From fcfcb37ab037a53cbc094e5faf0aaf5d3a8fe683 Mon Sep 17 00:00:00 2001
From: Dimitri Papadopoulos
 <3234522+DimitriPapadopoulos@users.noreply.github.com>
Date: Mon, 22 Apr 2024 10:44:10 +0200
Subject: [PATCH 01/74] =?UTF-8?q?anonymisation=20=E2=86=92=20deidentififca?=
 =?UTF-8?q?tion?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

In the vast majority of cases, strict anonymisation is impossible.
Use the more generic term deidentification instead.
---
 src/modality-agnostic-files.md                                | 2 +-
 .../magnetic-resonance-imaging-data.md                        | 2 +-
 src/modality-specific-files/positron-emission-tomography.md   | 2 +-
 src/schema/objects/columns.yaml                               | 4 ++--
 src/schema/objects/metadata.yaml                              | 2 +-
 src/schema/objects/suffixes.yaml                              | 2 +-
 6 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/modality-agnostic-files.md b/src/modality-agnostic-files.md
index fb5b04ee3e..c6890aa6b4 100644
--- a/src/modality-agnostic-files.md
+++ b/src/modality-agnostic-files.md
@@ -534,7 +534,7 @@ ses-followup	2009-06-17T13:45:30	110
 Template: `code/*`
 
 Source code of scripts that were used to prepare the dataset MAY be stored here.
-Examples include anonymization or defacing of the data, or
+Examples include deidentification or defacing of the data, or
 the conversion from the format of the source data to the BIDS format
 (see [source vs. raw vs. derived data](./common-principles.md#source-vs-raw-vs-derived-data)).
 Extra care should be taken to avoid including original IDs or
diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 072410f528..06fb0b997c 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -925,7 +925,7 @@ NIfTI headers.
 
 ### `*_asllabeling.*`
 
-An anonymized screenshot of the planning of the labeling slab/plane
+A deidentified screenshot of the planning of the labeling slab/plane
 with respect to the imaging slab or slices.
 This screenshot is based on DICOM macro C.8.13.5.14.
 
diff --git a/src/modality-specific-files/positron-emission-tomography.md b/src/modality-specific-files/positron-emission-tomography.md
index 5ea5f8bbcb..f15f3fad40 100644
--- a/src/modality-specific-files/positron-emission-tomography.md
+++ b/src/modality-specific-files/positron-emission-tomography.md
@@ -177,7 +177,7 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table("pet.PETTime") }}
 
-We refer to the common principles for the standards for describing dates and timestamps, including possibilities for anonymization (see [Units](../common-principles.md#units)).
+We refer to the common principles for the standards for describing dates and timestamps, including possibilities for deidentification (see [Units](../common-principles.md#units)).
 
 #### Reconstruction
 
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 3ccb32d324..5ca387a007 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -19,7 +19,7 @@ acq_time__scans:
     Acquisition time refers to when the first data point in each run was acquired.
     Furthermore, if this header is provided, the acquisition times of all files
     from the same recording MUST be identical.
-    Datetime format and their anonymization are described in
+    Datetime format and their deidentification are described in
     [Units](SPEC_ROOT/common-principles.md#units).
   type: string
   format: datetime
@@ -28,7 +28,7 @@ acq_time__sessions:
   display_name: Session acquisition time
   description: |
     Acquisition time refers to when the first data point of the first run was acquired.
-    Datetime format and their anonymization are described in
+    Datetime format and their deidentification are described in
     [Units](SPEC_ROOT/common-principles.md#units).
   type: string
   format: datetime
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 57515dd6f0..1b13a6a614 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -1646,7 +1646,7 @@ LabelingLocationDescription:
     Description of the location of the labeling plane (`"CASL"` or `"PCASL"`) or
     the labeling slab (`"PASL"`) that cannot be captured by fields
     `LabelingOrientation` or `LabelingDistance`.
-    May include a link to an anonymized screenshot of the planning of the
+    May include a link to a deidentified screenshot of the planning of the
     labeling slab/plane with respect to the imaging slab or slices
     `*_asllabeling.*`.
     Based on DICOM macro C.8.13.5.14.
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 0ddc8647d2..4ed5a281b0 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -505,7 +505,7 @@ asllabeling:
   value: asllabeling
   display_name: ASL Labeling Screenshot
   description: |
-    An anonymized screenshot of the planning of the labeling slab/plane
+    A deidentified screenshot of the planning of the labeling slab/plane
     with respect to the imaging slab or slices.
     This screenshot is based on DICOM macro C.8.13.5.14.
 beh:

From cbb94e11dea2e6a94d9e68f6782494d3c36c9c79 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 25 Apr 2024 06:41:47 -0400
Subject: [PATCH 02/74] [MAINT] Update contributor table generator style
 (#1805)

* chore(code-style): Rewrite f-strings in print_contributors.py to outrage flake8 less

* chore(render): Rerender contributors.md

* chore(style): Ignore linting errors in auto-generated table
---
 src/appendices/contributors.md | 13 +++++++------
 tools/print_contributors.py    | 20 +++++++++-----------
 2 files changed, 16 insertions(+), 17 deletions(-)

diff --git a/src/appendices/contributors.md b/src/appendices/contributors.md
index 2ffab4740f..f48586f04d 100644
--- a/src/appendices/contributors.md
+++ b/src/appendices/contributors.md
@@ -37,6 +37,7 @@ ecosystem (in alphabetical order).
 If you contributed to the BIDS ecosystem and your name is not listed, please add it.
 
 <!-- THE SECTION BELOW IS AUTOMATICALLY GENERATED -->
+<!--lint ignore -->
 
 | name                                                 | contributions                          |
 | ---------------------------------------------------- | -------------------------------------- |
@@ -121,7 +122,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 | Dianne Patterson                                     | 📖                                     |
 | Dimitri Papadopoulos Orfanos                         | 📖💡🤔💬💻                             |
 | Dmitry Petrov                                        | 📖💻                                   |
-| Dora Hermes                                          | 📖💻✅🔍🤔                              |
+| Dora Hermes                                          | 📖💻✅🔍🤔                             |
 | Dorien Huijser                                       | 📖                                     |
 | Douglas N. Greve                                     | 📖                                     |
 | Duncan Macleod                                       | 📖🚇                                   |
@@ -194,7 +195,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 | Jeanette Mumford                                     | 📖                                     |
 | Jefferson Casimir                                    | 🔧                                     |
 | Jeffrey G. Ojemann                                   | 📖                                     |
-| Jeffrey S. Grethe                                    | 💬🐛✅📢💻                              |
+| Jeffrey S. Grethe                                    | 💬🐛✅📢💻                             |
 | JegouA                                               | 💻                                     |
 | Jelle Dalenberg                                      | 📖                                     |
 | Jeremy Moreau                                        | 📖💡                                   |
@@ -211,7 +212,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 | Jose Manuel Saborit                                  | 📖                                     |
 | Joseph Wexler                                        | 📖💡                                   |
 | Joseph Woods                                         | 📖                                     |
-| Julia Guiomar Niso Galán                             | 🤔🎨🔍👀📋📝🔧🐛💻🔣✅💬📖💡📢          |
+| Julia Guiomar Niso Galán                             | 🤔🎨🔍👀📋📝🔧🐛💻🔣✅💬📖💡📢         |
 | Julia Sprenger                                       | 📖                                     |
 | Julien Cohen-Adad                                    | 📖🔣🤔                                 |
 | Julius Welzel                                        | 📖💡🐛💻🔣🤔💬📓                       |
@@ -269,7 +270,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 | Michael Hanke                                        | 📖🤔🔧🐛📢                             |
 | Michael P. Harms                                     | 📖⚠️🔧                                 |
 | Michael P. Milham                                    | 💡🔍                                   |
-| Michael P. Notter                                    | 💬📝✅📢📖                              |
+| Michael P. Notter                                    | 💬📝✅📢📖                             |
 | Michael Schirner                                     | 📖                                     |
 | Mikaël Naveau                                        | 🐛                                     |
 | Nader Pouratian                                      | 📖                                     |
@@ -288,7 +289,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 | Patricia Clement                                     | 💬🐛💻📖🔣💡📋🤔📆⚠️📢                 |
 | Patrick Park                                         | 📖💡💬💻                               |
 | Paule-Joanne Toussaint                               | 📖                                     |
-| Peer Herholz                                         | 💬📖👀🔧✅📢                            |
+| Peer Herholz                                         | 💬📖👀🔧✅📢                           |
 | Petra Ritter                                         | 📖                                     |
 | Pierre Rioux                                         | 📖                                     |
 | Pieter Vandemaele                                    | 📖💻                                   |
@@ -318,7 +319,7 @@ If you contributed to the BIDS ecosystem and your name is not listed, please add
 | Shashank Bansal                                      | 📖                                     |
 | Sjoerd B. Vos                                        | 📖                                     |
 | Soichi Hayashi                                       | 📖🔧🐛                                 |
-| Stefan Appelhoff                                     | 📖💬🤔🐛💡💻👀⚠️📢✅🔧🔌📝🚧🔣          |
+| Stefan Appelhoff                                     | 📖💬🤔🐛💡💻👀⚠️📢✅🔧🔌📝🚧🔣         |
 | Stephan Bickel                                       | 📖                                     |
 | Steven Meisler                                       | 🐛💻💬🔧📓                             |
 | Suyash Bhogawar                                      | 📖💡⚠️🔧💬                             |
diff --git a/tools/print_contributors.py b/tools/print_contributors.py
index c49ca6f823..29db86a39c 100644
--- a/tools/print_contributors.py
+++ b/tools/print_contributors.py
@@ -15,8 +15,9 @@
 
 
 def contributor_table_header(max_name_length, max_contrib_length):
-    return f"""| name{" " * (max_name_length-4)} | contributions{" " * (max_contrib_length-13)} |
-| {"-" * max_name_length} | {"-"*max_contrib_length} |
+    return f"""\
+| {"name":<{max_name_length}} | {"contributions":<{max_contrib_length}} |
+| {"":-<{max_name_length}} | {"":-<{max_contrib_length}} |
 """
 
 
@@ -24,16 +25,13 @@ def create_line_contributor(
     contributor: dict[str, str], max_name_length: int, max_contrib_length: int
 ):
     name = contributor["name"]
+    emap = emoji_map()
+    contributions = "".join(
+        emoji.emojize(emap[cont]) for cont in contributor["contributions"]
+    )
 
-    line = f"| {name}{' '*(max_name_length-len(name))} | "
-
-    nb_contrib = len(contributor["contributions"]) * 2
-    for contrib in contributor["contributions"]:
-        line += emoji.emojize(emoji_map()[contrib])
-
-    line += f"{' '*(max_contrib_length-nb_contrib)} |\n"
-
-    return line
+    pad = max_contrib_length - len(contributor["contributions"]) * 2
+    return f"| {name:<{max_name_length}} | {contributions}{'':<{pad}} |\n"
 
 
 def main():

From 90ec07f1e8357d1ba209570fdac3a1394a9d677b Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu, 25 Apr 2024 14:55:51 -0400
Subject: [PATCH 03/74] [FIX] Move `rawdata/` into `sourcedata/raw` in
 alternative structure example, clarify on naming of datasets themselves
 (#1741)

* RF: move `rawdata/` to `sourcedata/raw` in an example + make overall dataset to be BIDS dataset

This is my take on an extended discussion about ambiguity of
`rawdata/` example:
https://github.com/bids-standard/bids-specification/pull/1734/files#r1534475631

* Minor rewording in description of sourcedata/ content

Prior one bundled naming aspect under the same MUST. I separated into
separate sentences, added explicit statement that BIDS does not
prescribe a particular naming scheme for source data. And added
explicit RECOMMENDED on the example how to organize/name files there.

* Add one dataset_description.json into an example to make it explicitly a BIDS dataset

* My take on dataset naming common principle

* [DATALAD RUNCMD] Replace use of rawdata in tests with explicit 'noncompliant'

=== Do not change lines below ===
{
 "chain": [],
 "cmd": "sed -i -e s,rawdata,noncompliant,g tools/schemacode/bidsschematools/validator.py tools/schemacode/bidsschematools/tests/test_validator.py tools/schemacode/bidsschematools/tests/data/expected_bids_validator_xs_write.log",
 "exit": 0,
 "extra_inputs": [],
 "inputs": [],
 "outputs": [],
 "pwd": "."
}
^^^ Do not change lines above ^^^

* Do not use e.g.

* Move dataset_description.json in the example to be listed after folders

* Remove the notion that example layout can in fact be a valid BIDS dataset

* Use lower case "recommended" as not part of BIDS spec, and recommend underscores too

* Make into a single sentence

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/common-principles.md                      | 53 ++++++++++---------
 .../data/expected_bids_validator_xs_write.log |  2 +-
 .../bidsschematools/tests/test_validator.py   |  4 +-
 tools/schemacode/bidsschematools/validator.py |  2 +-
 4 files changed, 33 insertions(+), 28 deletions(-)

diff --git a/src/common-principles.md b/src/common-principles.md
index 9b10ba19f2..3d9bc233af 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -97,6 +97,12 @@ and/or files (like `events.tsv`) are fully omitted *when they are unavailable or
 instead of specified with an `n/a` value, or included as an empty file
 (for example an empty `events.tsv` file with only the headers included).
 
+## Dataset naming
+
+BIDS does not prescribe a particular naming scheme for directories containing individual BIDS datasets.
+However, it is recommended to use a short descriptive name that reflects the content of the dataset, avoid spaces in the name, and use hyphens or underscores to separate words.
+BIDS datasets embedded within a larger BIDS dataset MAY follow some convention (see for example [Storage of derived datasets](#storage-of-derived-datasets)).
+
 ## Filesystem structure
 
 Data for each subject are placed in subdirectories named "`sub-<label>`",
@@ -252,9 +258,10 @@ recommending a particular naming scheme for including different types of
 source data (such as the raw event logs or parameter files, before conversion to BIDS).
 However, in the case that these data are to be included:
 
-1.  These data MUST be kept in separate `sourcedata` directory with a similar
-    directory structure as presented below for the BIDS-managed data. For example:
-    `sourcedata/sub-01/ses-pre/func/sub-01_ses-pre_task-rest_bold.dicom.tgz` or
+1.  These data MUST be kept in separate `sourcedata` directory.
+    BIDS does not prescribe a particular naming scheme for source data,
+    but it is recommended for it to follow BIDS naming convention where possible.
+    For example: `sourcedata/sub-01/ses-pre/func/sub-01_ses-pre_task-rest_bold.dicom.tgz` or
     `sourcedata/sub-01/ses-pre/func/MyEvent.sce`.
 
