feat: update dependencies

eslint.config.mjs

@@ -0,0 +1,16 @@
+import cheminfo from 'eslint-config-cheminfo';
+import globals from 'globals';
+
+export default [
+  ...cheminfo,
+  {
+    languageOptions: {
+      globals: {
+        ...globals.node,
+      },
+    },
+    rules: {
+      //      "camelcase": "off",
+    }
+  }
+]

package.json

@@ -4,15 +4,15 @@
   "description": "Machine learning tools",
   "main": "src/index.js",
   "scripts": {
-    "compile": "rollup -c",
     "build": "cheminfo-build --root ML",
+    "compile": "rollup -c",
     "eslint": "eslint src --cache",
     "eslint-fix": "npm run eslint -- --fix",
     "prepack": "npm run compile",
     "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"
   },
   "files": [
     "src",
@@ -71,38 +71,38 @@
     "ml-distance-matrix": "^2.0.1",
     "ml-fcnnls": "^3.0.0",
     "ml-fnn": "^5.0.0",
-    "ml-gsd": "^12.1.3",
+    "ml-gsd": "^12.1.8",
     "ml-hash-table": "^1.0.0",
     "ml-hclust": "^3.1.0",
     "ml-kernel": "^3.0.0",
     "ml-kmeans": "^6.0.0",
     "ml-knn": "^3.0.0",
     "ml-levenberg-marquardt": "^4.1.3",
-    "ml-matrix": "^6.11.0",
+    "ml-matrix": "^6.12.0",
     "ml-naivebayes": "^4.0.0",
     "ml-ngmca": "^1.0.0",
     "ml-pad-array": "^2.0.0",
     "ml-pca": "^4.1.1",
     "ml-performance": "^0.2.0",
     "ml-pls": "^4.3.2",
-    "ml-random": "^1.0.1",
+    "ml-random": "^2.0.0",
     "ml-random-forest": "^2.1.0",
-    "ml-regression": "^5.0.0",
+    "ml-regression": "^6.2.0",
     "ml-savitzky-golay": "^5.0.0",
     "ml-som": "^0.0.6",
     "ml-sparse-matrix": "^2.1.0",
-    "ml-xsadd": "^2.0.0",
+    "ml-xsadd": "^3.0.1",
     "num-sort": "^3.0.0"
   },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.23.3",
-    "@types/jest": "^29.5.12",
+    "@babel/plugin-transform-modules-commonjs": "^7.25.7",
+    "@vitest/coverage-v8": "^2.1.3",
     "cheminfo-build": "^1.2.0",
-    "eslint": "^8.56.0",
-    "eslint-config-cheminfo": "^9.1.1",
+    "eslint": "^9.12.0",
+    "eslint-config-cheminfo": "^12.0.1",
     "esm": "^3.2.25",
-    "jest": "^29.7.0",
-    "prettier": "^3.2.4",
-    "rollup": "^4.9.6"
+    "prettier": "^3.3.3",
+    "rollup": "^4.24.0",
+    "vitest": "^2.1.3"
   }
 }

src/__tests__/index.test.js

@@ -1,8 +1,39 @@
-/* eslint-disable import/namespace */
+import { it, describe, expect } from 'vitest';
+
 import * as ML from '..';
 
 describe('Check all properties are defined', () => {
+  const objectsAndNbKeys = {
+    Distance: 42,
+    Similarity: 11,
+    Array: 11,
+    ArrayXY: 10,
+    BitArray: 12,
+    KMeans: 2,
+    HClust: 2,
+    NaiveBayes: 2,
+    CrossValidation: 6,
+    FCNNLS: 2,
+    MatrixLib: 36,
+    GSD: 7,
+  };
+
   it.each(Object.keys(ML))('Check %s', (key) => {
+    // if a function it should key should start with lowercase
+    // if a class it should key should start with uppercase
     expect(ML[key]).toBeDefined();
+
+    if (objectsAndNbKeys[key]) {
+      expect(typeof ML[key]).toBe('object');
+      expect(Object.keys(ML[key]).length).toBe(objectsAndNbKeys[key]);
+    } else if (key[0] === key[0].toUpperCase()) {
+      // should be a class
+      expect(typeof ML[key]).toBe('function');
+      expect(typeof ML[key].prototype).toBe('object');
+      expect(ML[key].prototype?.constructor).toBe(ML[key]);
+    } else {
+      // should be function
+      expect(typeof ML[key]).toBe('function');
+    }
   });
 });

src/index.js

@@ -2,31 +2,17 @@
 /* eslint-disable import/order */
 /* eslint-disable import/first */
 
