chore!: update dependencies and do not export default

eslint.config.mjs

@@ -0,0 +1,6 @@
+import cheminfo from 'eslint-config-cheminfo';
+import globals from 'globals';
+
+export default [
+  ...cheminfo,
+]

ml-direct.d.ts

@@ -7,7 +7,7 @@ declare module 'ml-direct' {
     initialState?: any;
   }
 
-  export default function direct(
+  export function direct(
     objectiveFunction: (parameters: number[]) => number,
     lowerBoundaries: number[],
     upperBoundaries: number[],

package.json

@@ -18,7 +18,7 @@
     "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-only": "vitest run --coverage"
   },
   "repository": {
     "type": "git",
@@ -32,18 +32,19 @@
   },
   "homepage": "https://github.com/mljs/direct#readme",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.23.3",
+    "@babel/plugin-transform-modules-commonjs": "^7.25.7",
+    "@vitest/coverage-v8": "^2.1.3",
     "cheminfo-build": "^1.2.0",
-    "eslint": "^8.57.0",
-    "eslint-config-cheminfo": "^9.2.0",
+    "eslint": "^9.13.0",
+    "eslint-config-cheminfo": "^12.0.1",
     "esm": "^3.2.25",
-    "jest": "^29.7.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^3.2.5",
-    "rollup": "^4.12.1"
+    "prettier": "^3.3.3",
+    "rollup": "^4.24.0",
+    "vitest": "^2.1.3"
   },
   "dependencies": {
-    "ml-matrix": "^6.11.0",
-    "ml-spectra-processing": "^14.2.0"
+    "ml-matrix": "^6.12.0",
+    "ml-spectra-processing": "^14.6.0"
   }
-}
+}

src/__tests__/initialState.test.js

@@ -1,6 +1,7 @@
-import direct from '../index';
-// Test functions from https://www.sfu.ca/~ssurjano/optimization.html
+import { describe, expect, it } from 'vitest';
 
+import { direct } from '../index';
+// Test functions from https://www.sfu.ca/~ssurjano/optimization.html
 describe('Initial state option', () => {
   it('The result after two runs of 50 iterations should be equal to one of 100 iterations', () => {
     const lowerBoundaries = [-5, -2];

src/__tests__/optimization.test.js

@@ -1,6 +1,7 @@
-import direct from '../index';
-// Test functions from https://www.sfu.ca/~ssurjano/optimization.html
+import { describe, expect, it } from 'vitest';
 
+import { direct } from '../index';
+// Test functions from https://www.sfu.ca/~ssurjano/optimization.html
 describe('test Direct method', () => {
   it('Evaluating griewank test function in 3D', () => {
     const options = {

src/index.js

@@ -1,6 +1,6 @@
 import { xNorm, xMaxValue, xMinValue } from 'ml-spectra-processing';
 
-import antiLowerConvexHull from './util/antiLowerConvexHull';
+import { antiLowerConvexHull } from './util/antiLowerConvexHull';
 
 /**
  * Performs a global optimization of required parameters
@@ -9,19 +9,19 @@ import antiLowerConvexHull from './util/antiLowerConvexHull';
  * - `optima`: Array of Array of values for all the variables where the function reach its minimum value
  * - `iterations`: Number of iterations performed in the process
  * - `finalState`: Internal state allowing to continue optimization (initialState)
- * @param {function} objectiveFunction Function to evaluate. It should accept an array of variables
- * @param {Array} lowerBoundaries Array containing for each variable the lower boundary
- * @param {Array} upperBoundaries Array containing for each variable the higher boundary
- * @param {Object} [options={}]
+ * @param {Function} objectiveFunction - Function to evaluate. It should accept an array of variables
+ * @param {Array} lowerBoundaries - Array containing for each variable the lower boundary
+ * @param {Array} upperBoundaries - Array containing for each variable the higher boundary
+ * @param {object} [options={}]
  * @param {number} [options.iterations] - Number of iterations.
  * @param {number} [options.epsilon] - Tolerance to choose best current value.
  * @param {number} [options.tolerance] - Minimum tollerance of the function.
  * @param {number} [options.tolerance2] - Minimum tollerance of the function.
- * @param {Object} [options.initialState={}}] - finalState of previous optimization.
- * @return {Object} {finalState, iterations, minFunctionValue}
- * */
+ * @param {object} [options.initialState={}}] - finalState of previous optimization.
+ * @returns {object} {finalState, iterations, minFunctionValue}
+ */
 
