chore: update dependencies

.ncurc.yml

@@ -0,0 +1,5 @@
+dep: 'prod,dev'
+reject:
+  # https://github.com/cheminfo/eslint-config/issues/49
+  - eslint
+  - react-plot

eslint.config.mjs

@@ -0,0 +1,16 @@
+import cheminfo from 'eslint-config-cheminfo-typescript';
+import globals from 'globals';
+
+export default [
+  ...cheminfo,
+  {
+    languageOptions: {
+      globals: {
+        ...globals.node,
+      },
+    },
+    rules: {
+      "unicorn/no-object-as-default-parameter": "off",
+    }
+  }
+]

package.json

@@ -14,7 +14,7 @@
     "build": "npm run tsc && cheminfo-build -r CommonSpectrum",
     "check-types": "tsc --noEmit",
     "clean": "rimraf lib lib-esm",
-    "eslint": "eslint src --ext ts --cache",
+    "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
     "prepack": "npm run tsc",
     "prettier": "prettier --check src",
@@ -49,10 +49,10 @@
     "@types/js-quantities": "^1.6.6",
     "cheminfo-build": "^1.2.0",
     "eslint": "^8.57.0",
-    "eslint-config-cheminfo-typescript": "^12.4.0",
+    "eslint-config-cheminfo-typescript": "^15.0.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "prettier": "^3.3.3",
-    "rimraf": "^5.0.5",
+    "rimraf": "^6.0.1",
     "typescript": "^5.4.5"
   },
   "dependencies": {

src/AnalysesManager.ts

@@ -157,7 +157,7 @@ export class AnalysesManager {
     for (const spectrum of this.getSpectra()) {
       if (spectrum.variables) {
         for (const [, variable] of Object.entries(spectrum.variables)) {
-          appendDistinctValue(values, variable.label.replace(/\s+[[(].*$/, ''));
+          appendDistinctValue(values, variable.label.replace(/\s+[([].*$/, ''));
         }
       }
     }
@@ -198,6 +198,7 @@ export class AnalysesManager {
 
   /**
    * Remove the analysis from the AnalysesManager for the specified id
+   * @param id
    */
   public removeAnalysis(id: string) {
     const index = this.getAnalysisIndex(id);
@@ -207,6 +208,7 @@ export class AnalysesManager {
 
   /**
    * Returns the index of the analysis in the analyses array
+   * @param id
    */
   public getAnalysisIndex(id: string) {
     if (!id) return undefined;
@@ -219,10 +221,11 @@ export class AnalysesManager {
 
   /**
    * Checks if the ID of an analysis exists in the AnalysesManager
+   * @param id
    */
   public includes(id: string) {
     const index = this.getAnalysisIndex(id);
-    return index === undefined ? false : !isNaN(index);
+    return index === undefined ? false : !Number.isNaN(index);
   }
 }
 
@@ -233,8 +236,8 @@ function normalizeLabelUnits(
   if (!originalLabel) {
     return { units: '', label: '' };
   }
-  if (originalLabel.search(/[[(]]/) >= 0) {
-    const [units, label] = originalLabel.split(/\s*[[(]/);
+  if (originalLabel.search(/[([]]/) >= 0) {
+    const [units, label] = originalLabel.split(/\s*[([]/);
     return { units: originalUnits || units, label };
   }
   return { label: originalLabel, units: originalUnits };

src/Analysis.ts

@@ -41,7 +41,7 @@ export class Analysis {
   };
 
   public constructor(options: AnalysisOptions = {}) {
-    this.id = options.id || Math.random().toString(36).substring(2, 10);
+    this.id = options.id || Math.random().toString(36).slice(2, 10);
     this.label = options.label || this.id;
     this.spectrumCallback = options.spectrumCallback;
     this.spectra = [];
@@ -81,6 +81,8 @@ export class Analysis {
 
   /**
    * Add a spectrum in the internal spectra variable
+   * @param variables
+   * @param options
    */
   public pushSpectrum(
     variables: SpectrumVariables,
@@ -96,6 +98,7 @@ export class Analysis {
 
   /**
    * Retrieve a Spectrum based on x/y units
+   * @param selector
    */
   public getXYSpectrum(selector: SpectrumSelector = {}) {
     const id = JSON.stringify(selector);
@@ -107,6 +110,7 @@ export class Analysis {
 
   /**
    * Retrieve spectra matching selector
+   * @param selector
    */
   public getXYSpectra(selector: SpectrumSelector = {}) {
     const id = JSON.stringify(selector);
@@ -118,9 +122,10 @@ export class Analysis {
 