 1.  A README file SHOULD be found at the root of the `sourcedata` directory or the
@@ -271,41 +278,38 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_filetree_example(
     {
-    "my_dataset-1": {
-            "sourcedata": "",
-            "...": "",
-            "rawdata": {
-                "dataset_description.json": "",
-                "participants.tsv": "",
+    "my_project-1": {
+        "sourcedata": {
+            "dicoms": {},
+            "raw": {
                 "sub-01": {},
                 "sub-02": {},
                 "...": "",
+                "dataset_description.json": "",
+				"...": "",
             },
-            "derivatives": {
-                "pipeline_1": {},
-                "pipeline_2": {},
-                "...": "",
-            },
+            "..." : "",
+        },
+        "derivatives": {
+            "pipeline_1": {},
+            "pipeline_2": {},
+            "...": "",
         }
     }
+   }
 ) }}
 
-In this example, where `sourcedata` and `derivatives` are not nested inside
-`rawdata`, **only the `rawdata` subdirectory** needs to be a BIDS-compliant
-dataset.
+In this example, `sourcedata/dicoms` is not nested inside
+`sourcedata/raw`, **and only the `sourcedata/raw` subdirectory** is a BIDS-compliant dataset among `sourcedata/` subfolders.
 The subdirectories of `derivatives` MAY be BIDS-compliant derivatives datasets
 (see [Non-compliant derivatives](#non-compliant-derivatives) for further discussion).
-This specification does not prescribe anything about the contents of `sourcedata`
-directories in the above example - nor does it prescribe the `sourcedata`,
-`derivatives`, or `rawdata` directory names.
-The above example is just a convention that can be useful for organizing raw,
-source, and derived data while maintaining BIDS compliance of the raw data
-directory. When using this convention it is RECOMMENDED to set the `SourceDatasets`
+The above example is just a convention useful for organizing source, raw BIDS, and derived BIDS data while maintaining BIDS compliance of the raw data directory.
+When using this convention it is RECOMMENDED to set the `SourceDatasets`
 field in `dataset_description.json` of each subdirectory of `derivatives` to:
 
 ```JSON
 {
-  "SourceDatasets": [ {"URL": "../../rawdata/"} ]
+  "SourceDatasets": [ {"URL": "../../sourcedata/raw/"} ]
 }
 ```
 
@@ -406,6 +410,7 @@ Derivatives can be stored/distributed in two ways:
             "sub-01": {},
             "sub-02": {},
             "...": "",
+            "dataset_description.json": "",
             }
         }
     ) }}
diff --git a/tools/schemacode/bidsschematools/tests/data/expected_bids_validator_xs_write.log b/tools/schemacode/bidsschematools/tests/data/expected_bids_validator_xs_write.log
index 4d410c3cc8..9b3bb24a91 100644
--- a/tools/schemacode/bidsschematools/tests/data/expected_bids_validator_xs_write.log
+++ b/tools/schemacode/bidsschematools/tests/data/expected_bids_validator_xs_write.log
@@ -3,5 +3,5 @@ SUMMARY:
 0 out of 1 files were successfully validated, using the following regular expressions:
 	- `.*?/sub-(?P<subject>[0-9a-zA-Z]+)/(|ses-(?P<session>[0-9a-zA-Z]+)/)anat/sub-(?P=subject)(|_ses-(?P=session))(|_acq-(?P<acquisition>[0-9a-zA-Z]+))(|_ce-(?P<ceagent>[0-9a-zA-Z]+))(|_rec-(?P<reconstruction>[0-9a-zA-Z]+))(|_run-(?P<run>[0-9a-zA-Z]+))(|_part-(?P<part>(mag|phase|real|imag)))_(T1w|T2w|PDw|T2starw|FLAIR|inplaneT1|inplaneT2|PDT2|angio|T2star)\.(nii.gz|nii|json)$`
 The following files were not matched by any regex schema entry:
-	* `/home/chymera/.data2/datalad/000026/rawdata/sub-EXC022/anat/sub-EXC022_ses-MRI_flip-1_VFA.nii.gz
+	* `/home/chymera/.data2/datalad/000026/noncompliant/sub-EXC022/anat/sub-EXC022_ses-MRI_flip-1_VFA.nii.gz
 The following mandatory regex schema entries did not match any files:
diff --git a/tools/schemacode/bidsschematools/tests/test_validator.py b/tools/schemacode/bidsschematools/tests/test_validator.py
index fd808fb709..abd11737f0 100644
--- a/tools/schemacode/bidsschematools/tests/test_validator.py
+++ b/tools/schemacode/bidsschematools/tests/test_validator.py
@@ -64,11 +64,11 @@ def test_write_report(tmp_path):
     ]
     validation_result["path_tracking"] = [
         "/home/chymera/.data2/datalad/000026/"
-        "rawdata/sub-EXC022/anat/sub-EXC022_ses-MRI_flip-1_VFA.nii.gz"
+        "noncompliant/sub-EXC022/anat/sub-EXC022_ses-MRI_flip-1_VFA.nii.gz"
     ]
     validation_result["path_listing"] = [
         "/home/chymera/.data2/datalad/000026/"
-        "rawdata/sub-EXC022/anat/sub-EXC022_ses-MRI_flip-1_VFA.nii.gz"
+        "noncompliant/sub-EXC022/anat/sub-EXC022_ses-MRI_flip-1_VFA.nii.gz"
     ]
 
     report_path = tmp_path / "output_bids_validator_xs_write.log"
diff --git a/tools/schemacode/bidsschematools/validator.py b/tools/schemacode/bidsschematools/validator.py
index 4ec04f6df6..bd5eba0ad4 100644
--- a/tools/schemacode/bidsschematools/validator.py
+++ b/tools/schemacode/bidsschematools/validator.py
@@ -599,7 +599,7 @@ def validate_bids(
     ::
 
         from bidsschematools import validator
-        bids_paths = '~/.data2/datalad/000026/rawdata'
+        bids_paths = '~/.data2/datalad/000026/noncompliant'
         validator.validate_bids(bids_paths)
 
     Notes

From 3322a4023f954931b074678f5f78c7779d13a619 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 26 Apr 2024 09:42:32 -0400
Subject: [PATCH 04/74] FIX: Re-add run entity to electrodes.tsv (#1722)

* FIX: Re-add run entity to electrodes.tsv

* [ENH] Recommend electrodes usage/require inheritance

* SCHEMA: Add check to warn against excessive electrode specificity
---
 .../electroencephalography.md                     |  6 ++++++
 .../intracranial-electroencephalography.md        |  6 ++++++
 src/schema/rules/checks/electrodes.yaml           | 15 +++++++++++++++
 src/schema/rules/files/raw/channels.yaml          |  1 +
 4 files changed, 28 insertions(+)
 create mode 100644 src/schema/rules/checks/electrodes.yaml

diff --git a/src/modality-specific-files/electroencephalography.md b/src/modality-specific-files/electroencephalography.md
index 6ba02cc13a..8a584bb7a0 100644
--- a/src/modality-specific-files/electroencephalography.md
+++ b/src/modality-specific-files/electroencephalography.md
@@ -308,6 +308,12 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_columns_table("eeg.EEGElectrodes") }}
 
+`*_electrodes.tsv` files SHOULD NOT be duplicated for each data file,
+for example, during multiple runs of a task.
+The [inheritance principle](../common-principles.md#the-inheritance-principle) MUST
+be used to find the appropriate electrode positions for a given data file.
+If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to indicate this.
+
 ### Example `*_electrodes.tsv`
 
 See also the corresponding [`electrodes.tsv` example](#example-channelstsv).
diff --git a/src/modality-specific-files/intracranial-electroencephalography.md b/src/modality-specific-files/intracranial-electroencephalography.md
index ae6a669a84..096b96f97d 100644
--- a/src/modality-specific-files/intracranial-electroencephalography.md
+++ b/src/modality-specific-files/intracranial-electroencephalography.md
@@ -349,6 +349,12 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_columns_table("ieeg.iEEGElectrodes") }}
 