-export default function direct(
+export function direct(
   objectiveFunction,
   lowerBoundaries,
   upperBoundaries,
@@ -83,10 +83,7 @@ export default function direct(
     initialState.originalCoordinates.length > 0
   ) {
     bestCurrentValue = xMinValue(functionValues);
-    choiceLimit =
-      epsilon * Math.abs(bestCurrentValue) > 1e-8
-        ? epsilon * Math.abs(bestCurrentValue)
-        : 1e-8;
+    choiceLimit = Math.max(epsilon * Math.abs(bestCurrentValue), 1e-8);
 
     smallerDistance = getMinIndex(
       functionValues,
@@ -115,10 +112,7 @@ export default function direct(
     //----------------------------------------------------------------------
 
     let S1 = [];
-    let idx = differentDistances.findIndex(
-      // eslint-disable-next-line no-loop-func
-      (e) => e === diagonalDistances[smallerDistance],
-    );
+    let idx = differentDistances.indexOf(diagonalDistances[smallerDistance]);
     let counter = 0;
     for (let i = idx; i < differentDistances.length; i++) {
       for (let f = 0; f < functionValues.length; f++) {
@@ -135,7 +129,7 @@ export default function direct(
     if (differentDistances.length - idx > 1) {
       let a1 = diagonalDistances[smallerDistance];
       let b1 = functionValues[smallerDistance];
-      let a2 = differentDistances[differentDistances.length - 1];
+      let a2 = differentDistances.at(-1);
       let b2 = smallerValuesByDistance[differentDistances.length - 1];
       let slope = (b2 - b1) / (a2 - a1);
       let constant = b1 - slope * a1;
@@ -230,10 +224,7 @@ export default function direct(
 
     bestCurrentValue = xMinValue(functionValues);
 
-    choiceLimit =
-      epsilon * Math.abs(bestCurrentValue) > 1e-8
-        ? epsilon * Math.abs(bestCurrentValue)
-        : 1e-8;
+    choiceLimit = Math.max(epsilon * Math.abs(bestCurrentValue), 1e-8);
 
     smallerDistance = getMinIndex(
       functionValues,
@@ -251,11 +242,12 @@ export default function direct(
       let minIndex;
       let minValue = Number.POSITIVE_INFINITY;
       for (let k = 0; k < diagonalDistances.length; k++) {
-        if (diagonalDistances[k] === differentDistances[i]) {
-          if (functionValues[k] < minValue) {
-            minValue = functionValues[k];
-            minIndex = k;
-          }
+        if (
+          diagonalDistances[k] === differentDistances[i] &&
+          functionValues[k] < minValue
+        ) {
+          minValue = functionValues[k];
+          minIndex = k;
         }
       }
       smallerValuesByDistance.push(functionValues[minIndex]);
@@ -330,6 +322,6 @@ function getMinIndex(
       diagonalDistances[i];
   }
   const min = xMinValue(item);
-  let result = item.findIndex((x) => x === min);
+  let result = item.indexOf(min);
   return result;
 }

src/util/__tests__/antiLowerConvexHull.test.js

@@ -1,4 +1,6 @@
-import antiLowerConvexHull from '../antiLowerConvexHull';
+import { describe, expect, it } from 'vitest';
+
+import { antiLowerConvexHull } from '../antiLowerConvexHull';
 
 describe('testing lower convexhull function', () => {
   it('Get anti clockwise lower convex hull', () => {

src/util/antiLowerConvexHull.js

@@ -2,10 +2,10 @@
  * Preparata, F. P., & Shamos, M. I. (2012). Computational geometry: an introduction. Springer Science & Business Media.
  * @param {Array} x - The array with x coordinates of the points.
  * @param {Array} y - The array with y coordinates of the points.
- * @return {Array} The indices of the points of anticlockwise lower convex hull
+ * @returns {Array} The indices of the points of anticlockwise lower convex hull
  * @private
  */
-export default function antiLowerConvexHull(x, y) {
+export function antiLowerConvexHull(x, y) {
   if (x.length !== y.length) {
     throw new RangeError('X and Y vectors has different dimensions');
   }
@@ -44,7 +44,7 @@ export default function antiLowerConvexHull(x, y) {
  * @param {number} currentPoint - The index of the current point to make the move
  * @param {number} nbPoints - The total number of points in the array
  * @param {Array} vector - The array with the points
- * @return {number} the index of the point after the move
+ * @returns {number} the index of the point after the move
  * @private
  */