chore: update dependencies

.eslintrc.yml

@@ -1,3 +1,4 @@
 extends: cheminfo
-parserOptions:
-  sourceType: module
+env:
+  jest: true
+  node: true

package.json

@@ -45,40 +45,40 @@
   },
   "homepage": "https://github.com/cheminfo/chromatography#readme",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.16.8",
-    "@types/jest": "^27.4.1",
-    "cheminfo-build": "^1.1.11",
-    "convert-to-jcamp": "^5.2.0",
-    "eslint": "^8.10.0",
-    "eslint-config-cheminfo": "^7.3.0",
+    "@babel/plugin-transform-modules-commonjs": "^7.24.1",
+    "@types/jest": "^29.5.12",
+    "cheminfo-build": "^1.2.0",
+    "convert-to-jcamp": "^5.4.10",
+    "eslint": "^8.57.0",
+    "eslint-config-cheminfo": "^9.2.0",
     "esm": "^3.2.25",
-    "jest": "^27.5.1",
+    "jest": "^29.7.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^2.5.1",
-    "rollup": "^2.70.0",
-    "spectrum-generator": "^8.0.0",
-    "typescript": "^4.6.2"
+    "prettier": "^3.2.5",
+    "rollup": "^4.17.1",
+    "spectrum-generator": "^8.0.11",
+    "typescript": "^5.4.5"
   },
   "dependencies": {
     "binary-search": "^1.3.6",
-    "is-any-array": "^2.0.0",
-    "isotopic-distribution": "^1.4.9",
-    "jcampconverter": "^8.2.5",
-    "mf-generator": "^1.3.20",
-    "mf-parser": "^1.4.5",
-    "ml-airpls": "^1.0.0",
+    "is-any-array": "^2.0.1",
+    "isotopic-distribution": "^3.1.2",
+    "jcampconverter": "^9.6.4",
+    "mf-generator": "^3.2.0",
+    "mf-parser": "^3.1.0",
+    "ml-airpls": "^1.0.3",
     "ml-array-max": "^1.2.4",
     "ml-array-mean": "^1.1.6",
     "ml-array-median": "^1.1.6",
     "ml-array-sum": "^1.1.6",
-    "ml-gsd": "^10.2.0",
-    "ml-matrix": "^6.9.0",
+    "ml-gsd": "^12.1.6",
+    "ml-matrix": "^6.11.0",
     "ml-ngmca": "^1.0.0",
-    "ml-pca": "^4.0.2",
-    "ml-regression-polynomial": "^2.2.0",
-    "ml-spectra-processing": "^11.0.0",
+    "ml-pca": "^4.1.1",
+    "ml-regression-polynomial": "^3.0.0",
+    "ml-spectra-processing": "^14.3.0",
     "mzdata": "^2.3.1",
     "netcdf-gcms": "^1.4.0",
-    "xy-parser": "^5.0.1"
+    "xy-parser": "^5.0.5"
   }
 }

src/ms/calculateForMF.js

@@ -1,5 +1,5 @@
-import IsotopicDistribution from 'isotopic-distribution';
-import generateMFs from 'mf-generator';
+import { IsotopicDistribution } from 'isotopic-distribution';
+import { generateMFs } from 'mf-generator';
 import { xyObjectSlotX } from 'ml-spectra-processing';
 /**
  * Calculate tic for specific molecular formula and ionizations

src/ms/deconvolution.js

@@ -41,8 +41,12 @@ export function deconvolution(chromatogram, options = {}) {
     scale: maxByRow.map((e) => 1 / e),
   });
 
-  return Object.assign(
-    { matrix, times, mzAxis, rank },
-    { profile: result.A, component: result.S },
-  );
+  return {
+    matrix,
+    times,
+    mzAxis,
+    rank,
+    profile: result.A,
+    component: result.S,
+  };
 }

src/scaleAlignment.js

@@ -1,11 +1,11 @@
-import Regression from 'ml-regression-polynomial';
+import { PolynomialRegression } from 'ml-regression-polynomial';
 
 export function scaleAlignment(reference, sample, options = {}) {
   const { computeQuality = false, polynomialDegree = 3 } = options;
   let referenceTime = reference.map((val) => val.retentionTime);
   let sampleTime = sample.map((val) => val.retentionTime);
 
-  const regression = new Regression(
+  const regression = new PolynomialRegression(
     sampleTime,
     referenceTime,
     polynomialDegree,

src/spectraComparison.js

@@ -36,7 +36,7 @@ const defaultOptions = {
 };
 
 export function spectraComparison(chrom1, chrom2, options = {}) {
-  options = Object.assign({}, defaultOptions, options);
+  options = { ...defaultOptions, ...options };
 
   // peak picking
   let reference = preprocessing(chrom1, options);
@@ -107,6 +107,6 @@ export function spectraComparison(chrom1, chrom2, options = {}) {
   return {
     peaksFirst: peaksChrom1,
     peaksSecond: peaksChrom2,
-    peaksSimilarity: peaksSimilarity,
+    peaksSimilarity,
   };
 }

src/vectorify.js

@@ -21,8 +21,7 @@ export function vectorify(ranges, options = {}) {
       };
       for (let j = 0; j < len; ++j) {
         vector[i].y[j] =
-          Math.pow(ranges[i].ms.x[j], massPower) *
-          Math.pow(ranges[i].ms.y[j], intPower);
+          ranges[i].ms.x[j] ** massPower * ranges[i].ms.y[j] ** intPower;
       }
 
       vector[i] = massFilter(vector[i], filterOptions);
@@ -36,8 +35,7 @@ export function vectorify(ranges, options = {}) {
       };
       for (let j = 0; j < len; ++j) {
         vector[i].y[j] =
-          Math.pow(ranges[i].ms.x[j], massPower) *
-          Math.pow(ranges[i].ms.y[j], intPower);
+          ranges[i].ms.x[j] ** massPower * ranges[i].ms.y[j] ** intPower;
       }
     }
   }