jcampconverter - npm Package Compare versions

Comparing version 8.2.1 to 8.2.2

CHANGELOG.md

 # Changelog
 
+### [8.2.2](https://www.github.com/cheminfo/jcampconverter/compare/v8.2.1...v8.2.2) (2021-11-05)
+
+
+### Bug Fixes
+
+* replace parseFloat by Number ([e65c194](https://www.github.com/cheminfo/jcampconverter/commit/e65c19483e8c429d73e540614e7e020cdd660e0b))
+
 ### [8.2.1](https://www.github.com/cheminfo/jcampconverter/compare/v8.2.0...v8.2.1) (2021-09-30)
@@ -4,0 +11,0 @@

lib/index.js

@@ -15,4 +15,5 @@ 'use strict';
 /**
- * Parse the jcamp to extract the structure as a tree
- * @param {string|ArrayBuffer jcamp
+ * Parse the jcamp to extract the structure as a tree.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
  * @param {object} [options={}]
@@ -128,3 +129,3 @@ * @param {boolean} [options.flatten=false]
     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]],
@@ -151,3 +152,3 @@ );
   for (let i = 0; i < stringArray.length; i++) {
-    floatArray.push(parseFloat(stringArray[i]));
+    floatArray.push(Number(stringArray[i]));
   }
@@ -365,5 +366,5 @@ return floatArray;
       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);
       }
@@ -394,5 +395,3 @@ } else {
         // todo should try to find a xFactor (y, ...)
-        currentData[variables[j % numberOfVariables]].push(
-          parseFloat(values[j]),
-        );
+        currentData[variables[j % numberOfVariables]].push(Number(values[j]));
       }
@@ -417,4 +416,4 @@ } else {
     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]));
   }
@@ -923,16 +922,18 @@ }
 /**
+ * Parse a jcamp.
  *
- * @param {string|ArrayBuffer} jcamp
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
  * @param {object} [options]
- * @param {number} [options.keepRecordsRegExp=/^$/] By default we don't keep meta information
- * @param {number} [options.canonicDataLabels=true] Canonize the Labels (uppercase without symbol)
- * @param {number} [options.canonicMetadataLabels=false] Canonize the metadata Labels (uppercase without symbol)
- * @param {number} [options.dynamicTyping=false] Convert numbers to Number
- * @param {number} [options.withoutXY=false] Remove the XY data
- * @param {number} [options.chromatogram=false] Special post-processing for GC / HPLC / MS
- * @param {number} [options.keepSpectra=false] Force to keep the spectra in case of 2D
- * @param {number} [options.noContour=false] Don't calculate countour in case of 2D
- * @param {number} [options.nbContourLevels=7] Number of positive / negative contour levels to calculate
- * @param {number} [options.noiseMultiplier=5] Define for 2D the level as 5 times the median as default
- * @param {number} [options.profiling=false] Add profiling information
+ * @param {number} [options.keepRecordsRegExp=/^$/] - 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.
+ * @returns {object}
  */
@@ -1074,25 +1075,25 @@
     } 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 (
@@ -1103,3 +1104,3 @@ canonicDataLabel === '.OBSERVEFREQUENCY' ||
       if (!spectrum.observeFrequency) {
-        spectrum.observeFrequency = parseFloat(dataValue);
+        spectrum.observeFrequency = Number(dataValue);
       }
@@ -1114,3 +1115,3 @@ } else if (canonicDataLabel === '.OBSERVENUCLEUS') {
       if (!spectrum.shiftOffsetVal) {
-        spectrum.shiftOffsetVal = parseFloat(dataValue);
+        spectrum.shiftOffsetVal = Number(dataValue);
       }
@@ -1157,6 +1158,6 @@ } else if (canonicDataLabel === '$REFERENCEPOINT') ; else if (canonicDataLabel === 'VARNAME') {
       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)) {
@@ -1163,0 +1164,0 @@ spectrum[convertMSFieldToLabel(canonicDataLabel)] = dataValue;

package.json

 {
   "name": "jcampconverter",
-  "version": "8.2.1",
+  "version": "8.2.2",
   "description": "Parse and convert JCAMP data",
@@ -22,4 +22,7 @@ "main": "lib/index.js",
     "eslint-fix": "npm run eslint -- --fix",
+    "jscpd": "jscpd -l 10 -i \"**/__tests__/**\" -t 1 src",
     "prepack": "rollup -c",
-    "test": "npm run test-coverage && npm run eslint",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
+    "test": "npm run test-coverage && npm run eslint && npm run prettier",
     "test-coverage": "jest --coverage",
@@ -49,16 +52,14 @@ "test-only": "jest",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.15.4",
+    "@babel/plugin-transform-modules-commonjs": "^7.16.0",
     "@types/jest": "^27.0.2",
     "benchmark": "^2.1.4",
     "cheminfo-build": "^1.1.11",
-    "eslint": "^7.32.0",
-    "eslint-config-cheminfo": "^5.5.0",
-    "eslint-plugin-import": "^2.24.2",
-    "eslint-plugin-jest": "^24.5.0",
-    "eslint-plugin-prettier": "^4.0.0",
+    "eslint": "^8.1.0",
+    "eslint-config-cheminfo": "^7.2.0",
     "esm": "^3.2.25",
-    "jest": "^27.2.4",
-    "jest-matcher-deep-close-to": "^3.0.0",
+    "jest": "^27.3.1",
+    "jest-matcher-deep-close-to": "^3.0.2",
+    "jscpd": "^3.3.26",
     "prettier": "^2.4.1",
-    "rollup": "^2.57.0"
+    "rollup": "^2.59.0"
   },
@@ -69,4 +70,4 @@ "dependencies": {
     "ml-array-median": "^1.1.5",
-    "nmr-processing": "^3.0.2"
+    "nmr-processing": "^3.4.0"
   }
 }

