Merge branch 'master' into file-formats

.circleci/config.yml

@@ -2,7 +2,7 @@ version: 2.1
 jobs:
   build_docs:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12-node
     steps:
       # checkout code to default ~/project
       - checkout
@@ -21,14 +21,15 @@ jobs:
       - persist_to_workspace:
           # the mkdocs build outputs are in ~/project/site
           root: ~/project
-          paths: site
+          paths:
+            - site
       - store_artifacts:
           path: ~/project/site/
           destination: dev_docs
 
   check_links:
     docker:
-      - image: cimg/python:3.8
+      - image: cimg/python:3.12
     steps:
       # checkout code to default ~/project
       - checkout
@@ -131,7 +132,8 @@ jobs:
       - persist_to_workspace:
           # raw generated changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Lint and fix the auto generated changes.md file
   lint_generated_changelog:
@@ -164,7 +166,8 @@ jobs:
       - persist_to_workspace:
           # linted and fixed changelog in ~/changelog_build/CHANGES.md
           root: ~/.
-          paths: changelog_build
+          paths:
+            - changelog_build
 
   # Push built changelog to repo
   commit_generated_changelog:
@@ -178,7 +181,7 @@ jobs:
       - attach_workspace:
           # fixed+linted changelog in ~/changelog_build/CHANGES.md
           at: ~/.
-      - deploy:
+      - run:
           name: Changelog deployment
           # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
           command: |
@@ -197,7 +200,6 @@ jobs:
             fi
 
 workflows:
-  version: 2
   search_build:
     jobs:
       - build_docs

.github/workflows/schemacode_ci.yml

@@ -44,7 +44,7 @@ jobs:
         run: python -m build tools/schemacode
       - name: "Check distribution metadata"
         run: twine check tools/schemacode/dist/*
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: dist
           path: tools/schemacode/dist/
@@ -76,7 +76,7 @@ jobs:
         run: python -c "import sys; print(sys.version)"
 
       - name: "Fetch packages"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
@@ -91,7 +91,7 @@ jobs:
               --cov-append --cov-report=xml --cov=bidsschematools --doctest-modules
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: unit_${{ matrix.os }}_${{ matrix.python-version }}
           path: coverage.xml
@@ -108,7 +108,7 @@ jobs:
         python-version: ["3.11"]
     steps:
       - name: "Fetch packages"
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
           name: dist
           path: dist/
@@ -146,7 +146,7 @@ jobs:
         run: python -m pytest --pyargs bidsschematools -m "validate_schema" --cov-append --cov-report=xml --cov=bidsschematools
 
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: schema_validation
           path: coverage.xml
@@ -161,10 +161,10 @@ jobs:
         uses: actions/checkout@v4
 
       - name: Download artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
 
       - name: Upload to CodeCov
-        uses: codecov/codecov-action@v3
+        uses: codecov/codecov-action@v4
         with:
           token: ${{ secrets.CODECOV_TOKEN }}  # not required but might help API rate limits
           fail_ci_if_error: true

.gitignore

@@ -7,6 +7,7 @@ venvs
 pdf_build_src/bids-spec.pdf
 pdf_build_src/bids-spec_pandoc_log.json
 pdf_build_src/src_copy
+pdf_build_src/tests/data/output
 
 # JS/NPM
 package-lock.json

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json'
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -13,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 23.12.1
+    rev: 24.4.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -43,13 +43,19 @@ repos:
       - id: prettier
         entry: env PRETTIER_LEGACY_CLI=1 prettier # temporary fix for https://github.com/prettier/prettier/issues/15742
         files: src/schema/.*/.*\.yaml
+  - repo: https://github.com/adrienverge/yamllint
+    rev: v1.35.1
+    hooks:
+      - id: yamllint
+        args: [-f=standard, -c=.yamllint.yml]
+        files: src/schema/.*/.*\.yaml
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.9.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing
@@ -62,5 +68,6 @@ repos:
           - pytest
           - types-PyYAML
           - types-tabulate
+          - types-jsonschema
         args: ["tools/schemacode/bidsschematools"]
         pass_filenames: false

.remarkrc

@@ -10,6 +10,7 @@
     ["lint-maximum-heading-length", false],
     ["lint-no-shortcut-reference-link", false],
     ["lint-no-trailing-spaces"],
+    ["remark-lint-code-block-style", false],
     ["lint-no-undefined-references", false]
   ]
 }

