Merge branch 'main' into fix/use_default_config_file

Author: rwblair

.git-blame-ignore-revs

@@ -1,5 +1,15 @@
+# 2026-01-27 11:50:03 -0500 - markiewicz@stanford.edu - chore: deno fmt [ignore-rev]
+03d6bdc6a4492607c0609e5aaa05099bf0937891
+# 2025-10-14 15:06:25 -0400 - markiewicz@stanford.edu - sty: deno fmt [ignore-rev]
+1560a880b30422b83c4016f1c18308079a95f367
+# 2025-10-14 08:26:35 -0400 - markiewicz@stanford.edu - sty: deno fmt [ignore-rev]
+54a4b9ae1841563d2dde099dbe98160190470eee
+# 2025-10-10 15:58:53 -0500 - markiewicz@stanford.edu - sty: deno fmt [ignore-rev]
+b75b43203bf0a3dfbfdbbf7239f61ecd6f4f3f43
 # 2025-09-22 14:52:13 -0400 - markiewicz@stanford.edu - [DATALAD RUNCMD] sty: Format [ignore-rev]
 fffce73a5b9b38fcf0cc0fc47c9e877be82d6cc5
+# 2025-09-17 10:59:35 -0400 - markiewicz@stanford.edu - sty: deno fmt [ignore-rev]
+3a1b37ab255708a567073acef60ebff1e11b64f7
 # 2025-09-10 09:32:33 -0400 - markiewicz@stanford.edu - sty: deno fmt [ignore-rev]
 55e4ad2a05683bf149ac9c805139f51bcc69cc94
 # 2025-08-22 14:13:47 -0400 - markiewicz@stanford.edu - sty: deno fmt [ignore-rev]

.github/workflows/deno_tests.yml

@@ -3,10 +3,10 @@ name: Deno build
 
 on:
   push:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
     tags: ['*']
   pull_request:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
@@ -38,7 +38,7 @@ jobs:
         run: echo version=$( git describe ) >> $GITHUB_OUTPUT
       - uses: denoland/setup-deno@e95548e56dfa95d4e1a28d6f422fafe75c4c26fb # v2
         with:
-          deno-version: v2.x
+          deno-version: v2.6.6
       - run: deno --node-modules-dir=auto -A ./build.ts
       - run: deno run -A ./dist/validator/bids-validator.js --version
       - uses: actions/upload-artifact@330a01c490aca151604b8cf639adc76d48f6c5d4 # v5

.github/workflows/docker-build-push.yml

@@ -2,10 +2,10 @@ name: Docker
 
 on:
   push:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
     tags: ['*']
   pull_request:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
   workflow_dispatch:
 
 concurrency:

.github/workflows/validation.yml

@@ -3,9 +3,9 @@ name: Validation
 
 on:
   push:
-    branches: [main]
+    branches: [main, dev, maint/*]
   pull_request:
-    branches: [main]
+    branches: [main, dev, maint/*]
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}

.github/workflows/web_build.yml

@@ -3,9 +3,9 @@ name: Web validator
 
 on:
   push:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
   pull_request:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
   release:
     types: [published]
   workflow_dispatch:
@@ -27,7 +27,7 @@ jobs:
       - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
       - uses: denoland/setup-deno@e95548e56dfa95d4e1a28d6f422fafe75c4c26fb # v2
         with:
-          deno-version: v2.x
+          deno-version: v2.6.6
       - run: deno task build
         working-directory: ./web
       - name: Upload GitHub Pages artifact
@@ -52,7 +52,7 @@ jobs:
           path: dev
       - uses: denoland/setup-deno@e95548e56dfa95d4e1a28d6f422fafe75c4c26fb # v2
         with:
-          deno-version: v2.x
+          deno-version: v2.6.6
       - name: Build release/target
         run: deno task build
         working-directory: stable/web

.github/workflows/wheels.yml

@@ -2,10 +2,10 @@ name: PyPI
 
 on:
   push:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
     tags: ['*']
   pull_request:
-    branches: [main, dev]
+    branches: [main, dev, maint/*]
   workflow_dispatch:
 
 concurrency:

