From 9e1092bf0f2ed79d698a816ebef6801a2d5245be Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 23 Jan 2024 12:14:15 +0100
Subject: [PATCH 01/18] Update schema.md (#1682)

---
 src/appendices/schema.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/appendices/schema.md b/src/appendices/schema.md
index 1616a6d5c9..fc0855881d 100644
--- a/src/appendices/schema.md
+++ b/src/appendices/schema.md
@@ -9,7 +9,7 @@ to the BIDS standard.
 
 The BIDS schema is available in two machine readable formats:
 
--   as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/src/schema)
+-   as a set of [YAML](https://en.wikipedia.org/wiki/YAML) files in the [BIDS specification repository](https://github.com/bids-standard/bids-specification/tree/master/src/schema)
 -   as a [single dereferenced json file](https://bids-specification.readthedocs.io/en/stable/schema.json)
 
 A didactic walkthrough of the schema can be found in the [BEP Guide](https://bids-extensions.readthedocs.io/en/latest/schema/),

From 16cb5fe42081ea3a7082087feeb64368956f9f88 Mon Sep 17 00:00:00 2001
From: Oscar Esteban <code@oscaresteban.es>
Date: Wed, 24 Jan 2024 16:12:28 +0100
Subject: [PATCH 02/18] [FIX] Add `part-<value>` to the pepolar fieldmaps
 (#1685)

---
 src/schema/rules/files/raw/fmap.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/rules/files/raw/fmap.yaml b/src/schema/rules/files/raw/fmap.yaml
index 94b03f7f6f..056ed1d67e 100644
--- a/src/schema/rules/files/raw/fmap.yaml
+++ b/src/schema/rules/files/raw/fmap.yaml
@@ -38,6 +38,7 @@ pepolar:
     ceagent: optional
     direction: required
     run: optional
+    part: optional
     chunk: optional
 
 TB1DAM:

From 436ebb58b5965b89ccfbe0499c3863d8c5a62a7d Mon Sep 17 00:00:00 2001
From: CPernet <wamcyril@gmail.com>
Date: Fri, 26 Jan 2024 10:30:52 +0100
Subject: [PATCH 03/18] just moving information to be more visible

---
 .../magnetic-resonance-imaging-data.md               | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 7099836c40..5758872f63 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -298,7 +298,11 @@ and a guide for using macros can be found at
       ])
 }}
 
-Currently supported parametric maps include:
+Parametric images listed in the table below are typically generated by
+processing a [file collection](../common-principles.md#entity-linked-file-collections).
+Please visit the [file collections appendix](../appendices/file-collections.md) to see the
+list of suffixes available for quantitative MRI (qMRI) applications associated
+with these maps (e.g. [MPM](../glossary.html#mpm-suffixes), [MP2RAGE](../glossary.html#mp2rage-suffixes), [MTR](../glossary.html#mtransfer-entities)). Currently supported parametric maps include:
 
 <!--
 This block generates a suffix table.
@@ -330,11 +334,7 @@ and a guide for using macros can be found at
    )
 }}
 
-Parametric images listed in the table above are typically generated by
-processing a [file collection](../common-principles.md#entity-linked-file-collections).
-Please visit the [file collections appendix](../appendices/file-collections.md) to see the
-list of suffixes available for quantitative MRI (qMRI) applications associated
-with these maps.
+
 For any other details on the organization of parametric maps, their
 recommended metadata fields, and the application specific entity or
 metadata requirement levels of [file collections](../appendices/file-collections.md) that can generate

From 9d78d69f78ae6b370d7525d988a315e2356fe418 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 26 Jan 2024 11:04:26 +0100
Subject: [PATCH 04/18] Update
 src/modality-specific-files/magnetic-resonance-imaging-data.md

---
 .../magnetic-resonance-imaging-data.md                     | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 5758872f63..cf45aaf2f5 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -302,7 +302,12 @@ Parametric images listed in the table below are typically generated by
 processing a [file collection](../common-principles.md#entity-linked-file-collections).
 Please visit the [file collections appendix](../appendices/file-collections.md) to see the
 list of suffixes available for quantitative MRI (qMRI) applications associated
-with these maps (e.g. [MPM](../glossary.html#mpm-suffixes), [MP2RAGE](../glossary.html#mp2rage-suffixes), [MTR](../glossary.html#mtransfer-entities)). Currently supported parametric maps include:
+with these maps
+(for example [MPM](../glossary.md#mpm-suffixes),
+[MP2RAGE](../glossary.md#mp2rage-suffixes),
+[MTR](../glossary.md#mtransfer-entities)).
+
+Currently supported parametric maps include:
 
 <!--
 This block generates a suffix table.