CONTRIBUTING.md

@@ -226,6 +226,37 @@ That would look like this:
 |--------------|----------------------------------------------------------|
 | Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) |
 
+
+#### MkDocs admonitions
+
+It is possible to use [Mkdocs admonitions](https://squidfunk.github.io/mkdocs-material/reference/admonitions/#inline-blocks-inline-end)
+to highlight certain aspect of the specification.
+
+Admonitions are written like this:
+
+````
+!!! note "displayed heading is preceded by a keyword and 3 `!`"
+
+    Body of the admonition
+    can be written on several lines,
+    but must be always preceded by 4 spaces.
+````
+
+The keyword for the heading must be one of the following:
+
+- note
+- abstract
+- info
+- tip
+- success
+- question
+- warning
+- failure: octicons
+- danger
+- bug
+- example
+- quote
+
 ## Using macros
 
 We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)

LICENSE

@@ -1,6 +1,6 @@
 Attribution 4.0 International
 
-Copyright (c) 2018-2022, BIDS Contributors.
+Copyright (c) 2018, BIDS Contributors.
 
 =======================================================================
 

README.md

@@ -1,7 +1,7 @@
 [![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml)
 [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification)
 [![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard)
-[![@BIDSstandard](http://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://twitter.com/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)
 
 <img src="./BIDS_logo/BIDS_logo_white_transparent_background_crop.png#gh-dark-mode-only" alt="bids-logo" width="600"/>
@@ -13,7 +13,6 @@ organization of neuroimaging data.
 In this repository, we develop the
 [BIDS specification](https://bids-specification.readthedocs.io/en/latest/).
 
-
 # When to use BIDS
 
 To organize your data in BIDS, all you need is neuro data, a computer, and the
@@ -44,10 +43,7 @@ The specification is provided in the form of a webpage, built using
 1. Read some introductory material, most likely the very basic problems have already been addressed!
   - [BIDS Starter Kit](https://github.com/bids-standard/bids-starter-kit) for tutorials, wikis, templates, ...
 2. Post your question in one of several channels where BIDS members are active
-  - the [NeuroStars](https://neurostars.org/tags/bids) discourse forum
-  - the [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html))
-  - the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions surrounding BIDS
-  - the [specification repository issue page](https://github.com/bids-standard/bids-specification/issues), if you found inconsistencies, typos, or other issues with the BIDS specification itself
+  - see: [BIDS communication channels](#bids-communication-channels)
 
 # Contributing to BIDS
 
@@ -58,11 +54,34 @@ For a current list of our contributors, please see our [Contributors appendix](h
 
 When you're ready to get started, check out [our contributing guidelines](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md).
 
-We ask that all contributions to BIDS across all project-related spaces (including but not limited to:
-[GitHub](https://github.com/bids-standard),
-the [Google group](https://groups.google.com/forum/#!forum/bids-discussion), and newsletter emails),
+We ask that all contributions to BIDS across all project-related spaces
+(including but not limited to:
+[GitHub](https://github.com/bids-standard), and the
+[Google group](https://groups.google.com/forum/#!forum/bids-discussion); see
+[BIDS communication channels](#bids-communication-channels))
 adhere to our [code of conduct](https://github.com/bids-standard/bids-specification/blob/master/CODE_OF_CONDUCT.md).
 
+# BIDS communication channels
+
+## Main communication channels
+
+  - "Issue" pages on the different GitHub repositories of the [`bids-standard` GitHub organization](https://github.com/bids-standard),
+    such as the [BIDS specification repository](https://github.com/bids-standard/bids-specification/issues),
+    for reporting problems or making suggestions
+  - The [NeuroStars Discourse forum](https://neurostars.org/tags/bids), for asking usage questions
+  - The [BrainHack Mattermost](https://mattermost.brainhack.org), for instant messaging
+    (see also this [news item](https://bids.neuroimaging.io/2020/06/24/Join-the-BIDS-community-on-the-BrainHack-Mattermost.html))
+  - The [Google group](https://groups.google.com/forum/#!forum/bids-discussion), for broader discussions and announcements surrounding BIDS
+  - The [BIDS website "news"](https://bids.neuroimaging.io/news.html), similar to the Google group, for broader discussions and announcements
+
+## Social media channels
+
+- [X](https://x.com/BIDSstandard)
+- [Mastodon](https://fosstodon.org/@bidsstandard)
+- [Bluesky](https://bsky.app/profile/bidsstandard.bsky.social)
+- [Youtube](https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw)
+- [Instagram](https://www.instagram.com/bidsstandard/)
+
 ## Contributors
 
 Thanks goes to these wonderful people.

