feat!: setup typescript (#66)

.eslintrc.yml

@@ -1,3 +1,3 @@
-extends: cheminfo
+extends: cheminfo-typescript
 parserOptions:
   sourceType: module

.github/workflows/nodejs.yml

@@ -5,36 +5,9 @@ on:
     branches: master
   pull_request:
 
-env:
-  NODE_VERSION: 14.x
-
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
-        with:
-          node-version: ${{ env.NODE_VERSION }}
-      - name: Install dependencies
-        run: npm install
-      - name: Run ESLint
-        run: npm run eslint
-  test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        node-version: [12.x, 14.x, 16.x]
-      fail-fast: false
-    steps:
-      - uses: actions/checkout@v2
-      - name: Use Node.js ${{ matrix.node-version }}
-        uses: actions/setup-node@v2
-        with:
-          node-version: ${{ matrix.node-version }}
-      - name: Install dependencies
-        run: npm install
-      - name: Run tests
-        run: npm run test-coverage
-      - name: Send coverage report to Codecov
-        uses: codecov/codecov-action@v1
+  nodejs:
+    uses: zakodium/workflows/.github/workflows/nodejs.yml@nodejs-v1
+    with:
+      node-version-matrix: '[14, 16]'
+      lint-check-types: true

.gitignore

@@ -6,3 +6,4 @@ dist
 lib
 coverage
 .eslintcache
+lib-esm

examples/example.js → examples/example.ts

@@ -10,7 +10,7 @@ import { join } from 'path';
 
 import { generateSpectrum } from 'spectrum-generator';
 
-import { gsd, optimizePeaks } from '../src';
+import { DataType, gsd, optimizePeaks } from '../src';
 
 const peaks = [
   { x: -0.1, y: 0.2, width: 0.3 },
@@ -20,14 +20,18 @@ const peaks = [
 const from = -1;
 const to = 1;
 
-const original = generateSpectrum(peaks, { from, to, nbPoints: 101 });
+const original = generateSpectrum(peaks, {
+  from,
+  to,
+  nbPoints: 101,
+});
 
 let peakList = gsd(original, {
   minMaxRatio: 0,
   realTopDetection: false,
   smoothY: false,
   heightFactor: 1,
-  shape: { kind: 'gaussian' },
+  shape: { kind: 'gaussian', width: 0 },
 });
 
 let optimizedPeaks = optimizePeaks(original, peakList);
@@ -63,8 +67,8 @@ let reconstructed = generateSpectrum(optimizedPeaks, {
   to,
   nbPoints: 5001,
 });
-reconstructed.x = Array.from(reconstructed.x)
-reconstructed.y = Array.from(reconstructed.y)
+reconstructed.x = Array.from(reconstructed.x);
+reconstructed.y = Array.from(reconstructed.y);
 
 original.x = Array.from(original.x);
 original.y = Array.from(original.y);

jest.config.js

@@ -0,0 +1,4 @@
+module.exports = {
+  preset: 'ts-jest',
+  testEnvironment: 'node',
+};