From 7157d4497d5ec47ace6edd964d33f451da0bea74 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 26 Jan 2024 11:12:50 +0100
Subject: [PATCH 05/18] Update
 src/modality-specific-files/magnetic-resonance-imaging-data.md

---
 src/modality-specific-files/magnetic-resonance-imaging-data.md | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index cf45aaf2f5..cc80cd99d9 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -339,7 +339,6 @@ and a guide for using macros can be found at
    )
 }}
 
-
 For any other details on the organization of parametric maps, their
 recommended metadata fields, and the application specific entity or
 metadata requirement levels of [file collections](../appendices/file-collections.md) that can generate

From 7f12ab91a9c657aae78ff4e929405ba58084be50 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 26 Jan 2024 13:29:48 +0100
Subject: [PATCH 06/18] update black pre-commit hook and run it (#1688)

---
 .pre-commit-config.yaml                                      | 2 +-
 tools/examplecode/__init__.py                                | 1 +
 tools/mkdocs_macros_bids/macros.py                           | 1 +
 tools/mkdocs_macros_bids/main.py                             | 1 +
 tools/pull_files.py                                          | 1 +
 tools/schemacode/bidsschematools/data/__init__.py            | 1 +
 tools/schemacode/bidsschematools/data/tests/test_rules.py    | 1 +
 tools/schemacode/bidsschematools/expressions.py              | 1 +
 tools/schemacode/bidsschematools/render/__init__.py          | 1 +
 tools/schemacode/bidsschematools/render/tables.py            | 1 +
 tools/schemacode/bidsschematools/render/text.py              | 1 +
 tools/schemacode/bidsschematools/render/utils.py             | 1 +
 tools/schemacode/bidsschematools/rules.py                    | 1 +
 tools/schemacode/bidsschematools/schema.py                   | 1 +
 tools/schemacode/bidsschematools/tests/data/__init__.py      | 1 +
 tools/schemacode/bidsschematools/tests/test_render_tables.py | 1 +
 tools/schemacode/bidsschematools/tests/test_render_text.py   | 1 +
 tools/schemacode/bidsschematools/tests/test_schema.py        | 1 +
 tools/schemacode/bidsschematools/types/namespace.py          | 1 +
 tools/schemacode/bidsschematools/utils.py                    | 1 +
 20 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 3780ff968a..f6b269a1ca 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -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: 24.1.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
diff --git a/tools/examplecode/__init__.py b/tools/examplecode/__init__.py
index 886bf1c86a..414983f48d 100644
--- a/tools/examplecode/__init__.py
+++ b/tools/examplecode/__init__.py
@@ -1,4 +1,5 @@
 """A Python package to render BIDS example with tree like output."""
+
 from examplecode.example import DirectoryTree
 
 __all__ = [
diff --git a/tools/mkdocs_macros_bids/macros.py b/tools/mkdocs_macros_bids/macros.py
index aa29f21b28..f68453c6b8 100644
--- a/tools/mkdocs_macros_bids/macros.py
+++ b/tools/mkdocs_macros_bids/macros.py
@@ -1,4 +1,5 @@
 """Functions used by the macros mkdocs plugin."""
+
 import os
 import sys
 
diff --git a/tools/mkdocs_macros_bids/main.py b/tools/mkdocs_macros_bids/main.py
index 30a93e6ce9..13bb5caf44 100644
--- a/tools/mkdocs_macros_bids/main.py
+++ b/tools/mkdocs_macros_bids/main.py
@@ -4,6 +4,7 @@
 Functions decorated in "define_env()" are callable throughout the
 specification and are run/rendered with the mkdocs plugin "macros".
 """
+
 import os
 import sys
 
diff --git a/tools/pull_files.py b/tools/pull_files.py
index 2e6658ba83..a2a32aa552 100644
--- a/tools/pull_files.py
+++ b/tools/pull_files.py
@@ -7,6 +7,7 @@
 https://github.com/alan-turing-institute/the-turing-way/blob/af98c94/tests/pull_files.py
 
 """
+
 import argparse
 
 import requests
diff --git a/tools/schemacode/bidsschematools/data/__init__.py b/tools/schemacode/bidsschematools/data/__init__.py
index e275ce39b4..14df1fc5ec 100644
--- a/tools/schemacode/bidsschematools/data/__init__.py
+++ b/tools/schemacode/bidsschematools/data/__init__.py
@@ -2,6 +2,7 @@
 
