Merge branch 'main' of github.com:bids-standard/bids-validator

Author: rwblair

.git-blame-ignore-revs

@@ -1,3 +1,5 @@
+# Tue Mar 25 15:43:26 2025 -0400 - [email protected] - chore(fmt): deno fmt [ignore-rev]
+51510f5ecd91027f6ab4bfd1d0d287aaf6300e8d
 # Wed Aug 28 11:37:33 2024 -0400 - [email protected] - chore(fmt): deno fmt [ignore-rev]
 ff6015b9b2d9b1f215905d71e7dc7a14b8f29f56
 # Fri Aug 16 17:23:33 2024 -0400 - [email protected] - chore(fmt): deno fmt [ignore-rev]

.github/scripts/scriv_check.sh

@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+# Modified from https://github.com/tarides/changelog-check-action/tree/main
+
+set -uo pipefail
+
+if [ "${NO_CHANGELOG_LABEL}" = "true" ]; then
+    # 'no changelog' set, so finish successfully
+    exit 0
+else
+    # a changelog check is required
+    # fail if the diff is empty
+    if git diff --exit-code "origin/${BASE_REF}" -- "changelog.d/"; then
+        cat <<END >&2
+User-visible changes should come with an entry in the changelog.
+Create a changelog blurb with "uvx scriv create --edit".
+If no changelog entry is needed, then set the "no changelog" label.
+END
+        exit 1
+    fi
+fi

.github/workflows/deno_tests.yml

@@ -72,10 +72,16 @@ jobs:
         run: echo 'PERMS=--allow-read --allow-write --allow-env --allow-run --deny-net' >> $GITHUB_ENV
         if: ${{ ! matrix.allow-net }}
       - name: Disable example that requires network access
-        run: touch tests/data/bids-examples/xeeg_hed_score/.SKIP_VALIDATION
+        run: |
+          for DS in eeg_ds003645s_hed_library xeeg_hed_score; do
+            touch tests/data/bids-examples/${DS}/.SKIP_VALIDATION
+          done
         if: ${{ ! matrix.allow-net }}
       - name: Disable unreleased examples
-        run: touch tests/data/bids-examples/dwi_deriv/.SKIP_VALIDATION
+        run: |
+          for DS in dwi_deriv pheno004; do
+            touch tests/data/bids-examples/${DS}/.SKIP_VALIDATION
+          done
         if: github.ref_name != 'dev' && github.base_ref != 'dev'
       - run: deno test --node-modules-dir=auto $PERMS --coverage=cov/ src/
       - name: Collect coverage

.github/workflows/validation.yml

@@ -22,3 +22,15 @@ jobs:
         python-version: 3
     - name: Validate CITATION.cff
       run: pipx run cffconvert --validate
+  check_change_log:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Check for changes in changelog
+      env:
+        BASE_REF: ${{ github.event.pull_request.base.ref }}
+        NO_CHANGELOG_LABEL: ${{ contains(github.event.pull_request.labels.*.name, 'no changelog') }}
+      run: .github/scripts/scriv_check.sh
+      shell: bash

changelog.d/20250324_121157_rosswilsonblair_scriv_for_180.md

@@ -0,0 +1,47 @@
+<!--
+A new scriv changelog fragment.
+
+Uncomment the section that is right (remove the HTML comment wrapper).
+-->
+
+### Added
+
+- Validate directory names names according to `schema.rules.directories` entries.
+  Use rules to identify "opaque" directories whose contents are unspecified by BIDS.
+
+<!--
+### Changed
+
+- A bullet item for the Changed category.
+
+-->
+<!--
+### 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.
+
+-->

