chore: update dependencies (#255)

* chore: update dependencies

* chore: fix prettier

eslint.config.mjs

@@ -0,0 +1,28 @@
+import cheminfo from 'eslint-config-cheminfo-typescript';
+import globals from 'globals';
+
+export default [
+  ...cheminfo,
+  {
+    languageOptions: {
+      globals: {
+        ...globals.node,
+      },
+    },
+    rules: {
+      "jsdoc/require-jsdoc": "off", // this would add automatically an empty bloc of JsDoc
+      "jsdoc/no-defaults": "off", // this would remove our default values https://github.com/gajus/eslint-plugin-jsdoc/blob/main/docs/rules/no-defaults.md#readme
+      "no-loss-of-precision": "off",
+      '@typescript-eslint/prefer-for-of': 'off',
+      "unicorn/import-style": [
+        "error",
+        {
+          "styles": {
+            "node:path": false
+          }
+        }
+      ]
+    }
+  }
+]
+

package.json

@@ -88,22 +88,22 @@
   },
   "homepage": "https://github.com/mljs/spectra-processing#readme",
   "devDependencies": {
-    "@vitest/coverage-v8": "^2.0.4",
+    "@vitest/coverage-v8": "^2.0.5",
     "cheminfo-build": "^1.2.0",
     "eslint": "^8.57.0",
-    "eslint-config-cheminfo-typescript": "^12.4.0",
+    "eslint-config-cheminfo-typescript": "^15.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "jscpd": "^3.5.10",
+    "jscpd": "^4.0.5",
     "ml-spectra-fitting": "^4.2.3",
     "prettier": "^3.3.3",
-    "rimraf": "^5.0.5",
+    "rimraf": "^6.0.1",
     "spectrum-generator": "^8.0.11",
     "typescript": "^5.5.4",
-    "vitest": "^2.0.4"
+    "vitest": "^2.0.5"
   },
   "dependencies": {
     "binary-search": "^1.3.6",
-    "cheminfo-types": "^1.7.3",
+    "cheminfo-types": "^1.8.0",
     "fft.js": "^4.0.4",
     "is-any-array": "^2.0.1",
     "ml-matrix": "^6.11.1",

src/matrix/__tests__/matrixApplyNumericalDecoding.test.ts

@@ -25,8 +25,6 @@ test('should return an array of numbers', () => {
     dictCategoricalToNumerical,
   );
 
-  const nonNumbers = matrix
-    .flat(2)
-    .filter((value) => typeof value !== 'number');
+  const nonNumbers = matrix.flat().filter((value) => typeof value !== 'number');
   expect(nonNumbers).toHaveLength(0);
 });

src/matrix/__tests__/matrixNumericalEncoding.test.ts

@@ -6,8 +6,6 @@ import { datasetForEncoding } from './fixtures/encoding';
 
 test('should return a matrix of numbers', () => {
   const { matrix } = matrixNumericalEncoding(datasetForEncoding);
-  const nonNumbers = matrix
-    .flat(2)
-    .filter((value) => typeof value !== 'number');
+  const nonNumbers = matrix.flat().filter((value) => typeof value !== 'number');
   expect(nonNumbers).toHaveLength(0);
 });

src/matrix/matrixAbsoluteMedian.ts

@@ -3,6 +3,7 @@ import { xMedian } from '../x';
 
 /**
  * Returns the median of the absolute matrix.
+ * @param matrix
  */
 export function matrixAbsoluteMedian(matrix: DoubleMatrix): number {
   const nbColumns = matrix[0].length;

src/matrix/matrixBoxPlot.ts

@@ -1,3 +1,5 @@
+import { DoubleArray } from 'cheminfo-types';
+
 import { DoubleMatrix } from '../types';
 
 export interface MatrixBoxPlot {
@@ -22,7 +24,7 @@ export function matrixBoxPlot(matrix: DoubleMatrix): MatrixBoxPlot {
     median: new Float64Array(nbColumns),
     q3: new Float64Array(nbColumns),
     min: Float64Array.from(matrix[0]),
-    max: Float64Array.from(matrix[matrix.length - 1]),
+    max: Float64Array.from(matrix.at(-1) as DoubleArray),
   };
 
   const columnArray = new Float64Array(matrix.length);

src/matrix/matrixCenterZMean.ts

@@ -4,7 +4,6 @@ import { matrixCreateEmpty } from './matrixCreateEmpty';
 