 .. autofunction:: load_resource
 """
+
 import atexit
 import os
 from contextlib import ExitStack
diff --git a/tools/schemacode/bidsschematools/data/tests/test_rules.py b/tools/schemacode/bidsschematools/data/tests/test_rules.py
index c44634f814..e8da90ee93 100644
--- a/tools/schemacode/bidsschematools/data/tests/test_rules.py
+++ b/tools/schemacode/bidsschematools/data/tests/test_rules.py
@@ -1,4 +1,5 @@
 """Simple validation tests on schema rules."""
+
 import warnings
 from collections.abc import Mapping
 
diff --git a/tools/schemacode/bidsschematools/expressions.py b/tools/schemacode/bidsschematools/expressions.py
index c850d24551..3c22673095 100644
--- a/tools/schemacode/bidsschematools/expressions.py
+++ b/tools/schemacode/bidsschematools/expressions.py
@@ -1,5 +1,6 @@
 """Parsing utilities for BIDS Schema expression language
 """
+
 from functools import partial
 
 from pyparsing import (
diff --git a/tools/schemacode/bidsschematools/render/__init__.py b/tools/schemacode/bidsschematools/render/__init__.py
index 506e6b4583..a251a1f3cd 100644
--- a/tools/schemacode/bidsschematools/render/__init__.py
+++ b/tools/schemacode/bidsschematools/render/__init__.py
@@ -1,4 +1,5 @@
 """Functions for rendering elements of the schema in the specification text."""
+
 from bidsschematools.render.tables import (
     make_columns_table,
     make_entity_table,
diff --git a/tools/schemacode/bidsschematools/render/tables.py b/tools/schemacode/bidsschematools/render/tables.py
index 90d091f5db..cf8645ffeb 100644
--- a/tools/schemacode/bidsschematools/render/tables.py
+++ b/tools/schemacode/bidsschematools/render/tables.py
@@ -1,4 +1,5 @@
 """Functions for rendering portions of the schema as text."""
+
 from __future__ import annotations
 
 import logging
diff --git a/tools/schemacode/bidsschematools/render/text.py b/tools/schemacode/bidsschematools/render/text.py
index 6468007625..1106e17185 100644
--- a/tools/schemacode/bidsschematools/render/text.py
+++ b/tools/schemacode/bidsschematools/render/text.py
@@ -1,4 +1,5 @@
 """Functions for rendering portions of the schema as text."""
+
 import logging
 import os
 
diff --git a/tools/schemacode/bidsschematools/render/utils.py b/tools/schemacode/bidsschematools/render/utils.py
index a482b54492..873699058e 100644
--- a/tools/schemacode/bidsschematools/render/utils.py
+++ b/tools/schemacode/bidsschematools/render/utils.py
@@ -1,4 +1,5 @@
 """Utility functions for specification rendering tools."""
+
 import math
 import posixpath
 
diff --git a/tools/schemacode/bidsschematools/rules.py b/tools/schemacode/bidsschematools/rules.py
index 6dd837629f..d0d6f5dae9 100644
--- a/tools/schemacode/bidsschematools/rules.py
+++ b/tools/schemacode/bidsschematools/rules.py
@@ -3,6 +3,7 @@
 This module is currently limited to constructing filename rules from
 ``schema.rules.files``.
 """
+
 import re
 import typing as ty
 from collections.abc import Mapping
diff --git a/tools/schemacode/bidsschematools/schema.py b/tools/schemacode/bidsschematools/schema.py
index 22dac02cb6..8a51725f1b 100644
--- a/tools/schemacode/bidsschematools/schema.py
+++ b/tools/schemacode/bidsschematools/schema.py
@@ -1,4 +1,5 @@
 """Schema loading- and processing-related functions."""
+
 import logging
 import os
 import re
diff --git a/tools/schemacode/bidsschematools/tests/data/__init__.py b/tools/schemacode/bidsschematools/tests/data/__init__.py
index 6415366aea..978e681be5 100644
--- a/tools/schemacode/bidsschematools/tests/data/__init__.py
+++ b/tools/schemacode/bidsschematools/tests/data/__init__.py
@@ -2,6 +2,7 @@
 
 .. autofunction:: load_test_data
 """
+
 from ...data import Loader
 
 __all__ = ("load_test_data",)
diff --git a/tools/schemacode/bidsschematools/tests/test_render_tables.py b/tools/schemacode/bidsschematools/tests/test_render_tables.py
index be41b8c5eb..9e1116fe68 100644
--- a/tools/schemacode/bidsschematools/tests/test_render_tables.py
+++ b/tools/schemacode/bidsschematools/tests/test_render_tables.py
@@ -1,4 +1,5 @@
 """Tests for the bidsschematools package."""
+
 from bidsschematools.render import tables
 
 
diff --git a/tools/schemacode/bidsschematools/tests/test_render_text.py b/tools/schemacode/bidsschematools/tests/test_render_text.py
index 3d25fd8b32..e6745c8780 100644
--- a/tools/schemacode/bidsschematools/tests/test_render_text.py
+++ b/tools/schemacode/bidsschematools/tests/test_render_text.py
@@ -1,4 +1,5 @@
 """Tests for the bidsschematools package."""
+
 import os
 