+`*_electrodes.tsv` files SHOULD NOT be duplicated for each data file,
+for example, during multiple runs of a task.
+The [inheritance principle](../common-principles.md#the-inheritance-principle) MUST
+be used to find the appropriate electrode positions for a given data file.
+If electrodes are repositioned, it is RECOMMENDED to use multiple sessions to indicate this.
+
 ### Example `*_electrodes.tsv`
 
 ```Text
diff --git a/src/schema/rules/checks/electrodes.yaml b/src/schema/rules/checks/electrodes.yaml
new file mode 100644
index 0000000000..29f81d3d44
--- /dev/null
+++ b/src/schema/rules/checks/electrodes.yaml
@@ -0,0 +1,15 @@
+---
+ElectrodeSpecificity:
+  issue:
+    code: EXCESSIVE_ELECTRODE_SPECIFICITY
+    message: |
+      Run or acquisition entities detected in electrodes.tsv.
+      Electrode definitions should generally not vary within a session.
+      Consider creating a new session each time electrodes are reconfigured.
+    level: warning
+  selectors:
+    - suffix == 'electrodes'
+    - extension == '.tsv'
+  checks:
+    - '!("run" in entities)'
+    - '!("acquisition" in entities)'
diff --git a/src/schema/rules/files/raw/channels.yaml b/src/schema/rules/files/raw/channels.yaml
index 06c213be17..25aa1deff3 100644
--- a/src/schema/rules/files/raw/channels.yaml
+++ b/src/schema/rules/files/raw/channels.yaml
@@ -70,6 +70,7 @@ electrodes:
     subject: required
     session: optional
     acquisition: optional
+    run: optional
     space: optional
 
 # MEG has an additional entity available

From f0bc97703017315c43cbb6fb6b8d5e354817436a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 26 Apr 2024 18:05:19 -0400
Subject: [PATCH 05/74] [INFRA] Refactor metaschema file rules into definitions
 (#1808)

* feat(metaschema): Factor out file rule types

* chore(sty): Run prettier on metaschema.json to reduce future diffs
---
 src/metaschema.json | 260 ++++++++++++++++++++++++++------------------
 1 file changed, 156 insertions(+), 104 deletions(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index 129e3f1c5d..a3e500dad7 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -7,8 +7,7 @@
       "properties": {
         "associations": {
           "type": "object",
-          "patternProperties":
-          {
+          "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "type": "object",
               "properties": {
@@ -28,7 +27,8 @@
                       "anyOf": [
                         {
                           "type": "string"
-                        }, {
+                        },
+                        {
                           "type": "array",
                           "items": {
                             "type": "string"
@@ -126,23 +126,23 @@
           "additionalProperties": false
         },
         "common_principles": {
-         "type": "object",
-         "patternProperties": {
-           "^[a-zA-Z0-9_]+$": {
-             "type": "object",
-             "properties": {
-               "display_name": {
-                 "type": "string"
-               },
-               "description": {
-                 "type": "string"
-               }
-             },
-             "required": ["display_name", "description"],
-             "additionalProperties": false
-           },
-           "additionalProperties": false
-         }
+          "type": "object",
+          "patternProperties": {
+            "^[a-zA-Z0-9_]+$": {
+              "type": "object",
+              "properties": {
+                "display_name": {
+                  "type": "string"
+                },
+                "description": {
+                  "type": "string"
+                }
+              },
+              "required": ["display_name", "description"],
+              "additionalProperties": false
+            },
+            "additionalProperties": false
+          }
         },
         "datatypes": {
           "type": "object",
@@ -191,7 +191,13 @@
                   "type": "array"
                 }
               },
-              "required": ["name", "display_name", "description", "type", "format"],
+              "required": [
+                "name",
+                "display_name",
+                "description",
+                "type",
+                "format"
+              ],
               "additionalProperties": false
             }
           },
@@ -312,7 +318,7 @@
                   "$ref": "http://json-schema.org/draft-07/schema#/properties/type"
                 }
               },
-              "required": ["name","display_name", "description"]
+              "required": ["name", "display_name", "description"]
             }
           },
           "additionalProperties": false
@@ -358,8 +364,20 @@
           }
         }
       },
-        "required": ["columns", "common_principles", "datatypes", "entities", "enums", "extensions", "files", "formats", "metadata", "modalities", "suffixes"],
-        "additionalProperties": false
+      "required": [
+        "columns",
+        "common_principles",
+        "datatypes",
+        "entities",
+        "enums",
+        "extensions",
+        "files",
+        "formats",
+        "metadata",
+        "modalities",
+        "suffixes"
+      ],
+      "additionalProperties": false
     },
     "rules": {
       "type": "object",
@@ -376,20 +394,20 @@
                     "issues": {
                       "type": "object",
                       "properties": {
-                        "code": {"type": "string"},
-                        "message": {"type": "string"},
-                        "level": {"enum": ["error", "warning"]}
+                        "code": { "type": "string" },
+                        "message": { "type": "string" },
+                        "level": { "enum": ["error", "warning"] }
                       },
                       "required": ["code", "message", "level"],
                       "additionalProperties": false
                     },
                     "selectors": {
                       "type": "array",
-                      "items": {"type": "string"}
+                      "items": { "type": "string" }
                     },
                     "checks": {
                       "type": "array",
-                      "items": {"type": "string"}
+                      "items": { "type": "string" }
                     }
                   },
                   "required": ["checks", "selectors"]
@@ -409,15 +427,10 @@
                   "type": "object",
                   "patternProperties": {
                     "^[a-zA-Z0-9_]+$": {
-                      "type": "object",
-                      "properties": {
-                        "level": {"type": "string"},
-                        "path": {"type": "string"},
-                        "extensions": {"type": "array"},
-                        "stem": {"type": "string"}
-                      },
-                      "required": ["level"],
-                      "additionalProperties": false
+                      "anyOf": [
+                        { "$ref": "#/definitions/pathRule" },
+                        { "$ref": "#/definitions/stemRule" }
+                      ]
                     }
                   },
                   "additionalProperties": false
@@ -426,17 +439,10 @@
                   "type": "object",
                   "patternProperties": {
                     "^[a-zA-Z0-9_]+$": {
-                      "type": "object",
-                      "properties": {
-                        "level": {"type": "string"},
-                        "path": {"type": "string"},
-                        "extensions": {"type": "array"},
-                        "stem": {"type": "string"},
-                        "entities": {"$ref": "#/definitions/entities"},
-                        "suffixes": {"type": "array"}
-                      },
-                      "required": ["level", "extensions"],
-                      "additionalProperties": false
+                      "anyOf": [
+                        { "$ref": "#/definitions/stemRule" },
+                        { "$ref": "#/definitions/suffixRule" }
+                      ]
                     }
                   },
                   "additionalProperties": false
@@ -471,24 +477,7 @@
                 "^[a-z]+$": {
                   "type": "object",
                   "patternProperties": {
-                    "^[a-zA-Z0-9_]+$": {
-                      "type": "object",
-                      "properties": {
-                        "suffixes": {
-                          "type": "array",
-                          "items": {"type": "string"}
-                        },
-                        "extensions": {
-                          "type": "array",
-                          "items": {"pattern": "^[./][a-z.]+|"}
-                        },
-                        "datatypes": {
-                          "type": "array",
-                          "items": {"pattern": "^[a-z]+$"}
-                        },
-                        "entities": {"$ref": "#/definitions/entities"}
-                      }
-                    }
+                    "^[a-zA-Z0-9_]+$": { "$ref": "#/definitions/suffixRule" }
                   },
                   "additionalProperties": false
                 }
@@ -505,7 +494,7 @@
             "^derivatives$": {
               "type": "object",
               "properties": {
-                "common_derivatives": {"$ref": "#/definitions/sidecar"}
+                "common_derivatives": { "$ref": "#/definitions/sidecar" }
               },
               "required": ["common_derivatives"],
               "additionalProperties": false
@@ -527,9 +516,7 @@
                   "$ref": "#/definitions/tabular_data"
                 }
               },
-              "required": [
-                "common_derivatives"
-              ],
+              "required": ["common_derivatives"],
               "additionalProperties": false
             },
             "^(?!derivatives$)[a-z_]+$": {
@@ -540,7 +527,7 @@
         },
         "common_principles": {
           "type": "array",
-          "items": {"type": "string"}
+          "items": { "type": "string" }
         },
         "dataset_metadata": {
           "type": "object"
@@ -550,7 +537,7 @@
         },
         "entities": {
           "type": "array",
-          "items": {"type": "string"}
+          "items": { "type": "string" }
         },
         "errors": {
           "type": "object",
@@ -558,9 +545,9 @@
             "^[a-zA-Z0-9_]+$": {
               "type": "object",
               "properties": {
-                "code": {"type": "string"},
-                "message": {"type": "string"},
-                "level": {"enum": ["error", "warning"]},
+                "code": { "type": "string" },
+                "message": { "type": "string" },
+                "level": { "enum": ["error", "warning"] },
                 "selectors": {
                   "type": "array",
                   "items": {
@@ -582,7 +569,7 @@
               "properties": {
                 "datatypes": {
                   "type": "array",
-                  "items": {"pattern": "^[a-z]+$"}
+                  "items": { "pattern": "^[a-z]+$" }
                 }
               },
               "required": ["datatypes"],
@@ -592,15 +579,15 @@
         }
       },
       "required": [
-          "entities",
-          "files",
-          "sidecars",
-          "tabular_data",
-          "common_principles",
-          "dataset_metadata",
-          "directories",
-          "errors",
-          "modalities"
+        "entities",
+        "files",
+        "sidecars",
+        "tabular_data",
+        "common_principles",
+        "dataset_metadata",
+        "directories",
+        "errors",
+        "modalities"
       ],
       "additionalProperties": false
     },
@@ -622,14 +609,14 @@
       "patternProperties": {
         "^[a-z]+$": {
           "anyOf": [
-            {"enum": ["optional", "required"]},
+            { "enum": ["optional", "required"] },
             {
               "type": "object",
               "properties": {
-                "level": {"enum": ["optional", "required"]},
+                "level": { "enum": ["optional", "required"] },
                 "enum": {
                   "type": "array",
-                  "items": {"type": "string"}
+                  "items": { "type": "string" }
                 }
               },
               "required": ["level", "enum"]
@@ -647,24 +634,38 @@
           "properties": {
             "selectors": {
               "type": "array",
-              "items": {"type": "string"}
+              "items": { "type": "string" }
             },
             "fields": {
               "type": "object",
               "patternProperties": {
                 "^[a-zA-Z0-9_]+$": {
                   "anyOf": [
-                    {"enum": ["recommended", "optional", "required", "deprecated"]},
                     {
-                      "type":  "object",
+                      "enum": [
+                        "recommended",
+                        "optional",
+                        "required",
+                        "deprecated"
+                      ]
+                    },
+                    {
+                      "type": "object",
                       "properties": {
-                        "level": {"enum": ["recommended", "optional", "required", "deprecated"]},
-                        "level_addendum": {"type": "string"}
+                        "level": {
+                          "enum": [
+                            "recommended",
+                            "optional",
+                            "required",
+                            "deprecated"
+                          ]
+                        },
+                        "level_addendum": { "type": "string" }
                       },
                       "required": ["level", "level_addendum"],
                       "additionalProperties": false
                     },
-                    {"pattern": "recommended.*"}
+                    { "pattern": "recommended.*" }
                   ]
                 }
               },
@@ -685,25 +686,39 @@
           "properties": {
             "selectors": {
               "type": "array",
-              "items": {"type": "string"}
+              "items": { "type": "string" }
             },
             "columns": {
               "type": "object",
               "patternProperties": {
                 "^[a-zA-Z0-9_]+$": {
                   "anyOf": [
-                    {"enum": ["recommended", "optional", "required", "deprecated"]},
                     {
-                      "type":  "object",
+                      "enum": [
+                        "recommended",
+                        "optional",
+                        "required",
+                        "deprecated"
+                      ]
+                    },
+                    {
+                      "type": "object",
                       "properties": {
-                        "level": {"enum": ["recommended", "optional", "required", "deprecated"]},
-                        "level_addendum": {"type": "string"},
-                        "description_addendum": {"type": "string"}
+                        "level": {
+                          "enum": [
+                            "recommended",
+                            "optional",
+                            "required",
+                            "deprecated"
+                          ]
+                        },
+                        "level_addendum": { "type": "string" },
+                        "description_addendum": { "type": "string" }
                       },
                       "required": ["level"],
                       "additionalProperties": false
                     },
-                    {"pattern": "recommended.*"}
+                    { "pattern": "recommended.*" }
                   ]
                 }
               },
@@ -712,16 +727,53 @@
             "additional_columns": {
               "type": "string"
             },
