fix: update dependencies (#55)

feat!: calculateForMF is now async and returns a Promise feat: getPeaks will make a baseline correction before calculate the noise chore!: remove support for Node.js 12 Co-authored-by: Luc Patiny <[email protected]>
cheminfo · Mar 8, 2022 · c173e22 · c173e22
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diff --git a/.github/workflows/lactame.yml b/.github/workflows/lactame.yml
@@ -5,7 +5,7 @@ on:
     types: [published]
 
 env:
-  NODE_VERSION: 14.x
+  NODE_VERSION: 16.x
 
 jobs:
   deploy:
@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v2
       - name: Get package name
         run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
         with:
           node-version: ${{ env.NODE_VERSION }}
       - name: Install dependencies

diff --git a/.github/workflows/nodejs.yml b/.github/workflows/nodejs.yml
@@ -2,39 +2,13 @@ name: Node.js CI
 
 on:
   push:
-    branches: master
+    branches:
+      - master
   pull_request:
 
-env:
-  NODE_VERSION: 14.x
-
 jobs:
-  lint:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
-        with:
-          node-version: ${{ env.NODE_VERSION }}
-      - name: Install dependencies
-        run: npm install
-      - name: Run ESLint
-        run: npm run eslint
-  test:
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        node-version: [12.x, 14.x, 16.x]
-      fail-fast: false
-    steps:
-      - uses: actions/checkout@v2
-      - name: Use Node.js ${{ matrix.node-version }}
-        uses: actions/setup-node@v2
-        with:
-          node-version: ${{ matrix.node-version }}
-      - name: Install dependencies
-        run: npm install
-      - name: Run tests
-        run: npm run test-coverage
-      - name: Send coverage report to Codecov
-        uses: codecov/codecov-action@v1
+  nodejs:
+    # Documentation: https://github.com/zakodium/workflows#nodejs-ci
+    uses: zakodium/workflows/.github/workflows/nodejs.yml@nodejs-v1
+    with:
+      node-version-matrix: '[14, 16]'
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -5,33 +5,12 @@ on:
     branches:
       - master
 
-env:
-  NODE_VERSION: 14.x
-
 jobs:
-  release-please:
-    runs-on: ubuntu-latest
-    steps:
-      - name: Get package name
-        run: echo "PACKAGE_NAME=$(jq .name package.json | tr -d '"')" >> $GITHUB_ENV
-      - uses: GoogleCloudPlatform/release-please-action@v2
-        id: release
-        with:
-          token: ${{ secrets.BOT_TOKEN }}
-          release-type: node
-          package-name: ${{ env.PACKAGE_NAME }}
-          bump-minor-pre-major: Yes
-      - uses: actions/checkout@v2
-        # These if statements ensure that a publication only occurs when a new release is created
-        if: ${{ steps.release.outputs.release_created }}
-      - uses: actions/setup-node@v2
-        with:
-          node-version: ${{ env.NODE_VERSION }}
-          registry-url: 'https://registry.npmjs.org'
-        if: ${{ steps.release.outputs.release_created }}
-      - run: npm install
-        if: ${{ steps.release.outputs.release_created }}
-      - run: npm publish  --access public
-        env:
-          NODE_AUTH_TOKEN: ${{ secrets.NPM_BOT_TOKEN }}
-        if: ${{ steps.release.outputs.release_created }}
+  release:
+    # Documentation: https://github.com/zakodium/workflows#release
+    uses: zakodium/workflows/.github/workflows/release.yml@release-v1
+    with:
+      npm: true
+    secrets:
+      github-token: ${{ secrets.BOT_TOKEN }}
+      npm-token: ${{ secrets.NPM_BOT_TOKEN }}
diff --git a/.github/workflows/typedoc.yml b/.github/workflows/typedoc.yml
@@ -6,15 +6,15 @@ on:
     types: [published]
 
 env:
-  NODE_VERSION: 14.x
+  NODE_VERSION: 16.x
   ENTRY_FILE: 'chromatography.d.ts'
 
 jobs:
   deploy:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v3
         with:
           node-version: ${{ env.NODE_VERSION }}
       - name: Install dependencies