 import pytest
diff --git a/tools/schemacode/bidsschematools/tests/test_schema.py b/tools/schemacode/bidsschematools/tests/test_schema.py
index b0703361a3..5e7b0e3575 100644
--- a/tools/schemacode/bidsschematools/tests/test_schema.py
+++ b/tools/schemacode/bidsschematools/tests/test_schema.py
@@ -1,4 +1,5 @@
 """Tests for the bidsschematools package."""
+
 import os
 from collections.abc import Mapping
 
diff --git a/tools/schemacode/bidsschematools/types/namespace.py b/tools/schemacode/bidsschematools/types/namespace.py
index b59e8bb586..39943ac3f0 100644
--- a/tools/schemacode/bidsschematools/types/namespace.py
+++ b/tools/schemacode/bidsschematools/types/namespace.py
@@ -4,6 +4,7 @@
 YAML files available as a single dictionary and allow attribute (``.``)
 lookups.
 """
+
 import json
 import typing as ty
 from collections.abc import ItemsView, KeysView, Mapping, MutableMapping, ValuesView
diff --git a/tools/schemacode/bidsschematools/utils.py b/tools/schemacode/bidsschematools/utils.py
index 308fd981f6..ec2947fb37 100644
--- a/tools/schemacode/bidsschematools/utils.py
+++ b/tools/schemacode/bidsschematools/utils.py
@@ -1,4 +1,5 @@
 """Utility functions for the bids-specification schema."""
+
 import logging
 
 from . import data

From 4492b173dcc7822aca48270bd192fd4080b76b10 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 29 Jan 2024 19:33:09 +0000
Subject: [PATCH 07/18] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 24.1.0 → 24.1.1](https://github.com/psf/black/compare/24.1.0...24.1.1)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index f6b269a1ca..8d7578c843 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 24.1.0
+    rev: 24.1.1
     hooks:
       - id: black
         files: ^tools/(?!schemacode)

From f48ca16c99edacee83a9e0d8aa0c416a358593f1 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 5 Feb 2024 09:08:08 +0000
Subject: [PATCH 08/18] Bump codecov/codecov-action from 3 to 4

Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4.
- [Release notes](https://github.com/codecov/codecov-action/releases)
- [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md)
- [Commits](https://github.com/codecov/codecov-action/compare/v3...v4)

---
updated-dependencies:
- dependency-name: codecov/codecov-action
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 .github/workflows/schemacode_ci.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index db52d30c60..6cf4dbcd4c 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -164,7 +164,7 @@ jobs:
         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

From a73a310b9439b7e3774f19f398f5d0ecd2d0dc07 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 5 Feb 2024 16:42:39 +0100
Subject: [PATCH 09/18] update circle ci config (#1696)

---
 .circleci/config.yml | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 9e6b41fa62..ee82d5b003 100644
--- a/.circleci/config.yml
+++ b/.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

From 365f3219aec261654220c4bb88e02498b5b39ad8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Julia=20Guiomar=20Niso=20Gal=C3=A1n?=
 <guiomar.niso@ctb.upm.es>
Date: Mon, 5 Feb 2024 16:51:05 +0100
Subject: [PATCH 10/18] [MISC] Restructure MEG empty room example texts (#1677)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Update magnetoencephalography.md

* Update magnetoencephalography.md

* Update magnetoencephalography.md

* Apply suggestions from code review

Co-authored-by: Julia Guiomar Niso Galán <guiomar.niso@ctb.upm.es>

* pull example descriptions under example subheadings

---------

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 .../magnetoencephalography.md                 | 26 ++++++++++---------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/modality-specific-files/magnetoencephalography.md b/src/modality-specific-files/magnetoencephalography.md
index 53b0a2edfe..08feb5af59 100644
--- a/src/modality-specific-files/magnetoencephalography.md
+++ b/src/modality-specific-files/magnetoencephalography.md
@@ -504,25 +504,24 @@ has to be updated, then for MEG it could be considered to be a new session.
 
 Empty-room MEG recordings capture the environmental and recording system's noise.
 
-It is RECOMMENDED to explicitly specify which empty-room recording should be used with which experimental run(s) or session(s). This can be done via the [`AssociatedEmptyRoom`](../glossary.md#associatedemptyroom-metadata) field in the `*_meg.json` sidecar files.
+It is RECOMMENDED to explicitly specify which empty-room recording should be used with which experimental run(s) or session(s).
+This can be done via the [`AssociatedEmptyRoom`](../glossary.md#associatedemptyroom-metadata) field in the `*_meg.json` sidecar files.
 
