jcampconverter - npm Package Compare versions

Comparing version 9.6.4 to 10.0.0

jcampconverter.d.ts

 import { Logger } from 'cheminfo-types';
+import type { Molecule } from 'openchemlib';
+import { openchemlib } from 'openchemlib';
 
+declare interface Add2DOptions extends GenerateContourLinesOptions {
+    /**
+     * Don't calculate contour in case of 2D.
+     */
+    noContour?: boolean;
+}
+
+declare interface Chromatogram {
+    times: number[];
+    series: Record<string, {
+        dimension: number;
+        data: any[];
+    }>;
+}
+
+declare interface ContourLines {
+    minX: number;
+    maxX: number;
+    minY: number;
+    maxY: number;
+    segments: Array<{
+        zValue?: number;
+        lines?: number[];
+    }>;
+}
+
 /**
- * Conversion options
- * @typedef {object} ConvertOptions@typedef {object} ConvertOptions
- * @property {RegExp} [keepRecordsRegExp=/^$/] - By default we don't keep meta information.
- * @property {boolean} [canonicDataLabels=true] - Canonize the Labels (uppercase without symbol).
- * @property {boolean} [canonicMetadataLabels=false] - Canonize the metadata Labels (uppercase without symbol).
- * @property {boolean} [dynamicTyping=false] - Convert numbers to Number.
- * @property {boolean} [withoutXY=false] - Remove the XY data.
- * @property {boolean} [chromatogram=false] - Special post-processing for GC / HPLC / MS.
- * @property {boolean} [keepSpectra=false] - Force to keep the spectra in case of 2D.
- * @property {RegExp} [noTrimRegExp=/^$/] - For which fields we should not trim ?
- * @property {boolean} [noContour=false] - Don't calculate countour in case of 2D.
- * @property {number} [nbContourLevels=7] - Number of positive / negative contour levels to calculate.
- * @property {number} [noiseMultiplier=5] - Define for 2D the level as 5 times the median as default.
- * @property {import('cheminfo-types').Logger} [logger] - A logger like 'pino'
- * @property {boolean} [profiling=false] - Add profiling information.
- */
-/**
- *
- * @typedef {object} Ntuples@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] - first X value
- * @property {number} [lastX] - last X value
- * @property {number} [deltaX] - distance between 2 consecutive x axis values
- * @property {number} [yFactor] - y axis scaling factor
- * @property {number} [xFactor] - x axis scaling factor
- * @property {number} [nbPoints] - Number of points
- */
-/**
- *
- * @typedef {object} MinMax@typedef {object} MinMax
- * @property {number[][]} [z]
- * @property {number} minX
- * @property {number} maxX
- * @property {number} minY
- * @property {number} maxY
- * @property {number} minZ
- * @property {number} maxZ
- * @property {number} median
- */
-/**
- *
- * @typedef {object} Entry@typedef {object} Entry
- * @property {Spectrum[]} spectra
- * @property {Ntuples} ntuples
- * @property {Record<String, string | string[] | number | number[] | boolean | boolean[] | undefined>} meta
- * @property {Record<String, string | string[] | number | number[] | boolean | boolean[] | undefined>} info
- * @property {Record<String, string | string[] | number | number[] | boolean | boolean[] | undefined>} tmp
- * @property {string} [title]
- * @property {string} [dataType]
- * @property {string} [dataClass]
- * @property {string?} [jcampDX]
- * @property {string?} [jcampCS]
- * @property {boolean} [twoD]
- * @property {MinMax} [minMax]
- */
-/**
- *
- * @typedef { object } ConvertResult@typedef { object } ConvertResult
- * @property { object[] | boolean } profiling
- * @property { string[] } logs
- * @property { object[] } entries
- * @property { Entry[] } flatten
- */
-/**
- * Parse a jcamp.
- * The data can be provide as a string or array buffer. In this later case
+ * Parse JCAMP-DX data.
+ * The data can be provided as a string or array buffer. In this latter case
  * we will convert it first to a string before parsing.
- * @param {string|ArrayBuffer|Uint8Array} jcamp
- * @param {ConvertOptions} [options]
- * @returns {ConvertResult}
+ * @param jcamp
+ * @param optionsParam
+ * @returns Converted result.
  */
-export declare function convert(jcamp: string | ArrayBuffer | Uint8Array, options?: ConvertOptions | undefined): ConvertResult;
+export declare function convert(jcamp: string | ArrayBuffer | Uint8Array, optionsParam?: ConvertOptions): ConvertResult;
 
