ml-gsd - npm Package Compare versions

Comparing version 11.3.0 to 12.0.0-pre.1661358412

lib-esm/gsd.d.ts

@@ -5,2 +5,4 @@ import type { DataXY } from 'cheminfo-types';
 import { GSDPeak } from './GSDPeak';
+import { MakeMandatory } from './utils/MakeMandatory';
+import { MakeOptional } from './utils/MakeOptional';
 export interface GSDOptions {
@@ -45,2 +47,4 @@ /**
 }
+export declare type GSDPeakID = MakeMandatory<GSDPeak, 'id'>;
+export declare type GSDPeakIDOptionalShape = MakeOptional<GSDPeak, 'shape'>;
 /**
@@ -53,3 +57,3 @@ * Global spectra deconvolution
  */
-export declare function gsd(data: DataXY, options?: GSDOptions): GSDPeak[];
+export declare function gsd(data: DataXY, options?: GSDOptions): GSDPeakID[];
 //# sourceMappingURL=gsd.d.ts.map

lib-esm/gsd.js

@@ -0,5 +1,6 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import { sgg } from 'ml-savitzky-golay-generalized';
 import { xIsEquallySpaced, xIsMonotoneIncreasing, xMinValue, xMaxValue, xNoiseStandardDeviation, } from 'ml-spectra-processing';
-import { appendShapeAndFWHM } from './utils/appendShapeAndFWHM';
 import { optimizeTop } from './utils/optimizeTop';
+import { setShape } from './utils/setShape';
 /**
@@ -164,2 +165,3 @@ * Global spectra deconvolution
                 peaks.push({
+                    id: generateID(),
                     x: deltaX,
@@ -190,4 +192,4 @@ y: yData[minddYIndex],
     });
-    return appendShapeAndFWHM(peaks, { shape });
+    return setShape(peaks, { shape });
 }
 //# sourceMappingURL=gsd.js.map

lib-esm/GSDBroadenPeak.d.ts

@@ -0,5 +1,8 @@
+import { Shape1D } from 'ml-peak-shape-generator';
 export interface GSDBroadenPeak {
+    id?: string;
     x: number;
     y: number;
     width: number;
+    shape?: Shape1D;
     index: number;
@@ -6,0 +9,0 @@ from: {

lib-esm/GSDPeak.d.ts

 import { Shape1D } from 'ml-peak-shape-generator';
 export interface GSDPeak {
+    id?: string;
     x: number;
@@ -4,0 +5,0 @@ y: number;

lib-esm/GSDPeakOptimized.d.ts

 import { Shape1D } from 'ml-peak-shape-generator';
 export interface GSDPeakOptimized {
+    id?: string;
     x: number;
@@ -4,0 +5,0 @@ y: number;

lib-esm/index.d.ts

@@ -6,3 +6,4 @@ export * from './gsd';
 export * from './post/broadenPeaks';
-export * from './utils/appendShapeAndFWHM';
+export * from './utils/setShape';
+export * from './utils/addMissingShape';
 export * from './GSDBroadenPeak';
@@ -9,0 +10,0 @@ export * from './GSDPeak';

lib-esm/index.js

@@ -6,3 +6,4 @@ export * from './gsd';
 export * from './post/broadenPeaks';
-export * from './utils/appendShapeAndFWHM';
+export * from './utils/setShape';
+export * from './utils/addMissingShape';
 export * from './GSDBroadenPeak';
@@ -9,0 +10,0 @@ export * from './GSDPeak';

lib-esm/post/broadenPeaks.d.ts

@@ -0,3 +1,19 @@
+import { Shape1D } from 'ml-peak-shape-generator';
 import { GSDBroadenPeak } from '../GSDBroadenPeak';
 import { GSDPeak } from '../GSDPeak';
+import { MakeOptional } from '../utils/MakeOptional';
+declare type GSDPeakOptionalShape = MakeOptional<GSDPeak, 'shape'>;
+declare type GSDBroadenPeakWithID = GSDBroadenPeak & {
+    id: string;
+};
+declare type GSDBroadenPeakWithShape = GSDBroadenPeak & {
+    shape: Shape1D;
+};
+declare type GSDBroadenPeakWithShapeID = GSDBroadenPeakWithID & {
+    shape: Shape1D;
+};
+export declare type WithOrWithout<T, ToExtends, TrueType, FalseType> = T extends ToExtends ? TrueType : FalseType;
+export declare type WithIDOrShape<T> = T extends {
+    id: string;
+} ? WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShapeID, GSDBroadenPeakWithID> : WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShape, GSDBroadenPeak>;
 /**
@@ -10,3 +26,3 @@ * This method will allow to enlarge peaks while preventing overlap between peaks
  */
-export declare function broadenPeaks(peakList: Omit<GSDPeak, 'shape'>[], options?: {
+export declare function broadenPeaks<T extends GSDPeakOptionalShape>(peakList: T[], options?: {
     /**
@@ -21,3 +37,4 @@ * @default 2
     overlap?: boolean;
-}): GSDBroadenPeak[];
+}): WithIDOrShape<T>[];
+export {};
 //# sourceMappingURL=broadenPeaks.d.ts.map

