refactor!: migrate to esm-only and update ml-levenberg-marquardt (#112)

* migrate jest to vitest
* switch to `@zakodium/tsconfig` base config
  override `noUncheckedIndexedAccess` to `false`
* update to eslint v9 with `eslint-config-cheminfo-typescript` base config

Refs: https://github.com/cheminfo/generator-cheminfo/blob/main/ts-migration.md
Closes: #111

Author: tpoisseau

.eslintrc.yml

@@ -11,4 +11,4 @@ jobs:
     uses: zakodium/workflows/.github/workflows/npm-prerelease.yml@npm-prerelease-v1
     secrets:
       github-token: ${{ secrets.BOT_TOKEN }}
-      npm-token: ${{ secrets.NPM_BOT_TOKEN }}
+      npm-token: ${{ secrets.NPM_BOT_TOKEN }}

.github/npm-prerelease.yml

@@ -1,16 +1,16 @@
-name: Release
-
-on:
-  push:
-    branches:
-      - main
-
-jobs:
-  release:
-    # Documentation: https://github.com/zakodium/workflows#release
-    uses: zakodium/workflows/.github/workflows/release.yml@release-v1
-    with:
-      npm: true
-    secrets:
-      github-token: ${{ secrets.BOT_TOKEN }}
-      npm-token: ${{ secrets.NPM_BOT_TOKEN }}
+name: Release
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  release:
+    # Documentation: https://github.com/zakodium/workflows#release
+    uses: zakodium/workflows/.github/workflows/release.yml@release-v1
+    with:
+      npm: true
+    secrets:
+      github-token: ${{ secrets.BOT_TOKEN }}
+      npm-token: ${{ secrets.NPM_BOT_TOKEN }}

.github/workflows/npm-prerelease.yml

@@ -0,0 +1,2 @@
+coverage
+CHANGELOG.md

.github/workflows/release.yml

@@ -0,0 +1,9 @@
+import { defineConfig, globalIgnores } from 'eslint/config';
+import ts from 'eslint-config-cheminfo-typescript/base';
+
+export default defineConfig(globalIgnores(['coverage', 'lib']), ts, {
+  files: ['script/**'],
+  rules: {
+    'no-console': 'off',
+  },
+});

.prettierignore

@@ -2,29 +2,25 @@
   "name": "ml-spectra-fitting",
   "version": "4.2.4",
   "description": "Fit spectra using gaussian or lorentzian",
-  "main": "./lib/index.js",
-  "module": "./lib-esm/index.js",
-  "types": "./lib/index.d.ts",
+  "type": "module",
+  "exports": "./lib/index.js",
   "files": [
     "lib",
-    "src",
-    "lib-esm"
+    "src"
   ],
   "scripts": {
-    "build": "npm run tsc && cheminfo-build --entry lib-esm/index.js --root SpectraFitting",
+    "build": "npm run tsc && cheminfo-build --entry lib/index.js --root SpectraFitting",
     "check-types": "tsc --noEmit",
-    "clean": "rimraf lib lib-esm",
-    "eslint": "eslint src",
-    "eslint-fix": "npm run eslint -- --fix",
+    "clean": "rimraf lib",
+    "eslint": "eslint .",
+    "eslint-fix": "eslint . --fix",
     "prepack": "npm run tsc",
-    "test": "npm run test-only && npm run eslint && npm run check-types && npm run prettier",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
-    "test-only": "jest --coverage",
-    "tsc": "npm run clean && npm run tsc-cjs && npm run tsc-esm",
-    "tsc-cjs": "tsc --project tsconfig.cjs.json",
-    "tsc-esm": "tsc --project tsconfig.esm.json",
-    "debug": "npm run prepublishOnly && node src/debug.js"
+    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
+    "prettier": "prettier --check .",
+    "prettier-write": "prettier --write .",
+    "test-only": "vitest --run --coverage",
+    "tsc": "npm run clean && npm run tsc-build",
+    "tsc-build": "tsc --project tsconfig.build.json"
   },
   "repository": {
     "type": "git",
@@ -46,23 +42,24 @@
   },
   "homepage": "https://github.com/mljs/spectra-fitting",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.23.3",
-    "@babel/preset-typescript": "^7.23.3",
-    "@types/jest": "^29.5.12",
+    "@types/node": "^24.0.1",
+    "@vitest/coverage-v8": "^3.2.3",
+    "@zakodium/tsconfig": "^1.0.1",
     "cheminfo-build": "^1.2.0",
-    "eslint": "^8.57.0",
-    "eslint-config-cheminfo-typescript": "^12.2.0",
-    "jest": "^29.7.0",
+    "eslint": "^9.28.0",
+    "eslint-config-cheminfo-typescript": "^18.0.1",
     "jest-matcher-deep-close-to": "^3.0.2",
     "prettier": "^3.2.5",
+    "rimraf": "^6.0.1",
     "spectrum-generator": "^8.0.11",
-    "typescript": "^5.4.2"
+    "typescript": "^5.8.3",
+    "vitest": "^3.2.3"
   },
   "dependencies": {
     "cheminfo-types": "^1.7.2",
     "ml-array-max": "^1.2.4",
     "ml-direct": "^1.0.0",
-    "ml-levenberg-marquardt": "^4.1.3",
+    "ml-levenberg-marquardt": "^5.0.0",
     "ml-peak-shape-generator": "^4.1.4",
     "ml-spectra-processing": "^14.2.0"
   }

