chore: migrate from jest to vitest

cheminfo · Oct 14, 2024 · 04542c7 · 04542c7
1 parent 3109cbf
commit 04542c7
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Showing 15 changed files with 266 additions and 11 deletions.
diff --git a/eslint.config.mjs b/eslint.config.mjs
@@ -6,7 +6,6 @@ export default [
   {
     languageOptions: {
       globals: {
-        ...globals.jest,
         ...globals.node,
       },
     },

diff --git a/package.json b/package.json
@@ -15,9 +15,9 @@
     "prepack": "rollup -c",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-coverage && npm run eslint",
-    "test-coverage": "jest --coverage",
-    "test-only": "jest"
+    "test": "npm run test-coverage && npm run eslint && npm run prettier",
+    "test-coverage": "vitest run --coverage",
+    "test-only": "vitest run"
   },
   "repository": {
     "type": "git",
@@ -30,22 +30,18 @@
     "url": "https://github.com/cheminfo/xps-analysis/issues"
   },
   "homepage": "https://github.com/cheminfo/xps-analysis#readme",
-  "jest": {
-    "testEnvironment": "node"
-  },
   "devDependencies": {
     "@babel/plugin-transform-modules-commonjs": "^7.25.7",
-    "@types/jest": "^29.5.13",
     "cheminfo-build": "^1.2.0",
     "eslint": "^9.12.0",
     "eslint-config-cheminfo": "^12.0.1",
     "globals": "^15.11.0",
-    "jest": "^29.7.0",
     "openchemlib": "^8.15.0",
     "papaparse": "^5.4.1",
     "prettier": "^3.3.3",
     "rollup": "^4.24.0",
-    "spectrum-generator": "^8.0.11"
+    "spectrum-generator": "^8.0.11",
+    "vitest": "^2.1.3"
   },
   "dependencies": {
     "common-spectrum": "2.12.0",

diff --git a/src/__tests__/index.test.js b/src/__tests__/index.test.js
@@ -1,6 +1,8 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
+import { describe, it, expect } from 'vitest';
+
 import { fromVamas, toJcamp } from '..';
 
 describe('fromVamas', () => {

diff --git a/src/__tests__/peakPicking.test.js b/src/__tests__/peakPicking.test.js
@@ -1,6 +1,8 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
+import { describe, it, expect } from 'vitest';
+
 import { fromVamas } from '..';
 import { peakPicking } from '../peakPicking';
 