lib-esm/post/broadenPeaks.js

@@ -0,1 +1,2 @@
+import { getShape1D } from 'ml-peak-shape-generator';
 /**
@@ -10,14 +11,3 @@ * This method will allow to enlarge peaks while preventing overlap between peaks
     const { factor = 2, overlap = false } = options;
-    const peaks = peakList.map((peak) => {
-        const xFrom = peak.x - (peak.x - peak.inflectionPoints.from.x) * factor;
-        const xTo = peak.x + (peak.inflectionPoints.to.x - peak.x) * factor;
-        return {
-            x: peak.x,
-            y: peak.y,
-            index: peak.index,
-            width: xTo - xFrom,
-            from: { x: xFrom },
-            to: { x: xTo },
-        };
-    });
+    const peaks = mapPeaks(peakList, factor);
     if (!overlap) {
@@ -35,7 +25,36 @@ for (let i = 0; i < peaks.length - 1; i++) {
     }
-    for (let peak of peaks) {
+    for (const peak of peaks) {
         peak.width = peak.to.x - peak.from.x;
+        if (peak.shape) {
+            const { shape, width } = peak;
+            if (shape.fwhm !== undefined) {
+                const shapeFct = getShape1D(shape);
+                peak.shape.fwhm = shapeFct.widthToFWHM(width);
+            }
+        }
     }
     return peaks;
 }
+function mapPeaks(peaks, factor) {
+    return peaks.map((peak) => {
+        const { id, shape } = peak;
+        const xFrom = peak.x - (peak.x - peak.inflectionPoints.from.x) * factor;
+        const xTo = peak.x + (peak.inflectionPoints.to.x - peak.x) * factor;
+        let result = {
+            x: peak.x,
+            y: peak.y,
+            index: peak.index,
+            width: xTo - xFrom,
+            from: { x: xFrom },
+            to: { x: xTo },
+        };
+        if (id) {
+            result = { ...result, id };
+        }
+        if (shape) {
+            result = { ...result, shape };
+        }
+        return result;
+    });
+}
 //# sourceMappingURL=broadenPeaks.js.map

lib-esm/post/joinBroadPeaks.d.ts

 import type { Shape1D } from 'ml-peak-shape-generator';
 import { OptimizationOptions } from 'ml-spectra-fitting';
 import { GSDPeak } from '../GSDPeak';
+import { MakeOptional } from '../utils/MakeOptional';
+import { GSDPeakOptimizedID } from './optimizePeaksWithLogs';
 export interface JoinBroadPeaksOptions {
@@ -27,3 +29,4 @@ /**
  */
-export declare function joinBroadPeaks(peakList: GSDPeak[], options?: JoinBroadPeaksOptions): GSDPeak[];
+export declare type GSDPeakOptionalShape = MakeOptional<GSDPeak, 'shape'>;
+export declare function joinBroadPeaks<T extends GSDPeakOptionalShape>(peakList: T[], options?: JoinBroadPeaksOptions): GSDPeakOptimizedID[];
 //# sourceMappingURL=joinBroadPeaks.d.ts.map

lib-esm/post/joinBroadPeaks.js

@@ -1,6 +0,5 @@
-import { appendShapeAndFWHM } from '../utils/appendShapeAndFWHM';
+import { v4 as generateID } from '@lukeed/uuid';
+import { addMissingIDs } from '../utils/addMissingIDs';
+import { addMissingShape } from '../utils/addMissingShape';
 import { optimizePeaks } from './optimizePeaks';
-/**
- * This function tries to join the peaks that seems to belong to a broad signal in a single broad peak.
- */
 export function joinBroadPeaks(peakList, options = {}) {
@@ -12,5 +11,5 @@ let { shape = { kind: 'gaussian' }, optimization = { kind: 'lm', options: { timeout: 10 } }, broadWidth = 0.25, broadRatio = 0.0025, } = options;
     const broadLines = [];
-    const peaks = appendShapeAndFWHM(peakList, { shape });
-    if (peaks.length < 2)
-        return peaks;
+    if (peakList.length < 2) {
+        return addMissingIDs(addMissingShape(peakList.map(getGSDPeakOptimizedStructure), { shape }));
+    }
     let maxDdy = peakList[0].ddY;
@@ -21,6 +20,10 @@ for (let i = 1; i < peakList.length; i++) {
     }
-    for (let i = peaks.length - 1; i >= 0; i--) {
-        if (Math.abs(peaks[i].ddY) <= broadRatio * maxDdy) {
-            broadLines.push(peaks.splice(i, 1)[0]);
+    const newPeaks = [];
+    for (const peak of peakList) {
+        if (Math.abs(peak.ddY) <= broadRatio * maxDdy) {
+            broadLines.push(peak);
         }
+        else {
+            newPeaks.push(getGSDPeakOptimizedStructure(peak));
+        }
     }
@@ -49,2 +52,3 @@ //@ts-expect-error Push a feke peak
                     {
+                        id: generateID(),
                         x: broadLines[maxI].x,
@@ -55,11 +59,9 @@ y: max,
                 ], { shape, optimization });
-                //@ts-expect-error type is equal as expected
-                peaks.push(fitted[0]);
+                newPeaks.push(fitted[0]);
             }
             else {
                 // Put back the candidates to the peak list
-                indexes.forEach((index) => {
-                    // @ts-expect-error todo 2
-                    peaks.push(broadLines[index]);
-                });
+                for (const index of indexes) {
+                    newPeaks.push(getGSDPeakOptimizedStructure(broadLines[index]));
+                }
             }
@@ -73,7 +75,19 @@ candidates = { x: [broadLines[i].x], y: [broadLines[i].y] };
     }
-    peaks.sort((a, b) => {
+    newPeaks.sort((a, b) => {
         return a.x - b.x;
     });
-    return peaks;
+    return addMissingIDs(newPeaks, { output: newPeaks });
 }
+function getGSDPeakOptimizedStructure(peak) {
+    const { id, shape, x, y, width } = peak;
+    let newPeak = {
+        x,
+        y,
+        width,
+        shape,
+    };
+    if (id)
+        newPeak.id = id;
+    return newPeak;
+}
 //# sourceMappingURL=joinBroadPeaks.js.map

lib-esm/post/optimizePeaks.d.ts

@@ -1,6 +0,6 @@
-import type { DataXY, PeakXYWidth } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 import { FromTo } from 'cheminfo-types';
 import { Shape1D } from 'ml-peak-shape-generator';
 import type { OptimizationOptions } from 'ml-spectra-fitting';
-import { GSDPeakOptimized } from '../GSDPeakOptimized';
+import { Peak } from './optimizePeaksWithLogs';
 export interface OptimizePeaksOptions {
@@ -41,3 +41,5 @@ /**
  */
-export declare function optimizePeaks(data: DataXY, peakList: PeakXYWidth[], options?: OptimizePeaksOptions): GSDPeakOptimized[];
+export declare function optimizePeaks<T extends Peak>(data: DataXY, peakList: T[], options?: OptimizePeaksOptions): (T extends {
+    id: string;
+} ? import("./optimizePeaksWithLogs").GSDPeakOptimizedID : import("..").GSDPeakOptimized)[];
 //# sourceMappingURL=optimizePeaks.d.ts.map

