jcampconverter 8.2.0 → 8.2.4

package/package.json

@@ -1,12 +1,14 @@
 {
   "name": "jcampconverter",
-  "version": "8.2.0",
+  "version": "8.2.4",
   "description": "Parse and convert JCAMP data",
   "main": "lib/index.js",
-  "module": "src/index.js",
+  "module": "lib-esm/index.js",
+  "types": "lib/index.d.ts",
   "files": [
     "lib",
-    "src"
+    "src",
+    "lib-esm"
   ],
   "prettier": {
     "arrowParens": "always",
@@ -17,13 +19,20 @@
   },
   "scripts": {
     "build": "cheminfo-build --entry src/index.js --root JcampConverter",
-    "compile": "rollup -c",
-    "prepack": "npm run compile",
+    "check-types": "tsc --noEmit",
+    "clean": "rimraf lib lib-esm",
     "eslint": "eslint src __tests__",
     "eslint-fix": "npm run eslint -- --fix",
-    "test": "npm run test-coverage && npm run eslint",
+    "jscpd": "jscpd -l 10 -i \"**/__tests__/**\" -t 1 src",
+    "prepack": "npm run tsc",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
+    "test": "npm run test-coverage && npm run eslint && npm run prettier && npm run check-types",
     "test-coverage": "jest --coverage",
     "test-only": "jest",
+    "tsc": "npm run clean && npm run tsc-cjs && npm run tsc-esm",
+    "tsc-cjs": "tsc --project tsconfig.cjs.json",
+    "tsc-esm": "tsc --project tsconfig.esm.json",
     "benchmark": "node benchmark/benchmark.js",
     "deopt": "node --trace-opt --trace-deopt --code-comments debug/deoptimize.js > deopt.log",
     "hydra": "node --trace-hydrogen --trace-phase=Z --trace-deopt --code-comments --hydrogen-track-positions --redirect-code-traces --redirect-code-traces-to=code.asm debug/deoptimize.js"
@@ -42,29 +51,25 @@
     "url": "https://github.com/cheminfo/jcampconverter/issues"
   },
   "homepage": "https://github.com/cheminfo/jcampconverter#readme",
-  "jest": {
-    "testEnvironment": "node"
-  },
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.15.4",
-    "@types/jest": "^27.0.1",
+    "@types/jest": "^27.0.3",
     "benchmark": "^2.1.4",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^7.32.0",
-    "eslint-config-cheminfo": "^5.4.0",
-    "eslint-plugin-import": "^2.24.2",
-    "eslint-plugin-jest": "^24.4.0",
-    "eslint-plugin-prettier": "^4.0.0",
+    "eslint": "^8.4.1",
+    "eslint-config-cheminfo-typescript": "^10.2.4",
     "esm": "^3.2.25",
-    "jest": "^27.1.0",
-    "jest-matcher-deep-close-to": "^2.0.1",
-    "prettier": "^2.3.2",
-    "rollup": "^2.56.3"
+    "jest": "^27.4.5",
+    "jest-matcher-deep-close-to": "^3.0.2",
+    "jscpd": "^3.4.2",
+    "prettier": "^2.5.1",
+    "rimraf": "^3.0.2",
+    "ts-jest": "^27.1.1",
+    "typescript": "^4.5.4"
   },
   "dependencies": {
-    "dynamic-typing": "^0.1.2",
-    "ensure-string": "^1.0.0",
+    "dynamic-typing": "^0.1.3",
+    "ensure-string": "^1.1.0",
     "ml-array-median": "^1.1.5",
-    "nmr-processing": "^2.5.0"
+    "nmr-processing": "^6.0.2"
   }
 }

package/src/complexChromatogram.js

@@ -29,7 +29,7 @@ export function complexChromatogram(result) {
     let spectrum = spectra[i];
     chromatogram.times[i] = spectrum.pageValue;
     for (let j = 0; j < existingGCMSFields.length; j++) {
-      chromatogram.series[existingGCMSFields[j]].data[i] = parseFloat(
+      chromatogram.series[existingGCMSFields[j]].data[i] = Number(
         spectrum[existingGCMSFields[j]],
       );
     }

package/src/convert.js

@@ -14,8 +14,6 @@ import profiling from './profiling';
 // the following RegExp can only be used for XYdata, some peakTables have values with a "E-5" ...
 const ntuplesSeparatorRegExp = /[ \t]*,[ \t]*/;
 