diff --git a/src/from/__tests__/__snapshots__/fromVamas.test.js.snap b/src/from/__tests__/__snapshots__/fromVamas.test.js.snap
@@ -1,4 +1,244 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
+// Vitest Snapshot v1, https://vitest.dev/guide/snapshot.html
+
+exports[`fromVamas > Cellulose with CASA information, regions and components 1`] = `
+{
+  "analyserMode": "FAT",
+  "analysisSource": {
+    "beamWidthX": {
+      "units": "um",
+      "value": 6000,
+    },
+    "beamWidthY": {
+      "units": "um",
+      "value": 500,
+    },
+    "characteristicEnergy": {
+      "units": "eV",
+      "value": 1486.6,
+    },
+    "label": "Al Ka, Monochromated",
+  },
+  "components": [
+    {
+      "area": {
+        "lowerBound": 1e-20,
+        "upperBound": 126904.8,
+        "value": 4830.0138,
+      },
+      "assignment": "C 1s 1",
+      "atomicMass": 12.011,
+      "bindingEnergy": {
+        "units": "eV",
+        "value": 286.7736,
+      },
+      "componentID": "C 1s 1",
+      "fwhm": {
+        "lowerBound": 0.25,
+        "upperBound": 6.25,
+        "value": 1.1057933,
+      },
+      "groupIndex": -1,
+      "kineticEnergy": {
+        "units": "eV",
+        "value": 1199.8264,
+      },
+      "position": {
+        "lowerBound": 1199.7,
+        "upperBound": 1199.87,
+        "value": 1199.8264,
+      },
+      "relativeSensitivityFactor": 0.278,
+      "shape": {
+        "kind": "lorentzianAsymmetric",
+        "options": {
+          "alpha": 1.4,
+          "beta": 1.7,
+          "m": 100,
+        },
+      },
+      "uncorrectedRSF": 0.278,
+    },
+    {
+      "area": {
+        "constrain": {
+          "factor": 0.2048,
+          "linkedComponent": 0,
+        },
+        "lowerBound": 0,
+        "upperBound": 2000,
+        "value": 989.18682,
+      },
+      "assignment": "C 1s 2",
+      "atomicMass": 12.011,
+      "bindingEnergy": {
+        "units": "eV",
+        "value": 288.1950999999999,
+      },
+      "componentID": "C 1s 2",
+      "fwhm": {
+        "lowerBound": 0.25,
+        "upperBound": 6.25,
+        "value": 1.1121055,
+      },
+      "groupIndex": -1,
+      "kineticEnergy": {
+        "units": "eV",
+        "value": 1198.4049,
+      },
+      "position": {
+        "lowerBound": 1198.34,
+        "upperBound": 1198.74,
+        "value": 1198.4049,
+      },
+      "relativeSensitivityFactor": 0.278,
+      "shape": {
+        "kind": "lorentzianAsymmetric",
+        "options": {
+          "alpha": 1.4,
+          "beta": 1.6,
+          "m": 100,
+        },
+      },
+      "uncorrectedRSF": 0.278,
+    },
+    {
+      "area": {
+        "lowerBound": 0,
+        "upperBound": 243,
+        "value": 56.812945,
+      },
+      "assignment": "C 1s degrad",
+      "atomicMass": 12.011,
+      "bindingEnergy": {
+        "units": "eV",
+        "value": 288.8453999999999,
+      },
+      "componentID": "C 1s degrad",
+      "fwhm": {
+        "lowerBound": 0.25,
+        "upperBound": 2,
+        "value": 0.82920074,
+      },
+      "groupIndex": -1,
+      "kineticEnergy": {
+        "units": "eV",
+        "value": 1197.7546,
+      },
+      "position": {
+        "lowerBound": 1197.3546,
+        "upperBound": 1197.7546,
+        "value": 1197.7546,
+      },
+      "relativeSensitivityFactor": 0.278,
+      "shape": {
+        "kind": "gaussianLorentzianProduct",
+        "options": {
+          "mixingRatio": 30,
+        },
+      },
+      "uncorrectedRSF": 0.278,
+    },
+    {
+      "area": {
+        "lowerBound": 1e-20,
+        "upperBound": 126904.8,
+        "value": 100.40835,
+      },
+      "assignment": "C 1s Adv.C",
+      "atomicMass": 12.011,
+      "bindingEnergy": {
+        "units": "eV",
+        "value": 284.8711999999998,
+      },
+      "componentID": "C 1s Adv.C",
+      "fwhm": {
+        "lowerBound": 0.25,
+        "upperBound": 6.25,
+        "value": 0.74742285,
+      },
+      "groupIndex": -1,
+      "kineticEnergy": {
+        "units": "eV",
+        "value": 1201.7288,
+      },
+      "position": {
+        "lowerBound": 1201.4,
+        "upperBound": 1201.8,
+        "value": 1201.7288,
+      },
+      "relativeSensitivityFactor": 0.278,
+      "shape": {
+        "kind": "gaussianLorentzianProduct",
+        "options": {
+          "mixingRatio": 30,
+        },
+      },
+      "uncorrectedRSF": 0.278,
+    },
+  ],
+  "energyType": {
+    "kind": "binding",
+    "units": "eV",
+  },
+  "from": 294.16,
+  "region": {
+    "auger": {
+      "element": null,
+      "transition": null,
+    },
+    "name": "C 1s",
+    "orbital": {
+      "angularMomentum": "s",
+      "element": "C",
+      "shell": 1,
+    },
+  },
+  "regions": [
+    {
+      "background": {
+        "parameters": {
+          "averageWidth": 1,
+          "bindingEnergyEnd": {
+            "units": "eV",
+            "value": 283.34839999999986,
+          },
+          "bindingEnergyStart": {
+            "units": "eV",
+            "value": 293.2871,
+          },
+          "crossSection": [
+            40.442441,
+            -450,
+            0,
+            0,
+          ],
+          "endOffset": 0,
+          "kineticEnergyEnd": {
+            "units": "eV",
+            "value": 1203.2516,
+          },
+          "kineticEnergyStart": {
+            "units": "eV",
+            "value": 1193.3129,
+          },
+          "relativeSensitivityFactor": 0.278,
+          "startOffset": 0,
+        },
+        "rawParameters": "1193.3129 1203.2516 0.278 2 0 0 40.442441 -450 0 0",
+        "type": "Shirley",
+      },
+      "block": {
+        "atomicMass": 12.011,
+        "regionBlockID": "C 1s",
+        "relativeSensitivityFactor": 0.278,
+      },
+      "regionID": "C 1s",
+    },
+  ],
+  "speciesLabel": "C",
+  "to": 282.16,
+}
+`;
 