lib-esm/post/optimizePeaksWithLogs.d.ts

 import type { DataXY, PeakXYWidth } from 'cheminfo-types';
 import { GSDPeakOptimized } from '../GSDPeakOptimized';
+import { MakeMandatory } from '../utils/MakeMandatory';
 import { OptimizePeaksOptions } from './optimizePeaks';
+export interface Peak extends PeakXYWidth {
+    id?: string;
+}
+export declare type GSDPeakOptimizedID = MakeMandatory<GSDPeakOptimized, 'id'>;
+declare type GSDPeakOptimizedIDOrNot<T extends Peak> = T extends {
+    id: string;
+} ? GSDPeakOptimizedID : GSDPeakOptimized;
 /**
@@ -10,6 +18,7 @@ * Optimize the position (x), max intensity (y), full width at half maximum (fwhm)
  */
-export declare function optimizePeaksWithLogs(data: DataXY, peakList: PeakXYWidth[], options?: OptimizePeaksOptions): {
+export declare function optimizePeaksWithLogs<T extends Peak>(data: DataXY, peakList: T[], options?: OptimizePeaksOptions): {
     logs: any[];
-    optimizedPeaks: GSDPeakOptimized[];
+    optimizedPeaks: GSDPeakOptimizedIDOrNot<T>[];
 };
+export {};
 //# sourceMappingURL=optimizePeaksWithLogs.d.ts.map

lib-esm/post/optimizePeaksWithLogs.js

 import { getShape1D } from 'ml-peak-shape-generator';
 import { optimize } from 'ml-spectra-fitting';
 import { xGetFromToIndex } from 'ml-spectra-processing';
-import { appendShapeAndFWHM } from '../utils/appendShapeAndFWHM';
+import { addMissingShape } from '../utils/addMissingShape';
 import { groupPeaks } from '../utils/groupPeaks';
@@ -30,3 +30,3 @@ /**
         // In order to make optimization we will add fwhm and shape on all the peaks
-        const peaks = appendShapeAndFWHM(peakGroup, { shape });
+        const peaks = addMissingShape(peakGroup, { shape });
         const firstPeak = peaks[0];
@@ -68,3 +68,3 @@ const lastPeak = peaks[peaks.length - 1];
         else {
-            results = results.concat(peaks);
+            results.push(...peaks);
             logs.push({
@@ -71,0 +71,0 @@ ...log,

lib/gsd.d.ts

@@ -5,2 +5,4 @@ import type { DataXY } from 'cheminfo-types';
 import { GSDPeak } from './GSDPeak';
+import { MakeMandatory } from './utils/MakeMandatory';
+import { MakeOptional } from './utils/MakeOptional';
 export interface GSDOptions {
@@ -45,2 +47,4 @@ /**
 }
+export declare type GSDPeakID = MakeMandatory<GSDPeak, 'id'>;
+export declare type GSDPeakIDOptionalShape = MakeOptional<GSDPeak, 'shape'>;
 /**
@@ -53,3 +57,3 @@ * Global spectra deconvolution
  */
-export declare function gsd(data: DataXY, options?: GSDOptions): GSDPeak[];
+export declare function gsd(data: DataXY, options?: GSDOptions): GSDPeakID[];
 //# sourceMappingURL=gsd.d.ts.map

lib/gsd.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.gsd = void 0;
+const uuid_1 = require("@lukeed/uuid");
 const ml_savitzky_golay_generalized_1 = require("ml-savitzky-golay-generalized");
 const ml_spectra_processing_1 = require("ml-spectra-processing");
-const appendShapeAndFWHM_1 = require("./utils/appendShapeAndFWHM");
 const optimizeTop_1 = require("./utils/optimizeTop");
+const setShape_1 = require("./utils/setShape");
 /**
@@ -167,2 +168,3 @@ * Global spectra deconvolution
                 peaks.push({
+                    id: (0, uuid_1.v4)(),
                     x: deltaX,
@@ -193,5 +195,5 @@ y: yData[minddYIndex],
     });
-    return (0, appendShapeAndFWHM_1.appendShapeAndFWHM)(peaks, { shape });
+    return (0, setShape_1.setShape)(peaks, { shape });
 }
 exports.gsd = gsd;
 //# sourceMappingURL=gsd.js.map

lib/GSDBroadenPeak.d.ts

@@ -0,5 +1,8 @@
+import { Shape1D } from 'ml-peak-shape-generator';
 export interface GSDBroadenPeak {
+    id?: string;
     x: number;
     y: number;
     width: number;
+    shape?: Shape1D;
     index: number;
@@ -6,0 +9,0 @@ from: {

lib/GSDPeak.d.ts

 import { Shape1D } from 'ml-peak-shape-generator';
 export interface GSDPeak {
+    id?: string;
     x: number;
@@ -4,0 +5,0 @@ y: number;

lib/GSDPeakOptimized.d.ts

 import { Shape1D } from 'ml-peak-shape-generator';
 export interface GSDPeakOptimized {
+    id?: string;
     x: number;
@@ -4,0 +5,0 @@ y: number;

lib/index.d.ts

@@ -6,3 +6,4 @@ export * from './gsd';
 export * from './post/broadenPeaks';
-export * from './utils/appendShapeAndFWHM';
+export * from './utils/setShape';
+export * from './utils/addMissingShape';
 export * from './GSDBroadenPeak';
@@ -9,0 +10,0 @@ export * from './GSDPeak';

lib/index.js

@@ -22,3 +22,4 @@ "use strict";
 __exportStar(require("./post/broadenPeaks"), exports);
-__exportStar(require("./utils/appendShapeAndFWHM"), exports);
+__exportStar(require("./utils/setShape"), exports);
+__exportStar(require("./utils/addMissingShape"), exports);
 __exportStar(require("./GSDBroadenPeak"), exports);
@@ -25,0 +26,0 @@ __exportStar(require("./GSDPeak"), exports);

