chore: update dependencies (#96)

BREAKING CHANGE: Move property fwhm to be into 'shape'. This ensure compability with our other packages.

Co-authored-by: Luc Patiny <[email protected]>

Author: targos

.github/workflows/lactame.yml

@@ -5,13 +5,13 @@ on:
     types: [published]
 
 env:
-  NODE_VERSION: 14.x
+  NODE_VERSION: 16.x
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Get package name
         run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV
       - uses: actions/setup-node@v2

.github/workflows/nodejs-ts.yml

@@ -11,5 +11,5 @@ jobs:
     # Documentation: https://github.com/zakodium/workflows#nodejs-ci
     uses: zakodium/workflows/.github/workflows/nodejs.yml@nodejs-v1
     with:
-      node-version-matrix: '[14, 16]'
-      lint-check-types: true
+      node-version-matrix: '[14, 16, 18]'
+      lint-check-types: true

.github/workflows/typedoc.yml

@@ -13,8 +13,8 @@ jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/checkout@v3
+      - uses: actions/setup-node@v3
         with:
           node-version: ${{ env.NODE_VERSION }}
       - name: Install dependencies
@@ -29,4 +29,4 @@ jobs:
           token: ${{ secrets.BOT_TOKEN }}
           branch: gh-pages
           folder: docs
-          clean: true
+          clean: true

babel.config.js

@@ -0,0 +1,4 @@
+module.exports = {
+  presets: ['@babel/preset-typescript'],
+  plugins: ['@babel/plugin-transform-modules-commonjs'],
+};

jest.config.js

@@ -58,30 +58,31 @@
     "trailingComma": "all"
   },
   "devDependencies": {
+    "@babel/plugin-transform-modules-commonjs": "^7.17.9",
+    "@babel/preset-typescript": "^7.16.7",
     "@types/jest": "^27.4.1",
     "chemcalc": "^3.4.1",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^8.10.0",
+    "eslint": "^8.14.0",
     "eslint-config-cheminfo-typescript": "^10.4.0",
-    "eslint-plugin-jest": "^26.1.1",
+    "eslint-plugin-jest": "^26.1.5",
     "esm": "^3.2.25",
-    "jest": "^27.5.1",
+    "jest": "^28.0.3",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "mf-global": "^1.4.23",
+    "mf-global": "^1.4.24",
     "ml-stat": "^1.3.3",
-    "nodemon": "^2.0.15",
-    "prettier": "^2.5.1",
+    "nodemon": "^2.0.16",
+    "prettier": "^2.6.2",
     "rimraf": "^3.0.2",
-    "spectrum-generator": "^8.0.0",
-    "ts-jest": "^27.1.3",
-    "typescript": "^4.6.2",
-    "xy-parser": "^5.0.1"
+    "spectrum-generator": "^8.0.1",
+    "typescript": "^4.6.4",
+    "xy-parser": "^5.0.2"
   },
   "dependencies": {
     "cheminfo-types": "^1.1.0",
     "ml-peak-shape-generator": "^4.1.1",
     "ml-savitzky-golay-generalized": "4.0.1",
-    "ml-spectra-fitting": "3.0.4",
-    "ml-spectra-processing": "^11.0.0"
+    "ml-spectra-fitting": "4.0.1",
+    "ml-spectra-processing": "^11.5.0"
   }
 }

package.json

@@ -4,6 +4,5 @@ export interface GSDPeakOptimized {
   x: number;
   y: number;
   width: number;
-  fwhm: number;
   shape: Shape1D;
 }

src/GSDPeakOptimized.ts

@@ -49,15 +49,13 @@ describe('gaussian overlapping', () => {
         x: -0.1,
         y: 1,
         width: 0.1,
-        fwhm: 0.11774128880591818,
-        shape: { kind: 'gaussian' },
+        shape: { kind: 'gaussian', fwhm: 0.11774128880591818 },
       },
       {
         x: 0.1,
         y: 1,
         width: 0.1,
-        fwhm: 0.11774128880591818,
-        shape: { kind: 'gaussian' },
+        shape: { kind: 'gaussian', fwhm: 0.11774128880591818 },
       },
     ]);
   });

src/__tests__/gaussian-overlapping.test.ts

@@ -31,17 +31,17 @@ describe('optimizePeaks', () => {
       {
         x: 0,
         y: 1,
-        fwhm: 0.14128970668640126,
         width: 0.12,
         shape: {
           kind: 'gaussian',
+          fwhm: 0.14128970668640126,
         },
       },
     ]);
 
     const options = {
       optimization: {
-        kind: 'lm',
+        kind: 'lm' as const,
         options: {
           timeout: 0,
         },

src/post/__tests__/optimizePeaks.test.ts

@@ -1,5 +1,4 @@
-import type { DataXY } from 'cheminfo-types';
-import { PeakXYWidth } from 'cheminfo-types';
+import type { DataXY, PeakXYWidth } from 'cheminfo-types';
 import { getShape1D, Shape1D } from 'ml-peak-shape-generator';
 import { optimize } from 'ml-spectra-fitting';
 import type { OptimizationOptions } from 'ml-spectra-fitting';
@@ -90,11 +89,10 @@ export function optimizePeaks(
       });
       for (let i = 0; i < peaks.length; i++) {
         results.push({
-          x: optimizedPeaks[i].x,
-          y: optimizedPeaks[i].y,
-          shape: peaks[i].shape,
-          fwhm: optimizedPeaks[i].fwhm || 0, // todo remove || 0 it should never happen after update spectra-fitting
-          width: getShape1D(peaks[i].shape).fwhmToWidth(optimizedPeaks[i].fwhm),
+          ...optimizedPeaks[i],
+          width: getShape1D(peaks[i].shape).fwhmToWidth(
+            optimizedPeaks[i].shape.fwhm,
+          ),
         });
       }
     } else {