package.json

@@ -2,27 +2,33 @@
   "name": "ml-gsd",
   "version": "7.0.1",
   "description": "Global Spectra Deconvolution",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "main": "./lib/index.js",
+  "module": "./lib-esm/index.js",
+  "types": "./lib/index.d.ts",
   "files": [
     "lib",
-    "src"
+    "src",
+    "lib-esm"
   ],
   "env": {
     "jest": true
   },
   "scripts": {
     "build": "rollup -c && cheminfo-build --entry src/index.js --root GSD",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf lib lib-esm",
     "example": "nodemon -w src -w examples/example.js -r esm examples/example.js",
     "eslint": "eslint src --cache",
     "eslint-fix": "npm run eslint -- --fix",
-    "compile": "rollup -c",
-    "prepack": "npm run compile",
+    "prepack": "npm run compile && npm run tsc",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-coverage && npm run eslint",
+    "test": "npm run test-coverage && npm run eslint && npm run check-types",
     "test-only": "jest",
-    "test-coverage": "jest --coverage"
+    "test-coverage": "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"
   },
   "repository": {
     "type": "git",
@@ -45,9 +51,6 @@
     "url": "https://github.com/mljs/global-spectral-deconvolution/issues"
   },
   "homepage": "https://github.com/mljs/global-spectral-deconvolution",
-  "jest": {
-    "testEnvironment": "node"
-  },
   "prettier": {
     "arrowParens": "always",
     "semi": true,
@@ -56,25 +59,28 @@
     "trailingComma": "all"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.15.4",
     "@types/jest": "^27.0.2",
     "chemcalc": "^3.4.1",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^7.32.0",
-    "eslint-config-cheminfo": "^5.5.0",
+    "eslint": "^8.1.0",
+    "eslint-config-cheminfo-typescript": "^10.1.1",
+    "eslint-plugin-import": "^2.25.2",
+    "eslint-plugin-jest": "^25.2.2",
     "esm": "^3.2.25",
-    "jest": "^27.2.4",
-    "jest-matcher-deep-close-to": "^3.0.0",
-    "mf-global": "^1.4.6",
+    "jest": "^27.3.1",
+    "jest-matcher-deep-close-to": "^3.0.2",
+    "mf-global": "^1.4.7",
     "ml-stat": "^1.3.3",
-    "nodemon": "^2.0.13",
+    "nodemon": "^2.0.14",
     "prettier": "^2.4.1",
-    "rollup": "^2.58.0",
-    "spectrum-generator": "^5.4.0",
+    "rimraf": "^3.0.2",
+    "spectrum-generator": "^5.4.1",
+    "ts-jest": "^27.0.7",
+    "typescript": "^4.4.4",
     "xy-parser": "^3.2.0"
   },
   "dependencies": {
-    "cheminfo-types": "^0.5.0",
+    "cheminfo-types": "^0.6.0",
     "ml-peak-shape-generator": "^2.0.2",
     "ml-savitzky-golay-generalized": "2.0.3",
     "ml-spectra-fitting": "^2.0.0",

src/__tests__/bigLowS2NSpectrum.test.js → src/__tests__/bigLowS2NSpectrum.test.ts

@@ -5,11 +5,11 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
-let { gsd, joinBroadPeaks } = require('..');
+import { gsd, joinBroadPeaks } from '..';
 
 describe('Global spectra deconvolution NMR spectra', () => {
   it('Should give 120 peaks', () => {
-    let spectrum = JSON.parse(
+    let spectrum: number[][] = JSON.parse(
       readFileSync(join(__dirname, '/data/bigLowS2NSpectrum.json'), 'utf8'),
     );
 
@@ -22,7 +22,6 @@ describe('Global spectra deconvolution NMR spectra', () => {
         sgOptions: { windowSize: 13, polynomial: 3 },
       },
     );
-
     pp = joinBroadPeaks(pp, { width: 0.25 });
 
     expect(pp).toHaveLength(91);

src/__tests__/broadNMR.test.js → src/__tests__/broadNMR.test.ts

@@ -1,12 +1,12 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
-let { gsd, joinBroadPeaks } = require('..');
+import { gsd, joinBroadPeaks } from '..';
 
 describe('Global spectra deconvolution NMR spectra', () => {
   // Test case obtained from Pag 443, Chap 8.
   it('Should give 1 broad peak and around 14 other peaks', () => {
-    let spectrum = JSON.parse(
+    let spectrum: number[][] = JSON.parse(
       readFileSync(join(__dirname, '/data/broadNMR.json'), 'utf-8'),
     );
     let result = gsd(
@@ -21,7 +21,10 @@ describe('Global spectra deconvolution NMR spectra', () => {
         },
       },
     );
-    const newResult = joinBroadPeaks(result, { width: 0.25, shape: { kind: 'lorentzian' } });
+    const newResult = joinBroadPeaks(result, {
+      width: 0.25,
+      shape: { kind: 'lorentzian', width: 0 },
+    });
     expect(newResult).toHaveLength(14);
     newResult.forEach((peak) => {
       if (Math.abs(peak.x - 4.31) < 0.01) {

