refactor!: migration to typescript

.eslintrc.yml

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

.github/workflows/nodejs.yml → .github/workflows/nodejs-ts.yml

@@ -3,12 +3,12 @@ name: Node.js CI
 on:
   push:
     branches:
-      - master
+      - main
   pull_request:
 
 jobs:
   nodejs:
     # Documentation: https://github.com/zakodium/workflows#nodejs-ci
     uses: zakodium/workflows/.github/workflows/nodejs.yml@nodejs-v1
     with:
-      node-version-matrix: '[14, 16]'
+      lint-check-types: true

.github/workflows/release.yml

@@ -3,7 +3,7 @@ name: Release
 on:
   push:
     branches:
-      - master
+      - main
 
 jobs:
   release:
@@ -14,4 +14,3 @@ jobs:
     secrets:
       github-token: ${{ secrets.BOT_TOKEN }}
       npm-token: ${{ secrets.NPM_BOT_TOKEN }}
-

.github/workflows/typedoc.yml

@@ -0,0 +1,32 @@
+name: Deploy TypeDoc on GitHub pages
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+env:
+  NODE_VERSION: 18.x
+  ENTRY_FILE: 'src/index.ts'
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-node@v3
+        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@v4
+        with:
+          token: ${{ secrets.BOT_TOKEN }}
+          branch: gh-pages
+          folder: docs
+          clean: true

.gitignore

@@ -37,3 +37,5 @@ jspm_packages
 .node_repl_history
 
 lib
+
+lib-esm

README.md

@@ -64,5 +64,5 @@ For intercepting at zero using an array, skip the zero in the array (the option
 [download-url]: https://npmjs.org/package/ml-regression-polynomial
 [codecov-image]: https://img.shields.io/codecov/c/github/mljs/regression-polynomial.svg
 [codecov-url]: https://codecov.io/gh/mljs/regression-polynomial
-[ci-image]: https://github.com/mljs/regression-polynomial/workflows/Node.js%20CI/badge.svg?branch=master
+[ci-image]: https://github.com/mljs/regression-polynomial/workflows/Node.js%20CI/badge.svg?branch=main
 [ci-url]: https://github.com/mljs/regression-polynomial/actions?query=workflow%3A%22Node.js+CI%22

package.json

@@ -2,21 +2,26 @@
   "name": "ml-regression-polynomial",
   "version": "2.2.0",
   "description": "Polynomial Regression",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "main": "./lib/index.js",
+  "module": "./lib-esm/index.js",
   "files": [
+    "src",
     "lib",
-    "src"
+    "lib-esm"
   ],
   "scripts": {
-    "compile": "rollup -c",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf lib lib-esm",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepack": "npm run compile",
+    "prepack": "npm run tsc",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-only && npm run eslint && npm run prettier",
-    "test-only": "jest --coverage"
+    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
+    "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"
   },
   "repository": {
     "type": "git",
@@ -30,16 +35,18 @@
   },
   "homepage": "https://github.com/mljs/regression-polynomial#readme",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.23.0",
+    "@vitest/coverage-v8": "^0.34.5",
     "eslint": "^8.50.0",
-    "eslint-config-cheminfo": "^9.0.2",
-    "jest": "^29.7.0",
+    "eslint-config-cheminfo-typescript": "^12.0.4",
     "prettier": "^3.0.3",
-    "rollup": "^3.29.3"
+    "rimraf": "^5.0.5",
+    "typescript": "^5.2.2",
+    "vitest": "^0.34.5"
   },
   "dependencies": {
-    "@jest/globals": "^29.7.0",
+    "cheminfo-types": "^1.7.2",
     "ml-matrix": "^6.10.5",
     "ml-regression-base": "^3.0.0"
-  }
-}
+  },
+  "types": "./lib/index.d.ts"
+}

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

@@ -1,10 +1,14 @@
-import { expect, describe, it } from '@jest/globals';
+import { NumberArray } from 'cheminfo-types';
+import { expect, it, describe } from 'vitest';
 
 import { PolynomialRegression } from '..';
 
