feat: migrate fully to ESM

.github/workflows/lactame-head.yml

@@ -7,13 +7,13 @@ on:
       - main
 
 env:
-  NODE_VERSION: 20.x
+  NODE_VERSION: 24.x
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Get package name
         run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV
       - uses: actions/setup-node@v4

.github/workflows/lactame.yml

@@ -5,13 +5,13 @@ on:
     types: [published]
 
 env:
-  NODE_VERSION: 20.x
+  NODE_VERSION: 24.x
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
       - name: Get package name
         run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV
       - uses: actions/setup-node@v4

.github/workflows/typedoc.yml

@@ -1,32 +1,15 @@
-name: Deploy TypeDoc on GitHub pages
+name: TypeDoc
 
 on:
   workflow_dispatch:
   release:
     types: [published]
 
-env:
-  NODE_VERSION: 20.x
-  ENTRY_FILE: 'src/index.ts'
-
 jobs:
-  deploy:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: actions/setup-node@v4
-        with:
-          node-version: ${{ env.NODE_VERSION }}
-      - name: Install dependencies
-        run: npm install
-      - name: Build documentation
-        uses: zakodium/typedoc-action@v2
-        with:
-          entry: ${{ env.ENTRY_FILE }}
-      - name: Deploy to GitHub pages
-        uses: JamesIves/github-pages-deploy-action@releases/v4
-        with:
-          token: ${{ secrets.BOT_TOKEN }}
-          branch: gh-pages
-          folder: docs
-          clean: true
+  typedoc:
+    # Documentation: https://github.com/zakodium/workflows#typedoc
+    uses: zakodium/workflows/.github/workflows/typedoc.yml@typedoc-v1
+    with:
+      entry: 'src/index.ts'
+    secrets:
+      github-token: ${{ secrets.BOT_TOKEN }}

.gitignore

@@ -40,10 +40,7 @@ jspm_packages
 .node_repl_history
 
 lib
-lib-esm
-
 dist
 
 .DS_Store
-
-docs
+.eslintcache

.prettierignore

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

README.md

@@ -1,19 +1,19 @@
 # ml-spectra-processing
 
-[![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-spectra-processing.svg)](https://www.npmjs.com/package/ml-spectra-processing)
+[![npm download](https://img.shields.io/npm/dm/ml-spectra-processing.svg)](https://www.npmjs.com/package/ml-spectra-processing)
+[![test coverage](https://img.shields.io/codecov/c/github/mljs/spectra-processing.svg)](https://codecov.io/gh/mljs/spectra-processing)
+[![license](https://img.shields.io/npm/l/ml-spectra-processing.svg)](https://github.com/mljs/spectra-processing/blob/main/LICENSE)
 [![DOI](https://www.zenodo.org/badge/196417515.svg)](https://www.zenodo.org/badge/latestdoi/196417515)
 
 Various functions to process spectra. Those are `pure` functions.
 
 They are sorted in various categories:
 
-- matrix: functions on ml-matrix instances (or array or array)
+- matrix: functions on ml-matrix instances (or array of arrays)
 - x: functions that apply on a 1D array
 - xy: functions that apply on an object `{x: [], y:[]}`
-- xy2: functions that apply on an array of array of 2 numbers `[[x,y], [x,y]]`
+- xy2: functions that apply on an array of arrays of 2 numbers `[[x,y], [x,y]]`
 - xyArray: functions that apply on an array of objects `{x: [], y:[]}`
 - xyObject: functions that apply on an array of point `[{x,y}]`
 - xreim: functions that apply on an object `{x: [], re:[], im:[]}`
@@ -25,7 +25,9 @@ The name of the functions start with the first argument on which they apply.
 
 ## Installation
 
-`$ npm i ml-spectra-processing`
+```console
+npm install ml-spectra-processing
+```
 