 /**
  * Center mean of matrix columns.
- *
  * @param matrix - matrix [rows][cols]
  */
 export function matrixCenterZMean(matrix: DoubleMatrix): Float64Array[] {

src/matrix/matrixClone.ts

@@ -1,5 +1,6 @@
 /**
  * Clone a matrix.
+ * @param matrix
  */
 export function matrixClone<ValueType>(matrix: ValueType[][]): ValueType[][] {
   return matrix.map((row) => row.slice(0));

src/matrix/matrixColumnsCorrelation.ts

@@ -5,7 +5,6 @@ import { xCorrelation } from '../x';
 
 /**
  * Calculates a correlation matrix based on the columns of the initial matrix.
- *
  * @param A - matrix [rows][cols]
  */
 export function matrixColumnsCorrelation(A: DoubleMatrix): Float64Array[] {

src/matrix/matrixCreateEmpty.ts

@@ -12,16 +12,19 @@ export interface MatrixCreateEmptyOptions<
    * Matrix from which to extract nbRows and nbColumns
    */
   matrix?: DoubleMatrix;
+
   /**
    * Matrix from which to extract nbRows and nbColumns
    * @default matrix.length || 1
    */
   nbRows?: number;
+
   /**
    * Matrix from which to extract nbRows and nbColumns
    * @default matrix[0].length || 1
    */
   nbColumns?: number;
+
   /**
    * Allows to specify the type of array to use
    * @default Float64Array
@@ -31,6 +34,7 @@ export interface MatrixCreateEmptyOptions<
 
 /**
  * Create a new matrix based on the size of the current one or by using specific dimensions.
+ * @param options
  */
 export function matrixCreateEmpty<
   ArrayConstructorType extends NumberArrayConstructor = Float64ArrayConstructor,

src/matrix/matrixHistogram.ts

@@ -10,44 +10,50 @@ export interface MatrixHistogramOptions {
   /**
    * Center the X value. We will enlarge the first and
    * @default true
-   * */
+   */
   centerX?: boolean;
+
   /**
    * histogram
-   * */
+   */
   histogram?: DataXY;
+
   /**
    * Number of slots
    * @default 256
-   * */
+   */
   nbSlots?: number;
+
   /**
    * We can first apply a log on the x-axis.
-   * */
+   */
   logBaseX?: number;
+
   /**
    * We can apply a log on the resulting histogram
    */
   logBaseY?: number;
+
   /**
    * Take the absolute value
    */
   absolute?: boolean;
+
   /**
    * Maximal value to calculate used to calculate slot size
    * @default maxValue
-   * */
+   */
   max?: number;
+
   /**
    * Minimum value to calculate used to calculate slot size
    * @default minValue
-   * */
+   */
   min?: number;
 }
 
 /**
  * Calculates a histogram of defined number of slots.
- *
  * @param matrix - matrix [rows][cols].
  * @param options - options
  * @returns - Result of the histogram.
@@ -63,17 +69,17 @@ export function matrixHistogram(
     throw new Error('matrix must have at least one column and one row');
   }
 
-  if (typeof min === 'undefined' || typeof max === 'undefined') {
+  if (min === undefined || max === undefined) {
     const minMax = absolute
       ? matrixMinMaxAbsoluteZ(matrix)
       : matrixMinMaxZ(matrix);
-    if (typeof min === 'undefined') {
+    if (min === undefined) {
       min =
         logBaseX && minMax.min
           ? Math.log(minMax.min) / Math.log(logBaseX)
           : minMax.min;
     }
-    if (typeof max === 'undefined') {
+    if (max === undefined) {
       max =
         logBaseX && minMax.max
           ? Math.log(minMax.max) / Math.log(logBaseX)

src/matrix/matrixMaxAbsoluteZ.ts

@@ -2,7 +2,6 @@ import { NumberArray } from 'cheminfo-types';
 
 /**
  * Returns the max absolute values of Z.
- *
  * @param matrix - matrix [rows][cols].
  */
 export function matrixMaxAbsoluteZ(matrix: NumberArray[]): number {

src/matrix/matrixMedian.ts

@@ -5,6 +5,7 @@ import { matrixToArray } from './matrixToArray';
 