babel.config.js

@@ -1,10 +1,8 @@
 import type { DataXY } from 'cheminfo-types';
-import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { generateSpectrum } from 'spectrum-generator';
+import { describe, expect, it } from 'vitest';
 
-import { optimize } from '../index';
-
-expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
+import { optimize } from '../index.ts';
 
 describe('Optimize sum of Gaussians', () => {
   const peaks = [
@@ -59,7 +57,7 @@ describe('Optimize sum of Gaussians', () => {
     for (const key in peak) {
       //@ts-expect-error to be improved
       const value = peak[key];
-      // eslint-disable-next-line @typescript-eslint/no-loop-func
+
       it(`peak at ${peak.x} key: ${key}`, () => {
         //@ts-expect-error to be improved
         expect(result.peaks[i][key]).toMatchCloseTo(value, 2);

eslint.config.mjs

@@ -1,10 +1,8 @@
 import type { DataXY } from 'cheminfo-types';
-import { toBeDeepCloseTo, toMatchCloseTo } from 'jest-matcher-deep-close-to';
 import { generateSpectrum } from 'spectrum-generator';
+import { describe, expect, it } from 'vitest';
 
-import { optimize } from '../index';
-
-expect.extend({ toBeDeepCloseTo, toMatchCloseTo });
+import { optimize } from '../index.ts';
 
 describe('Sum of a mix of distributions', () => {
   it('2 peaks', () => {
@@ -94,7 +92,8 @@ describe('Sum of a mix of distributions', () => {
       expect(result.peaks[i]).toMatchCloseTo(peaks[i], 3);
     }
   });
-  it('20 peaks with overlap', () => {
+  // it seems CI needs extra time for this test
+  it('20 peaks with overlap', { timeout: 10000 }, () => {
     const nbPeaks = 5;
     const peaks = [];
     for (let i = 0; i < nbPeaks; i++) {
@@ -119,7 +118,7 @@ describe('Sum of a mix of distributions', () => {
       optimization: { options: { maxIterations: 10 } },
     });
     // we have a little bit more error on mu
-    //@ts-expect-error we ignoere this ts error
+    //@ts-expect-error we ignore this ts error
     peaks.forEach((peak) => peak.shape.mu && delete peak.shape.mu);
     for (let i = 0; i < result.peaks.length; i++) {
       expect(result.peaks[i]).toMatchCloseTo(peaks[i], 3);