Merge remote-tracking branch 'upstream/main' into dev

Author: effigies

CHANGELOG.md

@@ -1,4 +1,46 @@
 
+<a id='changelog-2.0.2'></a>
+# 2.0.2 — 2025-02-10
+
+## Added
+
+- Enable glob-style wildcards for `location` field in configuration files. (#134)
+
+## Changed
+
+- Ensure HED schemas are loaded only once, improving efficiency. (#156)
+
+- Change the output of the `intersects()` function in the expression language
+  to return the intersection, if non-empty.
+  Corresponds to [bids-standard/bids-specification#2044]. (#150)
+
+- Update to BIDS schema version 1.0.1 (BIDSVersion 1.10.0) (#152)
+
+- Limit TSV validation to first 1000 rows by default,
+  adding the `--max-rows` flag to control this behavior. (#139)
+
+[bids-standard/bids-specification#2044]: https://github.com/bids-standard/bids-specification/pull/2044
+
+## Fixed
+
+- TSV files may now have columns named `set`, `clear`, `delete`, `keys`, or `value`.
+  These were previously masked by the methods on the data structure
+  representing columns. (#155)
+
+- Improve handling of `.bidsignore` files in the web validator.
+  Ignores matching directories but not the files they contained could fail to match.
+  (#113)
+
+- Resolve issue with parsing headers of NIfTI files with large extensions.
+  Fixes [issue 126].
+
+[issue 126]: https://github.com/bids-standard/bids-validator/issues/126
+
+## Infrastructure
+
+- Adopting [scriv](https://scriv.readthedocs.io/en/latest/) for changelog
+  management.
+
 <a id='changelog-2.0.1'></a>
 # 2.0.1 — 2024-12-10
 

changelog.d/20241114_165444_effigies.md renamed to changelog.d/20250214_094554_markiewicz_load_subjects.md

@@ -4,12 +4,6 @@ A new scriv changelog fragment.
 Uncomment the section that is right (remove the HTML comment wrapper).
 -->
 
-<!--
-### Removed
-
-- A bullet item for the Removed category.
-
--->
 <!--
 ### Added
 
@@ -22,21 +16,36 @@ Uncomment the section that is right (remove the HTML comment wrapper).
 - A bullet item for the Changed category.
 
 -->
+
+### Fixed
+
+- Subject detection in `participants.tsv` and `phenotype/` directories
+  has been restored, enabling checks that were deactivated by the missing
+  data. ([#162])
+
+[#162]: https://github.com/bids-standard/bids-validator/pull/162
+
 <!--
 ### Deprecated
 
 - A bullet item for the Deprecated category.
 
 -->
-### Fixed
+<!--
+### Removed
 
-- Improve handling of `.bidsignore` files in the web validator.
-  Ignores matching directories but not the files they contained could fail to match.
-  (#113)
+- A bullet item for the Removed category.
 
+-->
 <!--
 ### Security
 
 - A bullet item for the Security category.
 
 -->
+<!--
+### Infrastructure
+
+- A bullet item for the Infrastructure category.
+
+-->

changelog.d/20241204_103403_effigies_nifti_headers.md renamed to changelog.d/20250214_101021_markiewicz_scrivening.md

@@ -16,12 +16,13 @@ Uncomment the section that is right (remove the HTML comment wrapper).
 - A bullet item for the Changed category.
 
 -->
+
 ### Fixed
 
-- Resolve issue with parsing headers of NIfTI files with large extensions.
-  Fixes [issue 126].
+- Skip HED tests if schema cannot be loaded. This was exhibiting
+  as a `HED_ERROR` with "cannot read property null". ([#160])
 
-[issue 126]: https://github.com/bids-standard/bids-validator/issues/126
+[#160]: https://github.com/bids-standard/bids-validator/pull/160
 
 <!--
 ### Deprecated

changelog.d/20241114_192344_effigies_scriv.md renamed to changelog.d/20250216_174252_dominik.welke_fix_warn_message.md

@@ -16,12 +16,12 @@ Uncomment the section that is right (remove the HTML comment wrapper).
 - A bullet item for the Changed category.
 