-            "index_columns": {"type": "array", "items": {"type": "string"}},
+            "index_columns": { "type": "array", "items": { "type": "string" } },
             "initial_columns": {
               "type": "array",
-              "items": {"type": "string"}
+              "items": { "type": "string" }
             }
           },
           "required": ["selectors", "columns"],
           "additionalProperties": false
         }
       }
+    },
+    "pathRule": {
+      "type": "object",
+      "properties": {
+        "level": { "enum": ["optional", "required"] },
+        "path": { "type": "string" }
+      },
+      "required": ["level", "path"],
+      "additionalProperties": false
+    },
+    "stemRule": {
+      "type": "object",
+      "properties": {
+        "level": { "enum": ["optional", "recommended", "required"] },
+        "stem": { "type": "string" },
+        "extensions": { "type": "array", "items": { "type": "string" } }
+      },
+      "required": ["level", "stem", "extensions"],
+      "additionalProperties": false
+    },
+    "suffixRule": {
+      "type": "object",
+      "properties": {
+        "level": { "enum": ["optional", "recommended", "required"] },
+        "datatypes": {
+          "type": "array",
+          "items": { "pattern": "^[a-z]+$" }
+        },
+        "suffixes": {
+          "type": "array",
+          "items": { "pattern": "^[a-zA-Z0-9]+$" }
+        },
+        "extensions": { "type": "array", "items": { "type": "string" } },
+        "entities": { "$ref": "#/definitions/entities" }
+      },
+      "required": ["suffixes", "extensions", "entities"],
+      "additionalProperties": false
     }
   }
 }

From 7ee24d16ae4e5df14b8f55186e418e038cba7fea Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 29 Apr 2024 21:11:22 +0000
Subject: [PATCH 06/74] [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: 24.4.0 → 24.4.2](https://github.com/psf/black/compare/24.4.0...24.4.2)
- [github.com/pre-commit/mirrors-mypy: v1.9.0 → v1.10.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.9.0...v1.10.0)
---
 .pre-commit-config.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b2f40321ca..8d032c6a49 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: 24.4.0
+    rev: 24.4.2
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -55,7 +55,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

From 3fd21ff095ecc9ac8e2b7bf092f5ee09e055e45b Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu, 16 May 2024 04:48:06 -0400
Subject: [PATCH 07/74] [MISC] Add shellcheck checks to ensure that those few
 shell scripts we have are "robust" (#1774)

* Add pre-commit definition for shellcheck

* Add "" for a variable use in a test_tag script

* Add github action to shellcheck master on push and PRs

* Skip shellcheck on ci for pre-commit -- needs docker
---
 .github/workflows/shellcheck.yml | 26 ++++++++++++++++++++++++++
 .pre-commit-config.yaml          |  6 ++++++
 scripts/test_tag                 |  2 +-
 3 files changed, 33 insertions(+), 1 deletion(-)
 create mode 100644 .github/workflows/shellcheck.yml

diff --git a/.github/workflows/shellcheck.yml b/.github/workflows/shellcheck.yml
new file mode 100644
index 0000000000..c4e38c1d1d
--- /dev/null
+++ b/.github/workflows/shellcheck.yml
@@ -0,0 +1,26 @@
+---
+name: Shellcheck
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  shellcheck:
+    name: Check shell scripts
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt update && sudo apt install -y shellcheck
+      - name: shellcheck
+        run: |
+          git grep -l '^#\( *shellcheck \|!\(/bin/\|/usr/bin/env \)\(sh\|bash\|dash\|ksh\)\)' | xargs shellcheck
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8d032c6a49..9812b4d133 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,5 +1,7 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
+ci:
+  skip: [shellcheck]
 exclude: 'tools/schemacode/bidsschematools/tests/data/broken_dataset_description.json'
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -71,3 +73,7 @@ repos:
           - types-jsonschema
         args: ["tools/schemacode/bidsschematools"]
         pass_filenames: false
+  - repo: https://github.com/koalaman/shellcheck-precommit
+    rev: v0.9.0
+    hooks:
+      - id: shellcheck
diff --git a/scripts/test_tag b/scripts/test_tag
index f11ef697dd..64e0ddd20f 100755
--- a/scripts/test_tag
+++ b/scripts/test_tag
@@ -9,7 +9,7 @@
 EPOCH="$(date +%s)"
 
 GIT_DIR=$( git rev-parse --git-dir )
-REPO_ROOT=$( ls -d ${GIT_DIR%.git} )
+REPO_ROOT=$( ls -d "${GIT_DIR%.git}" )
 
 VERSION_FILE="$REPO_ROOT/src/schema/SCHEMA_VERSION"
 

From 181c50e08fd143d481e22be9a15c31f612e6f906 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 21 May 2024 09:54:53 -0400
Subject: [PATCH 08/74] [pre-commit.ci] pre-commit autoupdate (#1829)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/koalaman/shellcheck-precommit: v0.9.0 → v0.10.0](https://github.com/koalaman/shellcheck-precommit/compare/v0.9.0...v0.10.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 9812b4d133..c074a6681e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -74,6 +74,6 @@ repos:
         args: ["tools/schemacode/bidsschematools"]
         pass_filenames: false
   - repo: https://github.com/koalaman/shellcheck-precommit
-    rev: v0.9.0
+    rev: v0.10.0
     hooks:
       - id: shellcheck

From 606c3fd7d0eca9d7d603c105d90bef9e329b78a2 Mon Sep 17 00:00:00 2001
From: Robert Smith <robert.smith@florey.edu.au>
Date: Wed, 22 May 2024 23:42:02 +1000
Subject: [PATCH 09/74] [ENH] Common Principles: Describe Inheritance Principle
 (#1807)

* Common Principles: Describe Inheritance Principle

* Inheritance Principle: Simplify wording

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>

* Update src/common-principles.md

---------

Co-authored-by: Yaroslav Halchenko <debian@onerussian.com>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/common-principles.md | 19 ++++++++++++++++++-
 1 file changed, 18 insertions(+), 1 deletion(-)

diff --git a/src/common-principles.md b/src/common-principles.md
index 3d9bc233af..08ef8e6a4f 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -658,6 +658,21 @@ for more information.
 
 ## The Inheritance Principle
 
+In some circumstances, there can be multiple data files for which
+all or a subset of the relevant metadata is precisely equivalent.
+Where this occurs,
+it may be preferable to define those metadata *only once*,
+and be placed on the filesystem in such a way that those files
+are deemed to be *applicable* to each relevant data file individually,
+but *not* be erroneously associated with other data files
+to which the metadata contained within are not applicable.
+The Inheritance Principle defines a systematized set of rules
+to determine which metadata files to associate with which data files.
+Further, because multiple metadata files may apply to an individual data file,
+the Principle defines the *order of precedence* of such metadata files contents.
+
+### Rules
+
 1.  Any metadata file (such as `.json`, `.bvec` or `.tsv`) MAY be defined at any directory level.
 
 1.  For a given data file, any metadata file is applicable to that data file if:
@@ -687,7 +702,7 @@ for more information.
         same key present in another metadata file at a lower level
         (though it is RECOMMENDED to minimize the extent of such overrides).
 
-Corollaries:
+### Corollaries
 
 1.  As per rule 3, metadata files applicable only to a specific participant / session
     MUST be defined in or below the directory corresponding to that participant / session;
@@ -704,6 +719,8 @@ Corollaries:
     a key-value in a later file does not imply the "unsetting" of that field
     (indeed removal of existing fields is not possible).
 
+### Examples
+
 Example 1: Demonstration of inheritance principle
 
 <!-- This block generates a file tree.

From a0e8c31654cf3e1074fe832f6b12fd74874a19c6 Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Wed, 22 May 2024 09:44:25 -0400
Subject: [PATCH 10/74] [ENH] Add use of session entity as example of encoding
 multi-site studies in a single dataset (#1803)

* Fix syntax (add closing ')') + point to specific issue for multi-site

* Add additional way (session-level) for multi-site studies

Reflecting up on discussion within https://github.com/bids-standard/bids-2-devel/issues/11

---------

Co-authored-by: Taylor Salo <salot@pennmedicine.upenn.edu>
---
 src/longitudinal-and-multi-site-studies.md | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/src/longitudinal-and-multi-site-studies.md b/src/longitudinal-and-multi-site-studies.md
index bf9cb92eec..b64ae016e8 100644
--- a/src/longitudinal-and-multi-site-studies.md
+++ b/src/longitudinal-and-multi-site-studies.md
@@ -80,7 +80,7 @@ for practical guidance when curating a new longitudinal dataset.
 
 This version of the BIDS specification does not explicitly cover studies with
 data coming from multiple sites or multiple centers (such extension is planned
-in [BIDS `2.0`](https://github.com/bids-standard/bids-2-devel).
+in [BIDS `2.0`](https://github.com/bids-standard/bids-2-devel/issues/11)).
 There are however ways to model your data without any loss in terms of metadata.
 
 ### Option 1: Treat each site/center as a separate dataset
@@ -92,11 +92,21 @@ Apps and everything should just work.
 
 ### Option 2: Combining sites/centers into one dataset
 
-Alternatively you can combine data from all sites into one dataset. To identify
-which site each subjects comes from you can add a `site` column in the
+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
 `participants.tsv` file indicating the source site. This solution allows you to
-analyze all of the subjects together in one dataset. One caveat is that subjects
+analyze all subjects together in one dataset. One caveat is that subjects
 from all sites will have to have unique labels. To enforce that and improve
 readability you can use a subject label prefix identifying the site. For example
 `sub-NUY001`, `sub-MIT002`, `sub-MPG002` and so on. Remember that hyphens and
 underscores are not allowed in subject labels.
+
+#### Option 2.b: Use different sessions for different sites
+
+In case of studies such as "Traveling Human Phantom" it is possible to incorporate site within session label.
+For example `sub-human1/ses-NUY`, `sub-human1/ses-MIT`, `sub-phantom1/ses-NUY`, `sub-phantom1/ses-MIT` and so on.

From 1d929e587775fa09489f95c94ffc0470b76020eb Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Wed, 22 May 2024 13:13:17 -0400
Subject: [PATCH 11/74] [ENH] Specify the naming of scanner-generated TRACE and
 ADC volumes (#1725)

* feat(schema): Define ADC/TRACE suffixes

* feat(schema): Add isotropic DWI volumes

* feat(spec): Specify the naming of scanner-generated TRACE and ADC volumes

* feat(schema): Add derivative rule for TRACE/ADC

* clarity: Split raw and scanner-derivative suffix tables

* Update wording to avoid confusion about "derivatives"
---
 .../magnetic-resonance-imaging-data.md        | 26 ++++++++++++++-----
 src/schema/objects/suffixes.yaml              | 10 +++++++
 src/schema/rules/files/deriv/imaging.yaml     |  9 +++++++
 src/schema/rules/files/raw/dwi.yaml           | 20 ++++++++++++++
 4 files changed, 58 insertions(+), 7 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 9a17c36686..6396aa0e8c 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -656,13 +656,18 @@ The definitions of these fields can be found in
 and a guide for using macros can be found at
  https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
 -->
-{{ MACROS___make_suffix_table(
-      [
-         "dwi",
-         "sbref",
-      ]
-   )
-}}
+{{ MACROS___make_suffix_table(["dwi", "sbref"]) }}
+
+Additionally, the following suffixes are used for scanner-generated images:
+
+<!--
+This block generates a suffix table.
+The definitions of these fields can be found in
+  src/schema/rules/files/raw
+and a guide for using macros can be found at
+ https://github.com/bids-standard/bids-specification/blob/master/macros_doc.md
+-->
+{{ MACROS___make_suffix_table(["ADC", "TRACE"]) }}
 
 <!--
 This block generates a filename templates.
@@ -691,6 +696,13 @@ In such a case, two files could have the following names:
 The user is free to choose any other label than `singleband` and
 `multiband`, as long as they are consistent across subjects and sessions.
 
+Scanner-generated TRACE and ADC volumes MAY be included using the
+`TRACE` and `ADC` suffixes.
+If TRACE or ADC volume filenames match a diffusion series with all applicable entities,
+such volumes SHOULD be computed from that series.
+Otherwise, some entity, such as [`acq-<label>`](../appendices/entities.md#acq),
+SHOULD be used to indicate that the files are unrelated.
+
 ### REQUIRED gradient orientation information
 
 The REQUIRED gradient orientation information corresponding to a DWI acquisition
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 06bceb83de..5f57b28ba8 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -6,6 +6,11 @@ TwoPE:
   display_name: 2-photon excitation microscopy
   description: |
     2-photon excitation microscopy imaging data
+ADC:
+  value: ADC
+  display_name: Apparent diffusion coefficient (ADC)
+  description:
+    Apparent diffusion coefficient (ADC) map
 BF:
   value: BF
   display_name: Bright-field microscopy
@@ -460,6 +465,11 @@ TEM:
   display_name: Transmission electron microscopy
   description: |
     Transmission electron microscopy imaging data
+TRACE:
+  value: TRACE
+  display_name: Trace diffusion weighted image
+  description: |
+    Diffusion images proportional to the trace of the diffusion tensor
 UNIT1:
   value: UNIT1
   display_name: Homogeneous (flat) T1-weighted MP2RAGE image
diff --git a/src/schema/rules/files/deriv/imaging.yaml b/src/schema/rules/files/deriv/imaging.yaml
index e037dcc10c..c9a0e12877 100644
--- a/src/schema/rules/files/deriv/imaging.yaml
+++ b/src/schema/rules/files/deriv/imaging.yaml
@@ -26,6 +26,15 @@ dwi_volumetric:
     density: optional
     description: optional
 
+dwi_isotropic:
+  $ref: rules.files.raw.dwi.isotropic
+  entities:
+    $ref: rules.files.raw.dwi.isotropic.entities
+    space: optional
+    resolution: optional
+    density: optional
+    description: optional
+
 func_volumetric:
   $ref: rules.files.raw.func.func
   entities:
diff --git a/src/schema/rules/files/raw/dwi.yaml b/src/schema/rules/files/raw/dwi.yaml
index 22b224b023..ff18501af9 100644
--- a/src/schema/rules/files/raw/dwi.yaml
+++ b/src/schema/rules/files/raw/dwi.yaml
@@ -38,3 +38,23 @@ sbref:
     run: optional
     part: optional
     chunk: optional
+
+# Common scanner-generated derivatives need raw names
+isotropic:
+  suffixes:
+    - ADC
+    - TRACE
+  extensions:
+    - .nii.gz
+    - .nii
+    - .json
+  datatypes:
+    - dwi
+  entities:
+    subject: required
+    session: optional
+    acquisition: optional
+    reconstruction: optional
+    direction: optional
+    run: optional
+    chunk: optional

From 2246cd82edac088f294ee52c45b1a6f3a9f694b5 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 23 May 2024 11:06:57 -0400
Subject: [PATCH 12/74] SCHEMA: Add file rule for phenotype tables (#1672)

* TEST: Add example to test phenotypic data

* SCHEMA: Add file rule for phenotype

* ENH: Update stem rule to accept datatypes, glob stems

* TEST: Update expected regexes for stem rules

* TEST: Make phenotype an exception for now

* feat(metaschema): Allow datatypes in stem rules

* feat(regex): Capture paths and stems, and match string ends
---
 src/metaschema.json                           |  4 +++
 src/schema/rules/files/common/tables.yaml     | 13 ++++++++++
 tools/schemacode/bidsschematools/conftest.py  |  1 +
 .../bidsschematools/data/tests/test_rules.py  |  5 ++++
 tools/schemacode/bidsschematools/rules.py     | 20 ++++++++++----
 .../bidsschematools/tests/test_rules.py       | 26 ++++++++++++++-----
 6 files changed, 58 insertions(+), 11 deletions(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index a3e500dad7..5d01c8862f 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -751,6 +751,10 @@
       "type": "object",
       "properties": {
         "level": { "enum": ["optional", "recommended", "required"] },
+        "datatypes": {