-import { DecisionTreeClassifier, DecisionTreeRegression } from 'ml-cart';
-import {
-  RandomForestClassifier,
-  RandomForestRegression,
-} from 'ml-random-forest';
-
 // Try to keep this list in the same structure as the README.
 
 // Unsupervised learning
 export { PCA } from 'ml-pca';
-import * as HClust from 'ml-hclust';
-export { HClust };
-import * as KMeans from 'ml-kmeans';
-export { KMeans };
 
 // Supervised learning
-import * as NaiveBayes from 'ml-naivebayes';
-export { NaiveBayes };
+
 export { default as KNN } from 'ml-knn';
 export { PLS, KOPLS, OPLS, oplsNipals } from 'ml-pls';
-import * as CrossValidation from 'ml-cross-validation';
-export { CrossValidation };
+
 export { ConfusionMatrix } from 'ml-confusion-matrix';
-export { DecisionTreeClassifier };
-export { RandomForestClassifier };
 
 // Artificial neural networks
 export { default as FNN } from 'ml-fnn';
@@ -42,13 +28,9 @@ export {
   TheilSenRegression,
   RobustPolynomialRegression,
 } from 'ml-regression';
-export { DecisionTreeRegression };
-export { RandomForestRegression };
 
 // Optimization
 export { levenbergMarquardt } from 'ml-levenberg-marquardt';
-import * as FCNNLS from 'ml-fcnnls';
-export { FCNNLS };
 
 // Math
 import * as MatrixLib from 'ml-matrix';
@@ -61,7 +43,6 @@ const {
   QrDecomposition,
 } = MatrixLib;
 export {
-  MatrixLib,
   Matrix,
   SVD,
   EVD,
@@ -72,10 +53,9 @@ export {
 
 export { SparseMatrix } from 'ml-sparse-matrix';
 export { default as Kernel } from 'ml-kernel';
-import { distance, similarity } from 'ml-distance';
-export { distance as Distance, similarity as Similarity };
+export { distance as Distance, similarity as Similarity } from 'ml-distance';
 export { default as distanceMatrix } from 'ml-distance-matrix';
-export { default as XSadd } from 'ml-xsadd';
+export { XSadd } from 'ml-xsadd';
 export { nGMCA } from 'ml-ngmca';
 
 // Statistics
@@ -89,9 +69,7 @@ export { default as BitArray } from 'ml-bit-array';
 export { default as HashTable } from 'ml-hash-table';
 export { default as padArray } from 'ml-pad-array';
 export { default as binarySearch } from 'binary-search';
-export { default as Random } from 'ml-random';
-import * as GSD from 'ml-gsd';
-export { GSD };
+export { Random } from 'ml-random';
 
 import min from 'ml-array-min';
 import max from 'ml-array-max';
@@ -140,3 +118,15 @@ export const ArrayXY = {
   equallySpaced,
   filterX,
 };
+export { DecisionTreeClassifier, DecisionTreeRegression } from 'ml-cart';
+export {
+  RandomForestClassifier,
+  RandomForestRegression,
+} from 'ml-random-forest';
+export * as HClust from 'ml-hclust';
+export * as KMeans from 'ml-kmeans';
+export * as NaiveBayes from 'ml-naivebayes';
+export * as CrossValidation from 'ml-cross-validation';
+export * as FCNNLS from 'ml-fcnnls';
+export * as MatrixLib from 'ml-matrix';
+export * as GSD from 'ml-gsd';