 Empty-room recordings may be collected once per day, where a single empty-room recording may be shared between multiple subjects and/or sessions (see [Example 1](#example-1)).
-Empty-room recordings can also be collected for each individual experimental session (see [Example 2](#example-2)).
-
-In the case of empty-room recordings being associated with multiple subjects and/or sessions, it is RECOMMENDED to store the empty-room recording inside a subject directory named `sub-emptyroom`.
-If a [`session-<label>`](../appendices/entities.md#ses) entity is present, its label SHOULD be the date of the empty-room recording in the format `YYYYMMDD`, that is `ses-YYYYMMDD`.
-The `scans.tsv` file containing the date and time of the acquisition SHOULD also be included.
-The rationale is that this naming scheme will allow users to easily retrieve the empty-room recording that best matches a particular experimental session, based on date and time of the recording.
-It should be possible to query empty-room recordings just like usual subject recordings, hence all metadata sidecar files (such as the `channels.tsv`) file SHOULD be present as well.
-
-In the case of empty-room recordings being collected for the individual experimental session, it is recommended to store the empty-room recording along with that subject and session.
-
+Empty-room recordings may also be collected for each individual experimental session (see [Example 2](#example-2)).
 In either case, the label for the [`task-<label>`](../appendices/entities.md#task) entity in the empty-room recording SHOULD be set to `noise`.
 
 ### Example 1
 
 One empty-room recording per day, applying to all subjects for that day.
 
+In the case of empty-room recordings being associated with multiple subjects and/or sessions,
+it is RECOMMENDED to store the empty-room recording inside a subject directory named `sub-emptyroom`.
+If a [`session-<label>`](../appendices/entities.md#ses) entity is present, its label SHOULD be the date of the empty-room recording in the format `YYYYMMDD`, that is `ses-YYYYMMDD`.
+The `scans.tsv` file containing the date and time of the acquisition SHOULD also be included.
+The rationale is that this naming scheme will allow users to easily retrieve the empty-room recording that best matches a particular experimental session, based on date and time of the recording.
+It should be possible to query empty-room recordings just like usual subject recordings, hence all metadata sidecar files (such as the `channels.tsv`) file SHOULD be present as well.
+
 <!-- This block generates a file tree.
 A guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
@@ -546,7 +545,10 @@ A guide for using macros can be found at
 
 ### Example 2
 
-One recording per session, stored within the session directory.
+One empty-room recording per each participant's session, stored within the session directory.
+
+In the case of empty-room recordings being collected for the individual experimental session,
+it is RECOMMENDED to store the empty-room recording along with that subject and session.
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at

From 2d9c9905fa899489480a778e268be2c6dd6df71e Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 12 Feb 2024 22:54:20 +0000
Subject: [PATCH 11/18] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 24.1.1 → 24.2.0](https://github.com/psf/black/compare/24.1.1...24.2.0)
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8d7578c843..1129a080c0 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 24.1.1
+    rev: 24.2.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)

From fea966caf650be90813ac07a6d65788752984d86 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 13 Feb 2024 14:28:13 +0100
Subject: [PATCH 12/18] [FIX] Remove task entity from DWI and PERF time series
 file templates (#1703)

* fix physio

* allow stim
---
 src/schema/rules/files/raw/task.yaml | 33 ++++++++++++++++++----------
 1 file changed, 22 insertions(+), 11 deletions(-)

diff --git a/src/schema/rules/files/raw/task.yaml b/src/schema/rules/files/raw/task.yaml
index cda1e45dec..b7171e568f 100644
--- a/src/schema/rules/files/raw/task.yaml
+++ b/src/schema/rules/files/raw/task.yaml
@@ -38,6 +38,25 @@ timeseries:
     run: optional
     recording: optional
 
+timeseries__mri_no_task:
+  suffixes:
+    - physio
+    - stim
+  extensions:
+    - .tsv.gz
+    - .json
+  datatypes:
+    - dwi
+    - perf
+  entities:
+    subject: required
+    session: optional
+    acquisition: optional
+    run: optional
+    reconstruction: optional
+    direction: optional
+    recording: optional
+
 # Specializations
 # In these rules, we use $ref to retrieve most of an object, and then override
 
@@ -72,23 +91,15 @@ events__pet:
     reconstruction: optional
     run: optional
 
-timeseries__mri:
-  $ref: rules.files.raw.task.timeseries
-  datatypes:
-    - dwi
-    - perf
-  entities:
-    $ref: rules.files.raw.task.timeseries.entities
-    reconstruction: optional
-    direction: optional
-
 timeseries__func:
   $ref: rules.files.raw.task.timeseries
   datatypes:
     - func
   entities:
-    $ref: rules.files.raw.task.timeseries__mri.entities
+    $ref: rules.files.raw.task.timeseries.entities
     ceagent: optional
+    reconstruction: optional
+    direction: optional
 
 timeseries__meg:
   $ref: rules.files.raw.task.timeseries

From fd6612eebea08cd0bc1000a3c90301e5f4c8adc9 Mon Sep 17 00:00:00 2001
From: Taylor Salo <tsalo006@fiu.edu>
Date: Fri, 16 Feb 2024 11:11:26 -0500
Subject: [PATCH 13/18] Fix links. (#1708)

