fix: cleanup package and remove uuid generator package (#129)

Author: targos

.github/workflows/lactame.yml

@@ -5,16 +5,16 @@ on:
     types: [published]
 
 env:
-  NODE_VERSION: 20.x
+  NODE_VERSION: 22.x
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Get package name
         run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v4
         with:
           node-version: ${{ env.NODE_VERSION }}
       - name: Install dependencies

.github/workflows/typedoc.yml

@@ -6,15 +6,15 @@ on:
     types: [published]
 
 env:
-  NODE_VERSION: 20.x
+  NODE_VERSION: 22.x
   ENTRY_FILE: 'src/index.ts'
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-node@v3
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v4
         with:
           node-version: ${{ env.NODE_VERSION }}
       - name: Install dependencies

README.md

@@ -1,11 +1,13 @@
-# global-spectral-deconvolution and peak optimizer
+# ml-gsd
 
-[![NPM version][npm-image]][npm-url]
-[![build status][ci-image]][ci-url]
-[![Test coverage][codecov-image]][codecov-url]
-[![npm download][download-image]][download-url]
+[![NPM version](https://img.shields.io/npm/v/ml-gsd.svg)](https://www.npmjs.com/package/ml-gsd)
+[![npm download](https://img.shields.io/npm/dm/ml-gsd.svg)](https://www.npmjs.com/package/ml-gsd)
+[![test coverage](https://img.shields.io/codecov/c/github/mljs/global-spectral-deconvolution.svg)](https://codecov.io/gh/mljs/global-spectral-deconvolution)
+[![license](https://img.shields.io/npm/l/ml-gsd.svg)](https://github.com/mljs/global-spectral-deconvolution/blob/main/LICENSE)
 
-## Global Spectra Deconvolution
+Global spectral deconvolution and peak optimizer.
+
+## [API documentation](http://mljs.github.io/global-spectral-deconvolution/)
 
 `gsd`is using an algorithm that is searching for inflection points to determine the position and width of peaks. The width is defined as the distance between the 2 inflection points. Depending the shape of the peak this width may differ from 'fwhm' (Full Width Half Maximum).
 
@@ -29,7 +31,7 @@ The result of GSD is an array of GSDPeak:
   - from: { x, index }
   - to: { x, index }
 
-## Parameters
+### Parameters
 
 #### minMaxRatio=0.00025 (0-1)
 
@@ -51,14 +53,14 @@ Use a quadratic optimizations with the peak and its 3 closest neighbors to deter
 
 Savitzky-Golay parameters. windowSize should be odd; polynomial is the degree of the polynomial to use in the approximations. It should be bigger than 2.
 
-## Post methods
+### Post methods
 
-### GSD.broadenPeaks(peakList, {factor=2, overlap=false})
+#### GSD.broadenPeaks(peakList, {factor=2, overlap=false})
 
 We enlarge the peaks and add the properties from and to.
 By default we enlarge of a factor 2 and we don't allow overlap.
 
-### GSD.optimizePeaks(data, peakList, options)
+#### GSD.optimizePeaks(data, peakList, options)
 
 Optimize the position (x), max intensity (y), full width at half maximum (fwhm) and the ratio of gaussian contribution (mu) if it's required. It currently supports three kind of shapes: gaussian, lorentzian and pseudovoigt
 