src/complexChromatogram.js

@@ -32,3 +32,3 @@ const GC_MS_FIELDS = ['TIC', '.RIC', 'SCANNUMBER'];
     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]],
@@ -35,0 +35,0 @@ );

src/convert.js

@@ -34,19 +34,21 @@ import { parseString } from 'dynamic-typing';
 /**
+ * Parse a jcamp.
  *
- * @param {string|ArrayBuffer} jcamp
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
  * @param {object} [options]
- * @param {number} [options.keepRecordsRegExp=/^$/] By default we don't keep meta information
- * @param {number} [options.canonicDataLabels=true] Canonize the Labels (uppercase without symbol)
- * @param {number} [options.canonicMetadataLabels=false] Canonize the metadata Labels (uppercase without symbol)
- * @param {number} [options.dynamicTyping=false] Convert numbers to Number
- * @param {number} [options.withoutXY=false] Remove the XY data
- * @param {number} [options.chromatogram=false] Special post-processing for GC / HPLC / MS
- * @param {number} [options.keepSpectra=false] Force to keep the spectra in case of 2D
- * @param {number} [options.noContour=false] Don't calculate countour in case of 2D
- * @param {number} [options.nbContourLevels=7] Number of positive / negative contour levels to calculate
- * @param {number} [options.noiseMultiplier=5] Define for 2D the level as 5 times the median as default
- * @param {number} [options.profiling=false] Add profiling information
+ * @param {number} [options.keepRecordsRegExp=/^$/] - 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.
+ * @returns {object}
  */
 
-export default function convert(jcamp, options = {}) {
+export function convert(jcamp, options = {}) {
   jcamp = ensureString(jcamp);
@@ -185,25 +187,25 @@ options = { ...defaultOptions, ...options };
     } 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 (
@@ -214,3 +216,3 @@ canonicDataLabel === '.OBSERVEFREQUENCY' ||
       if (!spectrum.observeFrequency) {
-        spectrum.observeFrequency = parseFloat(dataValue);
+        spectrum.observeFrequency = Number(dataValue);
       }
@@ -225,3 +227,3 @@ } else if (canonicDataLabel === '.OBSERVENUCLEUS') {
       if (!spectrum.shiftOffsetVal) {
-        spectrum.shiftOffsetVal = parseFloat(dataValue);
+        spectrum.shiftOffsetVal = Number(dataValue);
       }
@@ -234,3 +236,3 @@ } else if (canonicDataLabel === '$REFERENCEPOINT') {
       //                 currentEntry.shiftOffsetNum = parseInt(parts[2].trim());
-      //                 spectrum.shiftOffsetVal = parseFloat(parts[3].trim());
+      //                 spectrum.shiftOffsetVal = Number(parts[3].trim());
     } else if (canonicDataLabel === 'VARNAME') {
@@ -276,6 +278,6 @@ currentEntry.ntuples.varname = dataValue.split(ntuplesSeparatorRegExp);
       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)) {
@@ -282,0 +284,0 @@ spectrum[convertMSFieldToLabel(canonicDataLabel)] = dataValue;

src/convertToFloatArray.js

 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;
 }

src/createTree.js

 import { ensureString } from 'ensure-string';
 
 /**
- * Parse the jcamp to extract the structure as a tree
- * @param {string|ArrayBuffer jcamp
+ * Parse the jcamp to extract the structure as a tree.
+ *
+ * @param {string|ArrayBuffer|Uint8Array} jcamp
  * @param {object} [options={}]
@@ -10,3 +11,3 @@ * @param {boolean} [options.flatten=false]
  */
-export default function createTree(jcamp, options = {}) {
+export function createTree(jcamp, options = {}) {
   jcamp = ensureString(jcamp);
@@ -13,0 +14,0 @@ const { flatten = false } = options;

src/index.js

@@ -1,2 +0,2 @@
-export { default as createTree } from './createTree';
-export { default as convert } from './convert';
+export { createTree } from './createTree';
+export { convert } from './convert';

src/parse/parsePeakTable.js

@@ -35,5 +35,5 @@ const removeCommentRegExp = /\$\$.*/;
       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);
       }
@@ -64,5 +64,3 @@ } else {
         // todo should try to find a xFactor (y, ...)
-        currentData[variables[j % numberOfVariables]].push(
-          parseFloat(values[j]),
-        );
+        currentData[variables[j % numberOfVariables]].push(Number(values[j]));
       }
@@ -69,0 +67,0 @@ } else {

src/parse/parseXYA.js

@@ -13,5 +13,5 @@ export default function parseXYA(spectrum, value) {
     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]));
   }
 }

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

97422

increased by0.26%

Dev dependency count

12

decreased by-14.29%

Lines of code

2240

increased by0.09%

Dependency changes

• Updatednmr-processing@^3.4.0