 /**
- * Conversion options
+ * Conversion options.
  */
-declare type ConvertOptions = {
+declare interface ConvertOptions extends Partial<Add2DOptions> {
     /**
-     * - By default we don't keep meta information.
+     * By default we don't keep meta information.
+     * @default `/^$/`
      */
-    keepRecordsRegExp?: RegExp | undefined;
+    keepRecordsRegExp?: RegExp;
     /**
-     * - Canonize the Labels (uppercase without symbol).
+     * Canonize the Labels (uppercase without symbol).
      */
-    canonicDataLabels?: boolean | undefined;
+    canonicDataLabels?: boolean;
     /**
-     * - Canonize the metadata Labels (uppercase without symbol).
+     * Canonize the metadata Labels (uppercase without symbol).
      */
-    canonicMetadataLabels?: boolean | undefined;
+    canonicMetadataLabels?: boolean;
     /**
-     * - Convert numbers to Number.
+     * Convert numbers to Number.
      */
-    dynamicTyping?: boolean | undefined;
+    dynamicTyping?: boolean;
     /**
-     * - Remove the XY data.
+     * Remove the XY data.
      */
-    withoutXY?: boolean | undefined;
+    withoutXY?: boolean;
     /**
-     * - Special post-processing for GC / HPLC / MS.
+     * Special post-processing for GC / HPLC / MS.
      */
-    chromatogram?: boolean | undefined;
+    chromatogram?: boolean;
     /**
-     * - Force to keep the spectra in case of 2D.
+     * Force to keep the spectra in case of 2D.
      */
-    keepSpectra?: boolean | undefined;
+    keepSpectra?: boolean;
     /**
-     * - For which fields we should not trim ?
+     * For which fields we should not trim ?
+     * @default `/^$/`
      */
-    noTrimRegExp?: RegExp | undefined;
+    noTrimRegExp?: RegExp;
     /**
-     * - Don't calculate countour in case of 2D.
+     * A logger like `pino`.
      */
-    noContour?: boolean | undefined;
+    logger?: Logger;
     /**
-     * - Number of positive / negative contour levels to calculate.
+     * Add profiling information.
      */
-    nbContourLevels?: number | undefined;
-    /**
-     * - Define for 2D the level as 5 times the median as default.
-     */
-    noiseMultiplier?: number | undefined;
-    /**
-     * - A logger like 'pino'
-     */
-    logger?: Logger | undefined;
-    /**
-     * - Add profiling information.
-     */
-    profiling?: boolean | undefined;
-};
+    wantXY?: boolean;
+    start?: number;
+    fastParse?: boolean;
+}
 
-declare type ConvertResult = {
-    profiling: object[] | boolean;
-    logs: string[];
-    entries: object[];
+declare interface ConvertResult {
+    entries: Entry[];
     flatten: Entry[];
-};
+}
 
 /**
- *
- * @typedef {object} CreateTreeOptions@typedef {object} CreateTreeOptions
- * @property {boolean} [flatten=false]
+ * Parse the JCAMP-DX to extract the structure as a tree.
+ * @param jcamp
+ * @param options
+ * @returns Tree.
  */
-/**
- *
- * @typedef {object} Tree@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 declare function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions | undefined): Tree[];
+export declare function createTree(jcamp: string | ArrayBuffer | Uint8Array, options?: CreateTreeOptions): Stack[];
 
-declare type CreateTreeOptions = {
-    flatten?: boolean | undefined;
-};
+declare interface CreateTreeOptions {
+    flatten?: boolean;
+}
 
-declare type Entry = {
+declare interface Entry {
     spectra: Spectrum[];
@@ -188,13 +114,33 @@ ntuples: Ntuples;
     tmp: Record<string, string | string[] | number | number[] | boolean | boolean[] | undefined>;
-    title?: string | undefined;
-    dataType?: string | undefined;
-    dataClass?: string | undefined;
-    jcampDX?: string | null | undefined;
-    jcampCS?: string | null | undefined;
-    twoD?: boolean | undefined;
-    minMax?: MinMax | undefined;
-};
+    title?: string;
+    dataType?: string;
+    dataClass?: string;
+    jcampDX?: string;
+    jcampCS?: string;
+    twoD?: boolean;
+    minMax?: MinMax;
+    children?: Entry[];
+    shiftOffsetVal?: number;
+    shiftOffsetNum?: number;
+    xType?: string;
+    yType?: string;
+    chromatogram?: Chromatogram;
+    contourLines?: ContourLines;
+}
 