---
 src/schema/objects/metadata.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 7e85b4ac75..1c0d84e0e8 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -2661,10 +2661,10 @@ RepetitionTime:
     and the beginning of acquisition of the volume following it (TR).
     When used in the context of functional acquisitions this parameter best
     corresponds to
-    [DICOM Tag 0020, 0110](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0020,0110)):
+    [DICOM Tag 0020, 0110](http://dicomlookup.com/dicomtags/(0020,0110)):
     the "time delta between images in a
     dynamic of functional set of images" but may also be found in
-    [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080)):
+    [DICOM Tag 0018, 0080](http://dicomlookup.com/dicomtags/(0018,0080)):
     "the period of time in msec between the beginning
     of a pulse sequence and the beginning of the succeeding
     (essentially identical) pulse sequence".
@@ -2681,7 +2681,7 @@ RepetitionTimeExcitation:
   display_name: Repetition Time Excitation
   description: |
     The interval, in seconds, between two successive excitations.
-    [DICOM Tag 0018, 0080](http://dicomlookup.com/lookup.asp?sw=Tnumber&q=(0018,0080))
+    [DICOM Tag 0018, 0080](http://dicomlookup.com/dicomtags/(0018,0080))
     best refers to this parameter.
     This field may be used together with the `"RepetitionTimePreparation"` for
     certain use cases, such as

From ac801d024cb7c699402c4113e168f2a91936fe31 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 16 Feb 2024 13:26:20 -0500
Subject: [PATCH 14/18] Update
 src/modality-specific-files/magnetic-resonance-imaging-data.md

---
 .../magnetic-resonance-imaging-data.md                        | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index cc80cd99d9..48566b01b5 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -303,9 +303,9 @@ processing a [file collection](../common-principles.md#entity-linked-file-collec
 Please visit the [file collections appendix](../appendices/file-collections.md) to see the
 list of suffixes available for quantitative MRI (qMRI) applications associated
 with these maps
-(for example [MPM](../glossary.md#mpm-suffixes),
+(for example, [MPM](../glossary.md#mpm-suffixes),
 [MP2RAGE](../glossary.md#mp2rage-suffixes),
-[MTR](../glossary.md#mtransfer-entities)).
+and [MTR](../glossary.md#mtransfer-entities)).
 
 Currently supported parametric maps include:
 

From f320abae329d8e2966e3bd99fee85c06e99e1386 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 22 Feb 2024 14:26:02 -0500
Subject: [PATCH 15/18] ENH: Clarify the relation of motion.tsv columns to
 channels.tsv rows (#1699)

* ENH: Clarify the relation of motion.tsv columns to channels.tsv rows

* ENH: Add motion as exception to TSV rules in common principles
---
 src/common-principles.md              | 3 ++-
 src/modality-specific-files/motion.md | 5 ++++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/src/common-principles.md b/src/common-principles.md
index d3ff223dcb..f56f420c08 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -430,7 +430,8 @@ Tabular data MUST be saved as tab delimited values (`.tsv`) files, that is, CSV
 files where commas are replaced by tabs. Tabs MUST be true tab characters and
 MUST NOT be a series of space characters. Each TSV file MUST start with a header
 line listing the names of all columns (with the exception of
-[physiological and other continuous recordings](modality-specific-files/physiological-and-other-continuous-recordings.md)).
+[physiological and other continuous recordings](modality-specific-files/physiological-and-other-continuous-recordings.md)
+as well as [motion recording data](modality-specific-files/motion.md)).
 It is RECOMMENDED that the column names in the header of the TSV file are
 written in [`snake_case`](https://en.wikipedia.org/wiki/Snake_case) with the
 first letter in lower case (for example, `variable_name`, not `Variable_name`).
diff --git a/src/modality-specific-files/motion.md b/src/modality-specific-files/motion.md
index 9fa8d8ffad..88ac991d54 100644
--- a/src/modality-specific-files/motion.md
+++ b/src/modality-specific-files/motion.md
@@ -42,7 +42,10 @@ each of which is accompanied by `*_tracksys-<label>_motion.json` and `*_tracksys
 Between `tracksys-<label>` entity and `*_motion.tsv`, `*_motion.json`, or `*_channels.tsv` suffixes, optional [`acq-<label>`](../appendices/entities.md#acq) or [`run-<index>`](../appendices/entities.md#run) entity MAY be inserted.
 
 One column in the `*_tracksys-<label>_motion.tsv` file represents one data channel.
-The ordering of columns MUST match the order of rows in the `*_channels.tsv` file for unambiguous assignment.
+Motion files MUST NOT have a header row;
+the ordering of columns is given by the order of rows in the associated `*_channels.tsv` file.
+The number of columns in `_motion.tsv` files MUST equal the number of rows
+in the associated `_channels.tsv` file.
 All relevant metadata about a tracking systems is stored in accompanying sidecar `*_tracksys-<label>_motion.json` file.
 
