From aacabff3e0b6303d0c800a073a7cf79c82c4dbe4 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Wed, 16 Oct 2024 16:58:59 +0200
Subject: [PATCH 1/5] feat: update dependencies

---
 package.json | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/package.json b/package.json
index a48b1c0..6fd148f 100644
--- a/package.json
+++ b/package.json
@@ -71,14 +71,14 @@
     "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",
@@ -87,7 +87,7 @@
     "ml-pls": "^4.3.2",
     "ml-random": "^1.0.1",
     "ml-random-forest": "^2.1.0",
-    "ml-regression": "^5.0.0",
+    "ml-regression": "^6.1.0",
     "ml-savitzky-golay": "^5.0.0",
     "ml-som": "^0.0.6",
     "ml-sparse-matrix": "^2.1.0",
@@ -95,14 +95,14 @@
     "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",
+    "@types/jest": "^29.5.13",
     "cheminfo-build": "^1.2.0",
     "eslint": "^8.56.0",
     "eslint-config-cheminfo": "^9.1.1",
     "esm": "^3.2.25",
     "jest": "^29.7.0",
-    "prettier": "^3.2.4",
-    "rollup": "^4.9.6"
+    "prettier": "^3.3.3",
+    "rollup": "^4.24.0"
   }
 }

From 5aa5a83180eef420bcf36dbd94c6e4c3e727c974 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Thu, 17 Oct 2024 15:29:45 +0200
Subject: [PATCH 2/5] fix: migrate to vitest and update ml-regression

---
 .eslintrc.yml               |  5 ----
 eslint.config.mjs           | 16 +++++++++++
 package.json                | 14 +++++-----
 src/__tests__/index.test.js |  3 ++-
 src/index.js                | 53 ++++++++++++++++++++-----------------
 5 files changed, 54 insertions(+), 37 deletions(-)
 delete mode 100644 .eslintrc.yml
 create mode 100644 eslint.config.mjs

diff --git a/.eslintrc.yml b/.eslintrc.yml
deleted file mode 100644
index f4ab74d..0000000
--- a/.eslintrc.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-extends: cheminfo
-parserOptions:
-  sourceType: module
-env:
-  jest: true
diff --git a/eslint.config.mjs b/eslint.config.mjs
new file mode 100644
index 0000000..210a66d
--- /dev/null
+++ b/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",
+    }
+  }
+]
\ No newline at end of file
diff --git a/package.json b/package.json
index 6fd148f..1d1787d 100644
--- a/package.json
+++ b/package.json
@@ -12,7 +12,7 @@
     "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"
   },
   "files": [
     "src",
@@ -87,7 +87,7 @@
     "ml-pls": "^4.3.2",
     "ml-random": "^1.0.1",
     "ml-random-forest": "^2.1.0",
-    "ml-regression": "^6.1.0",
+    "ml-regression": "^6.2.0",
     "ml-savitzky-golay": "^5.0.0",
     "ml-som": "^0.0.6",
     "ml-sparse-matrix": "^2.1.0",
@@ -96,13 +96,13 @@
   },
   "devDependencies": {
     "@babel/plugin-transform-modules-commonjs": "^7.25.7",
-    "@types/jest": "^29.5.13",
+    "@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": "^3.3.3",
-    "rollup": "^4.24.0"
+    "rollup": "^4.24.0",
+    "vitest": "^2.1.3"
   }
 }
diff --git a/src/__tests__/index.test.js b/src/__tests__/index.test.js
index ae29b38..61c1f93 100644
--- a/src/__tests__/index.test.js
+++ b/src/__tests__/index.test.js
@@ -1,4 +1,5 @@
-/* eslint-disable import/namespace */
+import { it, describe, expect } from 'vitest';
+
 import * as ML from '..';
 
 describe('Check all properties are defined', () => {
diff --git a/src/index.js b/src/index.js
index c49e505..b0af69f 100644
--- a/src/index.js
+++ b/src/index.js
@@ -2,31 +2,28 @@
 /* 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 +39,13 @@ 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 +58,7 @@ const {
   QrDecomposition,
 } = MatrixLib;
 export {
-  MatrixLib,
+
   Matrix,
   SVD,
   EVD,
@@ -72,8 +69,7 @@ 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 { nGMCA } from 'ml-ngmca';
@@ -90,8 +86,8 @@ 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 };
+
+
 
 import min from 'ml-array-min';
 import max from 'ml-array-max';
@@ -140,3 +136,12 @@ 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';

From c1da1b7b74b8878a78231562274c4e1143c46d97 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Thu, 17 Oct 2024 15:30:57 +0200
Subject: [PATCH 3/5] chore: fix prettier

---
 src/index.js | 23 ++++-------------------
 1 file changed, 4 insertions(+), 19 deletions(-)

diff --git a/src/index.js b/src/index.js
index b0af69f..d3a3dcd 100644
--- a/src/index.js
+++ b/src/index.js
@@ -2,29 +2,18 @@
 /* eslint-disable import/order */
 /* eslint-disable import/first */
 
-
-
-
 // Try to keep this list in the same structure as the README.
 
