feat: modernize package to latest standards

.github/workflows/typedoc.yml

@@ -0,0 +1,14 @@
+name: TypeDoc
+
+on:
+  workflow_dispatch:
+  release:
+    types: [published]
+
+jobs:
+  typedoc:
+    uses: zakodium/workflows/.github/workflows/typedoc.yml@typedoc-v1
+    with:
+      entry: 'src/index.ts'
+    secrets:
+      github-token: ${{ secrets.BOT_TOKEN }}

.gitignore

@@ -115,6 +115,7 @@ dist
 .yarn/install-state.gz
 .pnp.*
 
+.claude
 .DS_Store
 
 lib

package.json

@@ -35,25 +35,25 @@
     "url": "https://github.com/cheminfo/arraybuffer-xml-parser/issues"
   },
   "homepage": "https://github.com/cheminfo/arraybuffer-xml-parser#readme",
+  "dependencies": {
+    "dynamic-typing": "^2.0.0"
+  },
   "devDependencies": {
     "@types/he": "^1.2.3",
-    "@vitest/coverage-v8": "4.0.12",
-    "@zakodium/tsconfig": "^1.0.2",
-    "cheminfo-build": "^1.3.1",
+    "@types/node": "^25.5.0",
+    "@vitest/coverage-v8": "4.1.2",
+    "@zakodium/tsconfig": "^1.0.3",
+    "cheminfo-build": "^1.3.2",
     "eslint": "^9.39.1",
-    "eslint-config-cheminfo-typescript": "^21.0.1",
-    "globals": "^16.5.0",
+    "eslint-config-cheminfo-typescript": "^21.1.0",
+    "globals": "^17.4.0",
     "he": "^1.2.0",
-    "ml-spectra-processing": "^14.18.1",
+    "ml-spectra-processing": "^14.22.0",
     "pako": "^2.1.0",
-    "prettier": "^3.6.2",
-    "rimraf": "^6.1.2",
+    "prettier": "^3.8.1",
+    "rimraf": "^6.1.3",
     "typescript": "^5.9.3",
     "uint8-base64": "^1.0.0",
-    "vitest": "^4.0.12"
-  },
-  "dependencies": {
-    "@types/node": "^24.10.1",
-    "dynamic-typing": "^1.0.1"
+    "vitest": "^4.1.2"
   }
 }

src/.npmignore

@@ -1,2 +1,3 @@
 __tests__
+.DS_Store
 .npmignore

src/XMLNode.ts

@@ -1,4 +1,4 @@
-import type { TagValueProcessor } from './traversable/defaultOptions.js';
+import type { TagValueProcessor } from './traversable/defaultOptions.ts';
 
 export type XMLNodeValue = string | Uint8Array | number | boolean;
 export type XMLAttributeValue = string | number | boolean;
@@ -36,7 +36,7 @@
     arrayConcat.set(toAppend, this.bytes.length);
     this.bytes = arrayConcat;
   }
   public get value(): any {
     if (this.cachedValue === undefined) {
       const value = this.tagValueProcessor(this.bytes, this);
       this.cachedValue = value;
@@ -44,9 +44,9 @@
     return this.cachedValue;
   }
   public addChild(child: XMLNode) {
-    if (Array.isArray(this.children[child.tagName])) {
-      //already presents
-      this.children[child.tagName].push(child);
+    const existing = this.children[child.tagName];
+    if (Array.isArray(existing)) {
+      existing.push(child);
     } else {
       this.children[child.tagName] = [child];
     }

src/__tests__/arrayModeSpec.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 

src/__tests__/arrayWithExtendedPrototypePropsSpec.test.js → src/__tests__/arrayWithExtendedPrototypePropsSpec.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 
@@ -15,8 +15,7 @@
       a: { b: [0, 1] },
     };
 
-    // eslint-disable-next-line no-extend-native
-    Array.prototype.someExtentionOfArrayPrototype =
+    (Array.prototype as any).someExtentionOfArrayPrototype =
       'someExtentionOfArrayPrototype';
 
     const result = parse(xmlData, {

src/__tests__/attributesSpec.test.ts

@@ -1,7 +1,7 @@
 import { describe, expect, it } from 'vitest';
 // import he from 'he';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 

src/__tests__/base64.test.js → src/__tests__/base64.test.ts

@@ -1,7 +1,7 @@
 import { decode as base64decode } from 'uint8-base64';
 import { expect, test } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 // library to convert base64 <--> arrayBuffer: https://github.com/niklasvh/base64-arraybuffer/blob/master/src/index.ts
 
 const encoder = new TextEncoder();
@@ -15,15 +15,15 @@
   <binary>AAAAAAAA8D8AAAAAAAAAQAAAAAAAAAhA</binary>
 </binaryDataArray>`);
 
-  let result = parse(xmlData, {
+  const result = parse(xmlData, {
     attributeNameProcessor: (name) => name,
     tagValueProcessor: (value, node) => {
       if (node.tagName !== 'binary') return decoder.decode(value);
       const decoded = base64decode(value);
       // isLittleEndian and the data were encoded in littleEndian
       return new Float64Array(decoded.buffer);
     },
-  });
+  }) as Record<string, any>;
 
   expect(result.binaryDataArray.binary).toStrictEqual(
     Float64Array.from([1, 2, 3]),

src/__tests__/cdataSpec.test.ts

@@ -3,7 +3,7 @@ import { join } from 'node:path';
 