+          "type": "array",
+          "items": { "pattern": "^[a-z]+$" }
+        },
         "stem": { "type": "string" },
         "extensions": { "type": "array", "items": { "type": "string" } }
       },
diff --git a/src/schema/rules/files/common/tables.yaml b/src/schema/rules/files/common/tables.yaml
index 5a304dbfd7..21f03f6579 100644
--- a/src/schema/rules/files/common/tables.yaml
+++ b/src/schema/rules/files/common/tables.yaml
@@ -30,3 +30,16 @@ sessions: # This file may only exist if session is present in the dataset.
     - .json
   entities:
     subject: required
+
+# Phenotype is a special case where there are no applicable entities, but a
+# parent directory is specified. This most closely matches datatype in the current
+# structure. We also require a stem that can match any value, as there are no
+# constraints on the filename except extension.
+phenotype:
+  level: optional
+  datatypes:
+    - phenotype
+  stem: '*'
+  extensions:
+    - .tsv
+    - .json
diff --git a/tools/schemacode/bidsschematools/conftest.py b/tools/schemacode/bidsschematools/conftest.py
index 3154e3e5cf..2e5eaec86f 100644
--- a/tools/schemacode/bidsschematools/conftest.py
+++ b/tools/schemacode/bidsschematools/conftest.py
@@ -25,6 +25,7 @@
     "qmri_tb1tfl",  # fmap, _TB1TFL
     "qmri_vfa",  # derivatives
     "ds000248",  # .bidsignore
+    "fnirs_automaticity",  # phenotypic
 ]
 # Errors are described in the README of the respective datasets:
 # https://github.com/bids-standard/bids-error-examples
diff --git a/tools/schemacode/bidsschematools/data/tests/test_rules.py b/tools/schemacode/bidsschematools/data/tests/test_rules.py
index 6c46a5da5d..39fce83a3a 100644
--- a/tools/schemacode/bidsschematools/data/tests/test_rules.py
+++ b/tools/schemacode/bidsschematools/data/tests/test_rules.py
@@ -87,6 +87,11 @@ def test_rule_objects(schema_obj):
 
                 # Build a list of items mentioned in rules, but not found in objects.
                 if use not in object_values:
+                    if (use, object_type) == ("phenotype", "datatypes"):
+                        # Special case: phenotype is a top-level directory
+                        # that acts like a datatype, but we don't want to
+                        # define it that way in the glossary, currently.
+                        continue
                     temp_path = path[:]
                     if is_list:
                         temp_path[-1] += f"[{i_use}]"
diff --git a/tools/schemacode/bidsschematools/rules.py b/tools/schemacode/bidsschematools/rules.py
index 22e1fce649..6004b0363b 100644
--- a/tools/schemacode/bidsschematools/rules.py
+++ b/tools/schemacode/bidsschematools/rules.py
@@ -4,6 +4,7 @@
 ``schema.rules.files``.
 """
 
+import fnmatch
 import re
 import typing as ty
 from collections.abc import Mapping
@@ -125,7 +126,7 @@ def _entity_rule(rule: Mapping, schema: bst.types.Namespace):
     ext_regex = f"(?P<extension>{ext_match})"
 
     return {
-        "regex": "".join(dir_regex + entity_regex + [suffix_regex, ext_regex]),
+        "regex": "".join(dir_regex + entity_regex + [suffix_regex, ext_regex, r"\Z"]),
         "mandatory": False,
     }
 
@@ -170,15 +171,24 @@ def _sanitize_extension(ext: str) -> str:
 
 
 def _stem_rule(rule: bst.types.Namespace):
-    stem_regex = re.escape(rule.stem)
+    # translate includes a trailing \Z (end of string) but we expect extensions
+    stem_match = fnmatch.translate(rule.stem)[:-2]
+    stem_regex = f"(?P<stem>{stem_match})"
+
+    dtypes = set(rule.get("datatypes", ()))
+    dir_regex = f"(?P<datatype>{'|'.join(dtypes)})/" if dtypes else ""
+
     ext_match = "|".join(_sanitize_extension(ext) for ext in rule.extensions)
-    ext_regex = f"(?P<extension>{ext_match})"
+    ext_regex = rf"(?P<extension>{ext_match})\Z"
 
-    return {"regex": stem_regex + ext_regex, "mandatory": rule.level == "required"}
+    return {"regex": dir_regex + stem_regex + ext_regex, "mandatory": rule.level == "required"}
 
 
 def _path_rule(rule: bst.types.Namespace):
-    return {"regex": re.escape(rule.path), "mandatory": rule.level == "required"}
+    path_match = re.escape(rule.path)
+    # Exact path matches may be files or opaque directories
+    # Consider using rules.directories to identify opaque directories
+    return {"regex": rf"(?P<path>{path_match})(?:/.*)?\Z", "mandatory": rule.level == "required"}
 
 
 def regexify_filename_rules(
diff --git a/tools/schemacode/bidsschematools/tests/test_rules.py b/tools/schemacode/bidsschematools/tests/test_rules.py
index 693c4b24fe..35b167e199 100644
--- a/tools/schemacode/bidsschematools/tests/test_rules.py
+++ b/tools/schemacode/bidsschematools/tests/test_rules.py
@@ -21,7 +21,7 @@ def test_entity_rule(schema_obj):
             r"sub-(?P=subject)_"
             r"(?:ses-(?P=session)_)?"
             r"(?P<suffix>T1w)"
-            r"(?P<extension>\.nii)"
+            r"(?P<extension>\.nii)\Z"
         ),
         "mandatory": False,
     }
@@ -43,7 +43,7 @@ def test_entity_rule(schema_obj):
             r"(?:sub-(?P=subject)_)?"
             r"(?:ses-(?P=session)_)?"
             r"(?P<suffix>T1w)"
-            r"(?P<extension>\.json)"
+            r"(?P<extension>\.json)\Z"
         ),
         "mandatory": False,
     }
@@ -84,7 +84,7 @@ def test_split_inheritance_rules():
 def test_stem_rule():
     rule = Namespace.build({"stem": "README", "level": "required", "extensions": ["", ".md"]})
     assert rules._stem_rule(rule) == {
-        "regex": r"README(?P<extension>|\.md)",
+        "regex": r"(?P<stem>(?s:README))(?P<extension>|\.md)\Z",
         "mandatory": True,
     }
 
@@ -92,7 +92,21 @@ def test_stem_rule():
         {"stem": "participants", "level": "optional", "extensions": [".tsv", ".json"]}
     )
     assert rules._stem_rule(rule) == {
-        "regex": r"participants(?P<extension>\.tsv|\.json)",
+        "regex": r"(?P<stem>(?s:participants))(?P<extension>\.tsv|\.json)\Z",
+        "mandatory": False,
+    }
+
+    # Wildcard stem, with datatype
+    rule = Namespace.build(
+        {
+            "stem": "*",
+            "datatypes": ["phenotype"],
+            "level": "optional",
+            "extensions": [".tsv", ".json"],
+        }
+    )
+    assert rules._stem_rule(rule) == {
+        "regex": r"(?P<datatype>phenotype)/(?P<stem>(?s:.*))(?P<extension>\.tsv|\.json)\Z",
         "mandatory": False,
     }
 
@@ -100,12 +114,12 @@ def test_stem_rule():
 def test_path_rule():
     rule = Namespace.build({"path": "dataset_description.json", "level": "required"})
     assert rules._path_rule(rule) == {
-        "regex": r"dataset_description\.json",
+        "regex": r"(?P<path>dataset_description\.json)(?:/.*)?\Z",
         "mandatory": True,
     }
 
     rule = Namespace.build({"path": "LICENSE", "level": "optional"})
-    assert rules._path_rule(rule) == {"regex": "LICENSE", "mandatory": False}
+    assert rules._path_rule(rule) == {"regex": r"(?P<path>LICENSE)(?:/.*)?\Z", "mandatory": False}
 
 
 def test_regexify_all():

From 6b7141ecd215e6ba67ca6e88a5f5043d1ee9cdb3 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 23 May 2024 15:17:08 -0400
Subject: [PATCH 13/74] rel(schema): 0.9.0

---
 src/schema/SCHEMA_VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index b1e9d95105..ac39a106c4 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.8.2-dev
+0.9.0

From 71d679dbd1ce874376adcec91a6fbd3ed605a880 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 23 May 2024 15:18:38 -0400
Subject: [PATCH 14/74] chore(schema-version): 0.9.1-dev

---
 src/schema/SCHEMA_VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index ac39a106c4..dc9bff91aa 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.9.0
+0.9.1-dev

From 2d7cfd0f20d4d0c422fcb62b8fc66cdb42a3ce90 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 23 May 2024 15:37:27 -0400
Subject: [PATCH 15/74] chore(schemacode-ci): Fix installation to not replicate
 test dependency list

---
 .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 6cf4dbcd4c..0b92cd9a4d 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -33,7 +33,7 @@ jobs:
       - name: "Install build dependencies"
         run: pip install --upgrade build twine
       - name: "Install test dependencies on tag"
-        run: pip install --upgrade pytest pyyaml pandas tabulate markdown-it-py pyparsing
+        run: pip install --upgrade tools/schemacode[test]
         if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
       - name: "Build archive on tag"
         run: pytest tools/schemacode/bidsschematools -k make_archive

From 9629ab0c65ac9f56828bf7519f1c78c6d6590451 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 23 May 2024 22:41:36 +0200
Subject: [PATCH 16/74] Update circleci docker image

as per: https://support.circleci.com/hc/en-us/articles/23614965074459-2024-Image-Deprecations-and-Brownouts-Android-Linux-VM-Remote-Docker-Linux-VM

see: https://discuss.circleci.com/t/remote-docker-image-deprecations-and-eol-for-2024/50176
---
 .circleci/config.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.circleci/config.yml b/.circleci/config.yml
index ee82d5b003..676383d1f1 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -174,8 +174,7 @@ jobs:
     docker:
       - image: cimg/base:stable
     steps:
-      - setup_remote_docker:
-          version: 17.11.0-ce
+      - setup_remote_docker
       # checkout code to default ~/project
       - checkout
       - attach_workspace:

From 40af25c0ed7ead0f67391286b2e81e7e1a68aefa Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 23 May 2024 20:00:13 -0400
Subject: [PATCH 17/74] fix(schema): Check paths with initial slashes (#1833)

---
 src/schema/rules/checks/dataset.yaml               | 14 +++++++-------
 src/schema/rules/checks/general.yaml               |  2 +-
 .../rules/tabular_data/modality_agnostic.yaml      |  4 ++--
 3 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/src/schema/rules/checks/dataset.yaml b/src/schema/rules/checks/dataset.yaml
index b0f0aba634..a569bc1f97 100644
--- a/src/schema/rules/checks/dataset.yaml
+++ b/src/schema/rules/checks/dataset.yaml
@@ -9,7 +9,7 @@ SubjectFolders:
       There are no subject directories (labeled "sub-*") in the root of this dataset.
     level: error
   selectors:
-    - path == 'dataset_description.json'
+    - path == '/dataset_description.json'
   checks:
     - length(dataset.subjects.sub_dirs) > 0
 
@@ -22,7 +22,7 @@ ParticipantIDMismtach:
       found in the participants.tsv file.
     level: error
   selectors:
-    - path == 'participants.tsv'
+    - path == '/participants.tsv'
   checks:
     - sorted(columns.participant_label) == sorted(dataset.subjects.sub_dirs)
 
@@ -34,7 +34,7 @@ PhenotypeSubjectsMissing:
       A phenotype/ .tsv file lists subjects that were not found in the dataset.
     level: error
   selectors:
-    - path == 'dataset_description.json'
+    - path == '/dataset_description.json'
   checks:
     - sorted(dataset.subjects.phenotype) == sorted(dataset.subjects.sub_dirs)
 
@@ -47,7 +47,7 @@ SamplesTSVMissing:
       See 'Modality agnostic files' section of the BIDS specification.
     level: error
   selectors:
-    - path == 'dataset_description.json'
+    - path == '/dataset_description.json'
     - '"micr" in dataset.modalities'
   checks:
     - "'samples.tsv' in dataset.files"
@@ -60,7 +60,7 @@ UnknownVersion:
       The BIDS Schema used for validation may be out of date.
     level: warning
   selectors:
-    - path == 'dataset_description.json'
+    - path == '/dataset_description.json'
   checks:
     - intersects([json.BIDSVersion], schema.meta.versions)
 
@@ -72,7 +72,7 @@ SingleSourceAuthors:
       'CITATION.cff' file found. The "Authors" field of 'dataset_description.json'
       must be removed to avoid inconsistency.
   selectors:
-    - path == 'CITATION.cff'
+    - path == '/CITATION.cff'
   checks:
     - '!("Authors" in dataset.dataset_description)'
 
@@ -85,7 +85,7 @@ SingleSourceCitationFields:
       The "HowToAckowledge", "License", and "ReferencesAndLinks" fields of
       'dataset_description.json' should be removed to avoid inconsistency.
   selectors:
-    - path == 'CITATION.cff'
+    - path == '/CITATION.cff'
   checks:
     - '!("HowToAcknowledge" in dataset.dataset_description)'
     - '!("License" in dataset.dataset_description)'
diff --git a/src/schema/rules/checks/general.yaml b/src/schema/rules/checks/general.yaml
index b0505250b3..3c03bac91d 100644
--- a/src/schema/rules/checks/general.yaml
+++ b/src/schema/rules/checks/general.yaml
@@ -20,6 +20,6 @@ ReadmeFileSmall:
       Please consider expanding it with additional information about the dataset.
     level: warning
   selectors:
-    - match(path, '^README')
+    - match(path, '^/README')
   checks:
     - size > 150
diff --git a/src/schema/rules/tabular_data/modality_agnostic.yaml b/src/schema/rules/tabular_data/modality_agnostic.yaml
index f33f2b597d..fcaa4b32d4 100644
--- a/src/schema/rules/tabular_data/modality_agnostic.yaml
+++ b/src/schema/rules/tabular_data/modality_agnostic.yaml
@@ -1,7 +1,7 @@
 ---
 Participants:
   selectors:
-    - path == "participants.tsv"
+    - path == "/participants.tsv"
   initial_columns:
     - participant_id
   columns:
@@ -20,7 +20,7 @@ Participants:
 
 Samples:
   selectors:
-    - path == "samples.tsv"
+    - path == "/samples.tsv"
   columns:
     sample_id: required
     participant_id: required

From f91e6514baf54442ee41a7ca8681d58b9714a1e0 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 24 May 2024 10:40:41 -0400
Subject: [PATCH 18/74] feat(schema): Add allequal(x: array, y: array) to
 expression language (#1837)

---
 src/schema/README.md                  | 4 ++++
 src/schema/meta/expression_tests.yaml | 6 ++++++
 src/schema/rules/checks/dataset.yaml  | 7 ++++---
 src/schema/rules/checks/events.yaml   | 2 +-
 src/schema/rules/checks/mri.yaml      | 4 ++--
 5 files changed, 17 insertions(+), 6 deletions(-)

diff --git a/src/schema/README.md b/src/schema/README.md
index e8cb197757..5f1abb4595 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -265,6 +265,7 @@ The following functions should be defined by an interpreter:
 | `exists(arg: str \| array, rule: str) -> int`   | Count of files in an array that exist in the dataset. String is array with length 1. Rules include `"bids-uri"`, `"dataset"`, `"subject"` and `"stimuli"`. | `exists(sidecar.IntendedFor, "subject")`               | True if all files in `IntendedFor` exist, relative to the subject directory.   |
 | `index(arg: array, val: any)`                   | Index of first element in an array equal to `val`, `null` if not found                                                                                     | `index(["i", "j", "k"], axis)`                         | The number, from 0-2 corresponding to the string `axis`                        |
 | `intersects(a: array, b: array) -> bool`        | `true` if arguments contain any shared elements                                                                                                            | `intersects(dataset.modalities, ["pet", "mri"])`       | True if either PET or MRI data is found in dataset                             |
+| `allequal(a: array, b: array) -> bool`          | `true` if arrays have the same length and paired elements are equal                                                                                        | `intersects(dataset.modalities, ["pet", "mri"])`       | True if either PET or MRI data is found in dataset                             |
 | `length(arg: array) -> int`                     | Number of elements in an array                                                                                                                             | `length(columns.onset) > 0`                            | True if there is at least one value in the onset column                        |
 | `match(arg: str, pattern: str) -> bool`         | `true` if `arg` matches the regular expression `pattern` (anywhere in string)                                                                              | `match(extension, ".gz$")`                             | True if the file extension ends with `.gz`                                     |
