ir-spectrum 3.1.0 → 3.2.0

package/package.json

@@ -1,11 +1,10 @@
 {
   "name": "ir-spectrum",
-  "version": "3.1.0",
-  "description": "",
-  "main": "lib/index.js",
-  "module": "src/index.js",
+  "version": "3.2.0",
+  "description": "Package used to handle IR spectra in SciPeaks.",
+  "type": "module",
+  "exports": "./src/index.js",
   "files": [
-    "lib",
     "src"
   ],
   "scripts": {
@@ -13,12 +12,11 @@
     "build-doc": "cheminfo doc",
     "eslint": "eslint src",
     "eslint-fix": "npm run eslint -- --fix",
-    "prepack": "rollup -c",
     "prettier": "prettier --check src",
     "prettier-write": "prettier --write src",
-    "test": "npm run test-coverage && npm run eslint && npm run prettier",
-    "test-coverage": "vitest run --coverage",
-    "test-only": "vitest run"
+    "test": "npm run test-only && npm run eslint && npm run prettier",
+    "test-only": "vitest run --coverage",
+    "test-import": "node -e \"import('file://' + process.cwd() + '/src/index.js').then(console.log)\""
   },
   "repository": {
     "type": "git",
@@ -31,25 +29,20 @@
     "url": "https://github.com/cheminfo/ir-spectrum/issues"
   },
   "homepage": "https://github.com/cheminfo/ir-spectrum#readme",
-  "jest": {
-    "testEnvironment": "node"
-  },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.25.9",
-    "@vitest/coverage-v8": "^2.1.5",
-    "cheminfo-build": "^1.2.0",
-    "codecov": "^3.8.3",
-    "eslint": "^9.14.0",
-    "eslint-config-cheminfo": "^12.0.1",
+    "@babel/plugin-transform-modules-commonjs": "^7.27.1",
+    "@vitest/coverage-v8": "^3.2.4",
+    "cheminfo-build": "^1.2.1",
+    "eslint": "^9.32.0",
+    "eslint-config-cheminfo": "^15.0.1",
     "esm": "^3.2.25",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "prettier": "^3.3.3",
-    "rollup": "^4.26.0",
-    "vitest": "^2.1.5"
+    "prettier": "^3.6.2",
+    "vitest": "^3.2.4"
   },
   "dependencies": {
     "common-spectrum": "2.12.0",
-    "ml-gsd": "^12.1.8",
+    "ml-gsd": "^13.0.1",
     "spc-parser": "^1.0.0",
     "uninstall": "^0.0.0"
   },

package/src/from/fromJcamp.js

@@ -1,6 +1,6 @@
 import { fromJcamp as commonFromJcamp } from 'common-spectrum';
 
-import { spectrumCallback } from './utils/spectrumCallback';
+import { spectrumCallback } from './utils/spectrumCallback.js';
 
 /**
  * Creates a new Analysis from a SPC buffer

package/src/from/fromSPC.js

@@ -1,7 +1,7 @@
 import { Analysis } from 'common-spectrum';
 import { parse } from 'spc-parser';
 
-import { spectrumCallback } from './utils/spectrumCallback';
+import { spectrumCallback } from './utils/spectrumCallback.js';
 
 /**
  * Creates a new Analysis from a SPC buffer

package/src/index.js

@@ -5,9 +5,9 @@ import {
 } from 'common-spectrum';
 
 import { convertPeak } from './convertPeak.js';
-import { getAnnotations } from './jsgraph/getAnnotations';
+import { getAnnotations } from './jsgraph/getAnnotations.js';
 
-export { Analysis, AnalysesManager, toJcamp } from 'common-spectrum';
+export { AnalysesManager, Analysis, toJcamp } from 'common-spectrum';
 
 export function peakPicking(spectrum, target, options) {
   const peak = originalPeakPicking(spectrum, target, options);
@@ -21,7 +21,7 @@ export function autoPeakPicking(spectrum, options) {
   return peaks.map((peak) => convertPeak(peak, spectrum));
 }
 
