PR of updated main branch

.github/dependabot.yml

@@ -1,24 +1,24 @@
 version: 2
 updates:
-  - package-ecosystem: 'github-actions'
-    directory: '/'
-    target-branch: 'main'
+  - package-ecosystem: github-actions
+    directory: /
+    target-branch: main
     schedule:
-      interval: 'weekly'
-  - package-ecosystem: 'npm'
-    directory: '/'
-    target-branch: 'main'
+      interval: weekly
+  - package-ecosystem: npm
+    directory: /
+    target-branch: main
     schedule:
-      interval: 'weekly'
+      interval: weekly
     ignore:
-      - dependency-name: 'chai'
+      - dependency-name: chai
         update-types:
-          - 'version-update:semver-major'
-      - dependency-name: 'esbuild'
+          - version-update:semver-major
+      - dependency-name: esbuild
         update-types:
-          - 'version-update:semver-minor'
-  - package-ecosystem: 'gitsubmodule'
-    directory: '/'
-    target-branch: 'main'
+          - version-update:semver-minor
+  - package-ecosystem: gitsubmodule
+    directory: /
+    target-branch: main
     schedule:
-      interval: 'daily'
+      interval: daily

.github/workflows/codeql.yml

@@ -16,9 +16,9 @@ permissions:
 
 on:
   push:
-    branches: [main]
+    branches: [typescript]
   pull_request:
-    branches: [main]
+    branches: [typescript]
   schedule:
     - cron: 26 6 * * 5
 

.github/workflows/coverage.yml

@@ -2,7 +2,9 @@ name: Test coverage
 
 on:
   push:
-    branches: [main]
+    branches: [main, typescript]
+  pull_request:
+    branches: [main, typescript]
 
 permissions:
   contents: read
@@ -22,7 +24,7 @@ jobs:
       - name: Download dependencies
         run: npm ci
       - name: Generate coverage report
-        run: ./node_modules/.bin/jest --coverage
+        run: npm run coverage
       - name: Upload coverage to Quality
         uses: qltysh/qlty-action/coverage@v2
         with:

.github/workflows/deploy-pages.yml

@@ -4,11 +4,11 @@ name: Deploy Vite App to GitHub Pages
 on:
   push:
     branches:
-      - main
+      - typescript
 
 # Allow only one concurrent deployment, cancelling any previously running ones.
 concurrency:
-  group: 'pages'
+  group: pages
   cancel-in-progress: true
 
 permissions: {}
@@ -28,9 +28,9 @@ jobs:
       - name: Set up Node.js
         uses: actions/setup-node@v6
         with:
-          node-version: 22
+          node-version: lts/*
           # Cache npm dependencies to speed up future builds
-          cache: 'npm'
+          cache: npm
           cache-dependency-path: |
             package-lock.json
             browser/package-lock.json

.github/workflows/publish.yml

@@ -14,8 +14,8 @@ jobs:
       # Setup .npmrc file to publish to npm
       - uses: actions/setup-node@v6
         with:
-          node-version: 'lts/*'
-          registry-url: 'https://registry.npmjs.org'
+          node-version: lts/*
+          registry-url: https://registry.npmjs.org
       - name: Update npm
         run: npm install -g npm@latest
       - run: npm ci

.github/workflows/tests.yml

@@ -2,20 +2,20 @@ name: Tests
 
 on:
   push:
-    branches: [main]
+    branches: [main, typescript]
   pull_request:
-    branches: [main]
+    branches: [main, typescript]
 
 permissions:
   contents: read
 
 jobs:
-  Build:
+  Main:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        node-version: [22.x, lts/*, 'node']
+        node-version: [22.x, lts/*, node]
 
     steps:
       - name: Check out the code
@@ -33,12 +33,12 @@ jobs:
       - name: Test with Node.js ${{ matrix.node-version }}
         run: npm test
 