 ## Usage
 
@@ -42,12 +44,3 @@ console.log(result);
 ## License
 
 [MIT](./LICENSE)
-
-[npm-image]: https://img.shields.io/npm/v/ml-spectra-processing.svg
-[npm-url]: https://www.npmjs.com/package/ml-spectra-processing
-[ci-image]: https://github.com/mljs/spectra-processing/actions/workflows/nodejs.yml/badge.svg
-[ci-url]: https://github.com/mljs/spectra-processing/actions/workflows/nodejs.yml
-[codecov-image]: https://img.shields.io/codecov/c/github/mljs/spectra-processing.svg
-[codecov-url]: https://codecov.io/gh/mljs/spectra-processing
-[download-image]: https://img.shields.io/npm/dm/ml-spectra-processing.svg
-[download-url]: https://www.npmjs.com/package/ml-spectra-processing

eslint.config.js

@@ -0,0 +1,4 @@
+import { defineConfig, globalIgnores } from 'eslint/config';
+import cheminfo from 'eslint-config-cheminfo-typescript';
+
+export default defineConfig(globalIgnores(['coverage', 'lib']), cheminfo);

package.json

@@ -1,109 +1,71 @@
 {
   "name": "ml-spectra-processing",
   "version": "14.16.1",
+  "license": "MIT",
   "description": "Various method to process spectra",
-  "main": "./lib/index.js",
-  "module": "./lib-esm/index.js",
-  "types": "./lib/index.d.ts",
+  "keywords": [],
+  "author": "Luc Patiny",
+  "type": "module",
   "exports": {
-    ".": {
-      "node": "./lib/index.js",
-      "default": "./lib-esm/index.js"
-    },
-    "./matrix": {
-      "node": "./lib/matrix/index.js",
-      "default": "./lib-esm/matrix/index.js"
-    },
-    "./reim": {
-      "node": "./lib/reim/index.js",
-      "default": "./lib-esm/reim/index.js"
-    },
-    "./utils": {
-      "node": "./lib/utils/index.js",
-      "default": "./lib-esm/utils/index.js"
-    },
-    "./x": {
-      "node": "./lib/x/index.js",
-      "default": "./lib-esm/x/index.js"
-    },
-    "./xreim": {
-      "node": "./lib/xreim/index.js",
-      "default": "./lib-esm/xreim/index.js"
-    },
-    "./xy": {
-      "node": "./lib/xy/index.js",
-      "default": "./lib-esm/xy/index.js"
-    },
-    "./xy2": {
-      "node": "./lib/xy2/index.js",
-      "default": "./lib-esm/xy2/index.js"
-    },
-    "./xyArray": {
-      "node": "./lib/xyArray/index.js",
-      "default": "./lib-esm/xyArray/index.js"
-    },
-    "./xyObject": {
-      "node": "./lib/xyObject/index.js",
-      "default": "./lib-esm/xyObject/index.js"
-    },
-    "./zones": {
-      "node": "./lib/zones/index.js",
-      "default": "./lib-esm/zones/index.js"
-    }
+    ".": "./lib/index.js",
+    "./matrix": "./lib/matrix/index.js",
+    "./reim": "./lib/reim/index.js",
+    "./utils": "./lib/utils/index.js",
+    "./x": "./lib/x/index.js",
+    "./xreim": "./lib/xreim/index.js",
+    "./xy": "./lib/xy/index.js",
+    "./xy2": "./lib/xy2/index.js",
+    "./xyArray": "./lib/xyArray/index.js",
+    "./xyObject": "./lib/xyObject/index.js",
+    "./zones": "./lib/zones/index.js"
   },
   "files": [
-    "src",
     "lib",
-    "lib-esm"
+    "src"
   ],
   "scripts": {
-    "build": "npm run tsc-esm && cheminfo-build --entry lib-esm/index.js --root SpectraProcessing",
+    "build": "npm run tsc && cheminfo-build --entry lib/index.js --root SpectraProcessing",
     "check-types": "tsc --noEmit",
-    "clean": "rimraf lib lib-esm",
-    "eslint": "eslint src",
-    "eslint-fix": "npm run eslint -- --fix",
-    "jscpd": "jscpd -l 10 -i \"**/__tests__/**\" -t 1 src",
+    "clean": "rimraf coverage dist lib",
+    "eslint": "eslint . --cache",
+    "eslint-fix": "eslint . --cache --fix",
     "prepack": "npm run tsc",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
-    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
+    "prettier": "prettier --check .",
+    "prettier-write": "prettier --write .",
+    "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier",
     "test-only": "vitest run --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"
+    "tsc": "npm run clean && npm run tsc-build",
+    "tsc-build": "tsc --project tsconfig.build.json"
   },
-  "repository": {
-    "type": "git",
-    "url": "git+https://github.com/mljs/spectra-processing.git"
-  },
-  "keywords": [],
-  "author": "Luc Patiny",
-  "license": "MIT",
-  "bugs": {
-    "url": "https://github.com/mljs/spectra-processing/issues"
+  "dependencies": {
+    "binary-search": "^1.3.6",
+    "cheminfo-types": "^1.8.1",
+    "fft.js": "^4.0.4",
+    "is-any-array": "^2.0.1",
+    "ml-matrix": "^6.12.1",
+    "ml-xsadd": "^3.0.1"
   },
-  "homepage": "https://github.com/mljs/spectra-processing#readme",
   "devDependencies": {
-    "@types/node": "^24.2.0",
+    "@types/node": "^24.3.0",
     "@vitest/coverage-v8": "^3.2.4",
+    "@zakodium/tsconfig": "^1.0.2",
     "cheminfo-build": "^1.2.1",
-    "eslint": "^9.32.0",
+    "eslint": "^9.33.0",
     "eslint-config-cheminfo-typescript": "^19.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "jscpd": "^4.0.5",
-    "ml-spectra-fitting": "^4.2.4",
+    "ml-spectra-fitting": "^5.0.1",
     "prettier": "^3.6.2",
     "rimraf": "^6.0.1",
     "spectrum-generator": "^8.1.0",
     "typescript": "^5.9.2",
     "vitest": "^3.2.4"
   },
-  "dependencies": {
-    "binary-search": "^1.3.6",
-    "cheminfo-types": "^1.8.1",
-    "fft.js": "^4.0.4",
-    "is-any-array": "^2.0.1",
-    "ml-matrix": "^6.12.1",
-    "ml-xsadd": "^3.0.1"
-  }
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/mljs/spectra-processing.git"
+  },
+  "bugs": {
+    "url": "https://github.com/mljs/spectra-processing/issues"
+  },
+  "homepage": "https://github.com/mljs/spectra-processing#readme"
 }