src/__tests__/data/test.json

@@ -1 +1,36 @@
-[[7,9,9.1,9.2,9.3,9.4,9.5,9.6,9.7,9.8,9.9,10,10.1,10.2,10.3,10.4,10.5,10.6,10.7,10.8,10.9,11,11.1,11.2,11.3,11.4,11.5,11.6,11.7,11.8,11.9,12,12.1,12.2,12.3,12.4,12.5,12.6,12.7,12.8,12.9,13,13.1,13.2,13.3,13.4,13.5,13.6,13.7,13.8,13.9,14,14.1,14.2,14.3,14.4,14.5,14.6,14.7,14.8,14.9,15,15.1,15.2,15.3,15.4,15.5,15.6,15.7,15.8,15.9,16,18],[0,1.3670611642005019e-12,7.018086806749659e-12,3.408530039598323e-11,1.566149139777829e-10,6.807955480447043e-10,2.799741264282628e-9,1.0892728768715286e-8,4.0093417978312345e-8,1.3961339042194703e-7,4.5993733696714487e-7,0.0000014334675420984624,0.000004226634174912734,0.000011790142647798723,0.00003111437370683429,0.00007768204955055934,0.00018348387377726662,0.0004100083945771263,0.0008667727242782787,0.001733546091298024,0.0032800711886719187,0.005871498495868112,0.009943347114095245,0.01593068598959557,0.0241465479122752,0.03462542672692695,0.046973848446379925,0.06028934116907687,0.07320700001112898,0.0841007412472281,0.09141030799602905,0.09400723223468063,0.09148237573734981,0.08425429229202339,0.0734587840992098,0.06065939675121234,0.04747989885270652,0.0352766117093386,0.024937897013924,0.016839966447159693,0.010931586752334044,0.0068875528273207405,0.004268351566479456,0.0026429525578170743,0.001658457916881255,0.001062033447037501,0.0006915187612199856,0.00045217216244198535,0.00029227323368097015,0.00018409073424885283,0.00011177068037381833,0.00006493783224280769,0.00003593624229100207,0.00001888916056485795,0.000009414867005196313,0.000004445430848023085,0.0000019873111386235026,8.408686570700081e-7,3.366812086048201e-7,1.2755306072424386e-7,4.5721144094463724e-8,1.5505362353033094e-8,4.974557268319468e-9,1.5100204968309241e-9,4.3363951518037203e-10,1.1781279472885229e-10,3.028124080443153e-11,7.363299670553255e-12,1.6939043561733317e-12,3.6865734785911304e-13,7.590572003661311e-14,1.4785762111538834e-14,0]]
+[
+  [
+    7, 9, 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7, 9.8, 9.9, 10, 10.1, 10.2, 10.3,
+    10.4, 10.5, 10.6, 10.7, 10.8, 10.9, 11, 11.1, 11.2, 11.3, 11.4, 11.5, 11.6,
+    11.7, 11.8, 11.9, 12, 12.1, 12.2, 12.3, 12.4, 12.5, 12.6, 12.7, 12.8, 12.9,
+    13, 13.1, 13.2, 13.3, 13.4, 13.5, 13.6, 13.7, 13.8, 13.9, 14, 14.1, 14.2,
+    14.3, 14.4, 14.5, 14.6, 14.7, 14.8, 14.9, 15, 15.1, 15.2, 15.3, 15.4, 15.5,
+    15.6, 15.7, 15.8, 15.9, 16, 18
+  ],
+  [
+    0, 1.3670611642005019e-12, 7.018086806749659e-12, 3.408530039598323e-11,
+    1.566149139777829e-10, 6.807955480447043e-10, 2.799741264282628e-9,
+    1.0892728768715286e-8, 4.0093417978312345e-8, 1.3961339042194703e-7,
+    4.5993733696714487e-7, 0.0000014334675420984624, 0.000004226634174912734,
+    0.000011790142647798723, 0.00003111437370683429, 0.00007768204955055934,
+    0.00018348387377726662, 0.0004100083945771263, 0.0008667727242782787,
+    0.001733546091298024, 0.0032800711886719187, 0.005871498495868112,
+    0.009943347114095245, 0.01593068598959557, 0.0241465479122752,
+    0.03462542672692695, 0.046973848446379925, 0.06028934116907687,
+    0.07320700001112898, 0.0841007412472281, 0.09141030799602905,
+    0.09400723223468063, 0.09148237573734981, 0.08425429229202339,
+    0.0734587840992098, 0.06065939675121234, 0.04747989885270652,
+    0.0352766117093386, 0.024937897013924, 0.016839966447159693,
+    0.010931586752334044, 0.0068875528273207405, 0.004268351566479456,
+    0.0026429525578170743, 0.001658457916881255, 0.001062033447037501,
+    0.0006915187612199856, 0.00045217216244198535, 0.00029227323368097015,
+    0.00018409073424885283, 0.00011177068037381833, 0.00006493783224280769,
+    0.00003593624229100207, 0.00001888916056485795, 0.000009414867005196313,
+    0.000004445430848023085, 0.0000019873111386235026, 8.408686570700081e-7,
+    3.366812086048201e-7, 1.2755306072424386e-7, 4.5721144094463724e-8,
+    1.5505362353033094e-8, 4.974557268319468e-9, 1.5100204968309241e-9,
+    4.3363951518037203e-10, 1.1781279472885229e-10, 3.028124080443153e-11,
+    7.363299670553255e-12, 1.6939043561733317e-12, 3.6865734785911304e-13,
+    7.590572003661311e-14, 1.4785762111538834e-14, 0
+  ]
+]

