Merge branch 'bids-standard:master' into master

.circleci/config.yml

@@ -55,11 +55,12 @@ jobs:
               # failures for local file:/// -- yoh found no better way,
               linkchecker -t 1 --check-extern \
                 --ignore-url 'file:///.*' \
+                --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
+                --ignore-url 'https://doi.org/.*' \
                 --ignore-url 'https://fonts.gstatic.com' \
-                --ignore-url 'https://github.com/bids-standard/bids-specification/(pull|tree)/.*' \
                 --ignore-url 'https://github.com/[^/]*' \
-                --ignore-url 'https://doi.org/.*' \
-                --ignore-url 'https://bids-specification.readthedocs.io/en/stable/.*' \
+                --ignore-url 'https://github.com/bids-standard/bids-specification/(pull|tree)/.*' \
+                --ignore-url 'https://www.incf.org' \
                 ~/project/site/*html ~/project/site/*/*.html
             else
               echo "Release PR - do nothing"

.codespellrc

@@ -1,6 +1,7 @@
 [codespell]
-skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build
-ignore-words-list = fo,te,als,Acknowledgements,acknowledgements,weill,bu,winn,manuel
+skip = *.js,*.svg,*.eps,.git,node_modules,env,venv,.mypy_cache,package-lock.json,CITATION.cff,tools/new_contributors.tsv,./tools/schemacode/docs/build,venvs
+ignore-regex = \bHEP\b
+ignore-words-list = acknowledgements,als,bu,fo,te,weill,winn
 builtin = clear,rare,en-GB_to_en-US
 # this overloads default dictionaries and I have not yet figured out
 # how to have multiple https://github.com/codespell-project/codespell/issues/2727

.pre-commit-config.yaml

@@ -17,7 +17,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.30.0
+    rev: 0.31.0
     hooks:
       - id: check-dependabot
       - id: check-github-workflows
@@ -69,7 +69,7 @@ repos:
       - id: pretty-format-toml
         args: [--autofix, --indent, '4', --no-sort]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.0
     hooks:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]

README.md

@@ -4,7 +4,7 @@
 ![YouTube Channel Subscribers](https://img.shields.io/youtube/channel/subscribers/UCxZUcYfd_nvIVWAbzRB1tlw)
 [![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard)
 [![@BIDSstandard](https://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://x.com/BIDSstandard)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10175845.svg)](https://doi.org/10.5281/zenodo.10175845)
 
 <img src="./BIDS_logo/BIDS_logo_white_transparent_background_crop.png#gh-dark-mode-only" alt="bids-logo" width="600"/>
 <img src="./BIDS_logo/BIDS_logo_black_transparent_background_crop.png#gh-light-mode-only" alt="bids-logo" width="600"/>
@@ -20,7 +20,8 @@ In this repository, we develop the
 To organize your data in BIDS, all you need is neuro data, a computer, and the
 [BIDS specification](https://bids-specification.readthedocs.io/en/stable/).
 
-BIDS currently supports the following data modalities with more to come in the future:
+BIDS currently supports the following data modalities with
+[more to come in the future](https://bids.neuroimaging.io/get_involved.html#extending-the-bids-specification):
 
 - MRI
 - MEG

src/common-principles.md

@@ -15,9 +15,9 @@ REQUIRED, RECOMMENDED, and OPTIONAL.
 The guiding principles for when particular data is placed under a given requirement level
 can be loosely described as below:
 
-* REQUIRED: Data cannot be be interpreted without this information (or the ambiguity is unacceptably high)
-* RECOMMENDED: Interpretation/utility would be dramatically improved with this information
-* OPTIONAL: Users and/or tools might find it useful to have this information
+-   REQUIRED: Data cannot be be interpreted without this information (or the ambiguity is unacceptably high)
+-   RECOMMENDED: Interpretation/utility would be dramatically improved with this information
+-   OPTIONAL: Users and/or tools might find it useful to have this information
 
 Throughout this specification we use a list of terms and abbreviations.
 To avoid misunderstanding we clarify them here.
@@ -484,6 +484,7 @@ with two exceptions:
 1.  [compressed tabular files](#compressed-tabular-files),
     for which column names are defined in a sidecar metadata
     [JSON object](https://www.json.org/json-en.html) described below; and
+
 1.  [motion recording data](modality-specific-files/motion.md),
     which use plain-text TSV and columns are defined as described
     in its corresponding section of the specifications.
@@ -606,8 +607,10 @@ Rules for formatting plain-text tabular files apply to TSVGZ files with three ex
 
 1.  The contents of TSVGZ files MUST be compressed with
     [gzip](https://datatracker.ietf.org/doc/html/rfc1952).
+
 1.  Compressed tabular files MUST NOT contain a header in the first row
     indicating the column names.
+
 1.  TSVGZ files MUST have an associated JSON file that defines the columns in the tabular file.
 