diff --git a/.ncurc b/.ncurc
diff --git a/.prettierrc → .prettierrc.json b/.prettierrc → .prettierrc.json
diff --git a/package.json b/package.json
@@ -25,19 +25,16 @@
     "build": "cheminfo-build --entry src/index.js --root Chromatography",
     "eslint": "eslint src --cache",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepublishOnly": "rollup -c",
-    "test": "npm run test-coverage && npm run eslint",
-    "test-only": "jest",
-    "test-coverage": "jest --coverage"
+    "prepack": "rollup -c",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
+    "test": "npm run test-only && npm run eslint && npm run prettier",
+    "test-only": "jest --coverage"
   },
   "repository": {
     "type": "git",
     "url": "git+https://github.com/cheminfo/chromatography.git"
   },
-  "jest": {
-    "testEnvironment": "node",
-    "transformIgnorePatterns": []
-  },
   "author": "Michaël Zasso",
   "contributors": [
     "Miguel Asencio <[email protected]>"
@@ -49,38 +46,39 @@
   "homepage": "https://github.com/cheminfo/chromatography#readme",
   "devDependencies": {
     "@babel/plugin-transform-modules-commonjs": "^7.16.8",
-    "@types/jest": "^27.4.0",
+    "@types/jest": "^27.4.1",
     "cheminfo-build": "^1.1.11",
-    "convert-to-jcamp": "^5.1.1",
-    "eslint": "^8.6.0",
-    "eslint-config-cheminfo": "^7.2.1",
+    "convert-to-jcamp": "^5.2.0",
+    "eslint": "^8.10.0",
+    "eslint-config-cheminfo": "^7.2.2",
     "esm": "^3.2.25",
-    "jest": "^27.4.7",
+    "jest": "^27.5.1",
     "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"
+    "rollup": "^2.70.0",
+    "spectrum-generator": "^8.0.0",
+    "typescript": "^4.6.2"
   },
   "dependencies": {
     "binary-search": "^1.3.6",
     "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": "^6.9.2",
-    "ml-matrix": "^6.8.2",
+    "isotopic-distribution": "^1.4.9",
+    "jcampconverter": "^8.2.5",
+    "mf-generator": "^1.3.20",
+    "mf-parser": "^1.4.5",
+    "ml-airpls": "^1.0.0",
+    "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": "^10.1.2",
+    "ml-matrix": "^6.9.0",
     "ml-ngmca": "^1.0.0",
     "ml-pca": "^4.0.2",
     "ml-regression-polynomial": "^2.2.0",
-    "ml-spectra-processing": "^8.0.3",
+    "ml-spectra-processing": "^11.0.0",
     "mzdata": "^2.3.1",
     "netcdf-gcms": "^1.4.0",
-    "xy-parser": "^4.0.1"
+    "xy-parser": "^5.0.1"
   }
 }
diff --git a/rollup.config.js b/rollup.config.js
@@ -16,7 +16,6 @@ const config = {
     'ml-array-median',
     'ml-array-sum',
     'ml-gsd',
-    'ml-gsd/src/gsd',
     'ml-regression-polynomial',
     'ml-spectra-processing',
     'mzdata',

diff --git a/src/Chromatogram.js b/src/Chromatogram.js
@@ -162,15 +162,15 @@ export class Chromatogram {
     return this.getSeries(seriesName);
   }
 
-  calculateForMF(targetMF, options = {}) {
+  async calculateForMF(targetMF, options = {}) {
     const {
       seriesName = `${targetMF}(${options.ionizations || 'H+'})±${
         options.slotWidth / 2 || 0.5
       }${options.threshold ? `(${options.threshold})` : ''}`,
       cache = false,
     } = options;
     if (cache && this.hasSeries(seriesName)) return this.getSeries(seriesName);
-    const result = calculateForMF(this, targetMF, options);
+    const result = await calculateForMF(this, targetMF, options);
     this.addSeries(seriesName, result, options);
     return this.getSeries(seriesName);
   }

diff --git a/src/__tests__/scaleAlignment.test.js b/src/__tests__/scaleAlignment.test.js
@@ -49,18 +49,10 @@ test('Simple case', () => {
 
   expect(compared.peaksSimilarity).toStrictEqual([1, 1, 1, 1, 1]);
   expect(compared.peaksFirst.map((val) => val.retentionTime)).toStrictEqual([
-    10,
-    20,
-    30,
-    40,
-    50,
+    10, 20, 30, 40, 50,
   ]);
   expect(compared.peaksSecond.map((val) => val.retentionTime)).toStrictEqual([
-    20,
-    30,
-    40,
-    50,
-    60,
+    20, 30, 40, 50, 60,
   ]);
 
   let aligned = scaleAlignment(compared.peaksFirst, compared.peaksSecond);
@@ -114,18 +106,10 @@ test('Quality and string', () => {
   let compared = spectraComparison(chrom1, chrom2, options);
   expect(compared.peaksSimilarity).toStrictEqual([1, 1, 1, 1, 1]);
   expect(compared.peaksFirst.map((val) => val.retentionTime)).toStrictEqual([
-    10,
-    20,
-    30,
-    40,
-    50,
+    10, 20, 30, 40, 50,
   ]);
   expect(compared.peaksSecond.map((val) => val.retentionTime)).toStrictEqual([
-    20,
-    30,
-    40,
-    50,
-    60,
+    20, 30, 40, 50, 60,
   ]);
 
