Merge pull request #258 from effigies/deno/2.5

type: Adapt to changes in ArrayBuffers in Typescript 5.9.2

Author: rwblair

.github/workflows/deno_tests.yml

@@ -38,7 +38,7 @@ jobs:
         run: echo version=$( git describe ) >> $GITHUB_OUTPUT
       - uses: denoland/setup-deno@v2
         with:
-          deno-version: v2.4
+          deno-version: v2.x
       - run: deno --node-modules-dir=auto -A ./build.ts
       - run: deno run -A ./dist/validator/bids-validator.js --version
       - uses: actions/upload-artifact@v4
@@ -64,7 +64,7 @@ jobs:
           submodules: true
       - uses: denoland/setup-deno@v2
         with:
-          deno-version: v2.4
+          deno-version: v2.x
       - name: Set permissions with network access
         run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --allow-net' >> $GITHUB_ENV
         if: ${{ matrix.allow-net }}
@@ -98,7 +98,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: denoland/setup-deno@v2
         with:
-          deno-version: v2.4
+          deno-version: v2.x
       - run: deno publish --dry-run
 
   publish:
@@ -117,7 +117,7 @@ jobs:
           TAG: ${{ github.ref_name }}
       - uses: denoland/setup-deno@v2
         with:
-          deno-version: v2.4
+          deno-version: v2.x
       - run: deno publish
 
   deploy:

.github/workflows/web_build.yml

@@ -27,7 +27,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: denoland/setup-deno@v2
         with:
-          deno-version: v2.4
+          deno-version: v2.x
       - run: deno task build
         working-directory: ./web
       - name: Upload GitHub Pages artifact
@@ -52,7 +52,7 @@ jobs:
           path: dev
       - uses: denoland/setup-deno@v2
         with:
-          deno-version: v2.4
+          deno-version: v2.x
       - name: Build release/target
         run: deno task build
         working-directory: stable/web

changelog.d/20250911_123931_markiewicz_2_5.md

@@ -0,0 +1,47 @@
+<!--
+A new scriv changelog fragment.
+
+Uncomment the section that is right (remove the HTML comment wrapper).
+For top level release notes, leave all the headers commented out.
+-->
+
+<!--
+### Added
+
+- A bullet item for the Added category.
+
+-->
+### Changed
+
+- Now supports Deno 2.5 and Typescript 5.9.2.
+
+<!--
+### Fixed
+
+- A bullet item for the Fixed category.
+
+-->
+<!--
+### Deprecated
+
+- A bullet item for the Deprecated category.
+
+-->
+<!--
+### Removed
+
+- A bullet item for the Removed category.
+
+-->
+<!--
+### Security
+
+- A bullet item for the Security category.
+
+-->
+<!--
+### Infrastructure
+
+- A bullet item for the Infrastructure category.
+
+-->

src/files/browser.ts

@@ -29,8 +29,8 @@ export class BIDSFileBrowser implements BIDSFile {
     return this.#file.size
   }
 
-  get stream(): ReadableStream<Uint8Array> {
-    return this.#file.stream()
+  get stream(): ReadableStream<Uint8Array<ArrayBuffer>> {
+    return this.#file.stream() as ReadableStream<Uint8Array<ArrayBuffer>>
   }
 
   get ignored(): boolean {

src/files/deno.ts

@@ -45,7 +45,7 @@ export class BIDSFileDeno implements BIDSFile {
     return this.#fileInfo ? this.#fileInfo.size : -1
   }
 
-  get stream(): ReadableStream<Uint8Array> {
+  get stream(): ReadableStream<Uint8Array<ArrayBuffer>> {
     const handle = this.#openHandle()
     return handle.readable
   }

src/files/tsv.test.ts

@@ -10,6 +10,12 @@ import { loadTSV, loadTSVGZ } from './tsv.ts'
 import { streamFromString } from '../tests/utils.ts'
 import { ColumnsMap } from '../types/columns.ts'
 
+function compressedStreamFromString(str: string): ReadableStream<Uint8Array<ArrayBuffer>> {
+  return streamFromString(str).pipeThrough(new CompressionStream('gzip')) as ReadableStream<
+    Uint8Array<ArrayBuffer>
+  >
+}
+
 Deno.test('TSV loading', async (t) => {
   await t.step('Empty file produces empty map', async () => {
     const file = pathToFile('/empty.tsv')
@@ -182,7 +188,7 @@ Deno.test('TSV loading', async (t) => {
 Deno.test('TSVGZ loading', async (t) => {
   await t.step('No header and empty file produces empty map', async () => {
     const file = pathToFile('/empty.tsv.gz')
-    file.stream = streamFromString('').pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString('')
 
     const map = await loadTSVGZ(file, [])
     // map.size looks for a column called map, so work around it
@@ -191,7 +197,7 @@ Deno.test('TSVGZ loading', async (t) => {
 
   await t.step('Empty file produces header-only map', async () => {
     const file = pathToFile('/empty.tsv.gz')
-    file.stream = streamFromString('').pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString('')
 