lib/post/broadenPeaks.d.ts

@@ -0,3 +1,19 @@
+import { Shape1D } from 'ml-peak-shape-generator';
 import { GSDBroadenPeak } from '../GSDBroadenPeak';
 import { GSDPeak } from '../GSDPeak';
+import { MakeOptional } from '../utils/MakeOptional';
+declare type GSDPeakOptionalShape = MakeOptional<GSDPeak, 'shape'>;
+declare type GSDBroadenPeakWithID = GSDBroadenPeak & {
+    id: string;
+};
+declare type GSDBroadenPeakWithShape = GSDBroadenPeak & {
+    shape: Shape1D;
+};
+declare type GSDBroadenPeakWithShapeID = GSDBroadenPeakWithID & {
+    shape: Shape1D;
+};
+export declare type WithOrWithout<T, ToExtends, TrueType, FalseType> = T extends ToExtends ? TrueType : FalseType;
+export declare type WithIDOrShape<T> = T extends {
+    id: string;
+} ? WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShapeID, GSDBroadenPeakWithID> : WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShape, GSDBroadenPeak>;
 /**
@@ -10,3 +26,3 @@ * This method will allow to enlarge peaks while preventing overlap between peaks
  */
-export declare function broadenPeaks(peakList: Omit<GSDPeak, 'shape'>[], options?: {
+export declare function broadenPeaks<T extends GSDPeakOptionalShape>(peakList: T[], options?: {
     /**
@@ -21,3 +37,4 @@ * @default 2
     overlap?: boolean;
-}): GSDBroadenPeak[];
+}): WithIDOrShape<T>[];
+export {};
 //# sourceMappingURL=broadenPeaks.d.ts.map

lib/post/broadenPeaks.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.broadenPeaks = void 0;
+const ml_peak_shape_generator_1 = require("ml-peak-shape-generator");
 /**
@@ -13,14 +14,3 @@ * This method will allow to enlarge peaks while preventing overlap between peaks
     const { factor = 2, overlap = false } = options;
-    const peaks = peakList.map((peak) => {
-        const xFrom = peak.x - (peak.x - peak.inflectionPoints.from.x) * factor;
-        const xTo = peak.x + (peak.inflectionPoints.to.x - peak.x) * factor;
-        return {
-            x: peak.x,
-            y: peak.y,
-            index: peak.index,
-            width: xTo - xFrom,
-            from: { x: xFrom },
-            to: { x: xTo },
-        };
-    });
+    const peaks = mapPeaks(peakList, factor);
     if (!overlap) {
@@ -38,4 +28,11 @@ for (let i = 0; i < peaks.length - 1; i++) {
     }
-    for (let peak of peaks) {
+    for (const peak of peaks) {
         peak.width = peak.to.x - peak.from.x;
+        if (peak.shape) {
+            const { shape, width } = peak;
+            if (shape.fwhm !== undefined) {
+                const shapeFct = (0, ml_peak_shape_generator_1.getShape1D)(shape);
+                peak.shape.fwhm = shapeFct.widthToFWHM(width);
+            }
+        }
     }
@@ -45,2 +42,24 @@ return peaks;
 exports.broadenPeaks = broadenPeaks;
+function mapPeaks(peaks, factor) {
+    return peaks.map((peak) => {
+        const { id, shape } = peak;
+        const xFrom = peak.x - (peak.x - peak.inflectionPoints.from.x) * factor;
+        const xTo = peak.x + (peak.inflectionPoints.to.x - peak.x) * factor;
+        let result = {
+            x: peak.x,
+            y: peak.y,
+            index: peak.index,
+            width: xTo - xFrom,
+            from: { x: xFrom },
+            to: { x: xTo },
+        };
+        if (id) {
+            result = { ...result, id };
+        }
+        if (shape) {
+            result = { ...result, shape };
+        }
+        return result;
+    });
+}
 //# sourceMappingURL=broadenPeaks.js.map

lib/post/joinBroadPeaks.d.ts

 import type { Shape1D } from 'ml-peak-shape-generator';
 import { OptimizationOptions } from 'ml-spectra-fitting';
 import { GSDPeak } from '../GSDPeak';
+import { MakeOptional } from '../utils/MakeOptional';
+import { GSDPeakOptimizedID } from './optimizePeaksWithLogs';
 export interface JoinBroadPeaksOptions {
@@ -27,3 +29,4 @@ /**
  */
-export declare function joinBroadPeaks(peakList: GSDPeak[], options?: JoinBroadPeaksOptions): GSDPeak[];
+export declare type GSDPeakOptionalShape = MakeOptional<GSDPeak, 'shape'>;
+export declare function joinBroadPeaks<T extends GSDPeakOptionalShape>(peakList: T[], options?: JoinBroadPeaksOptions): GSDPeakOptimizedID[];
 //# sourceMappingURL=joinBroadPeaks.d.ts.map