.pre-commit-config.yaml

@@ -0,0 +1,18 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: 3e8a8703264a2f4a69428a0aa4dcb512790b2c8c # v6.0.0
+    hooks:
+      - id: check-json
+      - id: check-toml
+      - id: check-yaml
+      - id: check-merge-conflict
+      - id: check-symlinks
+        exclude: tests/data/broken-symlink
+      - id: destroyed-symlinks
+      - id: end-of-file-fixer
+      - id: fix-byte-order-marker
+      - id: trailing-whitespace
+  - repo: https://github.com/nozaq/pre-commit-deno
+    rev: db9b2333832fdbbb36b9c36d252cd52c2f9d41dc # 0.1.0
+    hooks:
+      - id: deno-fmt

CHANGELOG.md

@@ -2,6 +2,102 @@
 
 <!-- scriv-insert-here -->
 
+<a id='changelog-"2.4.0"'></a>
+# "2.4.0" — 2026-02-05
+
+## Changed
+
+- Update to BIDS Schema v1.2.0 (BIDS v1.11.0)
+
+<a id='changelog-"2.3.2"'></a>
+# "2.3.2" — 2026-02-02
+
+## Changed
+
+- File reads are temporarily cached to avoid multiple fetches/opens.
+
+## Fixed
+
+- Retrieval of remote data on S3 is now more robust, avoiding resource leaks
+  by setting timeouts and a reasonable retry protocol.
+
+<a id='changelog-"2.3.1"'></a>
+# "2.3.1" — 2026-01-27
+
+Mismatch between version and tag. Re-releasing for consistency. No other changes.
+
+<a id='changelog-"2.3.0"'></a>
+# "2.3.0" — 2026-01-27
+
+## Changed
+
+- Improve types for memoized functions by passing argument and return types to callers.
+
+- Render Markdown links as OSC-8 links in terminals where support is detected.
+
+## Fixed
+
+- Exit with a non-zero exit code if nested datasets are validated and found to have errors.
+
+- Prevent HED check from failing for null values found in sidecar metadata.
+
+<a id='changelog-"2.2.10"'></a>
+# "2.2.10" — 2026-01-15
+
+## Changed
+
+- Improve types for memoized functions by passing argument and return types to callers.
+
+## Fixed
+
+- Extract AWS region from S3 special remote, defaulting to us-east-1.
+
+<a id='changelog-"2.2.9"'></a>
+# "2.2.9" — 2026-01-15
+
+## Changed
+
+- Reverted terminal URLs for the 2.2.x series. It should be back in 2.3.0.
+
+<a id='changelog-"2.2.8"'></a>
+# "2.2.8" — 2026-01-15
+
+## Changed
+
+- Render Markdown links as OSC-8 links in terminals where support is detected.
+
+## Fixed
+
+- Fix typo in S3 URL generation code that prevented reading remote files.
+
+<a id='changelog-"2.2.7"'></a>
+# "2.2.7" — 2026-01-13
+
+## Added
+
+- Maintainer documentation for creating and fixing releases.
+
+- Support for rendering Markdown in validation messages in the terminal.
+
+- Display validation summaries for derivative datasets when recursive validation
+  (`-r`/`--recursive`) is run.
+
+- Support for presigning S3 URLs if AWS credentials are detected.
+
+## Fixed
+
+- Validate derivative file paths relative to the derivative dataset root.
+
+- Have all three calls to fetch in HttpOpener use same error handling.
+
+- Fix memoization memory leak for readRemotes.
+
+- Replace SPEC_ROOT placeholder with actual documentation link in CLI output
+
+## Infrastructure
+
+- Pin Deno to 2.5.6 in wheel builds to account for bugs with MacOS binaries compiled with 2.6.0.
+
 <a id='changelog-"2.2.5"'></a>
 # "2.2.5" — 2025-12-10
 

CITATION.cff

@@ -46,7 +46,7 @@ authors:
     orcid: https://orcid.org/0000-0002-6533-2909
   - family-names: Gau
     given-names: Rémi
-    orcid: https://orcid.org/0000-0002-1535-9767  
+    orcid: https://orcid.org/0000-0002-1535-9767
   - family-names: Gorgolewski
     given-names: Krzysztof J.
     orcid: https://orcid.org/0000-0003-3321-7583

LICENSE

@@ -17,4 +17,4 @@ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
 FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
 COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
 IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.