 -->
-<!--
+
 ### Fixed
 
-- A bullet item for the Fixed category.
+- fix misleading ERROR/WARNING message
+
 
--->
 <!--
 ### Deprecated
 
@@ -40,7 +40,9 @@ Uncomment the section that is right (remove the HTML comment wrapper).
 - A bullet item for the Security category.
 
 -->
+<!--
 ### Infrastructure
 
-- Adopting [scriv](https://scriv.readthedocs.io/en/latest/) for changelog
-  management.
+- A bullet item for the Infrastructure category.
+
+-->

deno.json

@@ -33,19 +33,19 @@
     "@cliffy/table": "jsr:@effigies/[email protected]",
     "@hed/validator": "npm:[email protected]",
     "@ignore": "npm:[email protected]",
-    "@libs/xml": "jsr:@libs/[email protected].1",
+    "@libs/xml": "jsr:@libs/[email protected].4",
     "@mango/nifti": "npm:@bids/[email protected]",
     "@std/assert": "jsr:@std/[email protected]",
-    "@std/fmt": "jsr:@std/[email protected].3",
-    "@std/fs": "jsr:@std/[email protected].5",
-    "@std/io": "jsr:@std/[email protected].0",
-    "@std/log": "jsr:@std/[email protected].9",
+    "@std/fmt": "jsr:@std/[email protected].5",
+    "@std/fs": "jsr:@std/[email protected].13",
+    "@std/io": "jsr:@std/[email protected].2",
+    "@std/log": "jsr:@std/[email protected].14",
     "@std/path": "jsr:@std/[email protected]",
-    "@std/streams": "jsr:@std/[email protected].8",
-    "@std/yaml": "jsr:@std/yaml@^1.0.4"
+    "@std/streams": "jsr:@std/[email protected].9",
+    "@std/yaml": "jsr:@std/yaml@^1.0.5"
   },
   "tasks": {
-    "test": "deno test -A src/tests/"
+    "test": "deno test -A src/"
   },
   "fmt": {
     "lineWidth": 99,

deno.lock

@@ -41,7 +41,7 @@ export class BIDSFileBrowser implements BIDSFile {
     return this.#file.text()
   }
 
-  async readBytes(size: number, offset = 0): Promise<Uint8Array> {
+  async readBytes(size: number, offset = 0): Promise<Uint8Array<ArrayBuffer>> {
     return new Uint8Array(await this.#file.slice(offset, size).arrayBuffer())
   }
 }

src/files/browser.ts

@@ -78,7 +78,7 @@ export class BIDSFileDeno implements BIDSFile {
    * Reads up to size bytes, starting at offset.
    * If EOF is encountered, the resulting array may be smaller.
    */
-  async readBytes(size: number, offset = 0): Promise<Uint8Array> {
+  async readBytes(size: number, offset = 0): Promise<Uint8Array<ArrayBuffer>> {
     const handle = this.#openHandle()
     const buf = new Uint8Array(size)
     await handle.seek(offset, Deno.SeekMode.Start)

src/files/deno.ts

@@ -3,7 +3,7 @@ import type { BIDSFile } from '../types/filetree.ts'
 import { logger } from '../utils/logger.ts'
 import type { NiftiHeader } from '@bids/schema/context'
 
-async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array> {
+async function extract(buffer: Uint8Array, nbytes: number): Promise<Uint8Array<ArrayBuffer>> {
   // The fflate decompression that is used in nifti-reader does not like
   // truncated data, so pretend that we have a stream and stop reading
   // when we have enough bytes.

src/files/nifti.ts

@@ -7,7 +7,7 @@ import * as XML from '@libs/xml'
 import type { BIDSFile } from '../types/filetree.ts'
 
 function getImageDescription(
-  dataview: DataView,
+  dataview: DataView<ArrayBuffer>,
   littleEndian: boolean,
   IFDsize: number,
 ): string | undefined {