-class Spectrum {}
-
 const defaultOptions = {
   keepRecordsRegExp: /^$/,
   canonicDataLabels: true,
@@ -32,22 +30,79 @@ const defaultOptions = {
 
 /**
  *
- * @param {string|ArrayBuffer} jcamp
- * @param {object} [options]
- * @param {number} [options.keepRecordsRegExp=/^$/] By default we don't keep meta information
- * @param {number} [options.canonicDataLabels=true] Canonize the Labels (uppercase without symbol)
- * @param {number} [options.canonicMetadataLabels=false] Canonize the metadata Labels (uppercase without symbol)
- * @param {number} [options.dynamicTyping=false] Convert numbers to Number
- * @param {number} [options.withoutXY=false] Remove the XY data
- * @param {number} [options.chromatogram=false] Special post-processing for GC / HPLC / MS
- * @param {number} [options.keepSpectra=false] Force to keep the spectra in case of 2D
- * @param {number} [options.noContour=false] Don't calculate countour in case of 2D
- * @param {number} [options.nbContourLevels=7] Number of positive / negative contour levels to calculate
- * @param {number} [options.noiseMultiplier=5] Define for 2D the level as 5 times the median as default
- * @param {number} [options.profiling=false] Add profiling information
+ * @typedef {object} ConvertOptions
+ * @property {RegExp} [options.keepRecordsRegExp=/^$/] - By default we don't keep meta information.
+ * @property {boolean} [options.canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
+ * @property {boolean} [options.canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
+ * @property {boolean} [options.dynamicTyping=false] - Convert numbers to Number.
+ * @property {boolean} [options.withoutXY=false] - Remove the XY data.
+ * @property {boolean} [options.chromatogram=false] - Special post-processing for GC / HPLC / MS.
+ * @property {boolean} [options.keepSpectra=false] - Force to keep the spectra in case of 2D.
+ * @property {boolean} [options.noContour=false] - Don't calculate countour in case of 2D.
+ * @property {number} [options.nbContourLevels=7] - Number of positive / negative contour levels to calculate.
+ * @property {number} [options.noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
+ * @property {boolean} [options.profiling=false] - Add profiling information.
+ */
+
+/**
+ *
+ * @typedef {object} Ntuples
+ * @property {string[]} [varname]
+ * @property {string[]} [symbol]
+ * @property {string[]} [vartype]
+ * @property {string[]} [varform]
+ * @property {number[]} [vardim]
+ * @property {string[]} [units]
+ * @property {number[]} [factor]
+ * @property {number[]} [first]
+ * @property {number[]} [last]
+ * @property {number[]} [min]
+ * @property {number[]} [max]
+ * @property {string[]} [nucleus]
+ */
+
+/**
+ * @typedef { Record<string, any> } Spectrum
+ * @property {Record<string, number[]>} [data]
+ * @property {number} [firstX]
+ * @property {number} [lastX]
+ * @property {number} [deltaX]
+ * @property {number} [yFactor]
+ * @property {number} [xFactor]
+ * @property {number} [nbPoints]
+ */
+
+/**
+ *
+ * @typedef {object} Entry
+ * @property {Spectrum[]} spectra
+ * @property {Ntuples} ntuples
+ * @property {object} meta
+ * @property {object} tmp
+ * @property {string} [title]
+ * @property {string} [dataType]
+ * @property {string} [dataClass]
+ * @property {boolean} [twoD]
+ */
+
+/**
+ *
+ * @typedef { object } ConvertResult
+ * @property { object[] | boolean } profiling
+ * @property { string[] } logs
+ * @property { object[] } entries
+ * @property { Entry[] } flatten
+ */
+
+/**
+ * Parse a jcamp.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {ConvertOptions} [options]
+ * @returns {ConvertResult}
  */
 
-export default function convert(jcamp, options = {}) {
+export function convert(jcamp, options = {}) {
   jcamp = ensureString(jcamp);
   options = { ...defaultOptions, ...options };
   options.wantXY = !options.withoutXY;
@@ -65,7 +120,7 @@ export default function convert(jcamp, options = {}) {
   let currentEntry = tmpResult;
   let parentsStack = [];
 