-export { fromJcamp } from './from/fromJcamp';
-export { fromSPC } from './from/fromSPC';
+export { fromJcamp } from './from/fromJcamp.js';
+export { fromSPC } from './from/fromSPC.js';
 
 export const JSGraph = { ...OriginalJSGraph, getAnnotations };

package/lib/index.js

@@ -1,312 +0,0 @@
-'use strict';
-
-var commonSpectrum = require('common-spectrum');
-var spcParser = require('spc-parser');
-
-function convertPeak(peak, spectrum) {
-  return {
-    wavenumber: peak.x,
-    absorbance: peak.a,
-    transmittance: peak.t / 100,
-    kind: getPeakKind(
-      peak.t,
-      spectrum.variables.t.min,
-      spectrum.variables.t.max,
-    ),
-  };
-}
-
-function getPeakKind(transmittance, minTransmittance, maxTransmittance) {
-  let position =
-    (maxTransmittance - transmittance) / (maxTransmittance - minTransmittance);
-  if (position < 0.33) {
-    return 'w';
-  } else if (position < 0.66) {
-    return 'm';
-  }
-  return 'S';
-}
-
-/**
- * @typedef {object} Peak
- * @property {number} wavenumber
- * @property {number} transmittance
- * @property {number} absorbance
- * @property {number} kind
- * @property {number} assignment
- */
-
-/**
- * Creates annotations for jsgraph that allows to display the result of peak picking
- * @param {Array<Peak>} peaks
- * @param {object} [options={}]
- * @param {string} [options.fillColor='green']
- * @param {string} [options.strokeColor='red']
- * @param {string} [options.showKind=true] - Display the kind, 'm', 'w', 'S'
- * @param {string} [options.showAssignment=true] - Display the assignment
- * @param {Function} [options.createFct] - (annotation, peak) => {}: callback allowing to add properties
- * @param {string} [options.mode='t100'] - 't100'=transmittance in %, 't'=transmittance, 'a'=absorbance
- * @returns array
- */
-
-function getAnnotations(peaks, options = {}) {
-  const {
-    fillColor = 'green',
-    strokeColor = 'red',
-    creationFct,
-    mode = 't100',
-  } = options;
-  let annotations = peaks.map((peak) => {
-    let annotation = {
-      line: 1,
-      type: 'rect',
-      strokeColor,
-      strokeWidth: 0,
-      fillColor,
-    };
-    if (creationFct) {
-      creationFct(annotation, peak);
-    }
-    switch (mode) {
-      case 'a':
-        annotationAbsorbance(annotation, peak, options);
-        break;
-      case 't':
-        annotationTransmittance(annotation, peak, 1, options);
-        break;
-      case 't100':
-        annotationTransmittance(annotation, peak, 100, options);
-        break;
-    }
-    return annotation;
-  });
-  return annotations;
-}
-
-function annotationTransmittance(annotation, peak, factor = 1, options = {}) {
-  const { showKind = true, showAssignment = true } = options;
-  let labels = [];
-  let line = 0;
-
-  if (showKind) {
-    labels.push({
-      text: peak.kind,
-      size: '18px',
-      anchor: 'middle',
-      color: 'red',
-      position: {
-        x: peak.wavenumber,
-        y: peak.transmittance * factor,
-        dy: `${23 + line * 14}px`,
-      },
-    });
-    line++;
-  }
-
-  if (showAssignment) {
-    labels.push({
-      text: peak.assignment,
-      size: '18px',
-      anchor: 'middle',
-      color: 'darkred',
-      position: {
-        x: peak.wavenumber,
-        y: peak.transmittance * factor,
-        dy: `${23 + line * 14}px`,
-      },
-    });
-    line++;
-  }
-
-  annotation.labels = labels;
-  annotation.position = [
-    {
-      x: peak.wavenumber,
-      y: peak.transmittance * factor,
-      dy: '10px',
-      dx: '-1px',
-    },
-    {
-      x: peak.wavenumber,
-      y: peak.transmittance * factor,
-      dy: '5px',
-      dx: '1px',
-    },
-  ];
-}
-
-function annotationAbsorbance(annotation, peak, options = {}) {
-  const {
-    showKind = true,
-    showAssignment = true,
-    assignmentAngle = -45,
-  } = options;
-  let labels = [];
-  let line = 0;
-
-  if (showKind) {
-    labels.push({
-      text: peak.kind,
-      size: '18px',
-      anchor: 'middle',
-      color: 'red',
-      position: {
-        x: peak.wavenumber,
-        y: peak.absorbance,
-        dy: `${-15 - line * 14}px`,
-      },
-    });
-    line++;
-  }
-
-  if (showAssignment) {
-    labels.push({
-      text: peak.assignment,
-      size: '18px',