-declare type MinMax = {
-    z?: number[][] | undefined;
+declare interface GenerateContourLinesOptions {
+    /**
+     * Number of positive / negative contour levels to calculate.
+     * @default `7`
+     */
+    nbContourLevels: number;
+    /**
+     * Define for 2D the level as 5 times the median as default.
+     * @default `5`
+     */
+    noiseMultiplier: number;
+}
+
+declare interface MinMax {
+    z: number[][];
     minX: number;
@@ -206,50 +152,64 @@ maxX: number;
     maxZ: number;
-    median: number;
-};
+    median?: number;
+    noice?: number;
+}
 
-declare type Ntuples = {
-    varname?: string[] | undefined;
-    symbol?: string[] | undefined;
-    vartype?: string[] | undefined;
-    varform?: string[] | undefined;
-    vardim?: number[] | undefined;
-    units?: string[] | undefined;
-    factor?: number[] | undefined;
-    first?: number[] | undefined;
-    last?: number[] | undefined;
-    min?: number[] | undefined;
-    max?: number[] | undefined;
-    nucleus?: string[] | undefined;
-};
+declare interface Ntuples {
+    varname?: string[];
+    symbol?: string[];
+    vartype?: string[];
+    varform?: string[];
+    vardim?: number[];
+    units?: string[];
+    factor?: number[];
+    first?: number[];
+    last?: number[];
+    min?: number[];
+    max?: number[];
+    nucleus?: string[];
+    [key: string]: any | undefined;
+}
 
+declare type OCL = openchemlib;
+
+declare interface ParsedCS {
+    molfile: string;
+    molecule: Molecule;
+}
+
 /**
  *
- * @typedef {object} ParsedCS@typedef {object} ParsedCS
- * @property {string} molfile
- * @property {import("openchemlib").OCL} molecule
- */
-/**
- *
- * @param {import("./convert.js").Entry} entry
- * @param {object} [options={}]
- * @param {import("fifo-logger").Logger} [options.logger]
- * @param {import("openchemlib").OCL} [options.OCL]
+ * @param entry
+ * @param options
  * @returns ParsedCS
  */
-export declare function parseJcampCS(entry: Entry, options?: {
-    logger?: any;
-    OCL?: any;
-} | undefined): {
-    molecule: any;
-    molfile: any;
-} | undefined;
+export declare function parseJcampCS(entry: Entry, options: ParseJcampCSOptions): ParsedCS | undefined;
 
-declare type Spectrum = Record<string, any>;
+declare interface ParseJcampCSOptions {
+    OCL: OCL;
+    logger?: Logger;
+}
 
-declare type Tree = {
+declare interface Spectrum {
+    [key: string]: any;
+    data: Record<string, number[]>;
+    firstX?: number;
+    firstY?: number;
+    lastX?: number;
+    deltaX?: number;
+    yFactor?: number;
+    xFactor?: number;
+    nbPoints?: number;
+}
+
+declare interface Stack {
     title: string;
     jcamp: string;
-    children?: Tree[] | undefined;
-};
+    children: Stack[] | undefined;
+    jcampDX?: string;
+    jcampCS?: string;
+    dataType?: string;
+    dataClass?: string;
+}
 