 !!! warning "Attention"
@@ -889,7 +892,7 @@ have the form `<scheme>:[//<authority>]<path>[?<query>][#<fragment>]`, as specif
 in [RFC 3986](https://tools.ietf.org/html/rfc3986).
 This applies to URLs and other common URIs, including Digital Object Identifiers (DOIs),
 which may be fully specified as `doi:<path>`,
-for example, [doi:10.5281/zenodo.3686061](https://doi.org/10.5281/zenodo.3686061).
+for example, [doi:10.5281/zenodo.10175845](https://doi.org/10.5281/zenodo.10175845).
 A given resource may have multiple URIs.
 When selecting URIs to add to dataset metadata, it is important to consider
 specificity and persistence.

src/index.md

@@ -14,4 +14,4 @@ own datasets to match the BIDS specification, we recommend exploring the
 Alternatively, to get started please read [the introduction to the specification](introduction.md).
 
 For an overview of the BIDS ecosystem, visit the [BIDS homepage](https://bids.neuroimaging.io).
-The entire specification can also be [downloaded as PDF](https://doi.org/10.5281/zenodo.3686061).
+The entire specification can also be [downloaded as PDF](https://doi.org/10.5281/zenodo.10175845).

src/introduction.md

@@ -178,11 +178,11 @@ For example:
 
 #### Motion
 
--    Jeung, S., Cockx, H., Appelhoff, S., Berg, T., Gramann, K., Grothkopp, S., Warmerdam, E., Hansen, C.,
-     Oostenveld, R., BIDS maintainers, Welzel, J. (2023).
-     **Motion-BIDS: extending the Brain Imaging Data Structure specification to organize motion data for reproducible research**.
-     PsyArXiv.
-     [doi:10.31234/osf.io/w6z79](https://doi.org/10.31234/osf.io/w6z79)
+-   Jeung, S., Cockx, H., Appelhoff, S., Berg, T., Gramann, K., Grothkopp, S., Warmerdam, E., Hansen, C.,
+    Oostenveld, R., BIDS maintainers, Welzel, J. (2023).
+    **Motion-BIDS: extending the Brain Imaging Data Structure specification to organize motion data for reproducible research**.
+    PsyArXiv.
+    [doi:10.31234/osf.io/w6z79](https://doi.org/10.31234/osf.io/w6z79)
 
 #### MRS
 

src/longitudinal-and-multi-site-studies.md

@@ -95,7 +95,6 @@ Apps and everything should just work.
 Alternatively you can combine data from all sites into one dataset.
 This can be done in two ways:
 
-
 #### Option 2.a: Collate sites at subject level
 
 To identify which site each subjects comes from you can add a `site` column in the

src/modality-agnostic-files.md

@@ -545,9 +545,3 @@ code organization of these scripts at the moment.
 <!-- Link Definitions -->
 
 [bids uris]: ./common-principles.md#bids-uri
-
-[object]: https://www.json.org/json-en.html
-
-[string]: https://www.w3schools.com/js/js_json_datatypes.asp
-
-[uri]: ./common-principles.md#uniform-resource-indicator

src/schema/README.md

@@ -439,7 +439,7 @@ arrays or objects:
 | `properties`           | The object described has a given set of fields; the values of these fields may be constrained |
 | `additionalProperties` | The object described has constraints on its values, but not the names                         |
 
-### On re-used objects with different definitions
+### On reused objects with different definitions
 
 In a few cases, two objects with the same name appear multiple times in the specification.
 When this happens, it is preferred to find a common definition, and clarify it in the rules (see below).

src/schema/objects/metadata.yaml

@@ -523,7 +523,7 @@ ContinuousHeadLocalization:
   name: ContinuousHeadLocalization
   display_name: Continuous Head Localization
   description: |
-    `true` or `false` value indicating whether continuous head localisation
+    `true` or `false` value indicating whether continuous head localization
     was performed.
   type: boolean
 ContrastBolusIngredient:
@@ -1477,7 +1477,7 @@ HeadCoilFrequency:
   name: HeadCoilFrequency
   display_name: Head Coil Frequency
   description: |
-    List of frequencies (in Hz) used by the head localisation coils
+    List of frequencies (in Hz) used by the head localization coils
     ('HLC' in CTF systems, 'HPI' in Neuromag/Elekta/MEGIN, 'COH' in BTi/4D)
     that track the subject's head position in the MEG helmet
     (for example, `[293, 307, 314, 321]`).
@@ -2143,7 +2143,7 @@ MaxMovement:
   display_name: Max Movement
   description: |
     Maximum head movement (in mm) detected during the recording,
-    as measured by the head localisation coils (for example, `4.8`).
+    as measured by the head localization coils (for example, `4.8`).
   type: number
   unit: mm
 MeasurementToolMetadata:

tools/schemacode/src/bidsschematools/expressions.py

@@ -1,5 +1,4 @@
-"""Parsing utilities for BIDS Schema expression language
-"""
+"""Parsing utilities for BIDS Schema expression language"""
 
 from functools import partial
 

tools/schemacode/src/bidsschematools/validator.py

@@ -334,7 +334,7 @@ def select_schema_path(
 
     Notes
     -----
-    * This is a purely aspirational function, and is pre-empted by logic inside
+    * This is a purely aspirational function, and is preempted by logic inside
         `bst.validator.validate_bids()`, and further contingent on better schema stability and
         ongoing work in: https://github.com/bids-standard/bids-schema
     * The default `bids_reference_root` value is based on the FHS and ideally should be enforced.