src/.npmignore

@@ -1,2 +1,3 @@
 __tests__
+*.test.*
 .npmignore

src/__tests__/index.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
 
-import * as SpectraProcessing from '../index';
+import * as SpectraProcessing from '../index.ts';
 
 test('test existence of exported functions', () => {
   const exports = Object.keys(SpectraProcessing);

src/index.ts

@@ -1,19 +1,19 @@
-export * from './reim/index';
+export * from './reim/index.ts';
 
-export * from './x/index';
+export * from './x/index.ts';
 
-export * from './xy/index';
+export * from './xy/index.ts';
 
-export * from './xy2/index';
+export * from './xy2/index.ts';
 
-export * from './xreim/index';
+export * from './xreim/index.ts';
 
-export * from './xyArray/index';
-export * from './xyObject/index';
+export * from './xyArray/index.ts';
+export * from './xyObject/index.ts';
 
-export * from './zones/index';
+export * from './zones/index.ts';
 
-export * from './matrix/index';
-export * from './utils/index';
+export * from './matrix/index.ts';
+export * from './utils/index.ts';
 
-export * from './types/index';
+export * from './types/index.ts';

src/matrix/__tests__/matrixAbsoluteMedian.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
 
-import { matrixAbsoluteMedian } from '../matrixAbsoluteMedian';
+import { matrixAbsoluteMedian } from '../matrixAbsoluteMedian.ts';
 
 test('matrixAbsoluteMedian', () => {
   const matrix = [

src/matrix/__tests__/matrixApplyNumericalDecoding.test.ts

@@ -1,9 +1,9 @@
 import { expect, test } from 'vitest';
 
-import { matrixApplyNumericalEncoding } from '../matrixApplyNumericalEncoding';
-import { matrixNumericalEncoding } from '../matrixNumericalEncoding';
+import { matrixApplyNumericalEncoding } from '../matrixApplyNumericalEncoding.ts';
+import { matrixNumericalEncoding } from '../matrixNumericalEncoding.ts';
 
-import { datasetForEncoding } from './fixtures/encoding';
+import { datasetForEncoding } from './fixtures/encoding.ts';
 
 const datasetToEncode = [
   [78, 'o', 'ab', 147],

src/matrix/__tests__/matrixAutoCorrelation.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
 
-import { matrixAutoCorrelation } from '../matrixAutoCorrelation';
+import { matrixAutoCorrelation } from '../matrixAutoCorrelation.ts';
 
 test('simple', () => {
   const matrix = [