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 

src/__tests__/cheminfo.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 describe('XMLParser', () => {
   it('Try to parse a very simple example', () => {

src/__tests__/cyrillic.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 describe('XMLParser', () => {
   it('should parse XML with cyrillic characters to JSON string', () => {

src/__tests__/data.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 

src/__tests__/parseStream.test.ts

@@ -3,14 +3,14 @@
 
 import { describe, expect, it } from 'vitest';
 
-import { parseStream } from '../parseStream.js';
+import { parseStream } from '../parseStream.ts';
 
 describe('parseStream', () => {
   it('simple case', async () => {
     const file = await open(join(__dirname, 'assets/sample.xml'), 'r');
     const CHUNK_SIZE = 10;
     const transformStream = new TransformStream({
       start: function start() {}, // required.
       transform: async function transform(chunk, controller) {
         if (chunk === null) controller.terminate();
         chunk = new Uint8Array(await chunk);

src/__tests__/stopNodes.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 

src/__tests__/tagProcessors.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 describe('XMLParser', () => {
   it('tag name processor', () => {

src/__tests__/valueProcessors.test.ts

@@ -3,7 +3,7 @@ import he from 'he'; // HTML entity encoder/decoder
 import { describe, expect, it } from 'vitest';
 /* eslint-disable camelcase */
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 const decoder = new TextDecoder();
@@ -89,8 +89,9 @@ describe('XMLParser', () => {
     const resultMap: Record<string, Uint8Array[]> = {};
     parse(xmlData, {
       tagValueProcessor: (value, node) => {
-        if (resultMap[node.tagName]) {
-          resultMap[node.tagName].push(value);
+        const existing = resultMap[node.tagName];
+        if (existing) {
+          existing.push(value);
         } else {
           resultMap[node.tagName] = [value];
         }

src/__tests__/xmlParser.mz.test.ts

@@ -6,7 +6,7 @@
 import { decode } from 'uint8-base64';
 import { expect, test } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const decoder = new TextDecoder();
 
@@ -16,17 +16,17 @@
   const xmlData = readFileSync(fileNamePath);
 
   // eslint-disable-next-line unicorn/consistent-function-scoping
   const tagValueProcessor = async (bytes: Uint8Array, node: any) => {
     if (node.tagName !== 'binary') return decoder.decode(bytes);
     const ontologies = node.parent.children.cvParam.map(
       (entry: any) => entry.attributes.accession,
     );
     return decodeBase64(bytes, { ontologies });
   };
 
   const result = parse(xmlData, {
     tagValueProcessor,
   }) as any;
 
   await recursiveResolve(result);
 
@@ -48,7 +48,7 @@
   });
 });
 
 export async function decodeBase64(
   base64: Uint8Array,
   options: { ontologies?: string[] } = {},
 ) {
@@ -76,7 +76,9 @@
   switch (compression.toLowerCase()) {
     case 'zlib': {
       const ds = new DecompressionStream('deflate');
-      const decompressedStream = new Blob([uint8Array])
+      const decompressedStream = new Blob([
+        uint8Array as Uint8Array<ArrayBuffer>,
+      ])
         .stream()
         .pipeThrough(ds);
       const decompressedArrayBuffer = await new Response(
@@ -116,8 +118,8 @@
           i += step
         ) {
           for (let j = 0; j < step / 2; j++) {
-            const temp = uint8Array[i + j];
-            uint8Array[i + j] = uint8Array[i + step - 1 - j];
+            const temp = uint8Array[i + j] as number;
+            uint8Array[i + j] = uint8Array[i + step - 1 - j] as number;
             uint8Array[i + step - 1 - j] = temp;
           }
         }

src/__tests__/xmlParser.test.ts

@@ -5,7 +5,7 @@ import { parseString } from 'dynamic-typing';
 import { recursiveResolve } from 'ml-spectra-processing';
 import { describe, expect, it } from 'vitest';
 
-import { parse } from '../parse.js';
+import { parse } from '../parse.ts';
 
 const encoder = new TextEncoder();
 const decoder = new TextDecoder();

src/bufferUtils/__tests__/arrayIndexOf.test.ts

@@ -1,6 +1,6 @@
 import { describe, expect, it } from 'vitest';
 
-import { arrayIndexOf } from '../arrayIndexOf.js';
+import { arrayIndexOf } from '../arrayIndexOf.ts';
 
 describe('arrayIndexOf', () => {
   it('should find the index pointing to the begining of the found string in array', () => {

src/bufferUtils/__tests__/arrayTrim.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
 