-  let spectrum = new Spectrum();
+  let spectrum = {};
 
   if (typeof jcamp !== 'string') {
     throw new TypeError('the JCAMP should be a string');
@@ -125,7 +180,7 @@ export default function convert(jcamp, options = {}) {
           parsePeakTable(spectrum, dataValue, result);
         }
         currentEntry.spectra.push(spectrum);
-        spectrum = new Spectrum();
+        spectrum = {};
       }
       continue;
     } else if (canonicDataLabel === 'PEAKTABLE') {
@@ -133,7 +188,7 @@ export default function convert(jcamp, options = {}) {
         prepareSpectrum(spectrum);
         parsePeakTable(spectrum, dataValue, result);
         currentEntry.spectra.push(spectrum);
-        spectrum = new Spectrum();
+        spectrum = {};
       }
       continue;
     }
@@ -144,7 +199,7 @@ export default function convert(jcamp, options = {}) {
           parseXYA(spectrum, dataValue);
         }
         currentEntry.spectra.push(spectrum);
-        spectrum = new Spectrum();
+        spectrum = {};
       }
       continue;
     }
@@ -181,35 +236,35 @@ export default function convert(jcamp, options = {}) {
     } else if (canonicDataLabel === 'YUNITS') {
       spectrum.yUnits = dataValue;
     } else if (canonicDataLabel === 'FIRSTX') {
-      spectrum.firstX = parseFloat(dataValue);
+      spectrum.firstX = Number(dataValue);
     } else if (canonicDataLabel === 'LASTX') {
-      spectrum.lastX = parseFloat(dataValue);
+      spectrum.lastX = Number(dataValue);
     } else if (canonicDataLabel === 'FIRSTY') {
-      spectrum.firstY = parseFloat(dataValue);
+      spectrum.firstY = Number(dataValue);
     } else if (canonicDataLabel === 'LASTY') {
-      spectrum.lastY = parseFloat(dataValue);
+      spectrum.lastY = Number(dataValue);
     } else if (canonicDataLabel === 'NPOINTS') {
-      spectrum.nbPoints = parseFloat(dataValue);
+      spectrum.nbPoints = Number(dataValue);
     } else if (canonicDataLabel === 'XFACTOR') {
-      spectrum.xFactor = parseFloat(dataValue);
+      spectrum.xFactor = Number(dataValue);
     } else if (canonicDataLabel === 'YFACTOR') {
-      spectrum.yFactor = parseFloat(dataValue);
+      spectrum.yFactor = Number(dataValue);
     } else if (canonicDataLabel === 'MAXX') {
-      spectrum.maxX = parseFloat(dataValue);
+      spectrum.maxX = Number(dataValue);
     } else if (canonicDataLabel === 'MINX') {
-      spectrum.minX = parseFloat(dataValue);
+      spectrum.minX = Number(dataValue);
     } else if (canonicDataLabel === 'MAXY') {
-      spectrum.maxY = parseFloat(dataValue);
+      spectrum.maxY = Number(dataValue);
     } else if (canonicDataLabel === 'MINY') {
-      spectrum.minY = parseFloat(dataValue);
+      spectrum.minY = Number(dataValue);
     } else if (canonicDataLabel === 'DELTAX') {
-      spectrum.deltaX = parseFloat(dataValue);
+      spectrum.deltaX = Number(dataValue);
     } else if (
       canonicDataLabel === '.OBSERVEFREQUENCY' ||
       canonicDataLabel === '$SFO1'
     ) {
       if (!spectrum.observeFrequency) {
-        spectrum.observeFrequency = parseFloat(dataValue);
+        spectrum.observeFrequency = Number(dataValue);
       }
     } else if (canonicDataLabel === '.OBSERVENUCLEUS') {
       if (!spectrum.xType) {
@@ -219,7 +274,7 @@ export default function convert(jcamp, options = {}) {
       // OFFSET for Bruker spectra
       currentEntry.shiftOffsetNum = 0;
       if (!spectrum.shiftOffsetVal) {
-        spectrum.shiftOffsetVal = parseFloat(dataValue);
+        spectrum.shiftOffsetVal = Number(dataValue);
       }
     } else if (canonicDataLabel === '$REFERENCEPOINT') {
       // OFFSET for Varian spectra
@@ -227,7 +282,7 @@ export default function convert(jcamp, options = {}) {
       //         } else if (canonicDataLabel=='.SHIFTREFERENCE') {   // OFFSET FOR Bruker Spectra
       //                 var parts = dataValue.split(/ *, */);
       //                 currentEntry.shiftOffsetNum = parseInt(parts[2].trim());
-      //                 spectrum.shiftOffsetVal = parseFloat(parts[3].trim());
+      //                 spectrum.shiftOffsetVal = Number(parts[3].trim());
     } else if (canonicDataLabel === 'VARNAME') {
       currentEntry.ntuples.varname = dataValue.split(ntuplesSeparatorRegExp);
     } else if (canonicDataLabel === 'SYMBOL') {
@@ -268,10 +323,10 @@ export default function convert(jcamp, options = {}) {
       }
     } else if (canonicDataLabel === 'PAGE') {
       spectrum.page = dataValue.trim();
-      spectrum.pageValue = parseFloat(dataValue.replace(/^.*=/, ''));
+      spectrum.pageValue = Number(dataValue.replace(/^.*=/, ''));
       spectrum.pageSymbol = spectrum.page.replace(/[=].*/, '');
     } else if (canonicDataLabel === 'RETENTIONTIME') {
-      spectrum.pageValue = parseFloat(dataValue);
+      spectrum.pageValue = Number(dataValue);
     } else if (isMSField(canonicDataLabel)) {
       spectrum[convertMSFieldToLabel(canonicDataLabel)] = dataValue;
     } else if (canonicDataLabel === 'SAMPLEDESCRIPTION') {