-function assertCoefficientsAndPowers(result, expectedCs, expectedPowers) {
-  let i = 0;
-  for (i; i < expectedCs.length; ++i) {
+function assertCoefficientsAndPowers(
+  result: PolynomialRegression,
+  expectedCs: NumberArray,
+  expectedPowers: NumberArray,
+) {
+  for (let i = 0; i < expectedCs.length; ++i) {
     expect(result.coefficients[i]).toBeCloseTo(expectedCs[i], 10e-6);
     expect(result.powers).toStrictEqual(expectedPowers);
   }
@@ -16,9 +20,10 @@ describe('Polynomial regression', () => {
     const x = [-3, 0, 2, 4];
     const y = [3, 1, 1, 3];
     const result = new PolynomialRegression(x, y, 2);
-    const expected = [0.850519, -0.192495, 0.178462];
+    const expectedCoefficients = [0.850519, -0.192495, 0.178462];
+    const expectedPowers = [0, 1, 2];
 
-    assertCoefficientsAndPowers(result, expected, [0, 1, 2]);
+    assertCoefficientsAndPowers(result, expectedCoefficients, expectedPowers);
 
     const score = result.score(x, y);
     expect(score.r2).toBeGreaterThan(0.8);
@@ -35,9 +40,10 @@ describe('Polynomial regression', () => {
     const y = new Float64Array([3, 1, 1, 3]);
     const result = new PolynomialRegression(x, y, 2);
 
-    const expected = [0.850519, -0.192495, 0.178462];
+    const expectedCoefficients = [0.850519, -0.192495, 0.178462];
+    const expectedPowers = [0, 1, 2];
 
-    assertCoefficientsAndPowers(result, expected, [0, 1, 2]);
+    assertCoefficientsAndPowers(result, expectedCoefficients, expectedPowers);
 
     const score = result.score(x, y);
     expect(score.r2).toBeGreaterThan(0.8);
@@ -98,11 +104,16 @@ describe('Polynomial regression', () => {
     const solution = [0.018041553971009705, 1.0095279075485593];
     assertCoefficientsAndPowers(result, solution, [1, 2]);
   });
-  it('Fit a parabola inverting the degree array terms', () => {
+
+  it('We should get the same result using numeric degree', () => {
     const x = new Float64Array([-4, 4, 2, 3, 1, 8, 5, 7]);
+    // the .5 is to prove that we can force the origin on 0.
+    // remove .5 and it tends to y=x^2 as expected.
     const y = new Float64Array([16.5, 16.5, 4.5, 9.5, 1.5, 64.5, 25.5, 49.5]);
-    const result = new PolynomialRegression(x, y, [2, 1]);
-    const solution = [1.0095279075485593, 0.018041553971009705];
-    assertCoefficientsAndPowers(result, solution, [2, 1]);
+    const result = new PolynomialRegression(x, y, 2, {
+      interceptAtZero: true,
+    });
+    const solution = [0.018041553971009705, 1.0095279075485593];
+    assertCoefficientsAndPowers(result, solution, [1, 2]);
   });
 });

src/index.js → src/index.ts

@@ -1,15 +1,42 @@
+import { type NumberArray } from 'cheminfo-types';
 import { Matrix, MatrixTransposeView, solve } from 'ml-matrix';
 import BaseRegression, {
   checkArrayLength,
   maybeToPrecision,
 } from 'ml-regression-base';
 