 export { }

package.json

 {
   "name": "jcampconverter",
-  "version": "9.6.4",
+  "version": "10.0.0",
   "description": "Parse and convert JCAMP data",
-  "types": "jcampconverter.d.ts",
-  "main": "jcampconverter.cjs",
-  "module": "jcampconverter.mjs",
+  "keywords": [
+    "jcamp",
+    "converter"
+  ],
+  "author": "Luc Patiny",
+  "license": "MIT",
+  "types": "./jcampconverter.d.ts",
+  "require": "./jcampconverter.cjs",
+  "module": "./jcampconverter.mjs",
   "exports": {
@@ -22,5 +28,6 @@ ".": {
     "api-extractor": "api-extractor run --local",
-    "build": "cheminfo-build --entry src/index.js --root JcampConverter --no-source-map && rm dist/jcampconverter.js",
+    "benchmark": "node benchmark/benchmark.js",
+    "build": "tsc --project tsconfig.cheminfo-build.json && cheminfo-build --entry lib/index.js --root JcampConverter --no-source-map && rm dist/jcampconverter.js",
     "bundle": "npm run bundle-cjs && npm run bundle-esm",
-    "bundle-common": "esbuild src/index.js --bundle --packages=external --minify",
+    "bundle-common": "esbuild src/index.ts --bundle --packages=external --minify",
     "bundle-cjs": "npm run bundle-common -- --format=cjs --outfile=jcampconverter.cjs",
@@ -30,3 +37,5 @@ "bundle-esm": "npm run bundle-common -- --format=esm --outfile=jcampconverter.mjs",
     "check-types": "tsc --noEmit",
-    "clean": "rimraf dist types",
+    "clean": "rimraf dist lib types",
+    "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",
     "eslint": "eslint src __tests__",
@@ -36,17 +45,8 @@ "eslint-fix": "npm run eslint -- --fix",
     "prepack": "npm run bundle && npm run bundle-types",
-    "prettier": "prettier --check src",
-    "prettier-write": "prettier --write src",
-    "test": "npm run test-only && npm run eslint && npm run prettier && npm run check-types",
-    "test-only": "vitest run --globals --coverage",
-    "tsc": "tsc --project tsconfig.types.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"
+    "prettier": "prettier --check src __tests__",
+    "prettier-write": "prettier --write src __tests__",
+    "test": "npm run test-only && npm run check-types && npm run eslint && npm run prettier",
+    "test-only": "vitest run --coverage",
+    "tsc": "tsc --project tsconfig.types.json"
   },
-  "keywords": [
-    "jcamp",
-    "converter"
-  ],
-  "author": "Luc Patiny",
-  "license": "MIT",
   "bugs": {
@@ -56,30 +56,26 @@ "url": "https://github.com/cheminfo/nmrium/issues/new?title=%5Bjcampconverter%5D"
   "devDependencies": {
-    "@microsoft/api-extractor": "^7.42.3",
-    "@types/jest": "^29.5.12",
-    "@types/pino": "^7.0.5",
-    "@vitest/coverage-v8": "^1.3.1",
+    "@microsoft/api-extractor": "^7.47.10",
+    "@vitest/coverage-v8": "^2.1.3",
     "benchmark": "^2.1.4",
-    "c8": "^9.1.0",
     "cheminfo-build": "^1.2.0",
-    "esbuild": "^0.20.1",
-    "eslint": "^8.57.0",
-    "eslint-config-cheminfo-typescript": "^12.2.0",
-    "esm": "^3.2.25",
-    "fifo-logger": "^0.6.1",
+    "esbuild": "^0.24.0",
+    "eslint": "^9.12.0",
+    "eslint-config-cheminfo-typescript": "^16.0.0",
+    "fifo-logger": "^1.0.0",
     "jest-matcher-deep-close-to": "^3.0.2",
-    "jscpd": "^3.5.10",
-    "ml-spectra-processing": "^14.2.0",
-    "openchemlib": "^8.9.0",
-    "prettier": "^3.2.5",
-    "rimraf": "^5.0.5",
-    "typescript": "^5.4.2",
-    "vitest": "^1.3.1"
+    "jscpd": "^4.0.5",
+    "ml-spectra-processing": "^14.6.0",
+    "openchemlib": "^8.15.0",
+    "prettier": "^3.3.3",
+    "rimraf": "^6.0.1",
+    "typescript": "^5.6.3",
+    "vitest": "^2.1.3"
   },
   "dependencies": {
-    "cheminfo-types": "^1.7.2",
-    "dynamic-typing": "^1.0.0",
+    "cheminfo-types": "^1.8.0",
+    "dynamic-typing": "^1.0.1",
     "ensure-string": "^1.2.0",
-    "gyromagnetic-ratio": "^1.1.1",
+    "gyromagnetic-ratio": "^1.2.0",
     "ml-array-median": "^1.1.6"
   }
 }

README.md

 [![NPM version][npm-image]][npm-url]
 [![build status][ci-image]][ci-url]
-[![Test coverage][codecov-image]][codecov-url]
 [![npm download][download-image]][download-url]
@@ -85,4 +84,2 @@ [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5091526.svg)](https://doi.org/10.5281/zenodo.5091526)
 [npm-url]: https://npmjs.org/package/jcampconverter
-[codecov-image]: https://img.shields.io/codecov/c/github/cheminfo/jcampconverter.svg
-[codecov-url]: https://codecov.io/gh/cheminfo/jcampconverter
 [ci-image]: https://github.com/cheminfo/jcampconverter/workflows/Node.js%20CI/badge.svg?branch=main
@@ -89,0 +86,0 @@ [ci-url]: https://github.com/cheminfo/jcampconverter/actions?query=workflow%3A%22Node.js+CI%22

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Improved metrics

Dev dependency count

16

decreased by-20%

Worsened metrics

Total package byte prevSize

49074

decreased by-1.29%

Lines of code

349

decreased by-9.35%

Number of lines in readme file

88

decreased by-3.3%

Number of medium supply chain risk alerts

1

increased byInfinity%

Dependency changes

• Updatedcheminfo-types@^1.8.0

• Updateddynamic-typing@^1.0.1

• Updatedgyromagnetic-ratio@^1.2.0