 exports[`fromVamas Cellulose with CASA information, regions and components 1`] = `
 {

diff --git a/src/from/__tests__/fromVamas.test.js b/src/from/__tests__/fromVamas.test.js
@@ -1,6 +1,8 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
+import { describe, it, expect } from 'vitest';
+
 import { fromVamas } from '../fromVamas';
 
 describe('fromVamas', () => {

diff --git a/src/from/__tests__/getNormalizedMeta.test.js b/src/from/__tests__/getNormalizedMeta.test.js
@@ -1,3 +1,5 @@
+import { test, expect } from 'vitest';
+
 import { getNormalizedMeta } from '../getNormalizedMeta';
 
 import meta from './meta.json';

diff --git a/src/from/__tests__/mapComponents.test.js b/src/from/__tests__/mapComponents.test.js
@@ -1,4 +1,5 @@
 import { parseCASA } from 'vamas';
+import { describe, it, expect } from 'vitest';
 
 import { mapComponents } from '../mapComponents';
 

diff --git a/src/from/__tests__/parseRegion.test.js b/src/from/__tests__/parseRegion.test.js
@@ -1,3 +1,5 @@
+import { describe, it, expect } from 'vitest';
+
 import { parseRegion } from '../parseRegion.js';
 
 describe('XPS region parser', () => {

diff --git a/src/utilities/background/__tests__/appendBackground.test.js b/src/utilities/background/__tests__/appendBackground.test.js
@@ -1,6 +1,8 @@
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
+import { test } from 'vitest';
+
 import { fromVamas } from '../../../from/fromVamas.js';
 import { appendBackground } from '../appendBackground.js';
 

diff --git a/src/utilities/background/__tests__/linear.test.js b/src/utilities/background/__tests__/linear.test.js
@@ -1,3 +1,5 @@
+import { test, expect } from 'vitest';
+
 import { linear } from '../linear';
 
 test('linear', () => {

diff --git a/src/utilities/background/__tests__/shirley.test.js b/src/utilities/background/__tests__/shirley.test.js
@@ -1,3 +1,5 @@
+import { test, expect } from 'vitest';
+
 import { shirley } from '../shirley';
 
 test('shirley', () => {

diff --git a/src/utilities/prediction/__tests__/predictPolymer.test.js b/src/utilities/prediction/__tests__/predictPolymer.test.js
@@ -1,4 +1,5 @@
 import { Molecule } from 'openchemlib';
+import { test } from 'vitest';
 
 import { predictPolymer } from '../predictPolymer';
 

diff --git a/src/utilities/prediction/__tests__/predictUsingAI.test.js b/src/utilities/prediction/__tests__/predictUsingAI.test.js
@@ -1,4 +1,5 @@
 import OCL from 'openchemlib';
+import { test, expect } from 'vitest';
 
 import { predictUsingAI } from '../predictUsingAI.js';
 

diff --git a/src/utilities/prediction/__tests__/predictUsingHoseCodes.test.js b/src/utilities/prediction/__tests__/predictUsingHoseCodes.test.js
@@ -1,4 +1,5 @@
 import OCL from 'openchemlib';
+import { test, expect } from 'vitest';
 
 import { predictUsingHoseCodes } from '../predictUsingHoseCodes.js';