+interface PolynomialRegressionOptions {
+  interceptAtZero?: boolean;
+}
 export class PolynomialRegression extends BaseRegression {
-  constructor(x, y, degree, options = {}) {
+  degree: number;
+  powers: number[];
+  coefficients: number[];
+  /**
+   * @param x - independent or explanatory variable
+   * @param y - dependent or response variable
+   * @param degree - degree of the polynomial regression, or array of powers to be used. When degree is an array, intercept at zero is forced to false/ignored.
+   * @example `new PolynomialRegression(x, y, 2)`, in this case, you can pass the option `interceptAtZero`, if you need it.
+   * @example `new PolynomialRegression(x, y, [1, 3, 5])`
+   * Each of the degrees corresponds to a column, so if you have them switched, just do:
+   * @example `new PolynomialRegression(x, y, [3, 1, 5])`
+   *
+   * @param options.interceptAtZero - force the polynomial regression so that f(0) = 0
+   */
+  constructor(
+    x: NumberArray,
+    y: NumberArray,
+    degree: number | NumberArray,
+    options: PolynomialRegressionOptions = {},
+  ) {
     super();
+    // @ts-expect-error internal use only
     if (x === true) {
+      // @ts-expect-error internal use only
       this.degree = y.degree;
+      // @ts-expect-error internal use only
       this.powers = y.powers;
+      // @ts-expect-error internal use only
       this.coefficients = y.coefficients;
     } else {
       checkArrayLength(x, y);
@@ -20,7 +47,7 @@ export class PolynomialRegression extends BaseRegression {
     }
   }
 
-  _predict(x) {
+  _predict(x: number) {
     let y = 0;
     for (let k = 0; k < this.powers.length; k++) {
       y += this.coefficients[k] * Math.pow(x, this.powers[k]);
@@ -37,15 +64,15 @@ export class PolynomialRegression extends BaseRegression {
     };
   }
 
-  toString(precision) {
+  toString(precision: number) {
     return this._toFormula(precision, false);
   }
 
-  toLaTeX(precision) {
+  toLaTeX(precision: number) {
     return this._toFormula(precision, true);
   }
 
-  _toFormula(precision, isLaTeX) {
+  _toFormula(precision: number, isLaTeX: boolean) {
     let sup = '^';
     let closeSup = '';
     let times = ' * ';
@@ -78,37 +105,53 @@ export class PolynomialRegression extends BaseRegression {
       }
       fn = str + fn;
     }
-    if (fn.charAt(0) === '+') {
+    if (fn.startsWith('+')) {
       fn = fn.slice(1);
     }
 
     return `f(x) = ${fn}`;
   }
 
-  static load(json) {
+  static load(json: ReturnType<PolynomialRegression['toJSON']>) {
     if (json.name !== 'polynomialRegression') {
       throw new TypeError('not a polynomial regression model');
     }
+    // @ts-expect-error internal use only
     return new PolynomialRegression(true, json);
   }
 }
 
-function regress(x, y, degree, options) {
+/**
+ * Perform a polynomial regression on the given data set.
+ * This is an internal function.
+ * @param x - independent or explanatory variable
+ * @param y - dependent or response variable
+ * @param degree - degree of the polynomial regression
+ * @param options.interceptAtZero - force the polynomial regression so that $f(0) = 0$
+ */
+function regress(
+  x: NumberArray,
+  y: NumberArray,
+  degree: number | NumberArray,
+  options: PolynomialRegressionOptions = {},
+) {
   const n = x.length;
   let { interceptAtZero = false } = options;
-  let powers;
+  let powers: number[] = [];
   if (Array.isArray(degree)) {
     powers = degree;
     interceptAtZero = false; //must be false in this case
-  } else if (interceptAtZero) {
-    powers = new Array(degree);
-    for (let k = 0; k < degree; k++) {
-      powers[k] = k + 1;
-    }
-  } else {
-    powers = new Array(degree + 1);
-    for (let k = 0; k <= degree; k++) {
-      powers[k] = k;
+  } else if (typeof degree === 'number') {
+    if (interceptAtZero) {
+      powers = new Array(degree);
+      for (let k = 0; k < degree; k++) {
+        powers[k] = k + 1;
+      }
+    } else {
+      powers = new Array(degree + 1);
+      for (let k = 0; k <= degree; k++) {
+        powers[k] = k;
+      }
     }
   }
   const nCoefficients = powers.length; //1 per power, in any case.

tsconfig.cjs.json

@@ -0,0 +1,11 @@
+{
+  "extends": "./tsconfig.json",
+  "compilerOptions": {
+    "module": "commonjs",
+    "declaration": true,
+    "declarationMap": true
+  },
+  "exclude": [
+    "./src/**/__tests__"
+  ]
+}