lib/post/joinBroadPeaks.js

 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.joinBroadPeaks = void 0;
-const appendShapeAndFWHM_1 = require("../utils/appendShapeAndFWHM");
+const uuid_1 = require("@lukeed/uuid");
+const addMissingIDs_1 = require("../utils/addMissingIDs");
+const addMissingShape_1 = require("../utils/addMissingShape");
 const optimizePeaks_1 = require("./optimizePeaks");
-/**
- * This function tries to join the peaks that seems to belong to a broad signal in a single broad peak.
- */
 function joinBroadPeaks(peakList, options = {}) {
@@ -15,5 +14,5 @@ let { shape = { kind: 'gaussian' }, optimization = { kind: 'lm', options: { timeout: 10 } }, broadWidth = 0.25, broadRatio = 0.0025, } = options;
     const broadLines = [];
-    const peaks = (0, appendShapeAndFWHM_1.appendShapeAndFWHM)(peakList, { shape });
-    if (peaks.length < 2)
-        return peaks;
+    if (peakList.length < 2) {
+        return (0, addMissingIDs_1.addMissingIDs)((0, addMissingShape_1.addMissingShape)(peakList.map(getGSDPeakOptimizedStructure), { shape }));
+    }
     let maxDdy = peakList[0].ddY;
@@ -24,6 +23,10 @@ for (let i = 1; i < peakList.length; i++) {
     }
-    for (let i = peaks.length - 1; i >= 0; i--) {
-        if (Math.abs(peaks[i].ddY) <= broadRatio * maxDdy) {
-            broadLines.push(peaks.splice(i, 1)[0]);
+    const newPeaks = [];
+    for (const peak of peakList) {
+        if (Math.abs(peak.ddY) <= broadRatio * maxDdy) {
+            broadLines.push(peak);
         }
+        else {
+            newPeaks.push(getGSDPeakOptimizedStructure(peak));
+        }
     }
@@ -52,2 +55,3 @@ //@ts-expect-error Push a feke peak
                     {
+                        id: (0, uuid_1.v4)(),
                         x: broadLines[maxI].x,
@@ -58,11 +62,9 @@ y: max,
                 ], { shape, optimization });
-                //@ts-expect-error type is equal as expected
-                peaks.push(fitted[0]);
+                newPeaks.push(fitted[0]);
             }
             else {
                 // Put back the candidates to the peak list
-                indexes.forEach((index) => {
-                    // @ts-expect-error todo 2
-                    peaks.push(broadLines[index]);
-                });
+                for (const index of indexes) {
+                    newPeaks.push(getGSDPeakOptimizedStructure(broadLines[index]));
+                }
             }
@@ -76,8 +78,20 @@ candidates = { x: [broadLines[i].x], y: [broadLines[i].y] };
     }
-    peaks.sort((a, b) => {
+    newPeaks.sort((a, b) => {
         return a.x - b.x;
     });
-    return peaks;
+    return (0, addMissingIDs_1.addMissingIDs)(newPeaks, { output: newPeaks });
 }
 exports.joinBroadPeaks = joinBroadPeaks;
+function getGSDPeakOptimizedStructure(peak) {
+    const { id, shape, x, y, width } = peak;
+    let newPeak = {
+        x,
+        y,
+        width,
+        shape,
+    };
+    if (id)
+        newPeak.id = id;
+    return newPeak;
+}
 //# sourceMappingURL=joinBroadPeaks.js.map

lib/post/optimizePeaks.d.ts

@@ -1,6 +0,6 @@
-import type { DataXY, PeakXYWidth } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 import { FromTo } from 'cheminfo-types';
 import { Shape1D } from 'ml-peak-shape-generator';
 import type { OptimizationOptions } from 'ml-spectra-fitting';
-import { GSDPeakOptimized } from '../GSDPeakOptimized';
+import { Peak } from './optimizePeaksWithLogs';
 export interface OptimizePeaksOptions {
@@ -41,3 +41,5 @@ /**
  */
-export declare function optimizePeaks(data: DataXY, peakList: PeakXYWidth[], options?: OptimizePeaksOptions): GSDPeakOptimized[];
+export declare function optimizePeaks<T extends Peak>(data: DataXY, peakList: T[], options?: OptimizePeaksOptions): (T extends {
+    id: string;
+} ? import("./optimizePeaksWithLogs").GSDPeakOptimizedID : import("..").GSDPeakOptimized)[];
 //# sourceMappingURL=optimizePeaks.d.ts.map

lib/post/optimizePeaksWithLogs.d.ts

 import type { DataXY, PeakXYWidth } from 'cheminfo-types';
 import { GSDPeakOptimized } from '../GSDPeakOptimized';
+import { MakeMandatory } from '../utils/MakeMandatory';
 import { OptimizePeaksOptions } from './optimizePeaks';
+export interface Peak extends PeakXYWidth {
+    id?: string;
+}
+export declare type GSDPeakOptimizedID = MakeMandatory<GSDPeakOptimized, 'id'>;
+declare type GSDPeakOptimizedIDOrNot<T extends Peak> = T extends {
+    id: string;
+} ? GSDPeakOptimizedID : GSDPeakOptimized;
 /**
@@ -10,6 +18,7 @@ * Optimize the position (x), max intensity (y), full width at half maximum (fwhm)
  */
-export declare function optimizePeaksWithLogs(data: DataXY, peakList: PeakXYWidth[], options?: OptimizePeaksOptions): {
+export declare function optimizePeaksWithLogs<T extends Peak>(data: DataXY, peakList: T[], options?: OptimizePeaksOptions): {
     logs: any[];
-    optimizedPeaks: GSDPeakOptimized[];
+    optimizedPeaks: GSDPeakOptimizedIDOrNot<T>[];
 };
+export {};
 //# sourceMappingURL=optimizePeaksWithLogs.d.ts.map

lib/post/optimizePeaksWithLogs.js

@@ -7,3 +7,3 @@ "use strict";
 const ml_spectra_processing_1 = require("ml-spectra-processing");
-const appendShapeAndFWHM_1 = require("../utils/appendShapeAndFWHM");
+const addMissingShape_1 = require("../utils/addMissingShape");
 const groupPeaks_1 = require("../utils/groupPeaks");
@@ -34,3 +34,3 @@ /**
         // In order to make optimization we will add fwhm and shape on all the peaks
-        const peaks = (0, appendShapeAndFWHM_1.appendShapeAndFWHM)(peakGroup, { shape });
+        const peaks = (0, addMissingShape_1.addMissingShape)(peakGroup, { shape });
         const firstPeak = peaks[0];
@@ -72,3 +72,3 @@ const lastPeak = peaks[peaks.length - 1];
         else {
-            results = results.concat(peaks);
+            results.push(...peaks);
             logs.push({
@@ -75,0 +75,0 @@ ...log,

package.json

 {
   "name": "ml-gsd",
-  "version": "11.3.0",
+  "version": "12.0.0-pre.1661358412",
   "description": "Global Spectra Deconvolution",
@@ -82,8 +82,9 @@ "main": "./lib/index.js",
   "dependencies": {
+    "@lukeed/uuid": "^2.0.0",
     "cheminfo-types": "^1.1.0",
     "ml-peak-shape-generator": "^4.1.1",
-    "ml-savitzky-golay-generalized": "4.0.1",
-    "ml-spectra-fitting": "4.1.0",
+    "ml-savitzky-golay-generalized": "^4.0.1",
+    "ml-spectra-fitting": "^4.1.0",
     "ml-spectra-processing": "^11.6.0"
   }
 }

src/__tests__/gaussian-smooth.test.ts

@@ -36,2 +36,3 @@ import type { DataXY } from 'cheminfo-types';
       {
+        id: peakList[0].id,
         x: -0.5,
@@ -52,2 +53,3 @@ y: 0.6945098953985852,
       {
+        id: peakList[1].id,
         x: 0.5,
@@ -54,0 +56,0 @@ y: 0.6945098953985852,

src/__tests__/gaussian.test.ts

@@ -66,3 +66,3 @@ import type { DataXY } from 'cheminfo-types';
     ];
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
@@ -105,3 +105,3 @@
     ];
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
@@ -148,3 +148,3 @@
 
