Merge branch 'bids-standard:master' into master

Author: markmikkelsen

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
       - id: check-readthedocs
         files: readthedocs.yml
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -45,7 +45,7 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 7.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
@@ -67,7 +67,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.0
+    rev: v1.11.1
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

src/modality-specific-files/magnetic-resonance-imaging-data.md

@@ -721,7 +721,7 @@ within the `[*_]dwi.bval` and `[*_]dwi.bvec` files) MAY change across DWI runs.
 
 **Gradient orientation file formats**.
 The `[*_]dwi.bval` and `[*_]dwi.bvec` files MUST follow the
-[FSL format](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT):
+[FSL format](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/diffusion/index?id=diffusion-data-in-fsl):
 The `[*_]dwi.bvec` file contains 3 rows with *N* space-delimited floating-point numbers
 (corresponding to the *N* volumes in the corresponding NIfTI file.)
 The first row contains the *x* elements, the second row contains the *y* elements and

src/modality-specific-files/microscopy.md

@@ -55,7 +55,7 @@ Microscopy raw data MUST be stored in one of the following formats:
 
 -   [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#)
     (`.ome.tif` for standard TIFF files or `.ome.btf` for
-    [BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
+    [BigTIFF](https://web.archive.org/web/20240706160214/https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
 
 -   [OME-ZARR/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)
 

src/schema/SCHEMA_VERSION

@@ -1 +1 @@
-0.10.1-dev
+0.11.0-dev

src/schema/meta/context.yaml

@@ -29,9 +29,6 @@ properties:
       dataset_description:
         description: 'Contents of /dataset_description.json'
         type: object
-      files:
-        description: 'List of all files in dataset'
-        type: array
       tree:
         description: 'Tree view of all files in dataset'
         type: object

src/schema/rules/checks/dataset.yaml

@@ -51,7 +51,7 @@ SamplesTSVMissing:
     - path == '/dataset_description.json'
     - '"micr" in dataset.modalities'
   checks:
-    - "'samples.tsv' in dataset.files"
+    - exists('samples.tsv', 'dataset')
 
 UnknownVersion:
   issue:

src/schema/rules/checks/hints.yaml

@@ -34,6 +34,19 @@ TooFewAuthors:
   checks:
     - length(json.Authors) > 1
 
+# 115
+EmptyDatasetName:
+  issue:
+    code: EMPTY_DATASET_NAME
+    message: |
+      The Name field of dataset_description.json is present but empty of visible characters.
+    level: warning
+  selectors:
+    - path == '/dataset_description.json'
+    - type(json.Name) != 'null'
+  checks:
+    - match(json.Name, '\S')
+
 ### Functional files
 
 # 85

src/schema/rules/dataset_metadata.yaml

@@ -34,7 +34,7 @@ derivative_description:
 dataset_description_with_genetics:
   selectors:
     - path == "/dataset_description.json"
-    - intersects(dataset.files, ["/genetic_info.json"])
+    - exists('genetic_info.json', 'dataset')
   fields:
     Genetics: required