Merge remote-tracking branch 'origin/master' into contributors

.pre-commit-config.yaml

@@ -73,7 +73,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.13.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

macros_doc.md

@@ -1,3 +1,7 @@
+---
+render_macros: false
+---
+
 # Using MkDocs macros in the BIDS specification
 
 We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
@@ -9,23 +13,6 @@ in the specification.
 Below you will find answers to frequently asked questions regarding using macros
 in the BIDS specification.
 
-- [Using MkDocs macros in the BIDS specification](#using-mkdocs-macros-in-the-bids-specification)
-   - [What are macros and why use them?](#what-are-macros-and-why-use-them)
-   - [What kind of input information are required by macros?](#what-kind-of-input-information-are-required-by-macros)
-   - [What macros are available?](#what-macros-are-available)
-   - [When should I use a macro?](#when-should-i-use-a-macro)
-   - [Do I need learn how to program to use those macros?](#do-i-need-learn-how-to-program-to-use-those-macros)
-   - [Anything else I need to know if I need to insert a new macro call?](#anything-else-i-need-to-know-if-i-need-to-insert-a-new-macro-call)
-   - [How-To and Examples](#how-to-and-examples)
-      - [Writing directory content examples](#writing-directory-content-examples)
-      - [Generating tables](#generating-tables)
-         - [Modifying a term in the table](#modifying-a-term-in-the-table)
-         - [Why would you NOT want to modify the content of the yml file directly ?](#why-would-you-not-want-to-modify-the-content-of-the-yml-file-directly-)
-         - [Adding a new term to the table](#adding-a-new-term-to-the-table)
-         - [Should I create a macro if I need a new kind of table?](#should-i-create-a-macro-if-i-need-a-new-kind-of-table)
-   - [Why use macros at all?](#why-use-macros-at-all)
-   - [Links and references](#links-and-references)
-
 ## What are macros and why use them?
 
 A macro is a rule or pattern that specifies how an input should be mapped to
@@ -127,9 +114,6 @@ when you get back to the document you just edited) is to leave a comment before
 the macro to quickly explain what it does and where to find more information
 about it.
 