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
@@ -191,3 +191,3 @@
 
-    expect(peakList).toBeDeepCloseTo(expected);
+    expect(peakList).toBeDeepCloseTo(addMissingID(peakList, expected));
   });
@@ -203,1 +203,8 @@
 });
+
+function addMissingID(peaks, expected) {
+  for (let i = 0; i < expected.length; i++) {
+    expected[i].id = peaks[i].id;
+  }
+  return expected;
+}

src/__tests__/power.test.ts

@@ -54,2 +54,3 @@ import type { DataXY } from 'cheminfo-types';
       {
+        id: peakList[0].id,
         x: 5,
@@ -81,2 +82,3 @@ y: 10000,
       {
+        id: peakList[0].id,
         x: 4.45,
@@ -97,2 +99,3 @@ y: 7921,
       {
+        id: peakList[1].id,
         x: 5,
@@ -113,2 +116,3 @@ y: 10000,
       {
+        id: peakList[2].id,
         x: 5.55,
@@ -115,0 +119,0 @@ y: 7921,

src/__tests__/ubiquitin.test.ts

@@ -25,3 +25,5 @@ import { readFileSync } from 'fs';
     });
+
     expect(peaks[0]).toBeDeepCloseTo({
+      id: peaks[0].id,
       x: 200.05527917306466,
@@ -28,0 +30,0 @@ y: 28.795378784444413,

src/gsd.ts

@@ -0,1 +1,2 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import type { DataXY } from 'cheminfo-types';
@@ -13,4 +14,6 @@ import { Shape1D } from 'ml-peak-shape-generator';
 import { GSDPeak } from './GSDPeak';
-import { appendShapeAndFWHM } from './utils/appendShapeAndFWHM';
+import { MakeMandatory } from './utils/MakeMandatory';
+import { MakeOptional } from './utils/MakeOptional';
 import { optimizeTop } from './utils/optimizeTop';
+import { setShape } from './utils/setShape';
 
@@ -56,3 +59,4 @@ export interface GSDOptions {
 }
-
+export type GSDPeakID = MakeMandatory<GSDPeak, 'id'>;
+export type GSDPeakIDOptionalShape = MakeOptional<GSDPeak, 'shape'>;
 /**
@@ -66,3 +70,3 @@ * Global spectra deconvolution
 
-export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeak[] {
+export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
   let {
@@ -223,3 +227,3 @@ sgOptions = {
 
-  const peaks: GSDPeak[] = [];
+  const peaks: GSDPeakIDOptionalShape[] = [];
   for (const minddYIndex of minddY) {
@@ -252,2 +256,3 @@ let deltaX = x[minddYIndex];
         peaks.push({
+          id: generateID(),
           x: deltaX,
@@ -262,3 +267,3 @@ y: yData[minddYIndex],
           },
-        } as GSDPeak);
+        });
       }
@@ -283,3 +288,3 @@ }
 
-  return appendShapeAndFWHM(peaks, { shape });
+  return setShape(peaks, { shape }) as GSDPeakID[];
 }

src/GSDBroadenPeak.ts

@@ -0,5 +1,9 @@
+import { Shape1D } from 'ml-peak-shape-generator';
+
 export interface GSDBroadenPeak {
+  id?: string;
   x: number;
   y: number;
   width: number;
+  shape?: Shape1D;
   index: number;
@@ -6,0 +10,0 @@ from: { x: number };

src/GSDPeak.ts

 import { Shape1D } from 'ml-peak-shape-generator';
 
 export interface GSDPeak {
+  id?: string;
   x: number;
@@ -5,0 +6,0 @@ y: number;

src/GSDPeakOptimized.ts

 import { Shape1D } from 'ml-peak-shape-generator';
 
 export interface GSDPeakOptimized {
+  id?: string;
   x: number;
@@ -5,0 +6,0 @@ y: number;

src/index.ts

@@ -6,5 +6,6 @@ export * from './gsd';
 export * from './post/broadenPeaks';
-export * from './utils/appendShapeAndFWHM';
+export * from './utils/setShape';
+export * from './utils/addMissingShape';
 export * from './GSDBroadenPeak';
 export * from './GSDPeak';
 export * from './GSDPeakOptimized';

src/post/__tests__/broadenPeaks.test.ts

@@ -303,2 +303,3 @@ import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
         {
+          id: '1',
           x: -0.5,
@@ -331,2 +332,3 @@ y: 1,
           index: 575,
+          shape: { kind: 'gaussian' },
           inflectionPoints: {
@@ -340,29 +342,34 @@ from: { index: 573, x: 10.46 },
     );
-    expect(result).toBeDeepCloseTo([
-      {
-        x: -0.5,
-        y: 1,
-        index: 25,
-        width: 1.3,
-        from: { x: -1.3 },
-        to: { x: 0 },
-      },
-      {
-        x: 0.5,
-        y: 1,
-        index: 75,
-        width: 1.3,
-        from: { x: 0 },
-        to: { x: 1.3 },
-      },
-      {
-        x: 10.5,
-        y: 1,
-        index: 575,
-        width: 1.6,
-        from: { x: 9.7 },
-        to: { x: 11.3 },
-      },
-    ]);
+    expect(result).toBeDeepCloseTo(
+      [
+        {
+          id: '1',
+          x: -0.5,
+          y: 1,
+          index: 25,
+          width: 1.3,
+          from: { x: -1.3 },
+          to: { x: 0 },
+        },
+        {
+          x: 0.5,
+          y: 1,
+          index: 75,
+          width: 1.3,
+          from: { x: 0 },
+          to: { x: 1.3 },
+        },
+        {
+          x: 10.5,
+          y: 1,
+          index: 575,
+          shape: { kind: 'gaussian' },
+          width: 1.6,
+          from: { x: 9.7 },
+          to: { x: 11.3 },
+        },
+      ],
+      1,
+    );
   });
 });

src/post/__tests__/joinBroadPeaks.test.ts

@@ -29,3 +29,2 @@ import { generateSpectrum } from 'spectrum-generator';
     });
-
     expect(peaks.length).toBeGreaterThan(3);
@@ -32,0 +31,0 @@ expect(newPeaks).toHaveLength(3);

src/post/broadenPeaks.ts

@@ -0,4 +1,20 @@
+import { getShape1D, Shape1D } from 'ml-peak-shape-generator';
+
 import { GSDBroadenPeak } from '../GSDBroadenPeak';
 import { GSDPeak } from '../GSDPeak';
+import { MakeOptional } from '../utils/MakeOptional';
 
