fix: update ml-spectra-processing and dependencies

package.json

@@ -55,32 +55,32 @@
     "trailingComma": "all"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.21.2",
-    "@babel/preset-typescript": "^7.21.0",
-    "@types/jest": "^29.5.0",
+    "@babel/plugin-transform-modules-commonjs": "^7.23.3",
+    "@babel/preset-typescript": "^7.23.3",
+    "@types/jest": "^29.5.12",
     "chemcalc": "^3.4.1",
     "cheminfo-build": "^1.2.0",
-    "eslint": "^8.36.0",
-    "eslint-config-cheminfo-typescript": "^11.3.1",
-    "eslint-plugin-jest": "^27.2.1",
+    "eslint": "^8.57.0",
+    "eslint-config-cheminfo-typescript": "^12.2.0",
+    "eslint-plugin-jest": "^27.9.0",
     "esm": "^3.2.25",
-    "jest": "^29.5.0",
+    "jest": "^29.7.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "mf-global": "^2.1.2",
+    "mf-global": "^3.0.16",
     "ml-stat": "^1.3.3",
-    "nodemon": "^2.0.22",
-    "prettier": "^2.8.7",
-    "rimraf": "^4.4.1",
-    "spectrum-generator": "^8.0.6",
-    "typescript": "^5.0.2",
-    "xy-parser": "^5.0.4"
+    "nodemon": "^3.1.0",
+    "prettier": "^3.2.5",
+    "rimraf": "^5.0.5",
+    "spectrum-generator": "^8.0.11",
+    "typescript": "^5.4.2",
+    "xy-parser": "^5.0.5"
   },
   "dependencies": {
-    "@lukeed/uuid": "^2.0.0",
-    "cheminfo-types": "^1.4.0",
+    "@lukeed/uuid": "^2.0.1",
+    "cheminfo-types": "^1.7.2",
     "ml-peak-shape-generator": "^4.1.2",
     "ml-savitzky-golay-generalized": "^4.0.1",
-    "ml-spectra-fitting": "^4.2.1",
-    "ml-spectra-processing": "^14.0.0"
+    "ml-spectra-fitting": "^4.2.3",
+    "ml-spectra-processing": "^14.2.0"
   }
 }

src/__tests__/ethylvinylether.test.ts

@@ -5,10 +5,10 @@ import { gsd } from '../gsd';
 describe('Global spectra deconvolution NMR spectra', () => {
   // Test case obtained from Pag 443, Chap 8.
   it('Ethylvinylether should have 21 peaks', () => {
-    let spectrum: number[][] = JSON.parse(
+    const spectrum: number[][] = JSON.parse(
       readFileSync(`${__dirname}/data/ethylvinylether.json`, 'utf-8'),
     );
-    let result = gsd(
+    const result = gsd(
       { x: spectrum[0].reverse(), y: spectrum[1].reverse() },
       {
         minMaxRatio: 0.03,

src/__tests__/gaussian-noise.test.ts

@@ -29,15 +29,18 @@ describe('smooth:false option', () => {
   });
 
   it('positive maxima peaks', () => {
-    let peakList = gsd(data);
+    const peakList = gsd(data);
     expect(peakList).toMatchCloseTo([
       { x: -0.5, y: 1.131 },
       { x: 0.5, y: 1.05 },
     ]);
   });
 
   it('negative maxima peaks', () => {
-    let peakList = gsd({ x: data.x, y: data.y.map((value) => value - 2) }, {});
+    const peakList = gsd(
+      { x: data.x, y: data.y.map((value) => value - 2) },
+      {},
+    );
     expect(peakList).toMatchCloseTo([
       { x: -0.5, y: -0.868 },
       { x: 0.5, y: -0.95 },
@@ -46,7 +49,7 @@ describe('smooth:false option', () => {
 
   it('Negative peaks', () => {
     // we check negative peaks
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => -value) },
       { maxCriteria: false },
     );
@@ -58,7 +61,7 @@ describe('smooth:false option', () => {
 
   it('minima peaks', () => {
     // we check negative peaks
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => 1 - value) },
       { maxCriteria: false },
     );