-  JSON-spec-tests:
+  JSON:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        node-version: [22.x, lts/*, 'node']
+        node-version: [22.x, lts/*, node]
 
     steps:
       - name: Check out the code
@@ -56,12 +56,12 @@ jobs:
       - name: Run JSON spec tests with Node.js ${{ matrix.node-version }}
         run: npm run testSpecs
 
-  Browser-tests:
+  Browser:
     runs-on: ubuntu-latest
 
     strategy:
       matrix:
-        node-version: [22.x, lts/*, 'node']
+        node-version: [22.x, lts/*, node]
 
     steps:
       - name: Check out the code

babel.config.js

@@ -1,12 +1,14 @@
-module.exports = {
+export default {
   presets: [
-    ['@babel/preset-env', {
-      targets: {
-        node: '22'
+    [
+      '@babel/preset-env',
+      {
+        targets: {
+          node: '22',
+        },
       },
-      modules: 'commonjs'
-    }]
+    ],
+    '@babel/preset-typescript',
   ],
-  plugins: []
+  plugins: [],
 }
-

browser/src/bids/BidsWebAccessor.js

@@ -1,6 +1,6 @@
-import { BidsFileAccessor } from '../../../src/bids/datasetParser.js'
-import { buildSchemasFromVersion } from '../schema/init.js'
-import { BidsHedIssue } from '../../../src/bids/types/issues.js'
+import { BidsFileAccessor } from '../../../src/bids/datasetParser'
+import { buildSchemasFromVersion } from '../schema/init'
+import { BidsHedIssue } from '../../../src/bids/types/issues'
 
 /**
  * Build HED schemas from a dataset description for the browser environment.
@@ -90,8 +90,7 @@ export class BidsWebAccessor extends BidsFileAccessor {
    * @private
    */
   constructor(datasetRootDirectory, fileMap) {
-    super(datasetRootDirectory, fileMap)
-    this.schemaBuilder = buildBidsSchemas
+    super(datasetRootDirectory, fileMap, buildBidsSchemas)
   }
 
   async getFileContent(relativePath) {

browser/src/bids/BidsWebAccessor.spec.js

@@ -1,5 +1,5 @@
 import { describe, it, expect } from 'vitest'
-import { BidsWebAccessor } from './BidsWebAccessor.js'
+import { BidsWebAccessor } from './BidsWebAccessor'
 
 // Mock File object for BidsWebAccessor tests
 const MockFile = class {

browser/src/schema/init.js

@@ -7,11 +7,9 @@
 import zip from 'lodash/zip'
 
 import { loadSchema } from './loader'
-import { setParent } from '../../../src/utils/xml.js'
-
 import SchemaParser from '../../../src/schema/parser'
 import PartneredSchemaMerger from '../../../src/schema/schemaMerger'
-import { Schema, Schemas } from '../../../src/schema/containers'
+import { Schema, HedSchemas } from '../../../src/schema/containers'
 import { IssueError } from '../../../src/issues/issues'
 import { splitStringTrimAndRemoveBlanks } from '../../../src/utils/string'
 import { SchemasSpec } from '../../../src/schema/specs'
@@ -20,20 +18,18 @@ import { SchemasSpec } from '../../../src/schema/specs'
  * Build a single schema container object from an XML file.
  *
  * @param {Object} xmlData The schema's XML data
- * @returns {Schema} The HED schema object.
+ * @returns {HedSchema} The HED schema object.
  */
 const buildSchemaObject = function (xmlData) {
-  const rootElement = xmlData.HED
-  setParent(rootElement, null)
-  const schemaEntries = new SchemaParser(rootElement).parse()
+  const schemaEntries = new SchemaParser(xmlData.HED).parse()
   return new Schema(xmlData, schemaEntries)
 }
 