+type GSDPeakOptionalShape = MakeOptional<GSDPeak, 'shape'>;
+
+type GSDBroadenPeakWithID = GSDBroadenPeak & { id: string };
+type GSDBroadenPeakWithShape = GSDBroadenPeak & { shape: Shape1D };
+type GSDBroadenPeakWithShapeID = GSDBroadenPeakWithID & { shape: Shape1D };
+
+export type WithOrWithout<T, ToExtends, TrueType, FalseType> =
+  T extends ToExtends ? TrueType : FalseType;
+
+export type WithIDOrShape<T> = T extends { id: string }
+  ? WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShapeID, GSDBroadenPeakWithID>
+  : WithOrWithout<T, GSDPeak, GSDBroadenPeakWithShape, GSDBroadenPeak>;
+
 /**
@@ -12,4 +28,4 @@ * This method will allow to enlarge peaks while preventing overlap between peaks
 
-export function broadenPeaks(
-  peakList: Omit<GSDPeak, 'shape'>[],
+export function broadenPeaks<T extends GSDPeakOptionalShape>(
+  peakList: T[],
   options: {
@@ -26,17 +42,6 @@ /**
   } = {},
-): GSDBroadenPeak[] {
+) {
   const { factor = 2, overlap = false } = options;
 
-  const peaks = peakList.map((peak) => {
-    const xFrom = peak.x - (peak.x - peak.inflectionPoints.from.x) * factor;
-    const xTo = peak.x + (peak.inflectionPoints.to.x - peak.x) * factor;
-    return {
-      x: peak.x,
-      y: peak.y,
-      index: peak.index,
-      width: xTo - xFrom,
-      from: { x: xFrom },
-      to: { x: xTo },
-    };
-  });
+  const peaks = mapPeaks(peakList, factor);
 
@@ -56,4 +61,11 @@ if (!overlap) {
 
-  for (let peak of peaks) {
+  for (const peak of peaks) {
     peak.width = peak.to.x - peak.from.x;
+    if (peak.shape) {
+      const { shape, width } = peak;
+      if (shape.fwhm !== undefined) {
+        const shapeFct = getShape1D(shape);
+        peak.shape.fwhm = shapeFct.widthToFWHM(width);
+      }
+    }
   }
@@ -63,1 +75,33 @@
 }
+
+function mapPeaks<T extends GSDPeakOptionalShape>(
+  peaks: T[],
+  factor: number,
+): WithIDOrShape<T>[] {
+  return peaks.map((peak) => {
+    const { id, shape } = peak;
+    const xFrom = peak.x - (peak.x - peak.inflectionPoints.from.x) * factor;
+    const xTo = peak.x + (peak.inflectionPoints.to.x - peak.x) * factor;
+
+    let result = {
+      x: peak.x,
+      y: peak.y,
+      index: peak.index,
+      width: xTo - xFrom,
+      from: { x: xFrom },
+      to: { x: xTo },
+    } as GSDBroadenPeak;
+
+    if (id) {
+      result = { ...result, id } as GSDBroadenPeakWithID;
+    }
+
+    if (shape) {
+      result = { ...result, shape } as T extends { id: string }
+        ? GSDBroadenPeakWithShapeID
+        : GSDBroadenPeakWithShape;
+    }
+
+    return result as WithIDOrShape<T>;
+  });
+}

src/post/joinBroadPeaks.ts

@@ -0,1 +1,2 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import type { Shape1D } from 'ml-peak-shape-generator';
@@ -6,5 +7,8 @@ import { OptimizationOptions } from 'ml-spectra-fitting';
 import { GSDPeakOptimized } from '../GSDPeakOptimized';
-import { appendShapeAndFWHM } from '../utils/appendShapeAndFWHM';
+import { MakeOptional } from '../utils/MakeOptional';
+import { addMissingIDs } from '../utils/addMissingIDs';
+import { addMissingShape } from '../utils/addMissingShape';
 
 import { optimizePeaks } from './optimizePeaks';
+import { GSDPeakOptimizedID } from './optimizePeaksWithLogs';
 
@@ -36,6 +40,8 @@ export interface JoinBroadPeaksOptions {
 
-export function joinBroadPeaks(
-  peakList: GSDPeak[],
+export type GSDPeakOptionalShape = MakeOptional<GSDPeak, 'shape'>;
+
+export function joinBroadPeaks<T extends GSDPeakOptionalShape>(
+  peakList: T[],
   options: JoinBroadPeaksOptions = {},
-): GSDPeak[] {
+): GSDPeakOptimizedID[] {
   let {
@@ -51,6 +57,9 @@ shape = { kind: 'gaussian' },
   let count = 1;
-  const broadLines: GSDPeakOptimized[] = [];
-  const peaks = appendShapeAndFWHM(peakList, { shape });
+  const broadLines: T[] = [];
 
-  if (peaks.length < 2) return peaks;
+  if (peakList.length < 2) {
+    return addMissingIDs(
+      addMissingShape(peakList.map(getGSDPeakOptimizedStructure), { shape }),
+    );
+  }
 
@@ -62,5 +71,8 @@ let maxDdy = peakList[0].ddY;
 