   /**
    * Retrieve a xy object
-   * @param selector.units Units separated by vs like for example "g vs °C"
-   * @param selector.xUnits if undefined takes the first variable
-   * @param selector.yUnits if undefined takes the second variable
+   * @param selector.units - Units separated by vs like for example "g vs °C"
+   * @param selector.xUnits - if undefined takes the first variable
+   * @param selector.yUnits - if undefined takes the second variable
+   * @param selector
    */
   public getXY(selector: SpectrumSelector = {}) {
     const spectrum = this.getXYSpectrum(selector);
@@ -134,8 +139,9 @@ export class Analysis {
   /**
    * Return the data object for specific x/y units with possibly some
    * normalization options
-   * @param options.selector.xUnits // if undefined takes the first variable
-   * @param options.selector.yUnits // if undefined takes the second variable
+   * @param options.selector.xUnits - // if undefined takes the first variable
+   * @param options.selector.yUnits - // if undefined takes the second variable
+   * @param options
    */
   public getNormalizedSpectrum(options: NormalizedOptions = {}) {
     const { normalization, selector } = options;
@@ -145,6 +151,7 @@ export class Analysis {
   }
 
   /**
+   * @param options
    */
   public getNormalizedSpectra(options: NormalizedOptions = {}): Spectrum[] {
     const { normalization, selector } = options;
@@ -167,17 +174,19 @@ export class Analysis {
 
   /**
    * Returns the xLabel
-   * @param selector.xUnits // if undefined takes the first variable
-   * @param selector.yUnits // if undefined takes the second variable
+   * @param selector.xUnits - // if undefined takes the first variable
+   * @param selector.yUnits - // if undefined takes the second variable
+   * @param selector
    */
   public getXLabel(selector: SpectrumSelector) {
     return this.getXYSpectrum(selector)?.variables.x.label;
   }
 
   /**
    * Returns the yLabel
-   * @param selector.xUnits // if undefined takes the first variable
-   * @param selector.yUnits // if undefined takes the second variable
+   * @param selector.xUnits - // if undefined takes the first variable
+   * @param selector.yUnits - // if undefined takes the second variable
+   * @param selector
    */
   public getYLabel(selector: SpectrumSelector) {
     return this.getXYSpectrum(selector)?.variables.y.label;
@@ -186,6 +195,9 @@ export class Analysis {
 
 /**
  * Internal function that ensure the order of x / y array
+ * @param variables
+ * @param options
+ * @param analysisOptions
  */
 function standardizeData(
   variables: SpectrumVariables,
@@ -207,14 +219,14 @@ function standardizeData(
   const xVariable = variables.x;
   const yVariable = variables.y;
   if (!xVariable || !yVariable) {
-    throw Error('A spectrum must contain at least x and y variables');
+    throw new Error('A spectrum must contain at least x and y variables');
   }
   if (!isAnyArray(xVariable.data) || !isAnyArray(yVariable.data)) {
-    throw Error('x and y variables must contain an array data');
+    throw new Error('x and y variables must contain an array data');
   }
 
   const x = xVariable.data;
-  const reverse = x && x.length > 1 && x[0] > x[x.length - 1];
+  const reverse = x && x.length > 1 && x[0] > x.at(-1);
 
   for (const [key, variable] of Object.entries(variables)) {
     if (reverse) variable.data = variable.data.slice().reverse();

src/__tests__/AnalysesManager.test.ts

@@ -57,7 +57,7 @@ describe('AnalysisManager', () => {
     const analyses = analysesManager.getAnalyses();
     expect(analyses).toHaveLength(3);
     // we expect to have a total of 3 spectra without filtereing
-    expect(analyses.map((analysis) => analysis.spectra).flat()).toHaveLength(3);
+    expect(analyses.flatMap((analysis) => analysis.spectra)).toHaveLength(3);
 
     // we select the first analysis, we expect to have 2 spectra
     const filteredAnalyses = analysesManager.getAnalyses({ ids: ['abc'] });
@@ -83,7 +83,7 @@ describe('AnalysisManager', () => {
     const analysis2 = new Analysis({ id: 'def' });
     analysesManager.addAnalysis(analysis2);
 
-    const json = JSON.parse(JSON.stringify(analysesManager));
+    const json = structuredClone(analysesManager);
     const data = json.analyses[0].spectra[0].variables.x.data;
     expect(Array.isArray(data)).toBe(true);
     const spectraManager2 = AnalysesManager.fromJSON(json);

src/__tests__/Analysis.test.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join } from 'path';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
 import { describe, it, expect } from 'vitest';
 