 | `max(arg: array) -> number`                     | The largest non-`n/a` value in an array                                                                                                                    | `max(columns.onset)`                                   | The time of the last onset in an events.tsv file                               |
@@ -294,6 +295,9 @@ Most operations involving `null` simply resolve to `null`:
 | `null / 1`                 | `null` |
 | `match(null, pattern)`     | `null` |
 | `intersects(list, null)`   | `null` |
+| `intersects(null, list)`   | `null` |
+| `allequal(list, null)`     | `null` |
+| `allequal(null, list)`     | `null` |
 | `substr(null, 0, 1)`       | `null` |
 | `substr(str, null, 1)`     | `null` |
 | `substr(str, 0, null)`     | `null` |
diff --git a/src/schema/meta/expression_tests.yaml b/src/schema/meta/expression_tests.yaml
index e1f06fdedc..5ebb7dcec0 100644
--- a/src/schema/meta/expression_tests.yaml
+++ b/src/schema/meta/expression_tests.yaml
@@ -26,6 +26,10 @@
   result: false
 - expression: intersects(null, [])
   result: false
+- expression: allequal([], null)
+  result: false
+- expression: allequal(null, [])
+  result: false
 - expression: match(null, 'pattern')
   result: null
 - expression: match('string', null)
@@ -106,6 +110,8 @@
   result: null
 - expression: sorted([3, 2, 1])
   result: [1, 2, 3]
+- expression: allequal(sorted([3, 2, 1]), [1, 2, 3])
+  result: true
 - expression: min([-1, "n/a", 1])
   result: -1
 - expression: max([-1, "n/a", 1])
diff --git a/src/schema/rules/checks/dataset.yaml b/src/schema/rules/checks/dataset.yaml
index a569bc1f97..91704d32e4 100644
--- a/src/schema/rules/checks/dataset.yaml
+++ b/src/schema/rules/checks/dataset.yaml
@@ -14,7 +14,7 @@ SubjectFolders:
     - length(dataset.subjects.sub_dirs) > 0
 
 # 49
-ParticipantIDMismtach:
+ParticipantIDMismatch:
   issue:
     code: PARTICIPANT_ID_MISMATCH
     message: |
@@ -24,7 +24,7 @@ ParticipantIDMismtach:
   selectors:
     - path == '/participants.tsv'
   checks:
-    - sorted(columns.participant_label) == sorted(dataset.subjects.sub_dirs)
+    - allequal(sorted(columns.participant_id), sorted(dataset.subjects.sub_dirs))
 
 # 51
 PhenotypeSubjectsMissing:
@@ -35,8 +35,9 @@ PhenotypeSubjectsMissing:
     level: error
   selectors:
     - path == '/dataset_description.json'
+    - type(dataset.subjects.phenotype) != 'null'
   checks:
-    - sorted(dataset.subjects.phenotype) == sorted(dataset.subjects.sub_dirs)
+    - allequal(sorted(dataset.subjects.phenotype), sorted(dataset.subjects.sub_dirs))
 
 # 214
 SamplesTSVMissing:
diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index 1d6c52584c..234b9d078d 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -39,4 +39,4 @@ SortedOnsets:
     - extension == ".tsv"
   checks:
     # n/a values will likely cause false alarms if encountered. Consider alternatives.
-    - sorted(columns.onset) == columns.onset
+    - allequal(sorted(columns.onset), columns.onset)
diff --git a/src/schema/rules/checks/mri.yaml b/src/schema/rules/checks/mri.yaml
index 8837f5faa9..e2efc0216d 100644
--- a/src/schema/rules/checks/mri.yaml
+++ b/src/schema/rules/checks/mri.yaml
@@ -98,7 +98,7 @@ VolumeTimingNotMonotonicallyIncreasing:
     - modality == "mri"
     - sidecar.VolumeTiming != null
   checks:
-    - sorted(sidecar.VolumeTiming) == sidecar.VolumeTiming
+    - allequal(sorted(sidecar.VolumeTiming), sidecar.VolumeTiming)
 
 # 192
 BolusCutOffDelayTimeNotMonotonicallyIncreasing:
@@ -111,7 +111,7 @@ BolusCutOffDelayTimeNotMonotonicallyIncreasing:
     - modality == "mri"
     - sidecar.BolusCutoffDelayTime != null
   checks:
-    - sorted(sidecar.BolusCutoffDelayTime) == sidecar.BolusCutoffDelayTime
+    - allequal(sorted(sidecar.BolusCutoffDelayTime), sidecar.BolusCutoffDelayTime)
 
 # 201
 RepetitionTimePreparationNotConsistent:

From ed53091940dfea2535306a0672b5c619de8fc49e Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Fri, 24 May 2024 23:59:45 -0400
Subject: [PATCH 19/74] update PR template to include BEP header (#1797)

---
 .github/pull_request_template.md | 57 +++++++++++++++++++++++---------
 1 file changed, 41 insertions(+), 16 deletions(-)

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
index fa9d6566cf..b6be304f5b 100644
--- a/.github/pull_request_template.md
+++ b/.github/pull_request_template.md
@@ -2,27 +2,52 @@
 
 See the [CONTRIBUTING](https://github.com/bids-standard/bids-specification/blob/master/CONTRIBUTING.md) guide. Specifically:
 
-- Please keep the title of your Pull Request (PR) short but informative - it will
-  appear in the changelog.
+- Please keep the title of your Pull Request (PR) short but informative - it will appear in the changelog.
 - If you do **not** want a PR to appear in the changelog, it must receive the `exclude-from-changelog` label.
-- Please ensure your name is credited on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
-  To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors) and add your name with the type of contribution.
+
+- Please ensure your name is credited
+  on our [Contributors appendix](https://github.com/bids-standard/bids-specification/blob/master/src/appendices/contributors.md).
+  To add your name, please edit our [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Contributors)
+  and add your name with the type of contribution.
   For assistance, please tag @bids-standard/maintainers.
+
 - Use one of the following prefixes in the title of your PR:
-  - `[ENH]` - enhancement of the specification that adds a new feature or
-    support for a new data type
+  - `[ENH]` - enhancement of the specification that adds a new feature or support for a new data type
   - `[FIX]` - fix of a typo or language clarification
-  - `[INFRA]` - changes to the infrastructure automating the specification
-    release (for example building HTML docs)
+  - `[INFRA]` - changes to the infrastructure automating the specification release (for example building HTML docs)
   - `[SCHEMA]` - changes to the BIDS schema and/or related code
-  - `[MISC]` - everything else including changes to the file listing
-    contributors
-- If you are opening a PR to obtain early feedback, but the changes
-  are not ready to be merged (also known as a "Work in Progress" PR), please
-  use a [Draft PR](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
-- After opening the PR, our continuous integration services will automatically check your contribution  for formatting errors and render a preview of the BIDS specification with your changes.
+  - `[MISC]` - everything else including changes to the file listing contributors
+
+- If you are opening a PR to obtain early feedback,
+  but the changes are not ready to be merged (also known as a "Work in Progress" PR),
+  please use a [Draft PR](https://github.blog/2019-02-14-introducing-draft-pull-requests/).
+
+- After opening the PR, our continuous integration services will automatically check your contribution
+  for formatting errors and render a preview of the BIDS specification with your changes.
   To see the checks and preview, scroll down and click on the `show all checks` link.
-  From the list, select the `Details` link of the `ci/circleci: build_docs artifact` check to see the preview of the BIDS specification.
-- If you are updating the schema *and* you need to subsequently make changes to the bidsschematools code (validation, tests, rendering), this means your PR probably introduces a compatibility breaking change and you should increment the minor version (the second number) in `bids-specification/src/schema/SCHEMA_VERSION`.
+  From the list:
+    - select the `Details` link of the `docs/readthedocs.org:bids-specification` check to see the HTML preview of the BIDS specification.
+    - select the `Details` link of the `Check the rendered PDF version here! ` check to see the PDF preview of the BIDS specification.
+
+- If you are updating the schema *and* you need to subsequently make changes to the bidsschematools code (validation, tests, rendering),
+  this means your PR probably introduces a compatibility breaking change
+  and you should increment the minor version (the second number) in `bids-specification/src/schema/SCHEMA_VERSION`.
+
+- If you are opening a PR for a BIDS extension proposal (BEP),
+  make sure that your top message contains the following notes
+
+> [!Note]
+>
+> **We meet regularly to discuss this BEP**
+>
+> Next meeting: **insert date** on **URL to join**
+>
+> Communication channel on github repo / matrix / slack / discord : **insert URL to join**
+>
+
+> [!Tip]
+>
+> [**HTML preview of this BEP**](insert URL to HTML preview once available)
+>
 
 --- PLEASE READ AND DELETE THE TEXT ABOVE BEFORE OPENING THE PULL REQUEST ---

From 6d1df39346e41df40308bcc7a6a5c0775a7a1b61 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 27 May 2024 20:44:59 +0000
Subject: [PATCH 20/74] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/codespell-project/codespell: v2.2.6 → v2.3.0](https://github.com/codespell-project/codespell/compare/v2.2.6...v2.3.0)
---
 .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 c074a6681e..d6b5c19929 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -52,7 +52,7 @@ repos:
         args: [-f=standard, -c=.yamllint.yml]
         files: src/schema/.*/.*\.yaml
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.6
+    rev: v2.3.0
     hooks:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]

From 898ea86ec6445dca14766d177b5f1029b5d37f57 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 30 May 2024 17:31:30 -0400
Subject: [PATCH 21/74] feat(schema): Add schema check for README file (#1841)

---
 src/schema/rules/checks/hints.yaml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/src/schema/rules/checks/hints.yaml b/src/schema/rules/checks/hints.yaml
index 7c733d8d51..55b63c4784 100644
--- a/src/schema/rules/checks/hints.yaml
+++ b/src/schema/rules/checks/hints.yaml
@@ -4,6 +4,21 @@
 
 ### Dataset level
 
+# 101
+# This check should probably be replaced by making sure rules.files.common.core.README is
+# hit, but this is the short path forward.
+ReadmeFileMissing:
+  issue:
+    code: README_FILE_MISSING
+    message: |
+      The recommended file /README is missing.
+      See Section 03 (Modality agnostic files) of the BIDS specification.
+    level: warning
+  selectors:
+    - path == '/dataset_description.json'
+  checks:
+    - exists(["/README", "/README.txt", "/README.md", "/README.rst"], "dataset") > 0
+
 # 102
 TooFewAuthors:
   issue:

From 0f4f0b3dd5a9156db1b85a886563acd9d36f42df Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Fri, 31 May 2024 17:17:42 +0200
Subject: [PATCH 22/74] reduce hours stefan, clarify lead maintainer (#1843)

---
 DECISION-MAKING.md | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index a29b4b8632..af1547a3b9 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -21,25 +21,28 @@ Current and past members of the steering group can be found
 
 | Name                                                                      | Time commitment | Scope                                 | Joined   |
 |---------------------------------------------------------------------------|-----------------|---------------------------------------|----------|
-| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff))           | 5h/week         | Lead Maintainer                       | Mar 2020 |
+| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff))           | 1h/week         |                                       | Mar 2020 |
 | Chris Markiewicz ([@effigies](https://github.com/effigies))               | 5h/week         |                                       | Mar 2020 |
 | Ross Blair ([@rwblair](https://github.com/rwblair))                       |                 | Maintainer of the bids-validator      | Mar 2020 |
 | Taylor Salo ([@tsalo](https://github.com/tsalo))                          | 3h/week         | MRI                                   | Sep 2020 |
 | Remi Gau ([@Remi-Gau](https://github.com/Remi-Gau))                       | 3h/week         | Community development, MRI            | Oct 2020 |
 | Anthony Galassi  ([@bendhouseart](https://github.com/bendhouseart))       | 3h/week         | PET, Community development            | Sep 2021 |
 | Eric Earl ([@ericearl](https://github.com/ericearl))                      | 2h/week         |                                       | Dec 2021 |
-| Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/mo           | Interoperability, EEG and multi-modal | Apr 2023 |
+| Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/month        | Interoperability, EEG and multi-modal | Apr 2023 |
 | Nell Hardcastle ([@nellh](https://github.com/nellh))                      | 2h/week         |                                       | Jul 2023 |
-| Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay))                      | 1h/week         |                                       | Nov 2022 |
+| Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay))           | 1h/week         |                                       | Nov 2022 |
 
 In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
 classification of a maintainer, maintainers may declare a limited scope of responsibility.
 Such a scope can range from maintaining a modality supported in the specification to nurturing a
 welcoming BIDS community.
-One or more scopes can be chosen by the maintainer and agreed upon by the Maintainers Group.
+Any number of scopes can be chosen by the maintainer and agreed upon by the Maintainers Group.
 A maintainer is primarily responsible for issues within their chosen scope(s), although
 contributions elsewhere are welcome, as well.
 
+The role of the "lead maintainer", that is, the BIDS maintainer currently representing the maintainers group,
+is rotating among current maintainers.
+
 #### Past maintainers group members
 
 | Name                                                                           | Duration            |

From 124ac21a128ec14a0ebff6791a13d05e9503ba2e Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Sat, 1 Jun 2024 15:01:51 +0200
Subject: [PATCH 23/74] MAINT: Upgrade node for linting (#1845)

* try upgrade node

* tab-size -> tab

* try pipe fix

* remaining pipe fixes
---
 .github/workflows/validation.yml                     |  2 +-
 .remarkrc                                            |  2 +-
 CONTRIBUTING.md                                      |  8 ++++----
 DECISION-MAKING.md                                   |  4 ++--
 npm-requirements.txt                                 |  8 ++++----
 src/appendices/file-collections.md                   |  4 ++--
 src/appendices/licenses.md                           |  2 +-
 src/appendices/meg-systems.md                        |  2 +-
 src/appendices/qmri.md                               |  6 +++---
 src/appendices/units.md                              |  4 ++--
 src/derivatives/common-data-types.md                 |  2 +-
 src/derivatives/introduction.md                      |  2 +-
 .../magnetic-resonance-imaging-data.md               | 12 ++++++------
 src/modality-specific-files/motion.md                |  2 +-
 .../near-infrared-spectroscopy.md                    |  2 +-
 15 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 5be42a5b18..ee554f9f59 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -26,7 +26,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-node@v4
         with:
-          node-version: 14
+          node-version: 22
       - name: Install dependencies
         run: npm install `cat npm-requirements.txt`
       - name: Run style checks
diff --git a/.remarkrc b/.remarkrc
index 8d6c26487a..5f10c62bdf 100644
--- a/.remarkrc
+++ b/.remarkrc
@@ -4,7 +4,7 @@
     "preset-lint-recommended",
     "remark-gfm",
     ["lint-no-duplicate-headings", false],
-    ["lint-list-item-indent", "tab-size"],
+    ["lint-list-item-indent", "tab"],
     ["lint-emphasis-marker", "consistent"],
     ["lint-maximum-line-length", false],
     ["lint-maximum-heading-length", false],
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index c34f9cb514..208d0bd43b 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -202,28 +202,28 @@ Don't do this:
 