@@ -107,19 +109,6 @@ console.log(optimized);
 */
 ```
 
-i
-
-## [API documentation](http://mljs.github.io/global-spectral-deconvolution/)
-
 ## License
 
 [MIT](./LICENSE)
-
-[npm-image]: https://img.shields.io/npm/v/ml-gsd.svg
-[npm-url]: https://npmjs.org/package/ml-gsd
-[codecov-image]: https://img.shields.io/codecov/c/github/mljs/global-spectral-deconvolution.svg
-[codecov-url]: https://codecov.io/gh/mljs/global-spectral-deconvolution
-[ci-image]: https://github.com/mljs/global-spectral-deconvolution/workflows/Node.js%20CI/badge.svg?branch=main
-[ci-url]: https://github.com/mljs/global-spectral-deconvolution/actions?query=workflow%3A%22Node.js+CI%22
-[download-image]: https://img.shields.io/npm/dm/ml-gsd.svg
-[download-url]: https://npmjs.org/package/ml-gsd

eslint.config.mjs renamed to eslint.config.js

@@ -1,7 +1,7 @@
 {
   "name": "ml-gsd",
   "version": "13.0.0",
-  "description": "Global Spectra Deconvolution",
+  "description": "Global Spectral Deconvolution",
   "type": "module",
   "exports": "./lib/index.js",
   "files": [
@@ -52,28 +52,27 @@
   },
   "devDependencies": {
     "@types/node": "^24.0.1",
-    "@vitest/coverage-v8": "^1.6.0",
+    "@vitest/coverage-v8": "^3.2.3",
     "@zakodium/tsconfig": "^1.0.1",
-    "cheminfo-build": "^1.2.0",
+    "cheminfo-build": "^1.2.1",
     "eslint": "^9.28.0",
     "eslint-config-cheminfo-typescript": "^18.0.1",
     "esm": "^3.2.25",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "mf-global": "^3.0.20",
+    "mf-global": "^3.1.25",
     "ml-stat": "^1.3.3",
-    "prettier": "^3.2.5",
-    "rimraf": "^5.0.6",
-    "spectrum-generator": "^8.0.11",
+    "prettier": "^3.5.3",
+    "rimraf": "^6.0.1",
+    "spectrum-generator": "^8.1.0",
     "typescript": "^5.8.3",
-    "vitest": "^1.6.0",
+    "vitest": "^3.2.3",
     "xy-parser": "^5.0.5"
   },
   "dependencies": {
-    "@lukeed/uuid": "^2.0.1",
-    "cheminfo-types": "^1.7.3",
+    "cheminfo-types": "^1.8.1",
     "ml-peak-shape-generator": "^4.1.4",
     "ml-savitzky-golay-generalized": "^4.2.0",
     "ml-spectra-fitting": "^5.0.1",
-    "ml-spectra-processing": "^14.5.3"
+    "ml-spectra-processing": "^14.12.0"
   }
 }

package.json

@@ -1,12 +1,11 @@
-import { v4 as generateID } from '@lukeed/uuid';
 import type { DataXY } from 'cheminfo-types';
-import { sgg } from 'ml-savitzky-golay-generalized';
 import type { SGGOptions } from 'ml-savitzky-golay-generalized';
+import { sgg } from 'ml-savitzky-golay-generalized';
 import {
   xIsEquallySpaced,
   xIsMonotonic,
-  xNoiseStandardDeviation,
   xMinMaxValues,
+  xNoiseStandardDeviation,
 } from 'ml-spectra-processing';
 
 import type { GSDPeak } from './GSDPeak.ts';
@@ -213,7 +212,7 @@ export function gsd(data: DataXY, options: GSDOptions = {}): GSDPeakID[] {
       if (yData[minddYIndex] > yThreshold) {
         const width = Math.abs(intervalR[possible].x - intervalL[possible].x);
         peaks.push({
-          id: generateID(),
+          id: crypto.randomUUID(),
           x: deltaX,
           y: yData[minddYIndex],
           width,

src/gsd.ts

@@ -1,4 +1,3 @@
-import { v4 as generateID } from '@lukeed/uuid';
 import type { Shape1D } from 'ml-peak-shape-generator';
 import type { OptimizationOptions } from 'ml-spectra-fitting';
 
@@ -7,8 +6,8 @@ import type { GSDPeakOptimized } from '../GSDPeakOptimized.ts';
 import { addMissingIDs } from '../utils/addMissingIDs.ts';
 import { addMissingShape } from '../utils/addMissingShape.ts';
 
-import { optimizePeaksWithLogs } from './optimizePeaksWithLogs.ts';
 import type { GSDPeakOptimizedID } from './optimizePeaksWithLogs.ts';
+import { optimizePeaksWithLogs } from './optimizePeaksWithLogs.ts';
 
 export interface JoinBroadPeaksOptions {
   /**
@@ -99,7 +98,7 @@ export function joinBroadPeaks(
           candidates,
           [
             {
-              id: generateID(),
+              id: crypto.randomUUID(),
               x: broadLines[maxI].x,
               y: max,
               width: initialWidth,

src/post/joinBroadPeaks.ts

@@ -1,15 +1,11 @@
-import { v4 as generateID } from '@lukeed/uuid';
-
-const { parse, stringify } = JSON;
-
 export function addMissingIDs<T extends { id?: string }>(
   peaks: T[],
   options: { output?: T[] } = {},
 ) {
-  const { output = parse(stringify(peaks)) as T[] } = options;
+  const { output = structuredClone(peaks) } = options;
   for (const peak of output) {
     if (!('id' in peak)) {
-      peak.id = generateID();
+      peak.id = crypto.randomUUID();
     }
   }