@@ -9,7 +9,7 @@ describe('Analysis', () => {
   it('getXY', () => {
     const text = readFileSync(
       join(__dirname, '../../testFiles/xps.jdx'),
-      'utf-8',
+      'utf8',
     );
 
     const analysis = fromJcamp(text);

src/__tests__/AnalysisManager.distinct.test.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join } from 'path';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
 import { describe, it, expect } from 'vitest';
 

src/from/__tests__/fromJcamp.callback.test.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join } from 'path';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
 import { describe, it, expect } from 'vitest';
 

src/from/__tests__/fromJcamp.link.test.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join } from 'path';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
 import { test, expect } from 'vitest';
 

src/from/__tests__/fromJcamp.test.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join } from 'path';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
 import { describe, it, expect } from 'vitest';
 

src/from/__tests__/fromText.test.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join } from 'path';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
 import { test, expect } from 'vitest';
 

src/from/fromJcamp.ts

@@ -5,12 +5,12 @@ import { SpectrumVariable } from '../types/Cheminfo';
 
 /**
  * Creates a new Analysis from a JCAMP string
- * @param {string} jcamp - String containing the JCAMP data
- * @param {object} [options={}]
- * @param {object} [options.id=Math.random()]
- * @param {string} [options.label=options.id] human redeable label
- * @param {string} [options.spectrumCallback] a callback to apply on variables when creating spectrum
- * @return {Analysis} - New class element with the given data
+ * @param jcamp - String containing the JCAMP data
+ * @param [options={}]
+ * @param [options.id=Math.random()]
+ * @param [options.label=options.id] - human redeable label
+ * @param [options.spectrumCallback] - a callback to apply on variables when creating spectrum
+ * @returns - New class element with the given data
  */
 export function fromJcamp(jcamp: string | ArrayBuffer, options = {}): Analysis {
   const analysis = new Analysis(options);

src/from/fromText.ts

@@ -34,7 +34,8 @@ interface FromTextOptions {
 
 /**
  * Convert strings into JCAMP and add extra information
- * @param {string} data - values to add to the file, usually a csv or tsv values
+ * @param data - values to add to the file, usually a csv or tsv values
+ * @param options
  */
 
 export function fromText(

src/jsgraph/__tests__/getJSGraph.test.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join } from 'path';
+import { readFileSync } from 'node:fs';
+import { join } from 'node:path';
 
 import { test, expect, describe, it } from 'vitest';
 

src/jsgraph/addStyle.ts

@@ -13,7 +13,7 @@ export function addStyle(
   let { color = '#A9A9A9' } = options;
   const { opacity = 1, lineWidth = 1 } = options;
 
-  if (color.match(/#[0-9A-F]{6}$/i)) {
+  if (color.match(/#[\da-f]{6}$/i)) {
     color = (color + ((opacity * 255) >> 0).toString(16)).toUpperCase();
   } else {
     color = color.replace(/rgb ?\((.*)\)/, `rgba($1,${opacity})`);

src/jsgraph/getJSGraph.ts

@@ -9,6 +9,8 @@ import { COLORS } from './colors';
 
 /**
  * Generate a jsgraph chart format from an array of Analysis
+ * @param analyses
+ * @param options
  */
 export function getJSGraph(analyses: Analysis[], options: JSGraphOptions = {}) {
   const {

src/jsgraph/getNormalizationAnnotations.ts

@@ -1,17 +1,20 @@
 /**
  * Returns a JSGraph annotation that represents the normalization
  * @param {object} [filter={}]
- * @param {object} [filter.exclusions=[]] Array of exclusions zones
- * @param {object} [boundary={y: {min:'0px', max:'2000px'}}] Height of the annotation
+ * @param {object} [filter.exclusions=[]] - Array of exclusions zones
+ * @param {object} [boundary={y: {min:'0px', max:'2000px'}}] - Height of the annotation
  */
 interface AnnotationsFilter {
   exclusions?: Array<{ ignore?: boolean; from: number; to: number }>;
   from?: number;
   to?: number;
 }
+
+interface Boundary { y: { min: string; max: string } }
+
 export function getNormalizationAnnotations(
   filter: AnnotationsFilter = {},
-  boundary = { y: { min: '0px', max: '2000px' } },
+  boundary: Boundary = { y: { min: '0px', max: '2000px' } },
 ) {
   let { exclusions = [] } = filter;
 

src/reactPlot/getReactPlotJSON.ts

@@ -29,6 +29,9 @@ function getData(x: ListNumber, y: ListNumber) {
 
 /**
  * Generate a jsgraph chart format from an array of Analysis
+ * @param analyses
+ * @param query
+ * @param options
  */
 export function getReactPlotJSON(
   analyses: Analysis[],

src/types/SpectrumSelector.ts

@@ -15,11 +15,13 @@ export interface SpectrumSelector {
   yLabel?: string | RegExp;
   /** Allows to specify X and Y variables using a string like 'c vs d' */
   variables?: string;
-  /** Select a specific X variable by one letter name
+  /**
+   * Select a specific X variable by one letter name
    * @default 'x'
    */
   xVariable?: OneLowerCase;
-  /** Select a specific Y variable by one letter name
+  /**
+   * Select a specific Y variable by one letter name
    * @default 'y'
    */
   yVariable?: OneLowerCase;