package/src/convertToFloatArray.js

@@ -1,7 +1,7 @@
 export default function convertToFloatArray(stringArray) {
   let floatArray = [];
   for (let i = 0; i < stringArray.length; i++) {
-    floatArray.push(parseFloat(stringArray[i]));
+    floatArray.push(Number(stringArray[i]));
   }
   return floatArray;
 }

package/src/createTree.js

@@ -1,13 +1,27 @@
 import { ensureString } from 'ensure-string';
 
 /**
- * Parse the jcamp to extract the structure as a tree
- * @param {string|ArrayBuffer jcamp
- * @param {object} [options={}]
- * @param {boolean} [options.flatten=false]
- * @returns
+ *
+ * @typedef {object} CreateTreeOptions
+ * @property {boolean} [flatten=false]
  */
-export default function createTree(jcamp, options = {}) {
+
+/**
+ *
+ * @typedef {object} Tree
+ * @property {string} title
+ * @property {string} jcamp
+ * @property {Tree[]} [children]
+ */
+
+/**
+ * Parse the jcamp to extract the structure as a tree.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
+ * @param {CreateTreeOptions} [options={}]
+ * @returns {Tree[]}
+ */
+export function createTree(jcamp, options = {}) {
   jcamp = ensureString(jcamp);
   const { flatten = false } = options;
   if (typeof jcamp !== 'string') {

package/src/index.js

@@ -1,2 +1,2 @@
-export { default as createTree } from './createTree';
-export { default as convert } from './convert';
+export { createTree } from './createTree';
+export { convert } from './convert';

package/src/parse/parsePeakTable.js

@@ -32,9 +32,9 @@ function parseXY(spectrum, value, result) {
       .split(peakTableSplitRegExp);
     if (values.length % 2 === 0) {
       for (let j = 0; j < values.length; j = j + 2) {
-        // takes around 40% of the time to add and parse the 2 values nearly exclusively because of parseFloat
-        currentData.x.push(parseFloat(values[j]) * spectrum.xFactor);
-        currentData.y.push(parseFloat(values[j + 1]) * spectrum.yFactor);
+        // takes around 40% of the time to add and parse the 2 values nearly exclusively because of Number
+        currentData.x.push(Number(values[j]) * spectrum.xFactor);
+        currentData.y.push(Number(values[j + 1]) * spectrum.yFactor);
       }
     } else {
       result.logs.push(`Format error: ${values}`);
@@ -60,9 +60,7 @@ function parseXYZ(spectrum, value, result) {
     if (values.length % numberOfVariables === 0) {
       for (let j = 0; j < values.length; j++) {
         // todo should try to find a xFactor (y, ...)
-        currentData[variables[j % numberOfVariables]].push(
-          parseFloat(values[j]),
-        );
+        currentData[variables[j % numberOfVariables]].push(Number(values[j]));
       }
     } else {
       result.logs.push(`Format error: ${values}`);

package/src/parse/parseXYA.js

@@ -10,7 +10,7 @@ export default function parseXYA(spectrum, value) {
 
   for (let i = 1; i < lines.length; i++) {
     values = lines[i].trim().replace(removeSymbolRegExp, '').split(',');
-    currentData.x.push(parseFloat(values[0]));
-    currentData.y.push(parseFloat(values[1]));
+    currentData.x.push(Number(values[0]));
+    currentData.y.push(Number(values[1]));
   }
 }