 /**
  * Returns the median of the matrix.
+ * @param matrix
  */
 export function matrixMedian(matrix: DoubleMatrix): number {
   return xMedian(matrixToArray(matrix));

src/matrix/matrixMinMaxAbsoluteZ.ts

@@ -2,7 +2,6 @@ import { DoubleMatrix } from '../types';
 
 /**
  * Get min and max of the absolute values of Z.
- *
  * @param matrix - matrix [rows][cols].
  */
 export function matrixMinMaxAbsoluteZ(matrix: DoubleMatrix): {

src/matrix/matrixMinMaxZ.ts

@@ -4,7 +4,6 @@ import { matrixCheck } from './matrixCheck';
 
 /**
  * Get min and max Z.
- *
  * @param matrix - matrix [rows][cols].
  */
 export function matrixMinMaxZ(matrix: DoubleMatrix): {

src/matrix/matrixPQN.ts

@@ -7,8 +7,9 @@ export interface MatrixPQNOptions {
   /**
    * Normalization integral constant.
    * @default 100
-   * */
+   */
   max?: number;
+
   /**
    * min
    */
@@ -19,7 +20,6 @@ export interface MatrixPQNOptions {
  * Performs a Probabilistic quotient normalization (PQN) over the dataset to account dilution based in median spectrum.
  * Dieterle, F., Ross, A., Schlotterbeck, G., & Senn, H. (2006). Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Analytical chemistry, 78(13), 4281-4290.
  * DOI: 10.1021/ac051632c
- *
  * @param matrix - matrix [rows][cols].
  * @param options - options
  * @returns - {data: Normalized dataset, medianOfQuotients: The median of quotients of each variables}

src/matrix/matrixZPivotRescale.ts

@@ -11,8 +11,9 @@ export interface MatrixZPivotRescaleOptions<
   /**
    * max
    * @default 1
-   * */
+   */
   max?: number;
+
   /**
    * Allows to specify the type of array to use
    * @default Float64Array
@@ -22,7 +23,6 @@ export interface MatrixZPivotRescaleOptions<
 
 /**
  * Rescale a matrix around 0 taking into account the absolute max value.
- *
  * @param matrix - matrix [rows][cols].
  * @param options - Options.
  */

src/matrix/matrixZRescale.ts

@@ -10,13 +10,15 @@ export interface MatrixZRescaleOptions<
   /**
    * min
    * @default 0
-   * */
+   */
   min?: number;
+
   /**
    * max
    * @default 1
-   * */
+   */
   max?: number;
+
   /**
    * Allows to specify the type of array to use.
    * @default Float64Array
@@ -26,7 +28,6 @@ export interface MatrixZRescaleOptions<
 
 /**
  * Rescale a matrix between min and max values.
- *
  * @param matrix - matrix [rows][cols].
  * @param options - Options.
  */

src/matrix/matrixZRescalePerColumn.ts

@@ -6,18 +6,18 @@ export interface MatrixZRescalePerColumnOptions {
   /**
    * min
    * @default 0
-   * */
+   */
   min?: number;
+
   /**
    * max
    * @default 1
-   * */
+   */
   max?: number;
 }
 
 /**
  * Rescale the matrix per column for which we get the min and max values.
- *
  * @param matrix - matrix [rows][cols].
  * @param options - Options.
  */

src/reim/__tests__/reimAutoPhaseCorrection.test.ts

@@ -1,5 +1,5 @@
 import { readFileSync } from 'node:fs';
-import { join } from 'path';
+import { join } from 'node:path';
 
 import { expect, test } from 'vitest';
 

src/reim/reimAbsolute.ts

@@ -2,7 +2,6 @@ import { DataReIm } from '../types';
 
 /**
  * Calculates reimAbsolute value of a complex spectrum.
- *
  * @param data - complex spectrum
  * @returns - reimAbsolute value
  */
@@ -12,7 +11,7 @@ export function reimAbsolute(data: DataReIm): Float64Array {
   const im = data.im;
   const newArray = new Float64Array(length);
   for (let i = 0; i < length; i++) {
-    newArray[i] = Math.sqrt(re[i] ** 2 + im[i] ** 2);
+    newArray[i] = Math.hypot(re[i], im[i]);
   }
 
   return newArray;