deno.json

@@ -28,16 +28,16 @@
   },
   "imports": {
     "@ajv": "npm:[email protected]",
-    "@bids/schema": "jsr:@bids/[email protected].3",
+    "@bids/schema": "jsr:@bids/[email protected].4",
     "@cliffy/command": "jsr:@effigies/[email protected]",
     "@cliffy/table": "jsr:@effigies/[email protected]",
-    "@hed/validator": "npm:hed-validator@3.15.5",
+    "@hed/validator": "npm:hed-validator@4.0.1",
     "@ignore": "npm:[email protected]",
     "@libs/xml": "jsr:@libs/[email protected]",
     "@mango/nifti": "npm:@bids/[email protected]",
-    "@std/assert": "jsr:@std/[email protected].11",
-    "@std/fmt": "jsr:@std/[email protected].5",
-    "@std/fs": "jsr:@std/[email protected].13",
+    "@std/assert": "jsr:@std/[email protected].12",
+    "@std/fmt": "jsr:@std/[email protected].6",
+    "@std/fs": "jsr:@std/[email protected].15",
     "@std/io": "jsr:@std/[email protected]",
     "@std/log": "jsr:@std/[email protected]",
     "@std/path": "jsr:@std/[email protected]",

deno.lock

@@ -179,9 +179,6 @@ export const bidsIssues: IssueDefinitionRecord = {
     severity: 'error',
     reason: 'We were unable to read this file.',
   },
-}
-
-const hedIssues: IssueDefinitionRecord = {
   HED_ERROR: {
     severity: 'error',
     reason: 'The validation on this HED string returned an error.',
@@ -190,33 +187,6 @@ const hedIssues: IssueDefinitionRecord = {
     severity: 'warning',
     reason: 'The validation on this HED string returned a warning.',
   },
-  HED_INTERNAL_ERROR: {
-    severity: 'error',
-    reason: 'An internal error occurred during HED validation.',
-  },
-  HED_INTERNAL_WARNING: {
-    severity: 'warning',
-    reason: 'An internal warning occurred during HED validation.',
-  },
-  HED_MISSING_VALUE_IN_SIDECAR: {
-    severity: 'warning',
-    reason:
-      'The json sidecar does not contain this column value as a possible key to a HED string.',
-  },
-  HED_VERSION_NOT_DEFINED: {
-    severity: 'warning',
-    reason:
-      "You should define 'HEDVersion' for this file. If you don't provide this information, the HED validation will use the latest version available.",
-  },
-}
-
-export const hedOldToNewLookup: Record<number, Partial<keyof IssueDefinitionRecord>> = {
-  104: 'HED_ERROR',
-  105: 'HED_WARNING',
-  106: 'HED_INTERNAL_ERROR',
-  107: 'HED_INTERNAL_WARNING',
-  108: 'HED_MISSING_VALUE_IN_SIDECAR',
-  109: 'HED_VERSION_NOT_DEFINED',
 }
 
-export const nonSchemaIssues = { ...bidsIssues, ...hedIssues }
+export const nonSchemaIssues = { ...bidsIssues }

src/issues/list.ts

@@ -25,7 +25,6 @@ import { buildAssociations } from './associations.ts'
 import type { ValidatorOptions } from '../setup/options.ts'
 import { logger } from '../utils/logger.ts'
 
-
 export class BIDSContextDataset implements Dataset {
   #dataset_description: Record<string, unknown> = {}
   tree: FileTree
@@ -100,7 +99,6 @@ export class BIDSContextDataset implements Dataset {
   isOpaqueDirectory(file: FileTree): boolean {
     return this.opaqueDirectories.has(file.path)
   }
-
 }
 
 class BIDSContextDatasetSubjects implements Subjects {

src/schema/context.ts

@@ -11,7 +11,8 @@ const subjectJson = JSON.stringify({ subOverwrite: 'subject', subValue: 'subject
 const rootJson = JSON.stringify({ rootOverwrite: 'root', rootValue: 'root' })
 
 function readBytes(json: string) {
-  return (size: number) => Promise.resolve(new TextEncoder().encode(json) as Uint8Array<ArrayBuffer>)
+  return (size: number) =>
+    Promise.resolve(new TextEncoder().encode(json) as Uint8Array<ArrayBuffer>)
 }
 
 export const rootFileTree = pathsToTree([