src/__tests__/gaussian-noiseParam.test.ts

@@ -29,20 +29,20 @@ describe('smooth:false option', () => {
   });
 
   it('positive maxima peaks but noiseLevel over the peaks', () => {
-    let peakList = gsd(data, { noiseLevel: 1.2 });
+    const peakList = gsd(data, { noiseLevel: 1.2 });
     expect(peakList).toStrictEqual([]);
   });
 
   it('positive maxima peaks', () => {
-    let peakList = gsd(data, { noiseLevel: 0.5 });
+    const peakList = gsd(data, { noiseLevel: 0.5 });
     expect(peakList).toMatchCloseTo([
       { x: -0.5, y: 1.131 },
       { x: 0.5, y: 1.05 },
     ]);
   });
 
   it('negative maxima peaks', () => {
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => value - 2) },
       { noiseLevel: -1.5 },
     );
@@ -54,7 +54,7 @@ describe('smooth:false option', () => {
 
   it('Negative peaks', () => {
     // we check negative peaks
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => -value) },
       { maxCriteria: false, noiseLevel: -0.5 },
     );
@@ -66,7 +66,7 @@ describe('smooth:false option', () => {
 
   it('Negative peaks with noiseLevel too low', () => {
     // we check negative peaks
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => -value) },
       { maxCriteria: false, noiseLevel: -1.2 },
     );
@@ -75,7 +75,7 @@ describe('smooth:false option', () => {
 
   it('minima peaks', () => {
     // we check negative peaks
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => 1 - value) },
       { maxCriteria: false, noiseLevel: 0.5 },
     );

src/__tests__/gaussian-overlapping.test.ts

@@ -27,7 +27,7 @@ describe('gaussian overlapping', () => {
       },
     });
 
-    let peaks = gsd(data, {});
+    const peaks = gsd(data, {});
     expect(peaks).toMatchCloseTo([
       {
         x: -0.1,
@@ -43,7 +43,7 @@ describe('gaussian overlapping', () => {
       },
     ]);
 
-    let optimizedPeaks = optimizePeaks(data, peaks, { groupingFactor: 3 });
+    const optimizedPeaks = optimizePeaks(data, peaks, { groupingFactor: 3 });
     expect(optimizedPeaks).toMatchCloseTo([
       {
         x: -0.1,

src/__tests__/gaussian-smooth.test.ts

@@ -28,7 +28,7 @@ describe('gaussian simulated peaks', () => {
       },
     });
 
-    let peakList = gsd(data, {
+    const peakList = gsd(data, {
       smoothY: true,
     });
     expect(peakList).toBeDeepCloseTo([

src/__tests__/gaussian.test.ts

@@ -29,9 +29,9 @@ describe('smooth:false option', () => {
   // we have here a low resolution spectrum so the impact is big
 
   it('positive maxima peaks', () => {
-    let peakList = gsd(data);
+    const peakList = gsd(data);
 
-    let expected = [
+    const expected = [
       {
         x: -0.5,
         y: 1,
@@ -59,9 +59,12 @@ describe('smooth:false option', () => {
   });
 
   it('negative maxima peaks', () => {
-    let peakList = gsd({ x: data.x, y: data.y.map((value) => value - 2) }, {});
+    const peakList = gsd(
+      { x: data.x, y: data.y.map((value) => value - 2) },
+      {},
+    );
 
-    let expected = [
+    const expected = [
       {
         x: -0.5,
         y: -1,
@@ -90,11 +93,11 @@ describe('smooth:false option', () => {
 
   it('Negative peaks', () => {
     // we check negative peaks
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => -value) },
       { maxCriteria: false },
     );
-    let expected = [
+    const expected = [
       {
         x: -0.5,
         y: -1,
@@ -124,11 +127,11 @@ describe('smooth:false option', () => {
 
   it('minima peaks', () => {
     // we check negative peaks
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => 1 - value) },
       { maxCriteria: false },
     );
-    let expected = [
+    const expected = [
       {
         x: -0.5,
         y: 0,
@@ -157,7 +160,7 @@ describe('smooth:false option', () => {
   });
 
