Merge branch 'master' of https://github.com/markmikkelsen/bids-specif…

…ication

.pre-commit-config.yaml

@@ -49,7 +49,7 @@ repos:
       - 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

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.

mkdocs.yml

@@ -84,12 +84,16 @@ 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

readthedocs.yml

@@ -2,11 +2,14 @@ version: 2
 
 build:
   os: ubuntu-22.04
+  apt_packages:
+    - jq
   tools:
     python: "3.11"
   jobs:
     pre_build:
       - bst -v export --output src/schema.json
+      - tools/no-bad-schema-paths.sh src/schema.json  # README.md might need fixing
 
 mkdocs:
   configuration: mkdocs.yml

src/modality-specific-files/microscopy.md

@@ -26,7 +26,7 @@ and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
 {{ MACROS___make_filename_template("raw", datatypes=["micr"], suffixes=["TEM", "SEM", "uCT", "BF", "DF",
-"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM"], n_dupes_to_combine=4) }}
+"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM", "hipCT"], n_dupes_to_combine=4) }}
 
 Microscopy data MUST be stored in the `micr` directory.
 
@@ -89,6 +89,7 @@ and a guide for using macros can be found at
          "NLO",
          "OCT",
          "SPIM",
+         "hipCT",
       ]
    )
 }}

src/modality-specific-files/near-infrared-spectroscopy.md

@@ -22,7 +22,7 @@ and a guide for using macros can be found at
 {{ MACROS___make_filename_template(
    "raw",
    datatypes=["nirs"],
-   suffixes=["nirs", "events", "physio", "stim"])
+   suffixes=["nirs", "events", "channels", "optodes", "coordsystem", "physio", "stim"])
 }}
 
 Only the *Shared Near Infrared Spectroscopy Format* ([SNIRF](https://github.com/fNIRS/snirf))

src/schema/README.md

@@ -136,18 +136,20 @@ with the object being referenced.
 The following two prototypical examples are presented to clarify the semantics of
 references (the cases in which they are used will be presented later):
 
-1.  In `objects.metadata`:
+1.  In `objects.enums`:
     ```YAML
     _GeneticLevelEnum:
       type: string
       enum:
-        - Genetic
-        - Genomic
-        - Epigenomic
-        - Transcriptomic
-        - Metabolomic
-        - Proteomic
-
+        - $ref: objects.enums.Genetic.value
+        - $ref: objects.enums.Genomic.value
+        - $ref: objects.enums.Epigenomic.value
+        - $ref: objects.enums.Transcriptomic.value
+        - $ref: objects.enums.Metabolomic.value
+        - $ref: objects.enums.Proteomic.value
+    ```
+    and in `objects.metadata`:
+    ```YAML
     GeneticLevel:
       name: GeneticLevel
       display_name: Genetic Level
@@ -156,29 +158,29 @@ references (the cases in which they are used will be presented later):
         Values MUST be one of `"Genetic"`, `"Genomic"`, `"Epigenomic"`,
         `"Transcriptomic"`, `"Metabolomic"`, or `"Proteomic"`.
       anyOf:
-        - $ref: objects.metadata._GeneticLevelEnum
+        - $ref: objects.enums._GeneticLevelEnum
         - type: array
           items:
-            $ref: objects.metadata._GeneticLevelEnum
+            $ref: objects.enums._GeneticLevelEnum
     ```
     Here `_GeneticLevelEnum` is used to describe the valid values of `GeneticLevel`,
-    and the references inside `GeneticLevel.anyOf` indicate that there may be a single
+    (which are in turn references to individual values), and the references inside `GeneticLevel.anyOf` indicate that there may be a single
     such value or a list of values.
 
-1.  In `rules.datatypes.derivatives.common_derivatives`:
+1.  In [`rules.files.deriv.preprocessed_data`](./rules/files/deriv/preprocessed_data.yaml):
     ```YAML
     anat_nonparametric_common:
-      $ref: rules.datatypes.anat.nonparametric
+      $ref: rules.files.raw.anat.nonparametric
       entities:
-        $ref: rules.datatypes.anat.nonparametric.entities
+        $ref: rules.files.raw.anat.nonparametric.entities
         space: optional
         description: optional
     ```
     Here, the derivative datatype rule starts by copying the raw datatype rule
-    `rules.datatypes.anat.nonparametric`.
+    `rules.files.raw.anat.nonparametric`.
     It then *overrides* the `entities` portion of that rule with a new object.
     To *extend* the original `entities`, it again begins
-    by referencing `rules.datatypes.anat.nonparametric.entities`,
+    by referencing `rules.files.raw.anat.nonparametric.entities`,
     and adding the new entities `space` and `description`.
 
 ### Expressions
@@ -229,7 +231,10 @@ which (currently) contains at the top level:
 -   `associations`: associated files, discovered by the inheritance principle
 -   `columns`: the columns in the current TSV file
 -   `json`: the contents of the current JSON file
+-   `gzip`: the contents of the current file GZIP header
 -   `nifti_header`: selected contents of the current NIfTI file's header
+-   `ome`: the contents of the current OME-XML metadata
+-   `tiff`: the contents of the current TIFF file's header
 
 Some of these are strings, while others are nested objects.
 These are to be populated by an *interpreter* of the schema,

src/schema/objects/columns.yaml

@@ -397,7 +397,7 @@ reference_frame:
   description: |
     Specification of a reference frame in which the motion data are to be interpreted.
     The description of the levels in `*_channels.json` SHOULD use `RotationRule`,
-    `RotationOrder`, and `SpatialAxis`, and MAY use `Description` for the specification.
+    `RotationOrder`, and `SpatialAxes`, and MAY use `Description` for the specification.
   anyOf:
     - type: string
     - type: string

src/schema/objects/suffixes.yaml

@@ -595,6 +595,11 @@ headshape:
   description: |
     The 3-D locations of points that describe the head shape and/or electrode
     locations can be digitized and stored in separate files.
+hipCT:
+  value: hipCT
+  display_name: HiP-CT
+  description: |
+    Hierarchical Phase-Contrast Tomography imaging data
 ieeg:
   value: ieeg
   display_name: Intracranial Electroencephalography

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

@@ -18,6 +18,7 @@ microscopy:
     - NLO
     - OCT
     - SPIM
+    - hipCT
   extensions:
     - .ome.tif
     - .ome.btf

tools/no-bad-schema-paths.sh

@@ -0,0 +1,29 @@
+#!/bin/bash
+
+set -eu -o pipefail
+
+schema_json=$(readlink -f "$1")
+
+cd "$(dirname "$(readlink -f "$0")")/../src/schema"
+
+# Create a temporary file and ensure it gets deleted on exit
+tmpfile=$(mktemp)
+trap 'rm -f "$tmpfile"' EXIT
+
+grep -oE '(://)?([-_A-Za-z]+\.)+[-_A-Za-z]+' README.md \
+    | grep -v -e :// -e '\.\(md\|html\|json\|tsv\|yaml\)$' \
+    | grep -e '^\(meta\|objects\|rules\)' \
+    | grep -v 'objects.metadata.OtherObjectName' \
+    | sort | uniq | \
+    while IFS= read -r p; do
+        v=$(jq ".$p" < "$schema_json" | grep -v '^null$' || echo "fail")
+        if [ -z "$v" ] || [ "$v" = "fail" ]; then
+            echo "$p: not reachable" >> "$tmpfile"
+        fi
+    done
+
+# Check if the temporary file is empty
+if [ -s "$tmpfile" ]; then
+    cat "$tmpfile" # Display the not reachable paths
+    exit 1
+fi