 /**
  * Build a single merged schema container object from one or more XML files.
  *
  * @param {Object[]} xmlData The schemas' XML data.
- * @returns {Schema} The HED schema object.
+ * @returns {HedSchema} The HED schema object.
  */
 const buildSchemaObjects = function (xmlData) {
   const schemas = xmlData.map((data) => buildSchemaObject(data))
@@ -48,7 +44,7 @@ const buildSchemaObjects = function (xmlData) {
  * Build a schema collection object from a schema specification.
  *
  * @param {SchemasSpec} schemaSpecs The description of which schemas to use.
- * @returns {Promise<Schemas>} The schema container object and any issues found.
+ * @returns {Promise<HedSchemas>} The schema container object and any issues found.
  */
 export async function buildSchemas(schemaSpecs) {
   const schemaPrefixes = Array.from(schemaSpecs.data.keys())
@@ -62,14 +58,14 @@ export async function buildSchemas(schemaSpecs) {
   )
   const schemaObjects = schemaXmlData.map(buildSchemaObjects)
   const schemas = new Map(zip(schemaPrefixes, schemaObjects))
-  return new Schemas(schemas)
+  return new HedSchemas(schemas)
 }
 
 /**
  * Build HED schemas from a version specification string.
  *
  * @param {string} hedVersionString The HED version specification string (can contain comma-separated versions).
- * @returns {Promise<Schemas>} A Promise that resolves to the built schemas.
+ * @returns {Promise<HedSchemas>} A Promise that resolves to the built schemas.
  * @throws {IssueError} If the schema specification is invalid or schemas cannot be built.
  */
 export async function buildSchemasFromVersion(hedVersionString) {

browser/src/schema/loader.js

@@ -2,8 +2,8 @@
 
 /* Imports */
 import { IssueError } from '../../../src/issues/issues'
-import { parseSchemaXML } from '../../../src/utils/xml.js'
-import { schemaData } from './vite-importer.js'
+import parseSchemaXML from '../../../src/utils/xml.js'
+import { schemaData } from './vite-importer'
 
 /**
  * Load schema XML data from a schema version or path description.

browser/src/schema/loader.spec.js

@@ -1,6 +1,6 @@
 import { describe, it, expect } from 'vitest'
-import { loadSchema } from './loader.js'
-import { SchemaSpec } from '../../../src/schema/specs.js'
+import { loadSchema } from './loader'
+import { SchemaSpec } from '../../../src/schema/specs.ts'
 
 describe('Browser Schema Loader', () => {
   it('should return undefined when loading a bundled schema in test environment', async () => {

browser/src/utils/files.js

@@ -8,9 +8,9 @@ import { IssueError } from '../../../src/issues/issues'
  * @throws {IssueError} Always throws since local file reading is not supported in browsers.
  */
 export async function readFile(fileName) {
-  IssueError.generateAndThrow('fileReadError', { 
-    fileName: fileName, 
-    message: 'Local file reading is not supported in browser environment' 
+  IssueError.generateAndThrow('fileReadError', {
+    fileName: fileName,
+    message: 'Local file reading is not supported in browser environment',
   })
 }
 
@@ -26,7 +26,7 @@ export async function readHTTPSFile(url) {
   if (!response.ok) {
     IssueError.generateAndThrow('networkReadError', {
       url: url,
-      statusCode: response.status,
+      statusCode: response.status.toString(),
       statusText: response.statusText,
     })
   }

browser/src/validate_dataset.jsx

@@ -3,9 +3,9 @@ import { createRoot } from 'react-dom/client'
 import { FolderInput } from './components/FolderInput'
 import { ErrorDisplay } from './components/ErrorDisplay'
 import { BidsWebAccessor } from './bids/BidsWebAccessor.js'
-import { BidsDataset } from '@hed-javascript-root/src/bids/types/dataset.js'
-import { IssueError } from '@hed-javascript-root/src/issues/issues.js'
-import { BidsHedIssue } from '@hed-javascript-root/src/bids/types/issues.js'
+import { BidsDataset } from '@hed-javascript-root/src/bids/types/dataset'
+import { IssueError } from '@hed-javascript-root/src/issues/issues'
+import { BidsHedIssue } from '@hed-javascript-root/src/bids/types/issues'
 
 // --- Add TailwindCSS to the document head for immediate styling ---
 ;(() => {