 The source data from each tracking system in their original format, if different from `.tsv`,

From 830dbcb84a5d66d1542a43a0f716cce23b40955a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 22 Feb 2024 15:45:54 -0500
Subject: [PATCH 16/18] FIX: Implement inheritance for all TSV/JSON files
 (#1671)

---
 tools/schemacode/bidsschematools/rules.py | 40 ++++++++++-------------
 1 file changed, 18 insertions(+), 22 deletions(-)

diff --git a/tools/schemacode/bidsschematools/rules.py b/tools/schemacode/bidsschematools/rules.py
index d0d6f5dae9..22e1fce649 100644
--- a/tools/schemacode/bidsschematools/rules.py
+++ b/tools/schemacode/bidsschematools/rules.py
@@ -130,7 +130,7 @@ def _entity_rule(rule: Mapping, schema: bst.types.Namespace):
     }
 
 
-def _split_inheritance_rules(rule: Mapping) -> ty.List[Mapping]:
+def _split_inheritance_rules(rule: dict) -> ty.List[dict]:
     """Break composite rules into main and sidecar rules
 
     Implements the inheritance principle for file naming.
@@ -139,32 +139,28 @@ def _split_inheritance_rules(rule: Mapping) -> ty.List[Mapping]:
     rule_exts = set(rule["extensions"])
 
     main_exts = rule_exts - heritable_exts
-    # If a rule only has TSV or JSON files, entities can be
-    # made required
-    if not main_exts:
-        if ".tsv" in rule_exts:
-            main_exts = {".tsv"}
-        elif ".json" in rule_exts:
-            main_exts = {".json"}
-
     sidecar_exts = rule_exts - main_exts
     if not sidecar_exts:
         return [rule]
 
-    sidecar_dtypes = [""] + rule.get("datatypes", [])
-    sidecar_entities = {ent: "optional" for ent in rule["entities"]}
-
-    main_rule = {**rule, **{"extensions": list(main_exts)}}
-    sidecar_rule = {
-        **rule,
-        **{
-            "extensions": list(sidecar_exts),
-            "datatypes": sidecar_dtypes,
-            "entities": sidecar_entities,
-        },
-    }
+    rules = []
+
+    # Some rules only address metadata, such as events.tsv or coordsystem.json
+    if main_exts:
+        rules.append({**rule, **{"extensions": list(main_exts)}})
+
+    rules.append(
+        {
+            **rule,
+            **{
+                "extensions": list(sidecar_exts),
+                "datatypes": [""] + rule.get("datatypes", []),
+                "entities": {ent: "optional" for ent in rule["entities"]},
+            },
+        }
+    )
 
-    return [main_rule, sidecar_rule]
+    return rules
 
 
 def _sanitize_extension(ext: str) -> str:

From dcbcbbff1133c45dcc8853c661645841f6a7243c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 22 Feb 2024 21:07:28 -0500
Subject: [PATCH 17/18] SCHEMA: Add schema.rules.directories to specify
 directory layouts (#1693)

* SCHEMA: Add schema.rules.directories to specify directory layouts

* Alternative layout

* ENH: Adopt the alternative structure, add derivative

* STY: Fix Latin and indentation
---
 src/schema/rules/directories.yaml | 112 ++++++++++++++++++++++++++++++
 1 file changed, 112 insertions(+)
 create mode 100644 src/schema/rules/directories.yaml