-      angle: assignmentAngle,
-      anchor: 'left',
-      color: 'darkred',
-      position: {
-        x: peak.wavenumber,
-        y: peak.absorbance,
-        dy: `${-15 - line * 14}px`,
-      },
-    });
-    line++;
-  }
-
-  annotation.labels = labels;
-
-  annotation.position = [
-    {
-      x: peak.wavenumber,
-      y: peak.absorbance,
-      dy: '-10px',
-      dx: '-1px',
-    },
-    {
-      x: peak.wavenumber,
-      y: peak.absorbance,
-      dy: '-5px',
-      dx: '1px',
-    },
-  ];
-}
-
-function spectrumCallback(variables) {
-  // we add missing absorbance / transmittance
-  // variable a = absorbance
-  // variable t = transmittance
-  let yVariable = variables.y;
-  let absorbance = true;
-  if (yVariable.label.toLowerCase().includes('trans')) {
-    absorbance = false;
-  }
-  if (absorbance) {
-    variables.a = { ...yVariable, symbol: 'a', data: yVariable.data.slice() };
-    variables.t = {
-      data: yVariable.data.map((absorbance) => 10 ** -absorbance * 100),
-      label: 'Transmittance (%)',
-      symbol: 't',
-      units: '',
-    };
-  } else {
-    const factor =
-      yVariable.label.includes('%') ||
-      yVariable.label.toLowerCase().includes('percent')
-        ? 100
-        : 1;
-
-    variables.a = {
-      data: yVariable.data.map(
-        (transmittance) => -Math.log10(transmittance / factor),
-      ),
-      symbol: 'a',
-      label: 'Absorbance',
-      units: '',
-    };
-    if (factor === 100) {
-      variables.t = { ...yVariable, symbol: 't' };
-      variables.t.data = variables.t.data.slice();
-    } else {
-      variables.t = {
-        units: '',
-        label: 'Transmittance (%)',
-        symbol: 't',
-        data: yVariable.data.map((transmittance) => transmittance * 100),
-      };
-    }
-  }
-}
-
-/**
- * Creates a new Analysis from a SPC buffer
- * @param {ArrayBuffer|string} jcamp
- * @param {object} [options={}]
- * @param {string|number} [options.id=Math.random()]
- * @param {string} [options.label=options.id] - human redeable label
- * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
- * @returns {Analysis} - New class element with the given data
- */
-function fromJcamp(jcamp, options = {}) {
-  return commonSpectrum.fromJcamp(jcamp, { ...options, spectrumCallback });
-}
-
-/**
- * Creates a new Analysis from a SPC buffer
- * @param {ArrayBuffer} buffer
- * @param {object} [options={}]
- * @param {object} [options.id=Math.random()]
- * @param {string} [options.label=options.id] - human redeable label
- * @param {string} [options.spectrumCallback] - a callback to apply on variables when creating spectrum. Default will add a and t
- * @returns {Analysis} - New class element with the given data
- */
-
-function fromSPC(buffer, options = {}) {
-  let analysis = new commonSpectrum.Analysis({ ...options, spectrumCallback });
-  let result = spcParser.parse(buffer);
-
-  if (result.meta) delete result.meta.parameters;
-
-  for (let spectrum of result.spectra) {
-    if (spectrum.meta) delete spectrum.meta.parameters;
-    analysis.pushSpectrum(spectrum.variables, {
-      dataType: 'IR SPECTRUM',
-      title: '',
-      meta: { ...result.meta, ...spectrum.meta },
-    });
-  }
-  return analysis;
-}
-
-function peakPicking(spectrum, target, options) {
-  const peak = commonSpectrum.peakPicking(spectrum, target, options);
-  if (!peak) return undefined;
-  return convertPeak(peak, spectrum);
-}
-
-function autoPeakPicking(spectrum, options) {
-  const peaks = commonSpectrum.autoPeakPicking(spectrum, options);
-  if (!peaks) return [];
-  return peaks.map((peak) => convertPeak(peak, spectrum));
-}
-
-const JSGraph = { ...commonSpectrum.JSGraph, getAnnotations };
-
-Object.defineProperty(exports, "AnalysesManager", {
-  enumerable: true,
-  get: function () { return commonSpectrum.AnalysesManager; }
-});
-Object.defineProperty(exports, "Analysis", {
-  enumerable: true,
-  get: function () { return commonSpectrum.Analysis; }
-});
-Object.defineProperty(exports, "toJcamp", {
-  enumerable: true,
-  get: function () { return commonSpectrum.toJcamp; }
-});
-exports.JSGraph = JSGraph;
-exports.autoPeakPicking = autoPeakPicking;
-exports.fromJcamp = fromJcamp;
-exports.fromSPC = fromSPC;
-exports.peakPicking = peakPicking;