-  for (let i: number = peaks.length - 1; i >= 0; i--) {
-    if (Math.abs(peaks[i].ddY) <= broadRatio * maxDdy) {
-      broadLines.push(peaks.splice(i, 1)[0]);
+  const newPeaks: GSDPeakOptimized[] = [];
+  for (const peak of peakList) {
+    if (Math.abs(peak.ddY) <= broadRatio * maxDdy) {
+      broadLines.push(peak);
+    } else {
+      newPeaks.push(getGSDPeakOptimizedStructure(peak));
     }
@@ -93,2 +105,3 @@ }
             {
+              id: generateID(),
               x: broadLines[maxI].x,
@@ -101,10 +114,8 @@ y: max,
         );
-        //@ts-expect-error type is equal as expected
-        peaks.push(fitted[0]);
+        newPeaks.push(fitted[0]);
       } else {
         // Put back the candidates to the peak list
-        indexes.forEach((index) => {
-          // @ts-expect-error todo 2
-          peaks.push(broadLines[index]);
-        });
+        for (const index of indexes) {
+          newPeaks.push(getGSDPeakOptimizedStructure(broadLines[index]));
+        }
       }
@@ -119,7 +130,22 @@
   }
-  peaks.sort((a, b) => {
+  newPeaks.sort((a, b) => {
     return a.x - b.x;
   });
 
-  return peaks;
+  return addMissingIDs(newPeaks, { output: newPeaks });
 }
+
+function getGSDPeakOptimizedStructure<T extends GSDPeakOptionalShape>(peak: T) {
+  const { id, shape, x, y, width } = peak;
+
+  let newPeak = {
+    x,
+    y,
+    width,
+    shape,
+  } as GSDPeakOptimized;
+
+  if (id) newPeak.id = id;
+
+  return newPeak;
+}

src/post/optimizePeaks.ts

@@ -1,2 +0,2 @@
-import type { DataXY, PeakXYWidth } from 'cheminfo-types';
+import type { DataXY } from 'cheminfo-types';
 import { FromTo } from 'cheminfo-types';
@@ -6,6 +6,4 @@ import { Shape1D } from 'ml-peak-shape-generator';
 
-import { GSDPeakOptimized } from '../GSDPeakOptimized';
+import { Peak, optimizePeaksWithLogs } from './optimizePeaksWithLogs';
 
-import { optimizePeaksWithLogs } from './optimizePeaksWithLogs';
-
 export interface OptimizePeaksOptions {
@@ -47,8 +45,8 @@ /**
  */
-export function optimizePeaks(
+export function optimizePeaks<T extends Peak>(
   data: DataXY,
-  peakList: PeakXYWidth[],
+  peakList: T[],
   options: OptimizePeaksOptions = {},
-): GSDPeakOptimized[] {
+) {
   return optimizePeaksWithLogs(data, peakList, options).optimizedPeaks;
 }

src/post/optimizePeaksWithLogs.ts

@@ -7,3 +7,4 @@ import type { DataXY, PeakXYWidth } from 'cheminfo-types';
 import { GSDPeakOptimized } from '../GSDPeakOptimized';
-import { appendShapeAndFWHM } from '../utils/appendShapeAndFWHM';
+import { MakeMandatory } from '../utils/MakeMandatory';
+import { addMissingShape } from '../utils/addMissingShape';
 import { groupPeaks } from '../utils/groupPeaks';
@@ -13,2 +14,14 @@
 
+export interface Peak extends PeakXYWidth {
+  id?: string;
+}
+
+export type GSDPeakOptimizedID = MakeMandatory<GSDPeakOptimized, 'id'>;
+
+type GSDPeakOptimizedIDOrNot<T extends Peak> = T extends {
+  id: string;
+}
+  ? GSDPeakOptimizedID
+  : GSDPeakOptimized;
+
 /**
@@ -20,7 +33,7 @@ * Optimize the position (x), max intensity (y), full width at half maximum (fwhm)
  */
-export function optimizePeaksWithLogs(
+export function optimizePeaksWithLogs<T extends Peak>(
   data: DataXY,
-  peakList: PeakXYWidth[],
+  peakList: T[],
   options: OptimizePeaksOptions = {},
-): { logs: any[]; optimizedPeaks: GSDPeakOptimized[] } {
+): { logs: any[]; optimizedPeaks: GSDPeakOptimizedIDOrNot<T>[] } {
   const {
@@ -47,7 +60,7 @@ fromTo = {},
   let logs: any[] = [];
-  let results: GSDPeakOptimized[] = [];
+  let results: GSDPeakOptimizedIDOrNot<T>[] = [];
   groups.forEach((peakGroup) => {
     const start = Date.now();
     // In order to make optimization we will add fwhm and shape on all the peaks
-    const peaks = appendShapeAndFWHM(peakGroup, { shape });
+    const peaks = addMissingShape(peakGroup, { shape });
 
@@ -97,3 +110,3 @@ const firstPeak = peaks[0];
           ),
-        });
+        } as GSDPeakOptimizedIDOrNot<T>);
       }
@@ -107,3 +120,3 @@ logs.push({
     } else {
-      results = results.concat(peaks);
+      results.push(...(peaks as GSDPeakOptimizedIDOrNot<T>[]));
       logs.push({
@@ -110,0 +123,0 @@ ...log,

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Total package byte prevSize

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increased by1.12%

Number of package files

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increased by20.14%

Lines of code

10728

increased by5.65%

Worsened metrics

Dependency count

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increased by20%

Number of low quality alerts

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increased byInfinity%

Dependency changes

• + Added@lukeed/uuid@^2.0.0

• + Added@lukeed/csprng@1.1.0(transitive)

• + Added@lukeed/uuid@2.0.1(transitive)

• + Addedml-direct@1.0.0(transitive)

• + Addedml-savitzky-golay-generalized@4.2.0(transitive)

• + Addedml-spectra-fitting@4.2.4(transitive)

• + Addedml-spectra-processing@14.9.1(transitive)

• + Addedml-xsadd@3.0.1(transitive)

• - Removedml-savitzky-golay-generalized@4.0.1(transitive)

• - Removedml-spectra-fitting@4.1.0(transitive)

• Updatedml-savitzky-golay-generalized@^4.0.1

• Updatedml-spectra-fitting@^4.1.0