chore: fix ml-gsd version and update dependencies

.ncurc

@@ -0,0 +1,5 @@
+{
+  "reject": [
+    "ml-gsd",
+  ]
+}

package.json

@@ -48,38 +48,39 @@
   },
   "homepage": "https://github.com/cheminfo/chromatography#readme",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.15.4",
-    "@types/jest": "^27.0.1",
+    "@babel/plugin-transform-modules-commonjs": "^7.16.8",
+    "@types/jest": "^27.4.0",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^7.32.0",
-    "eslint-config-cheminfo": "^5.4.0",
+    "convert-to-jcamp": "^5.1.1",
+    "eslint": "^8.6.0",
+    "eslint-config-cheminfo": "^7.2.1",
     "esm": "^3.2.25",
-    "jest": "^27.1.0",
-    "jest-matcher-deep-close-to": "^2.0.1",
-    "prettier": "^2.3.2",
-    "rollup": "^2.56.3",
-    "spectrum-generator": "^5.1.0",
-    "typescript": "^4.4.2"
+    "jest": "^27.4.7",
+    "jest-matcher-deep-close-to": "^3.0.2",
+    "prettier": "^2.5.1",
+    "rollup": "^2.63.0",
+    "spectrum-generator": "^6.0.2",
+    "typescript": "^4.5.4"
   },
   "dependencies": {
     "binary-search": "^1.3.6",
-    "is-any-array": "^1.0.1",
-    "isotopic-distribution": "^1.2.1",
-    "jcampconverter": "^8.1.5",
-    "mf-generator": "^1.3.6",
-    "mf-parser": "^1.3.3",
+    "is-any-array": "^2.0.0",
+    "isotopic-distribution": "^1.4.0",
+    "jcampconverter": "^8.2.4",
+    "mf-generator": "^1.3.8",
+    "mf-parser": "^1.4.0",
     "ml-array-max": "^1.2.3",
     "ml-array-mean": "^1.1.5",
     "ml-array-median": "^1.1.5",
     "ml-array-sum": "^1.1.5",
-    "ml-gsd": "^6.7.0",
-    "ml-matrix": "^6.8.0",
+    "ml-gsd": "^6.9.2",
+    "ml-matrix": "^6.8.2",
     "ml-ngmca": "^1.0.0",
     "ml-pca": "^4.0.2",
     "ml-regression-polynomial": "^2.2.0",
-    "ml-spectra-processing": "^6.8.0",
+    "ml-spectra-processing": "^8.0.3",
     "mzdata": "^2.3.1",
     "netcdf-gcms": "^1.4.0",
-    "xy-parser": "^3.2.0"
+    "xy-parser": "^4.0.1"
   }
 }

src/Chromatogram.js

@@ -1,4 +1,4 @@
-import isAnyArray from 'is-any-array';
+import { isAnyArray } from 'is-any-array';
 import { xFindClosestIndex } from 'ml-spectra-processing';
 
 import { meanFilter } from './filter/meanFilter';

src/peaks/__tests__/appendMass.test.js

@@ -89,7 +89,10 @@ describe('appendMass', () => {
     let result = appendMass(simple4, peaks, {
       mergeThreshold: 2,
     })[0];
-    expect(Array.from(result.ms.x)).toBeDeepCloseTo([102, 202, 302], 1);
+    expect(Array.from(result.ms.x)).toBeDeepCloseTo(
+      [102.05, 202.03, 302.02],
+      1,
+    );
     expect(Array.from(result.ms.y)).toStrictEqual([36, 66, 96]);
   });
 });

src/peaks/appendMass.js

@@ -5,7 +5,7 @@ import { merge } from '../ms/merge';
  * @param {Chromatogram} chromatogram
  * @param {Array<object>} peaks - Array of range {from:, to:}
  * @param {object} [options={}] - Options for the integral filtering
- * @param {number} [options.mergeThreshold=0.3] - Peaks that are under this value (in Da) will be merged
+ * @param {number} [options.mergeThreshold=0.3] - Peaks that are closer than this value (in Da) will be merged
  * @param {number} [options.seriesName='ms'] - Maximum number of peaks for each mass spectra (when is Number.MAX_VALUE there's no filter)
  * @return {Array<object>} - A copy of ranges with ms appended
  */

src/seriesFromArray.js

@@ -1,4 +1,4 @@
-import isAnyArray from 'is-any-array';
+import { isAnyArray } from 'is-any-array';
 
 import { Series1D } from './Series1D';
 import { Series2D } from './Series2D';