 // Unsupervised learning
 export { PCA } from 'ml-pca';
 
-
-
-
-
 // Supervised learning
 
-
 export { default as KNN } from 'ml-knn';
 export { PLS, KOPLS, OPLS, oplsNipals } from 'ml-pls';
 
-
 export { ConfusionMatrix } from 'ml-confusion-matrix';
 
-
-
 // Artificial neural networks
 export { default as FNN } from 'ml-fnn';
 export { default as SOM } from 'ml-som';
@@ -40,13 +29,9 @@ export {
   RobustPolynomialRegression,
 } from 'ml-regression';
 
-
-
 // Optimization
 export { levenbergMarquardt } from 'ml-levenberg-marquardt';
 
-
-
 // Math
 import * as MatrixLib from 'ml-matrix';
 const {
@@ -58,7 +43,6 @@ const {
   QrDecomposition,
 } = MatrixLib;
 export {
-
   Matrix,
   SVD,
   EVD,
@@ -87,8 +71,6 @@ export { default as padArray } from 'ml-pad-array';
 export { default as binarySearch } from 'binary-search';
 export { default as Random } from 'ml-random';
 
-
-
 import min from 'ml-array-min';
 import max from 'ml-array-max';
 import median from 'ml-array-median';
@@ -137,7 +119,10 @@ export const ArrayXY = {
   filterX,
 };
 export { DecisionTreeClassifier, DecisionTreeRegression } from 'ml-cart';
-export { RandomForestClassifier, RandomForestRegression } from 'ml-random-forest';
+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';

From 681ce9f10265fd371685a7d540234170fd893332 Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Thu, 17 Oct 2024 17:01:18 +0200
Subject: [PATCH 4/5] chore: add `npm run dupe` to find duplicate dependencies

---
 package.json | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/package.json b/package.json
index 1d1787d..ddefe44 100644
--- a/package.json
+++ b/package.json
@@ -4,8 +4,9 @@
   "description": "Machine learning tools",
   "main": "src/index.js",
   "scripts": {
-    "compile": "rollup -c",
     "build": "cheminfo-build --root ML",
+    "compile": "rollup -c",
+    "dupe": "find-duplicate-dependencies",
     "eslint": "eslint src --cache",
     "eslint-fix": "npm run eslint -- --fix",
     "prepack": "npm run compile",
@@ -101,6 +102,7 @@
     "eslint": "^9.12.0",
     "eslint-config-cheminfo": "^12.0.1",
     "esm": "^3.2.25",
+    "find-duplicate-dependencies": "^3.0.0",
     "prettier": "^3.3.3",
     "rollup": "^4.24.0",
     "vitest": "^2.1.3"

From 53024d94d16eaea68eeb008e4f2e49804773e39b Mon Sep 17 00:00:00 2001
From: Luc Patiny <luc@patiny.com>
Date: Mon, 21 Oct 2024 08:50:19 +0200
Subject: [PATCH 5/5] test: try to add test to check if we didn't messup with
 default export

---
 package.json                |  6 ++----
 src/__tests__/index.test.js | 30 ++++++++++++++++++++++++++++++
 src/index.js                |  4 ++--
 3 files changed, 34 insertions(+), 6 deletions(-)

diff --git a/package.json b/package.json
index ddefe44..c88b149 100644
--- a/package.json
+++ b/package.json
@@ -6,7 +6,6 @@
   "scripts": {
     "build": "cheminfo-build --root ML",
     "compile": "rollup -c",
-    "dupe": "find-duplicate-dependencies",
     "eslint": "eslint src --cache",
     "eslint-fix": "npm run eslint -- --fix",
     "prepack": "npm run compile",
@@ -86,13 +85,13 @@
     "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": "^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": {
@@ -102,7 +101,6 @@
     "eslint": "^9.12.0",
     "eslint-config-cheminfo": "^12.0.1",
     "esm": "^3.2.25",
-    "find-duplicate-dependencies": "^3.0.0",
     "prettier": "^3.3.3",
     "rollup": "^4.24.0",
     "vitest": "^2.1.3"
diff --git a/src/__tests__/index.test.js b/src/__tests__/index.test.js
index 61c1f93..0e65101 100644
--- a/src/__tests__/index.test.js
+++ b/src/__tests__/index.test.js
@@ -3,7 +3,37 @@ 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');
+    }
   });
 });
diff --git a/src/index.js b/src/index.js
index d3a3dcd..67c7d94 100644
--- a/src/index.js
+++ b/src/index.js
@@ -55,7 +55,7 @@ export { SparseMatrix } from 'ml-sparse-matrix';
 export { default as Kernel } from 'ml-kernel';
 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
@@ -69,7 +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';
+export { Random } from 'ml-random';
 
 import min from 'ml-array-min';
 import max from 'ml-array-max';