-import { arrayTrim } from '../arrayTrim.js';
+import { arrayTrim } from '../arrayTrim.ts';
 
 test('arrayTrim', () => {
   const beginning = new Uint8Array([32, 32, 32, 32, 32, 32, 32, 33, 33, 97]);

src/bufferUtils/arrayTrim.ts

@@ -1,9 +1,9 @@
 /* eslint-disable @typescript-eslint/no-unused-vars */
 export function arrayTrim(array: Uint8Array, arg?: unknown) {
   let i = 0;
   let j = array.length - 1;
-  for (; i < array.length && array[i] <= 0x20; i++);
-  for (; j >= i && array[j] <= 0x20; j--);
+  for (; i < array.length && (array[i] as number) <= 0x20; i++);
+  for (; j >= i && (array[j] as number) <= 0x20; j--);
   if (i === 0 && j === array.length - 1) return array;
   return array.subarray(i, j + 1);
 }

src/index.ts

@@ -1,2 +1,2 @@
-export * from './parse.js';
-export * from './parseStream.js';
+export * from './parse.ts';
+export * from './parseStream.ts';

src/parse.ts

@@ -1,10 +1,10 @@
 import type {
   ParseOptions,
   RealParseOptions,
-} from './traversable/defaultOptions.js';
-import { defaultOptions } from './traversable/defaultOptions.js';
-import { getTraversable } from './traversable/getTraversable.js';
-import { traversableToJSON } from './traversableToJSON.js';
+} from './traversable/defaultOptions.ts';
+import { defaultOptions } from './traversable/defaultOptions.ts';
+import { getTraversable } from './traversable/getTraversable.ts';
+import { traversableToJSON } from './traversableToJSON.ts';
 
 /**
  * Parse an ArrayBuffer or Uint8Array representing an XML and return an object

src/parseStream.ts

@@ -1,7 +1,7 @@
-import type { StreamParseOptions } from './traversable/defaultOptions.js';
-import { defaultStreamOptions } from './traversable/defaultOptions.js';
-import { getTraversableGenerator } from './traversable/getTraversableGenerator.js';
-import { traversableToJSON } from './traversableToJSON.js';
+import type { StreamParseOptions } from './traversable/defaultOptions.ts';
+import { defaultStreamOptions } from './traversable/defaultOptions.ts';
+import { getTraversableGenerator } from './traversable/getTraversableGenerator.ts';
+import { traversableToJSON } from './traversableToJSON.ts';
 
 /**
  * Parse a web stream representing an XML and emit objects

src/traversable/__tests__/closingIndexForOpeningTag.test.ts

@@ -1,6 +1,6 @@
 import { expect, test } from 'vitest';
 
-import { closingIndexForOpeningTag } from '../closingIndexForOpeningTag.js';
+import { closingIndexForOpeningTag } from '../closingIndexForOpeningTag.ts';
 
 test('sclosingIndexForOpeningTag', () => {
   expect(

src/traversable/closingIndexForOpeningTag.ts

@@ -1,4 +1,4 @@
-import { decoder } from './utils/utf8Decoder.js';
+import { decoder } from './utils/utf8Decoder.ts';
 
 /**
  * Search for the corresponding closing tag '>'

src/traversable/defaultOptions.ts

@@ -1,6 +1,6 @@
 import { parseString } from 'dynamic-typing';
 
-import type { XMLAttributeValue, XMLNode } from '../XMLNode.js';
+import type { XMLAttributeValue, XMLNode } from '../XMLNode.ts';
 
 const utf8Decoder = new TextDecoder();
 

src/traversable/findClosingIndex.ts

@@ -1,4 +1,4 @@
-import { arrayIndexOf } from '../bufferUtils/arrayIndexOf.js';
+import { arrayIndexOf } from '../bufferUtils/arrayIndexOf.ts';
 
 export function findClosingIndex(
   xmlData: Uint8Array,

src/traversable/getTraversable.ts

@@ -1,13 +1,13 @@
-import { XMLNode } from '../XMLNode.js';
-import { arrayIndexOf } from '../bufferUtils/arrayIndexOf.js';
-import { arrayTrim } from '../bufferUtils/arrayTrim.js';
+import { XMLNode } from '../XMLNode.ts';
+import { arrayIndexOf } from '../bufferUtils/arrayIndexOf.ts';
+import { arrayTrim } from '../bufferUtils/arrayTrim.ts';
 
-import { closingIndexForOpeningTag } from './closingIndexForOpeningTag.js';
-import type { RealParseOptions } from './defaultOptions.js';
-import { findClosingIndex } from './findClosingIndex.js';
-import { parseAttributesString } from './parseAttributesString.js';
-import { removeNameSpaceIfNeeded } from './utils/removeNameSpaceIfNeeded.js';
-import { decoder } from './utils/utf8Decoder.js';
+import { closingIndexForOpeningTag } from './closingIndexForOpeningTag.ts';
+import type { RealParseOptions } from './defaultOptions.ts';
+import { findClosingIndex } from './findClosingIndex.ts';
+import { parseAttributesString } from './parseAttributesString.ts';
+import { removeNameSpaceIfNeeded } from './utils/removeNameSpaceIfNeeded.ts';
+import { decoder } from './utils/utf8Decoder.ts';
 
 export function getTraversable(xmlData: Uint8Array, options: RealParseOptions) {
   const { tagValueProcessor } = options;