Release_Protocol.md

@@ -278,5 +278,5 @@ Update the following files in the BIDS website repository (https://github.com/bi
 
 ### 12. Sharing news of the release
 
-Please share news of the release on the [identified platforms](https://docs.google.com/spreadsheets/d/16SAGK3zG93WM2EWuoZDcRIC7ygPc5b7PDNGpFyC3obA/edit#gid=0).
+Please share news of the release on the [identified platforms](https://github.com/bids-standard/bids-specification?tab=readme-ov-file#BIDS-communication-channels).
 Please use our previous release posts as a guide.

mkdocs.yml

@@ -12,7 +12,7 @@ nav:
           - Electroencephalography: modality-specific-files/electroencephalography.md
           - Intracranial Electroencephalography: modality-specific-files/intracranial-electroencephalography.md
           - Task events: modality-specific-files/task-events.md
-          - Physiological and other continuous recordings: modality-specific-files/physiological-and-other-continuous-recordings.md
+          - Physiological recordings: modality-specific-files/physiological-recordings.md
           - Behavioral experiments (with no neural recordings): modality-specific-files/behavioral-experiments.md
           - Genetic Descriptor: modality-specific-files/genetic-descriptor.md
           - Positron Emission Tomography: modality-specific-files/positron-emission-tomography.md
@@ -84,19 +84,25 @@ extra:
   social:
     - icon: fontawesome/brands/github
       link: https://github.com/bids-standard/bids-specification/
-    - icon: fontawesome/brands/twitter
-      link: https://twitter.com/BIDSstandard/
+    - icon: fontawesome/brands/x-twitter
+      link: https://x.com/BIDSstandard/
     - icon: fontawesome/brands/mastodon
       link: https://fosstodon.org/@bidsstandard
     - icon: fontawesome/brands/google
       link: https://groups.google.com/g/bids-discussion
+    - icon: fontawesome/brands/instagram
+      link: https://www.instagram.com/bidsstandard/
+    - icon: fontawesome/brands/youtube
+      link: https://www.youtube.com/channel/UCxZUcYfd_nvIVWAbzRB1tlw
 
 extra_javascript:
   - js/jquery-3.6.0.min.js
 markdown_extensions:
   - toc:
       anchorlink: true
   - pymdownx.superfences
+  - admonition
+  - pymdownx.details
 plugins:
   - search
   - branchcustomization:
@@ -116,7 +122,7 @@ plugins:
         "04-modality-specific-files/03-electroencephalography.md": "modality-specific-files/electroencephalography.md"
         "04-modality-specific-files/04-intracranial-electroencephalography.md": "modality-specific-files/intracranial-electroencephalography.md"
         "04-modality-specific-files/05-task-events.md": "modality-specific-files/task-events.md"
-        "04-modality-specific-files/06-physiological-and-other-continuous-recordings.md": "modality-specific-files/physiological-and-other-continuous-recordings.md"
+        "04-modality-specific-files/06-physiological-and-other-continuous-recordings.md": "modality-specific-files/physiological-recordings.md"
         "04-modality-specific-files/07-behavioral-experiments.md": "modality-specific-files/behavioral-experiments.md"
         "04-modality-specific-files/08-genetic-descriptor.md": "modality-specific-files/genetic-descriptor.md"
         "04-modality-specific-files/09-positron-emission-tomography.md": "modality-specific-files/positron-emission-tomography.md"

pdf_build_src/pandoc_script.py

@@ -2,6 +2,7 @@
 
 This is done once the duplicate src directory is processed.
 """
+
 import subprocess
 import yaml
 from pathlib import Path
@@ -11,9 +12,7 @@
 
 def _find(path, filename):
     return next(
-        parent / filename
-        for parent in path.parents
-        if Path.is_file(parent / filename)
+        parent / filename for parent in path.parents if Path.is_file(parent / filename)
     )