 ```Markdown
 | **Key name** | **Description**                                          |
-|--------------|----------------------------------------------------------|
+| ------------ | -------------------------------------------------------- |
 | Manufacturer | Manufacturer of the equipment, for example (`Siemens`)   |
 ```
 
 That would look like this:
 
 | **Key name** | **Description**                                          |
-|--------------|----------------------------------------------------------|
+| ------------ | -------------------------------------------------------- |
 | Manufacturer | Manufacturer of the equipment, for example (`Siemens`)   |
 
 But do this instead:
 
 ```Markdown
 | **Key name** | **Description**                                          |
-|--------------|----------------------------------------------------------|
+| ------------ | -------------------------------------------------------- |
 | Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) |
 ```
 
 That would look like this:
 
 | **Key name** | **Description**                                          |
-|--------------|----------------------------------------------------------|
+| ------------ | -------------------------------------------------------- |
 | Manufacturer | Manufacturer of the equipment, for example (`"Siemens"`) |
 
 
diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index af1547a3b9..f31b2eacbf 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -20,7 +20,7 @@ Current and past members of the steering group can be found
 ### Maintainers Group
 
 | Name                                                                      | Time commitment | Scope                                 | Joined   |
-|---------------------------------------------------------------------------|-----------------|---------------------------------------|----------|
+| ------------------------------------------------------------------------- | --------------- | ------------------------------------- | -------- |
 | Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff))           | 1h/week         |                                       | Mar 2020 |
 | Chris Markiewicz ([@effigies](https://github.com/effigies))               | 5h/week         |                                       | Mar 2020 |
 | Ross Blair ([@rwblair](https://github.com/rwblair))                       |                 | Maintainer of the bids-validator      | Mar 2020 |
@@ -46,7 +46,7 @@ is rotating among current maintainers.
 #### Past maintainers group members
 
 | Name                                                                           | Duration            |
-|--------------------------------------------------------------------------------|---------------------|
+| ------------------------------------------------------------------------------ | ------------------- |
 | Franklin Feingold ([@franklin-feingold](https://github.com/franklin-feingold)) | Mar 2020 - Jul 2022 |
 
 ### BEP Leads Group
diff --git a/npm-requirements.txt b/npm-requirements.txt
index 7ef67d23b8..c2eaebe9b7 100644
--- a/npm-requirements.txt
+++ b/npm-requirements.txt
@@ -1,5 +1,5 @@
-remark-cli@9.0.0
-remark-gfm@1
-remark-preset-lint-recommended@5.0.0
-remark-preset-lint-markdown-style-guide@4.0.0
+remark-cli@12
+remark-gfm@4
+remark-preset-lint-recommended@7
+remark-preset-lint-markdown-style-guide@6
 remark-lint-no-trailing-spaces@2
diff --git a/src/appendices/file-collections.md b/src/appendices/file-collections.md
index 93d8391c1d..1df4677c75 100644
--- a/src/appendices/file-collections.md
+++ b/src/appendices/file-collections.md
@@ -47,7 +47,7 @@ and a guide for using macros can be found at
 }}
 
 | **Suffix** | **Linking entities**  | **Application**                            | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                     |
-|------------|-----------------------|--------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| ---------- | --------------------- | ------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | VFA        | flip                  | Variable flip angle                        | The VFA method involves at least two spoiled gradient echo (SPGR) of steady-state free precession (SSFP) images acquired at different flip angles. Depending on the provided metadata fields and the sequence type, data may be eligible for DESPOT1, DESPOT2 and their variants ([Deoni et al. 2005](https://doi.org/10.1002/mrm.20314)).                                                                                          |
 | IRT1       | inv, part             | Inversion recovery T1 mapping              | The IRT1 method involves multiple inversion recovery spin-echo images acquired at different inversion times ([Barral et al. 2010](https://doi.org/10.1002/mrm.22497)).                                                                                                                                                                                                                                                              |
 | MP2RAGE    | flip, inv, echo, part | Magnetization prepared two gradient echoes | The MP2RAGE method is a special protocol that collects several images at different flip angles and inversion times to create a parametric T1map by combining the magnitude and phase images ([Marques et al. 2010](https://doi.org/10.1016/j.neuroimage.2009.10.002)).                                                                                                                                                              |
@@ -81,7 +81,7 @@ and a guide for using macros can be found at
 }}
 
 | **Suffix** | **Meta-data relevant entity**                          | **Application**                    | **Description**                                                                                                                                                                                                                                                                                                                                                                                                                                         |
-|------------|--------------------------------------------------------|------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| ---------- | ------------------------------------------------------ | ---------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | TB1DAM     | flip                                                   | Double-angle B1+ mapping           | The double-angle B1<sup>+</sup> method ([Insko and Bolinger 1993](https://doi.org/10.1006/jmra.1993.1133)) is based on the calculation of the actual angles from signal ratios, collected by two acquisitions at different nominal excitation flip angles. Common sequence types for this application include spin echo and echo planar imaging.                                                                                                        |
 | TB1EPI     | flip, echo                                             | B1<sup>+</sup> mapping with 3D EPI | This B1<sup>+</sup> mapping method ([Jiru and Klose 2006](https://doi.org/10.1002/mrm.21083)) is based on two EPI readouts to acquire spin echo (SE) and stimulated echo (STE) images at multiple flip angles in one sequence, used in the calculation of deviations from the nominal flip angle.                                                                                                                                                       |
 | TB1AFI     | Please see the [qMRI appendix](../appendices/qmri.md). | Actual Flip Angle Imaging (AFI)    | This method ([Yarnykh 2007](https://doi.org/10.1002/mrm.21120)) calculates a B1<sup>+</sup> map from two images acquired at interleaved (two) TRs with identical RF pulses using a steady-state sequence.                                                                                                                                                                                                                                               |
diff --git a/src/appendices/licenses.md b/src/appendices/licenses.md
index 90cb6aa73f..adc02c23af 100644
--- a/src/appendices/licenses.md
+++ b/src/appendices/licenses.md
@@ -9,7 +9,7 @@ The terms of any license should be consistent with the informed consent
 obtained from participants and any institutional limitations on distribution.
 
 | **Identifier** | **License name**                                       | **Description**                                                                                                                |
-| ---------------| ------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------ |
+| -------------- | ------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------ |
 | PD             | Public Domain                                          | No license required for any purpose; the work is not subject to copyright in any jurisdiction.                                 |
 | [PDDL][pddl]   | Open Data Commons Public Domain Dedication and License | License to assign public domain like permissions without giving up the copyright.                                              |
 | [CC0][cc0]     | Creative Commons Zero 1.0 Universal.                   | Use this if you are a holder of copyright or database rights, and you wish to waive all your interests in your work worldwide. |
diff --git a/src/appendices/meg-systems.md b/src/appendices/meg-systems.md
index 189d0ead31..9ae9fa3012 100644
--- a/src/appendices/meg-systems.md
+++ b/src/appendices/meg-systems.md
@@ -14,7 +14,7 @@ Preferred names of MEG systems comprise restricted keywords for Manufacturer fie
 Restricted keywords for ManufacturersModelName field in the `*_meg.json` file:
 
 | **System Model Name**     | **Manufacturer**      | **Details**                                                                                  |
-|-------------------------- | --------- ------------| -------------------------------------------------------------------------------------------- |
+| ------------------------- | --------- ----------- | -------------------------------------------------------------------------------------------- |
 | CTF-64                    | CTF                   |                                                                                              |
 | CTF-151                   | CTF                   | [https://www.ctf.com/products](https://www.ctf.com/products)                                 |
 | CTF-275                   | CTF                   | CTF-275: OMEGA 2000                                                                          |
diff --git a/src/appendices/qmri.md b/src/appendices/qmri.md
index 31e3b3ef7d..8aad465f24 100644
--- a/src/appendices/qmri.md
+++ b/src/appendices/qmri.md
@@ -208,7 +208,7 @@ but also by which metadata fields are provided in accompanying json files.
 #### Anatomy imaging data
 
 | **File collection**  | **REQUIRED metadata**                                                                                                        | **OPTIONAL metadata**      |
-|----------------------|------------------------------------------------------------------------------------------------------------------------------|----------------------------|
+| -------------------- | ---------------------------------------------------------------------------------------------------------------------------- | -------------------------- |
 | VFA                  | `FlipAngle`, `PulseSequenceType`, `RepetitionTimeExcitation`                                                                 | `SpoilingRFPhaseIncrement` |
 | IRT1                 | `InversionTime`                                                                                                              |                            |
 | MP2RAGE<sup>\*</sup> | `FlipAngle`, `InversionTime`, `RepetitionTimeExcitation`, `RepetitionTimePreparation`, `NumberShots`,`MagneticFieldStrength` | `EchoTime`                 |
@@ -282,7 +282,7 @@ and a guide for using macros can be found at
 }}
 
 | **File collection**  | **REQUIRED metadata**                                                                                |
-|----------------------|------------------------------------------------------------------------------------------------------|
+| -------------------- | ---------------------------------------------------------------------------------------------------- |
 | TB1DAM               | `FlipAngle`                                                                                          |
 | TB1EPI               | `EchoTime`, `FlipAngle`, `TotalReadoutTime`, `MixingTime`                                            |
 | TB1AFI               | `RepetitionTime`                                                                                     |
@@ -447,7 +447,7 @@ This approach aims at:
 -   keeping an inheritance track of the qMRI methods described within the specification.
 
 | **File-collection suffix** | **If REQUIRED metadata == Value** | **OPTIONAL metadata (`entity`/`fixed`)** | **Derived application name (NOT a suffix)** |
-|----------------------------|-----------------------------------|------------------------------------------|---------------------------------------------|
+| -------------------------- | --------------------------------- | ---------------------------------------- | ------------------------------------------- |
 | VFA                        | `PulseSequenceType` == `SPGR`     |                                          | DESPOT1                                     |
 | VFA                        | `PulseSequenceType` == `SSFP`     | `SpoilingRFPhaseIncrement` (`fixed`)     | DESPOT2                                     |
 | MP2RAGE                    |                                   | `EchoTime` (`echo`)                      | MP2RAGE-ME                                  |
diff --git a/src/appendices/units.md b/src/appendices/units.md
index 0edf271b16..4e4355483f 100644
--- a/src/appendices/units.md
+++ b/src/appendices/units.md
@@ -47,7 +47,7 @@ Examples for CMIXF-12 (including the five unicode symbols mentioned above):
 ## Unit table
 
 | **Unit name**  | **Unit symbol** | **Quantity name**                          |
-| ---------------| --------------- | ------------------------------------------ |
+| -------------- | --------------- | ------------------------------------------ |
 | meter          | m               | length                                     |
 | kilogram       | kg              | mass                                       |
 | liter          | L               | volume                                     |
@@ -84,7 +84,7 @@ Examples for CMIXF-12 (including the five unicode symbols mentioned above):
 ### Multiples
 
 | **Prefix name**                             | **Prefix symbol** | **Factor**      |
-| --------------------------------------------| ------------------| --------------- |
+| ------------------------------------------- | ----------------- | --------------- |
 | [deca](https://www.wikiwand.com/en/Deca-)   | da                | 10<sup>1</sup>  |
 | [hecto](https://www.wikiwand.com/en/Hecto-) | h                 | 10<sup>2</sup>  |
 | [kilo](https://www.wikiwand.com/en/Kilo-)   | k                 | 10<sup>3</sup>  |
diff --git a/src/derivatives/common-data-types.md b/src/derivatives/common-data-types.md
index 5a2e725e91..63f0809c55 100644
--- a/src/derivatives/common-data-types.md
+++ b/src/derivatives/common-data-types.md
@@ -329,7 +329,7 @@ A guide for using macros can be found at
 Contents of the `descriptions.tsv` file:
 
 | desc_id | description                                                                                     |
-|---------|-------------------------------------------------------------------------------------------------|
+| ------- | ----------------------------------------------------------------------------------------------- |
 | Filt    | low-pass filtered at 30Hz                                                                       |
 | FiltDs  | low-pass filtered at 30Hz, downsampled to 250Hz                                                 |
 | preproc | low-pass filtered at 30Hz, downsampled to 250Hz, and rereferenced to a common average reference |
diff --git a/src/derivatives/introduction.md b/src/derivatives/introduction.md
index 669719cdc1..af798f38bd 100644
--- a/src/derivatives/introduction.md
+++ b/src/derivatives/introduction.md
@@ -108,7 +108,7 @@ The following extension table is reproduced in part from Section 9.0 of the
 or combinations of data arrays.
 
 | Intent      | Extension     |
-|-------------|---------------|
+| ----------- | ------------- |
 | Coordinates | `.coord.gii`  |
 | Functional  | `.func.gii`   |
 | Labels      | `.label.gii`  |
diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index 6396aa0e8c..d5e8e6abc9 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -573,11 +573,11 @@ sparse sequences.
 
 |          | **`RepetitionTime`** | **`SliceTiming`** | **`AcquisitionDuration`** | **`DelayTime`** | **`VolumeTiming`** |
 | -------- | -------------------- | ----------------- | ------------------------- | --------------- | ------------------ |
-| option A |     \[ X ]           |                   |         \[ ]              |                 |     \[ ]           |
-| option B |      \[ ]            |    \[ X ]         |                           |    \[ ]         |    \[ X ]          |
-| option C |      \[ ]            |                   |        \[ X ]             |    \[ ]         |    \[ X ]          |
-| option D |     \[ X ]           |    \[ X ]         |         \[ ]              |                 |     \[ ]           |
-| option E |     \[ X ]           |                   |         \[ ]              |   \[ X ]        |     \[ ]           |
+| option A | \[ X ]               |                   | \[ ]                      |                 | \[ ]               |
+| option B | \[ ]                 | \[ X ]            |                           | \[ ]            | \[ X ]             |
+| option C | \[ ]                 |                   | \[ X ]                    | \[ ]            | \[ X ]             |
+| option D | \[ X ]               | \[ X ]            | \[ ]                      |                 | \[ ]               |
+| option E | \[ X ]               |                   | \[ ]                      | \[ X ]          | \[ ]               |
 
 **Legend**
 
@@ -1029,7 +1029,7 @@ imposed on the Dependent fields in column 3. See the [ASL Appendix](../appendice
 form of flowcharts.
 
 | **Source field**         | **Value**    | **Dependent field**  | **Requirements**                                 |
-|--------------------------|--------------|----------------------|--------------------------------------------------|
+| ------------------------ | ------------ | -------------------- | ------------------------------------------------ |
 | MRAcquisitionType        | 2D / 3D      | SliceTiming          | \[X\] / \[\]                                     |