   it('negative peaks with maxCriteria true', () => {
-    let peakList = gsd(
+    const peakList = gsd(
       { x: data.x, y: data.y.map((value) => -value) },
       { maxCriteria: true },
     );

src/__tests__/power.test.ts

@@ -48,8 +48,8 @@ describe('power', () => {
   // we have here a low resolution spectrum so the impact is big
 
   it('default options', () => {
-    let peakList = gsd(data);
-    let expected = [
+    const peakList = gsd(data);
+    const expected = [
       {
         id: peakList[0].id,
         x: 5,
@@ -66,7 +66,7 @@ describe('power', () => {
     expect(peakList).toBeDeepCloseTo(expected);
   });
   it('custom options', () => {
-    let peakList = gsd(data, {
+    const peakList = gsd(data, {
       smoothY: false,
       sgOptions: { windowSize: 7, polynomial: 3 },
     });

src/__tests__/ubiquitin.test.ts

@@ -12,11 +12,11 @@ expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
 
 describe('Global spectra deconvolution ubiquitin', () => {
   it('HR mass spectra', () => {
-    let spectrum = parseXY(
+    const spectrum = parseXY(
       readFileSync(`${__dirname}/data/ubiquitin.txt`, 'utf-8'),
     );
 
-    let peaks = gsd(spectrum, {
+    const peaks = gsd(spectrum, {
       minMaxRatio: 0.0,
       smoothY: false,
       realTopDetection: true,

src/__tests__/zero.test.ts

@@ -2,25 +2,25 @@ import { gsd } from '../gsd';
 
 describe('Simple test cases', () => {
   it('length = 0', () => {
-    let x = [];
-    let y = [];
+    const x = [];
+    const y = [];
     expect(() => {
       gsd({ x, y });
     }).toThrow('input must not be empty');
   });
 
   it('length = 2', () => {
-    let x = [1, 2];
-    let y = [2, 3];
+    const x = [1, 2];
+    const y = [2, 3];
     expect(() => {
       gsd({ x, y });
     }).toThrow('Window size is higher than the data length 9>2');
   });
 
   it('no peaks', () => {
-    let x = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15];
-    let y = [0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0];
-    let peaks = gsd({ x, y });
+    const x = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15];
+    const y = [0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0];
+    const peaks = gsd({ x, y });
     expect(peaks[0].x).toBe(8);
   });
 });

src/gsd.ts

@@ -57,19 +57,19 @@ export type GSDPeakID = MakeMandatory<GSDPeak, 'id'>;
  */
 
 export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
-  let {
+  let { noiseLevel } = options;
+  const {
     sgOptions = {
       windowSize: 9,
       polynomial: 3,
     },
-    noiseLevel,
     smoothY = false,
     maxCriteria = true,
     minMaxRatio = 0.00025,
     realTopDetection = false,
   } = options;
-
-  let { x, y } = data;
+  const { x } = data;
+  let { y } = data;
   if (xIsMonotonic(x) !== 1) {
     throw new Error('GSD only accepts monotone increasing x values');
   }
@@ -141,9 +141,9 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
 
   let lastMax: XIndex | null = null;
   let lastMin: XIndex | null = null;
-  let minddY: number[] = [];
-  let intervalL: XIndex[] = [];
-  let intervalR: XIndex[] = [];
+  const minddY: number[] = [];
+  const intervalL: XIndex[] = [];
+  const intervalR: XIndex[] = [];
 
   // By the intermediate value theorem We cannot find 2 consecutive maximum or minimum
   for (let i = 1; i < yData.length - 1; ++i) {
@@ -186,7 +186,7 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
 
   const peaks: GSDPeakID[] = [];
   for (const minddYIndex of minddY) {
-    let deltaX = x[minddYIndex];
+    const deltaX = x[minddYIndex];
     let possible = -1;
     let k = lastK + 1;
     let minDistance = Number.POSITIVE_INFINITY;
@@ -210,7 +210,7 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
 
     if (possible !== -1) {
       if (yData[minddYIndex] > yThreshold) {
-        let width = Math.abs(intervalR[possible].x - intervalL[possible].x);
+        const width = Math.abs(intervalR[possible].x - intervalL[possible].x);
         peaks.push({
           id: generateID(),
           x: deltaX,