Migrate src folder to TypeScript

[Copilot]

Migrates all JavaScript files in src/ to TypeScript while preserving existing behavior and test compatibility.

Migration approach

• Type definitions: Leverages types from cheminfo-types, ml-spectra-processing, and jcampconverter dependencies
• TSDoc conversion: Replaces JSDoc with proper TypeScript interfaces and type annotations
• Type safety: Adds type assertions where NumberArray/DoubleArray conversions are needed
• Default values: Documents defaults in interface definitions (e.g., @default '\t')

Files migrated

• Core: Kinds.ts, SpectraProcessor.ts, index.ts
• Parsers: parseText.ts, parseMatrix.ts, parseJcamp.ts
• Spectra processing: getMeanData.ts, getNormalizedData.ts, getPostProcessedData.ts, etc.
• Metadata: getMetadata.ts, getClasses.ts, getClassLabels.ts, getCategoriesStats.ts
• JSGraph utilities: getChart.ts, getBoxPlotChart.ts, getAutocorrelationChart.ts, etc.
• Scaled operations: integration.ts, min.ts, max.ts, minMax.ts, getFromToIndex.ts

Example type improvements

Before (JSDoc):

/**
 * @param {string} text - String containing the JCAMP data
 * @param options
 * @returns {Spectrum} - new instance of Spectrum
 */
export default function parseText(value, options = {}) {
  const { kind, parserOptions = {} } = options;
  const data = parseXY(value, parserOptions);
  return { data };
}

After (TypeScript):

export interface ParseTextOptions {
  kind?: Kind;
  parserOptions?: any;
}

export interface ParseTextResult {
  data: DataXY;
}

export default function parseText(
  value: string,
  options: ParseTextOptions = {},
): ParseTextResult {
  const { kind, parserOptions = {} } = options;
  const data = parseXY(value, parserOptions);
  return { data };
}

Dependencies added

• @types/chroma-js
• @types/object-hash

Original prompt

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This section details on the original issue you should resolve

<issue_title>Migrate to typescript</issue_title>
<issue_description>The setup is already done and we only need to migrate the src folder.

We should take care about types that are present in dependencies, especially ml-spectra-processing and cheminfo-types

We should take the opportunity to check the jsdoc and migrate to tsdoc.

We should not forget to add default values if they exists in the documentation of types.</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes Migrate to typescript #33

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