+     * `error` when the processor throws or the matrix comes out wrong;
+     * `warning` when it runs and the reader most likely did not mean it.
+     */
+    severity: ProblemSeverity;
+    /** Which part of the settings it is about, as the panel labels that part. */
+    where: string;
+    /** What is wrong, in one sentence a reader can act on. */
+    message: string;
+}
+/**
+ * A problem, spelled out.
+ * @param severity - How much it matters.
+ * @param where - Which part of the settings it is about.
+ * @param message - What is wrong.
+ * @returns The problem.
+ */
+export declare function problem(severity: ProblemSeverity, where: string, message: string): SettingsProblem;
+/**
+ * Whether a value is a number the processor can work with.
+ * @param value - What the settings hold.
+ * @returns True when it is a finite number.
+ */
+export declare function isNumber(value: unknown): value is number;
+/**
+ * Whether a value is a whole number.
+ * @param value - What the settings hold.
+ * @returns True when it is a finite integer.
+ */
+export declare function isWholeNumber(value: unknown): value is number;
+/**
+ * Whether a label can stand as the name of a variable.
+ *
+ * A range's label becomes a parameter of the function the calculations are
+ * compiled into, so a label with a space in it fails far from the field that
+ * caused it — which is why it is checked here instead.
+ * @param label - What the reader typed.
+ * @returns True when the label can be a variable name.
+ */
+export declare function isUsableLabel(label: string): boolean;
+/**
+ * What is wrong with an expression, as far as can be told without running it.
+ *
+ * The expression is compiled by the processor, not here, so this catches what
+ * a reader actually mistypes — an empty box, unclosed brackets, a variable that
+ * never appears — and stays silent about the rest rather than pretending to be
+ * a parser.
+ * @param formula - What the reader typed.
+ * @param variable - The one name the expression may read, `x` or `y`.
+ * @returns The complaint, or undefined when nothing obvious is wrong.
+ */
+export declare function formulaProblem(formula: string, variable: string): string | undefined;
+//# sourceMappingURL=problems.d.ts.map

package/lib/spectra/core/problems.d.ts.map

@@ -0,0 +1 @@
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