-<!-- - [ ] TODO for maintainers: actually add those comments in the current
-      specification. -->
-
 It could for example look like this:
 
 ```markdown

mkdocs.yml

@@ -95,6 +95,9 @@ extra:
       link: https://www.instagram.com/bidsstandard/
     - icon: fontawesome/brands/youtube
       link: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw
+  analytics:
+    provider: google
+    property: G-SBWH6YNMPX
 
 extra_javascript:
   - js/jquery-3.6.0.min.js

src/common-principles.md

@@ -739,9 +739,11 @@ A guide for using macros can be found at
             "sub-01_task-rest_acq-default_bold.nii.gz": "",
             "sub-01_task-rest_acq-longtr_bold.nii.gz": "",
             "sub-01_task-rest_acq-longtr_bold.json": "",
-            }
+            },
+        "sub-01_scans.tsv": "",
         },
     "task-rest_bold.json": "",
+    "scans.json": ""
     }
 ) }}
 
@@ -773,6 +775,10 @@ the value for field "`RepetitionTime`" is therefore overridden to the value `3.0
 The value for field "`EchoTime`" remains applicable to that image, and is not unset by its
 absence in the metadata file at the lower level (rule 5.b; corollary 3).
 
+A single `scans.json`, without any entity in the filename at the top level,
+is applicable to describe columns of the `sub-01_scans.tsv`
+and any other `_scans.tsv` potentially present in the dataset for other subjects.
+
 Example 2: Impermissible use of multiple metadata files at one directory level (rule 4)
 
 <!-- This block generates a file tree.

src/modality-specific-files/intracranial-electroencephalography.md

@@ -38,6 +38,7 @@ stored in one of the following formats:
 | [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php)                          | `.set`, `.fdt`           | The format used by the MATLAB toolbox [EEGLAB](https://sccn.ucsd.edu/eeglab/index.php). Each recording consists of a `.set` file with an OPTIONAL `.fdt` file.             |
 | [Neurodata Without Borders](https://nwb-schema.readthedocs.io/en/latest/) | `.nwb`                   | Each recording consists of a single `.nwb` file.                                                                                                                           |
 | [MEF3](https://osf.io/e3sf9/)                                             | `.mefd`                  | Each recording consists of a `.mefd` directory.                                                                                                                            |
+| [MED](https://medformat.org/)                                             | `.medd`                  | Each recording consists of a `.medd` directory.                                                                                                                            |
 
 It is RECOMMENDED to use the European data format, or the BrainVision data
 format. It is furthermore discouraged to use the other accepted formats over

src/schema/objects/columns.yaml

@@ -349,6 +349,8 @@ onset:
     (for example, "dummy volumes" in BOLD fMRI),
     a time of 0 corresponds to the first stored data point and not the first
     acquired data point.
+
+    A value of `n/a` value indicates the onset time is unknown or unavailable.
   type: number
   unit: s
 pathology:

src/schema/objects/extensions.yaml

@@ -153,6 +153,14 @@ md:
   display_name: Markdown
   description: |
     A Markdown file.
+medd:
+  value: .medd/
+  display_name: Multiscale Electrophysiology Data Format
+  description: |
+    A directory in the [MED](https://medformat.org/) format.
+    Successor to the MEF 3.0 format.
+
+    Each recording consists of a `.medd` directory.
 mefd:
   value: .mefd/
   display_name: Multiscale Electrophysiology File Format Version 3.0

src/schema/rules/checks/func.yaml

@@ -88,6 +88,8 @@ VolumeTimingRepetitionTimeMutex:
       or 'VolumeTiming' when variable times are used.
     level: error
   selectors:
+    - type(nifti_header) != "null"
+    - intersects([suffix], ["asl", "bold"])
     - type(sidecar.VolumeTiming) != "null"
   checks:
     - type(sidecar.RepetitionTime) == "null"
@@ -101,6 +103,8 @@ RepetitionTimeAcquisitionDurationMutex:
       (RepetitionTime - AcquisitionDuration).
     level: error
   selectors:
+    - type(nifti_header) != "null"
+    - intersects([suffix], ["asl", "bold"])
     - type(sidecar.AcquisitionDuration) != "null"
   checks:
     - type(sidecar.RepetitionTime) == "null"
@@ -113,6 +117,8 @@ VolumeTimingDelayTimeMutex:
       To specify acquisition duration, use 'AcquisitionDuration' or 'SliceTiming'.
     level: error
   selectors:
+    - type(nifti_header) != "null"
+    - intersects([suffix], ["asl", "bold"])
     - type(sidecar.VolumeTiming) != "null"
   checks:
     - type(sidecar.DelayTime) == "null"
@@ -124,6 +130,8 @@ VolumeTimingMissingAcquisitionDuration:
       The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
     level: error
   selectors:
+    - type(nifti_header) != "null"
+    - intersects([suffix], ["asl", "bold"])
     - type(sidecar.VolumeTiming) != "null"
   checks:
     - '"SliceTiming" in sidecar || "AcquisitionDuration" in sidecar'

src/schema/rules/files/raw/ieeg.yaml

@@ -3,6 +3,7 @@ ieeg:
   suffixes:
     - ieeg
   extensions:
+    - .medd/
     - .mefd/
     - .json
     - .edf

tools/schemacode/bidsschematools/conftest.py

@@ -1,12 +1,8 @@
 import logging
 import tempfile
+from importlib.resources import as_file, files
 from subprocess import run
 
-try:
-    from importlib.resources import as_file, files
-except ImportError:  # PY<3.9
-    from importlib_resources import as_file, files
-
 import pytest
 
 lgr = logging.getLogger()

tools/schemacode/bidsschematools/data/tests/test_rules.py

@@ -64,6 +64,7 @@ def test_rule_objects(schema_obj):
                 is_list = False
 
             for i_use, use in enumerate(instance):
+                assert isinstance(use, str)
                 if use == "derivatives":
                     # Skip derivatives dirs, because the dir is treated as a "use" instead.
                     continue
@@ -81,9 +82,21 @@ def test_rule_objects(schema_obj):
                     object_values = [
                         value["value"] for value in schema_obj["objects"][object_type].values()
                     ]
-                else:
+                elif object_type in [
+                    "columns",
+                    "common_principles",
+                    "datatypes",
+                    "entities",
+                    "enums",
+                    "files",
+                    "formats",
+                    "metadata",
+                    "modalities",
+                ]:
                     # But other object types are referenced via their keys
                     object_values = list(schema_obj["objects"][object_type].keys())
+                else:
+                    raise AssertionError(f"Object type {object_type} not implemented.")
 
                 # Build a list of items mentioned in rules, but not found in objects.
                 if use not in object_values:

tools/schemacode/bidsschematools/tests/test_make_testdata.py

@@ -1,10 +1,6 @@
 import os
 import shutil
-
-try:
-    from importlib.resources import files
-except ImportError:  # PY<3.9
-    from importlib_resources import files
+from importlib.resources import files
 
 import pytest