     const map = await loadTSVGZ(file, ['a', 'b', 'c'])
     assertEquals(map.a, [])
@@ -201,15 +207,15 @@ Deno.test('TSVGZ loading', async (t) => {
 
   await t.step('Single column file produces single column maps', async () => {
     const file = pathToFile('/single_column.tsv')
-    file.stream = streamFromString('1\n2\n3\n').pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString('1\n2\n3\n')
 
     const map = await loadTSVGZ(file, ['a'])
     assertEquals(map.a, ['1', '2', '3'])
   })
 
   await t.step('Mismatched header length throws issue', async () => {
     const file = pathToFile('/single_column.tsv.gz')
-    file.stream = streamFromString('1\n2\n3\n').pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString('1\n2\n3\n')
 
     try {
       await loadTSVGZ(file, ['a', 'b'])
@@ -220,17 +226,15 @@ Deno.test('TSVGZ loading', async (t) => {
 
   await t.step('Missing final newline is ignored', async () => {
     const file = pathToFile('/missing_newline.tsv.gz')
-    file.stream = streamFromString('1\n2\n3').pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString('1\n2\n3')
 
     const map = await loadTSVGZ(file, ['a'])
     assertEquals(map.a, ['1', '2', '3'])
   })
 
   await t.step('Empty row throws issue', async () => {
     const file = pathToFile('/empty_row.tsv.gz')
-    file.stream = streamFromString('1\t2\t3\n\n4\t5\t6\n').pipeThrough(
-      new CompressionStream('gzip'),
-    )
+    file.stream = compressedStreamFromString('1\t2\t3\n\n4\t5\t6\n')
 
     try {
       await loadTSVGZ(file, ['a', 'b', 'c'])
@@ -255,35 +259,33 @@ Deno.test('TSVGZ loading', async (t) => {
     // Use 1500 to avoid overlap with default initial capacity
     const headers = ['a', 'b', 'c']
     const text = '1\t2\t3\n'.repeat(1500)
-    file.stream = streamFromString(text).pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString(text)
 
     let map = await loadTSVGZ(file, headers, 0)
     assertEquals(map.a, [])
     assertEquals(map.b, [])
     assertEquals(map.c, [])
 
-    file.stream = streamFromString(text).pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString(text)
     map = await loadTSVGZ(file, headers, 1)
     assertEquals(map.a, ['1'])
     assertEquals(map.b, ['2'])
     assertEquals(map.c, ['3'])
 
-    file.stream = streamFromString(text).pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString(text)
     map = await loadTSVGZ(file, headers, 2)
     assertEquals(map.a, ['1', '1'])
     assertEquals(map.b, ['2', '2'])
     assertEquals(map.c, ['3', '3'])
 
-    file.stream = streamFromString(text).pipeThrough(new CompressionStream('gzip'))
+    file.stream = compressedStreamFromString(text)
     map = await loadTSVGZ(file, headers, -1)
     assertEquals(map.a, Array(1500).fill('1'))
     assertEquals(map.b, Array(1500).fill('2'))
     assertEquals(map.c, Array(1500).fill('3'))
 
     // Check that maxRows does not truncate shorter files
-    file.stream = streamFromString('1\t2\t3\n4\t5\t6\n7\t8\t9\n').pipeThrough(
-      new CompressionStream('gzip'),
-    )
+    file.stream = compressedStreamFromString('1\t2\t3\n4\t5\t6\n7\t8\t9\n')
     map = await loadTSVGZ(file, headers, 4)
     assertEquals(map.a, ['1', '4', '7'])
     assertEquals(map.b, ['2', '5', '8'])

src/tests/utils.ts

@@ -1,4 +1,6 @@
-export function streamFromUint8Array(arr: Uint8Array): ReadableStream<Uint8Array> {
+export function streamFromUint8Array<T extends ArrayBufferLike>(
+  arr: Uint8Array<T>,
+): ReadableStream<Uint8Array<T>> {
   return new ReadableStream({
     start(controller) {
       controller.enqueue(arr)
@@ -7,6 +9,6 @@ export function streamFromUint8Array(arr: Uint8Array): ReadableStream<Uint8Array
   })
 }
 
-export function streamFromString(str: string): ReadableStream<Uint8Array> {
-  return streamFromUint8Array(new TextEncoder().encode(str))
+export function streamFromString(str: string): ReadableStream<Uint8Array<ArrayBuffer>> {
+  return streamFromUint8Array(new TextEncoder().encode(str) as Uint8Array<ArrayBuffer>)
 }

src/types/filetree.ts

@@ -10,7 +10,7 @@ export interface BIDSFile {
   // BIDS ignore status of the file
   ignored: boolean
   // ReadableStream to file raw contents
-  stream: ReadableStream<Uint8Array>
+  stream: ReadableStream<Uint8Array<ArrayBuffer>>
   // Resolve stream to decoded utf-8 text
   text: () => Promise<string>
   // Read a range of bytes