   let aligned = scaleAlignment(compared.peaksFirst, compared.peaksSecond, {

diff --git a/src/__tests__/spectraComparison.test.js b/src/__tests__/spectraComparison.test.js
@@ -48,18 +48,10 @@ test('Simple case', () => {
   let compared = spectraComparison(chrom1, chrom2, options);
   expect(compared.peaksSimilarity).toStrictEqual([1, 1, 1, 1, 1]);
   expect(compared.peaksFirst.map((val) => val.retentionTime)).toStrictEqual([
-    10,
-    20,
-    30,
-    40,
-    50,
+    10, 20, 30, 40, 50,
   ]);
   expect(compared.peaksSecond.map((val) => val.retentionTime)).toStrictEqual([
-    20,
-    30,
-    40,
-    50,
-    60,
+    20, 30, 40, 50, 60,
   ]);
 });
 
@@ -110,16 +102,10 @@ test('Shifted peaks', () => {
   let compared = spectraComparison(chrom1, chrom2, options);
   expect(compared.peaksSimilarity).toStrictEqual([1, 1, 1, 1]);
   expect(compared.peaksFirst.map((val) => val.retentionTime)).toStrictEqual([
-    20,
-    30,
-    40,
-    50,
+    20, 30, 40, 50,
   ]);
   expect(compared.peaksSecond.map((val) => val.retentionTime)).toStrictEqual([
-    20,
-    30,
-    40,
-    50,
+    20, 30, 40, 50,
   ]);
 });
 
@@ -179,11 +165,9 @@ test('Remove similar peaks in the similarity matrix column', () => {
 
   expect(compared.peaksSimilarity).toStrictEqual([1, 1]);
   expect(compared.peaksFirst.map((val) => val.retentionTime)).toStrictEqual([
-    40,
-    50,
+    40, 50,
   ]);
   expect(compared.peaksSecond.map((val) => val.retentionTime)).toStrictEqual([
-    50,
-    60,
+    50, 60,
   ]);
 });
diff --git a/src/ms/__tests__/calculateForMF.test.js b/src/ms/__tests__/calculateForMF.test.js
@@ -2,41 +2,41 @@ import { Chromatogram } from '../..';
 import { simple } from '../../../testFiles/examples';
 
 describe('calculateForMF', () => {
-  it('basic', () => {
-    simple.calculateForMF('C8H3', { ionizations: 'H+' });
+  it('basic', async () => {
+    await simple.calculateForMF('C8H3', { ionizations: 'H+' });
     expect(simple.getSeries('C8H3(H+)±0.5').data).toStrictEqual([10, 11]);
   });
 
-  it('basic range', () => {
-    simple.calculateForMF('(CH)0-5C5', { ionizations: 'H+' });
+  it('basic range', async () => {
+    await simple.calculateForMF('(CH)0-5C5', { ionizations: 'H+' });
     expect(simple.getSeries('(CH)0-5C5(H+)±0.5').data).toStrictEqual([10, 11]);
   });
 
-  it('check threshold', () => {
-    simple.calculateForMF('C8H3', { threshold: 0.9, ionizations: 'H+' });
+  it('check threshold', async () => {
+    await simple.calculateForMF('C8H3', { threshold: 0.9, ionizations: 'H+' });
     expect(simple.getSeries('C8H3(H+)±0.5(0.9)').data).toStrictEqual([10, 0]);
   });
 
-  it('check many ionizations', () => {
-    simple.calculateForMF('C8H4', {
+  it('check many ionizations', async () => {
+    await simple.calculateForMF('C8H4', {
       slotWidth: 0.01,
       ionizations: '+,H+',
     });
     expect(simple.getSeries('C8H4(+,H+)±0.005').data).toStrictEqual([0, 0]);
   });
 
-  it('check many ionizations, default slotWidth', () => {
-    simple.calculateForMF('C8H4', { ionizations: '+,H+' });
+  it('check many ionizations, default slotWidth', async () => {
+    await simple.calculateForMF('C8H4', { ionizations: '+,H+' });
     expect(simple.getSeries('C8H4(+,H+)±0.5').data).toStrictEqual([10, 11]);
   });
 
-  it('Errors', () => {
+  it('Errors', async () => {
     const chromatogram = new Chromatogram([1, 2, 3, 5, 6]);
-    expect(() => {
-      chromatogram.calculateForMF();
-    }).toThrow('targetMF must be defined and a string');
-    expect(() => {
-      chromatogram.calculateForMF('C10');
-    }).toThrow('The series "ms" does not exist');
+    await expect(chromatogram.calculateForMF()).rejects.toThrow(
+      'targetMF must be defined and a string',
+    );
+    await expect(chromatogram.calculateForMF('C10')).rejects.toThrow(
+      'The series "ms" does not exist',
+    );
   });
 });