diff --git a/src/schema/rules/directories.yaml b/src/schema/rules/directories.yaml
new file mode 100644
index 0000000000..db3db194fe
--- /dev/null
+++ b/src/schema/rules/directories.yaml
@@ -0,0 +1,112 @@
+---
+# This file defines layouts of directories.
+#
+# A layout defines a collection of directory specifiers.
+# Each specifier has a naming convention, requirement level, opacity, and subdirectories.
+#
+# Naming conventions may take three forms:
+#   - name: The directory name has exactly this value.
+#   - entity: The directory name takes the form of {key}-{value} for the specified entity
+#   - value: The directory name takes the form of {value} for the specified term (like datatype)
+#
+# The requirement level indicates whether a directory MUST (required) or MAY (optional) exist.
+#
+# The opaque field indicates whether the contents of the directory are specified.
+#
+# The special "root" specifier describes the root of the dataset and only defines subdirectories.
+# No naming convention applies, and the requirement level and opacity would be superfluous.
+#
+raw:
+  root:
+    subdirs:
+      - code
+      - derivatives
+      - phenotype
+      - sourcedata
+      - stimuli
+      - subject
+  code:
+    name: code
+    level: optional
+    opaque: true
+  derivatives:
+    name: derivatives
+    level: optional
+    opaque: true
+  phenotype:
+    name: phenotype
+    level: optional
+    opaque: false
+  sourcedata:
+    name: sourcedata
+    level: optional
+    opaque: true
+  stimuli:
+    name: stimuli
+    level: optional
+    opaque: true
+  subject:
+    entity: subject
+    level: required
+    opaque: false
+    subdirs:
+      - oneOf:
+          - session
+          - datatype
+  session:
+    entity: session
+    level: optional
+    opaque: false
+    subdirs:
+      - datatype
+  datatype:
+    value: datatype
+    level: required
+    opaque: false
+
+derivative:
+  root:
+    subdirs:
+      - code
+      - derivatives
+      - phenotype
+      - sourcedata
+      - stimuli
+      - subject
+  code:
+    name: code
+    level: optional
+    opaque: true
+  derivatives:
+    name: derivatives
+    level: optional
+    opaque: true
+  phenotype:
+    name: phenotype
+    level: optional
+    opaque: false
+  sourcedata:
+    name: sourcedata
+    level: optional
+    opaque: true
+  stimuli:
+    name: stimuli
+    level: optional
+    opaque: true
+  subject:
+    entity: subject
+    level: optional
+    opaque: false
+    subdirs:
+      - session
+      - datatype
+  session:
+    entity: session
+    level: optional
+    opaque: false
+    subdirs:
+      - datatype
+  datatype:
+    value: datatype
+    level: optional
+    opaque: false

From f90fd70bfe988162066ecbdcd475fe08e4c09fb5 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 23 Feb 2024 05:29:24 -0500
Subject: [PATCH 18/18] ENH: Add sample metadata to MRI and PET (#1593)

Co-authored-by: Remi Gau <remi_gau@hotmail.com>
---
 .../magnetic-resonance-imaging-data.md               | 12 ++++++++++++
 .../positron-emission-tomography.md                  | 12 ++++++++++++
 src/schema/rules/sidecars/mri.yaml                   | 10 ++++++++++
 src/schema/rules/sidecars/pet.yaml                   | 11 +++++++++++
 4 files changed, 45 insertions(+)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 5d14903561..3b51755b1d 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -162,6 +162,18 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table("mri.MRIEchoPlanarImagingAndB0Mapping") }}
 
+#### Tissue description
+
+<!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/sidecars
+The definitions of the fields specified in these tables may be found in
+  src/schema/objects/metadata.yaml
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_sidecar_table("mri.MRISample") }}
+
 ## Anatomy imaging data
 
 Anatomy MRI sequences measure static, structural features of the brain.
diff --git a/src/modality-specific-files/positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md
index c16d144b4f..b63007ba10 100644
--- a/src/modality-specific-files/positron-emission-tomography.md
+++ b/src/modality-specific-files/positron-emission-tomography.md
@@ -216,6 +216,18 @@ A guide for using macros can be found at
 
 {{ MACROS___make_sidecar_table("pet.PETInstitutionInformation") }}
 
+#### Tissue description
+
+<!-- This block generates a metadata table.
+These tables are defined in
+  src/schema/rules/sidecars
+The definitions of the fields specified in these tables may be found in
+  src/schema/objects/metadata.yaml
+A guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_sidecar_table("pet.PETSample") }}
+
 #### Task
 
 If the OPTIONAL [`task-<label>`](../appendices/entities.md#task) is used,
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index 521a70c701..d9967c13c6 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -35,6 +35,16 @@ MRIHardware:
     MatrixCoilMode: recommended
     CoilCombinationMethod: recommended
 
+MRISample:
+  selectors:
+    - modality == "mri"
+  fields:
+    BodyPart:
+      level: optional
+      description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
+    BodyPartDetails: optional
+    BodyPartDetailsOntology: optional
+
 MRIScannerHardwareASL:
   selectors:
     - datatype == "perf"
diff --git a/src/schema/rules/sidecars/pet.yaml b/src/schema/rules/sidecars/pet.yaml
index a2cedd3f54..dc4ff9a572 100644
--- a/src/schema/rules/sidecars/pet.yaml
+++ b/src/schema/rules/sidecars/pet.yaml
@@ -35,6 +35,17 @@ PETInstitutionInformation:
       level: recommended
       description_addendum: Corresponds to DICOM Tag 0008, 1040 `Institutional Department Name`.
 
+PETSample:
+  selectors:
+    - modality == "pet"
+    - suffix == "pet"
+  fields:
+    BodyPart:
+      level: optional
+      description_addendum: Corresponds to DICOM Tag 0018, 0015 `Body Part Examined`.
+    BodyPartDetails: optional
+    BodyPartDetailsOntology: optional
+
 PETRadioChemistry:
   selectors:
     - datatype == "pet"