src/__tests__/ethylvinylether.test.js → src/__tests__/ethylvinylether.test.ts

@@ -1,11 +1,11 @@
 import { readFileSync } from 'fs';
 
-import { gsd } from '..';
+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 = JSON.parse(
+    let spectrum: number[][] = JSON.parse(
       readFileSync(`${__dirname}/data/ethylvinylether.json`, 'utf-8'),
     );
     let result = gsd(

src/__tests__/general.test.js → src/__tests__/general.test.ts

@@ -1,9 +1,9 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
-import { gsd } from '..';
+import { gsd } from '../gsd';
 
-function lorentzian(x, x0 = 0, gamma = 1) {
+function lorentzian(x: number, x0 = 0, gamma = 1) {
   return (
     (gamma * gamma) / (Math.PI * gamma * (gamma * gamma + (x - x0) * (x - x0)))
   );
@@ -12,7 +12,7 @@ function lorentzian(x, x0 = 0, gamma = 1) {
 describe('Global spectra deconvolution simple simulated spectrum', () => {
   // Test case obtained from Pag 443, Chap 8.
   it('Should provide the right result ...', () => {
-    let spectrum = JSON.parse(
+    let spectrum: number[][] = JSON.parse(
       readFileSync(join(__dirname, '/data//C2.json'), 'utf8'),
     );
     let result = gsd(
@@ -35,8 +35,8 @@ describe('Global spectra deconvolution simple simulated spectrum', () => {
   it('Should give 10 peaks', () => {
     const size = 300;
     const fourth = size / 11;
-    let times = new Array(size);
-    let tic = new Array(size);
+    let times: number[] = new Array(size);
+    let tic: number[] = new Array(size);
 
     for (let i = 0; i < size; ++i) {
       times[i] = i;

src/__tests__/infraRed.test.js → src/__tests__/infraRed.test.ts

@@ -1,11 +1,11 @@
 import { readFileSync } from 'fs';
 
-import { gsd } from '..';
+import { DataType, gsd } from '../gsd';
 
 describe('Global spectra deconvolution Infrared spectra', () => {
   // Test case obtained from Pag 443, Chap 8.
   it('Should get the correct result', () => {
-    let spectrum = JSON.parse(
+    let spectrum: DataType = JSON.parse(
       readFileSync(`${__dirname}/data/infraRed.json`, 'utf-8'),
     );
     gsd(spectrum, {

src/__tests__/massPeakPicking.test.js → src/__tests__/massPeakPicking.test.ts

@@ -1,18 +1,18 @@
-import { gsd, optimizePeaks } from '..';
+import CC from 'chemcalc';
+import Stat from 'ml-stat';
 
-let CC = require('chemcalc');
-let Stat = require('ml-stat');
+import { DataType, gsd, optimizePeaks } from '..';
 
 let spectrum = CC.analyseMF('Cl2.Br2', {
   isotopomers: 'arrayXXYY',
   fwhm: 0.01,
   gaussianWidth: 11,
 });
-let xy = spectrum.arrayXXYY;
-let x = xy[0];
-let y = xy[1];
+let xy: DataType = spectrum.arrayXXYY;
+let x: number[] = xy[0];
+let y: number[] = xy[1];
 let max = Stat.array.max(y);
-let noiseLevel = Stat.array.median(y.filter((a) => a > 0)) * 3;
+let noiseLevel = Stat.array.median(y.filter((a: number) => a > 0)) * 3;
 /*
 69.938 100
 71.935 63.99155
@@ -39,6 +39,7 @@ describe('Check the peak picking of a simulated mass spectrum', () => {
       factorWidth: 4,
       shape: {
         kind: 'gaussian',
+        width: 0,
       },
     });
     expect(result[0].x).toBeCloseTo(69.938, 1);