 | LookLocker               | true         | FlipAngle            | \[X\]                                            |
 | ArterialSpinLabelingType | PCASL        | LabelingDuration     | \[X\]                                            |
diff --git a/src/modality-specific-files/motion.md b/src/modality-specific-files/motion.md
index f0bbcb96ef..af357581e1 100644
--- a/src/modality-specific-files/motion.md
+++ b/src/modality-specific-files/motion.md
@@ -210,7 +210,7 @@ The description of the `reference_frame` column SHOULD use the `"Levels"`
 field to describe the named field using [objects][object] with following fields.
 
 | Key name      | Requirement Level                                      | Data type  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
-|---------------|--------------------------------------------------------|------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| ------------- | ------------------------------------------------------ | ---------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
 | RotationOrder | RECOMMENDED                                            | [string][] | The sequence in which the extrinsic rotations are applied around the three axes. One of `"XYZ"`, `"XZY"`, `"YXZ"`, `"YZX"`, `"ZXY"`, or `"ZYX"`.                                                                                                                                                                                                                                                                                                                   |
 | RotationRule  | RECOMMENDED                                            | [string][] | The direction of rotation around each axis. One of `"left-hand"` or `"right-hand"`.                                                                                                                                                                                                                                                                                                                                                                                |
 | SpatialAxes   | RECOMMENDED                                            | [string][] | The coordinate system in which the motion data are to be interpreted. A sequence of characters from the set `{'A', 'P', 'L', 'R', 'S', 'I', '_'}` indicating the direction of each axis. For example `"ARS"` indicates positive values in the X, Y, Z axes are respectively anterior, right, and superior of the origin, while `"PLI"` indicates positive values are posterior, left, and inferior of the origin. The `"_"` character may be used for unused axes. |
diff --git a/src/modality-specific-files/near-infrared-spectroscopy.md b/src/modality-specific-files/near-infrared-spectroscopy.md
index 16ffc1ba98..7382560a43 100644
--- a/src/modality-specific-files/near-infrared-spectroscopy.md
+++ b/src/modality-specific-files/near-infrared-spectroscopy.md
@@ -279,7 +279,7 @@ As several of these data types are commonly acquired using NIRS devices they are
 Note that upper-case is REQUIRED.
 
 | **Keyword**                 | **Description**                                                                                                                                            |
-| --------------------------- | -----------------------------------------------------------------------------------------------------------------------------------------------------------|
+| --------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | NIRSCWAMPLITUDE             | Continuous wave amplitude measurements. Equivalent to dataType 001 in SNIRF.                                                                               |
 | NIRSCWFLUORESCENSEAMPLITUDE | Continuous wave fluorescence amplitude measurements. Equivalent to dataType 051 in SNIRF.                                                                  |
 | NIRSCWOPTICALDENSITY        | Continuous wave change in optical density measurements. Equivalent to dataTypeLabel dOD in SNIRF.                                                          |

From be50185e5bbf7ce17ec5d4a30ac6b6057b53b986 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Sat, 1 Jun 2024 15:53:41 +0200
Subject: [PATCH 24/74]  Fix generation of BIDS changelog  (#1836)

* use default remote_docker_version

* run changelog gen and lint even if not Merge commit

* TMP: to be reverted. testing gen and lint on non-master

* try new token

* check which version we are running

* no docker, upgrade version

* try old token

* new token (again), different scope, and implicit

* try explicit again

* try with fine grained token

* try with new circleci setting

* try CHANGE_TOKEN, now that no longer on fork

* try gh action

* migrate circleci -> gh action

* tweaks: only on master, or PR to master; remove ad; fix path

* try with directory

* fix linting

* better portioning of output
---
 .circleci/config.yml                      | 121 -------------------
 .github/workflows/changelog_generator.yml | 137 ++++++++++++++++++++++
 .github/workflows/schemacode_ci.yml       |   4 +-
 3 files changed, 139 insertions(+), 123 deletions(-)
 create mode 100644 .github/workflows/changelog_generator.yml

diff --git a/.circleci/config.yml b/.circleci/config.yml
index 676383d1f1..63f1dd4ce8 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -93,111 +93,6 @@ jobs:
       - store_artifacts:
           path: bids-spec.pdf
 
-  # Automatically generate a changelog since migration from Google Docs to GitHub
-  github_changelog_generator:
-    docker:
-      - image: ferrarimarco/github-changelog-generator:1.14.3
-    steps:
-      - setup_remote_docker:
-          version: 18.06.0-ce
-      # checkout code to default ~/project
-      - checkout
-      - run:
-          name: Build changelog
-          # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
-          command: |
-            mkdir ~/changelog_build
-            git status
-            if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-              github_changelog_generator \
-                --exclude-tags-regex "^(?!v).*?$" \
-                --user bids-standard \
-                --project bids-specification \
-                --token ${CHANGE_TOKEN} \
-                --output ~/changelog_build/CHANGES.md \
-                --base ~/project/src/pregh-changes.md \
-                --header-label "# Changelog" \
-                --release-branch master \
-                --no-issues \
-                --no-filter-by-milestone \
-                --no-compare-link \
-                --pr-label "" \
-                --enhancement-label "" \
-                --bugs-label "" \
-                --exclude-labels "exclude-from-changelog"
-              cat ~/changelog_build/CHANGES.md
-            else
-              echo "Commit or Release, do nothing"
-            fi
-      - persist_to_workspace:
-          # raw generated changelog in ~/changelog_build/CHANGES.md
-          root: ~/.
-          paths:
-            - changelog_build
-
-  # Lint and fix the auto generated changes.md file
-  lint_generated_changelog:
-    docker:
-      - image: cimg/node:lts
-    steps:
-      # checkout code to default ~/project
-      - checkout
-      - attach_workspace:
-          # the freshly built CHANGES.md will be in ~/changelog_build/CHANGES.md
-          at: ~/.
-      - run:
-          name: install remark and extensions
-          command: npm install `cat npm-requirements.txt`
-      - run:
-          name: remark on autogenerated CHANGES.md
-          # format changelog, then use sed to change * to -, then lint changelog
-          command: |
-            git status
-            if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-              head -n 100 ~/changelog_build/CHANGES.md
-              npx remark-cli ~/changelog_build/CHANGES.md --rc-path ~/project/.remarkrc --output ~/changelog_build/CHANGES.md
-              head -n 100 ~/changelog_build/CHANGES.md
-              sed -i 's/*   /-   /' ~/changelog_build/CHANGES.md
-              head -n 100 ~/changelog_build/CHANGES.md
-              npx remark-cli ~/changelog_build/CHANGES.md --frail --rc-path ~/project/.remarkrc
-            else
-              echo "Commit or Release, do nothing"
-            fi
-      - persist_to_workspace:
-          # linted and fixed changelog in ~/changelog_build/CHANGES.md
-          root: ~/.
-          paths:
-            - changelog_build
-
-  # Push built changelog to repo
-  commit_generated_changelog:
-    docker:
-      - image: cimg/base:stable
-    steps:
-      - setup_remote_docker
-      # checkout code to default ~/project
-      - checkout
-      - attach_workspace:
-          # fixed+linted changelog in ~/changelog_build/CHANGES.md
-          at: ~/.
-      - run:
-          name: Changelog deployment
-          # $CHANGE_TOKEN is generated via the GitHub web UI, and then securely stored within CircleCI web UI
-          command: |
-            if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-              mv ~/changelog_build/CHANGES.md ~/project/src/CHANGES.md
-              merge_message=$(git log -1 | grep Merge | grep "pull")
-              PR_number=$(echo $merge_message | cut -d ' ' -f 4)
-              git config credential.helper 'cache --timeout=120'
-              git config user.email "bids.maintenance@gmail.com"
-              git config user.name "bids-maintenance"
-              git add ~/project/src/CHANGES.md
-              git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
-              git push https://${CHANGE_TOKEN}@github.com/bids-standard/bids-specification.git master
-            else
-              echo "Commit or Release, do nothing"
-            fi
-
 workflows:
   search_build:
     jobs:
@@ -205,20 +100,4 @@ workflows:
       - check_links:
           requires:
             - build_docs
-      - github_changelog_generator:
-          filters:
-            branches:
-              only: master
-      - lint_generated_changelog:
-          requires:
-            - github_changelog_generator
-          filters:
-            branches:
-              only: master
-      - commit_generated_changelog:
-          requires:
-            - lint_generated_changelog
-          filters:
-            branches:
-              only: master
       - build_docs_pdf
diff --git a/.github/workflows/changelog_generator.yml b/.github/workflows/changelog_generator.yml
new file mode 100644
index 0000000000..fc06117e39
--- /dev/null
+++ b/.github/workflows/changelog_generator.yml
@@ -0,0 +1,137 @@
+---
+name: GitHub_Changelog_Generator
+
+on:
+    push:
+      branches: ["master"]
+    pull_request:
+      branches: ["master"]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  cancel-in-progress: true
+
+jobs:
+    github_changelog_generator:
+        runs-on: ubuntu-latest
+        strategy:
+          fail-fast: false
+          matrix:
+            ruby-version: ["3.2"]
+        steps:
+        - uses: actions/checkout@v4
+        - name: Set up Ruby ${{ matrix.ruby-version }}
+          uses: ruby/setup-ruby@v1
+          with:
+            ruby-version: ${{ matrix.ruby-version }}
+        - name: Install dependencies
+          run: |
+            gem install github_changelog_generator
+        - name: Check version
+          run: |
+            github_changelog_generator --version
+        - name: Build changelog
+          run: |
+            mkdir ~/changelog_build
+            github_changelog_generator \
+                --exclude-tags-regex "^(?!v).*?$" \
+                --user bids-standard \
+                --project bids-specification \
+                --token ${{ secrets.GITHUB_TOKEN }} \
+                --output ~/changelog_build/CHANGES.md \
+                --header-label "# Changelog" \
+                --release-branch master \
+                --no-issues \
+                --no-filter-by-milestone \
+                --no-compare-link \
+                --pr-label "" \
+                --enhancement-label "" \
+                --bugs-label "" \
+                --exclude-labels "exclude-from-changelog"
+        - name: Append changelog from pre-GitHub times
+          run: |
+            cat ${{ github.workspace }}/src/pregh-changes.md >> ~/changelog_build/CHANGES.md
+        - name: Remove the inserted advert from the file
+          run: |
+            sed -i '/This Changelog was automatically generated by/d' ~/changelog_build/CHANGES.md
+        - name: Print out complete changelog
+          run: |
+            cat ~/changelog_build/CHANGES.md
+        - name: Archive changelog
+          uses: actions/upload-artifact@v4
+          with:
+            name: changelog_pre_lint
+            path: |
+              ~/changelog_build/CHANGES.md
+
+    lint_generated_changelog:
+        needs: github_changelog_generator
+        runs-on: ubuntu-latest
+        steps:
+        - uses: actions/checkout@v4
+        - name: Download previously build changelog
+          uses: actions/download-artifact@v4
+          with:
+            name: changelog_pre_lint
+            path: ~/changelog_build
+        - name: Set up Node
+          uses: actions/setup-node@v4
+          with:
+            node-version: 20
+        - name: Install remark and extensions
+          run: |
+            npm install `cat npm-requirements.txt`
+        - name: Remark on autogenerated CHANGES.md
+          # first remove empty lines
+          # then run remark to re-organize
+          # replace remark's bullet list "*" with "-"
+          # final run of remark to check everything passes now
+          run: |
+            head -n 25 ~/changelog_build/CHANGES.md
+            sed -i '/^$/d' ~/changelog_build/CHANGES.md
+            echo $'\n------------------------------\n'
+            head -n 25 ~/changelog_build/CHANGES.md
+            npx remark ~/changelog_build/CHANGES.md --rc-path ${{ github.workspace }}/.remarkrc --output ~/changelog_build/CHANGES.md --quiet
+            echo $'\n------------------------------\n'
+            head -n 25 ~/changelog_build/CHANGES.md
+            sed -i 's/^* /-   /' ~/changelog_build/CHANGES.md
+            echo $'\n------------------------------\n'
+            head -n 25 ~/changelog_build/CHANGES.md
+            npx remark ~/changelog_build/CHANGES.md --rc-path ${{ github.workspace }}/.remarkrc --frail --quiet --no-stdout
+        - name: Archive linted changelog
+          uses: actions/upload-artifact@v4
+          with:
+            name: changelog_post_lint
+            path: |
+              ~/changelog_build/CHANGES.md
+
+    commit_generated_changelog:
+        permissions:
+            # Give the default GITHUB_TOKEN write permission to commit and push the
+            # added or changed files to the repository.
+            contents: write
+        needs: lint_generated_changelog
+        if: github.ref == 'refs/heads/master'
+        runs-on: ubuntu-latest
+        steps:
+        - uses: actions/checkout@v4
+        - name: Download previously build changelog
+          uses: actions/download-artifact@v4
+          with:
+            name: changelog_post_lint
+            path: ~/changelog_build
+        - name: Changelog deployment
+          run: |
+            if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
+              mv ~/changelog_build/CHANGES.md ${{ github.workspace }}/src/CHANGES.md
+              merge_message=$(git log -1 | grep Merge | grep "pull")
+              PR_number=$(echo $merge_message | cut -d ' ' -f 4)
+              git config credential.helper 'cache --timeout=120'
+              git config user.email "bids.maintenance@gmail.com"
+              git config user.name "bids-maintenance"
+              git add ${{ github.workspace }}/src/CHANGES.md
+              git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
+              git push https://${{ secrets.GITHUB_TOKEN }}@github.com/bids-standard/bids-specification.git master
+            else
+              echo "Did not detect a "Merge commit" to master, or detected a Release ... doing nothing."
+            fi
diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index 0b92cd9a4d..14746534db 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -117,8 +117,8 @@ jobs:
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/
-          skip_existing: true
+          repository-url: https://test.pypi.org/legacy/
+          skip-existing: true
       - name: "Upload to PyPI (on tags)"
         if: startsWith(github.ref, 'refs/tags/schema-')
         uses: pypa/gh-action-pypi-publish@release/v1

From 70d7750629bf8b1cb12f1f9120c457fb6ad43a4a Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Sat, 1 Jun 2024 16:51:25 +0200
Subject: [PATCH 25/74] do not build changelog for PRs to master

---
 .github/workflows/changelog_generator.yml | 17 +++++------------
 1 file changed, 5 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/changelog_generator.yml b/.github/workflows/changelog_generator.yml
index fc06117e39..45d9948d32 100644
--- a/.github/workflows/changelog_generator.yml
+++ b/.github/workflows/changelog_generator.yml
@@ -2,28 +2,22 @@
 name: GitHub_Changelog_Generator
 
 on:
-    push:
-      branches: ["master"]
-    pull_request:
-      branches: ["master"]
+  push:
+    branches: ["master"]
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.event.number }}-${{ github.event.ref }}
+  group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
     github_changelog_generator:
         runs-on: ubuntu-latest
-        strategy:
-          fail-fast: false
-          matrix:
-            ruby-version: ["3.2"]
         steps:
         - uses: actions/checkout@v4
-        - name: Set up Ruby ${{ matrix.ruby-version }}
+        - name: Set up Ruby
           uses: ruby/setup-ruby@v1
           with:
-            ruby-version: ${{ matrix.ruby-version }}
+            ruby-version: '3.2'
         - name: Install dependencies
           run: |
             gem install github_changelog_generator
@@ -111,7 +105,6 @@ jobs:
             # added or changed files to the repository.
             contents: write
         needs: lint_generated_changelog
-        if: github.ref == 'refs/heads/master'
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4

From 82674bca3a7f299116926ec9ffbb4a1b7f8a4d79 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 6 Jun 2024 09:28:40 +0200
Subject: [PATCH 26/74] add deprecation check

---
 src/schema/rules/checks/deprecations.yml | 53 ++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 src/schema/rules/checks/deprecations.yml

diff --git a/src/schema/rules/checks/deprecations.yml b/src/schema/rules/checks/deprecations.yml
new file mode 100644
index 0000000000..d7a3c27372
--- /dev/null
+++ b/src/schema/rules/checks/deprecations.yml
@@ -0,0 +1,53 @@
+AnatomicalLandmarkCoordinateSystemDeprecation:
+  issue:
+    code: ELEKTA_NEUROMAG_DEPRECATED
+    message: |
+        "ElektaNeuromag" as a coordinate system is deprecated.
+        Use "NeuromagElektaMEGIN" instead.
+    level: warning
+  selectors:
+    - sidecar.AnatomicalLandmarkCoordinateSystem
+  checks:
+    - sidecar.AnatomicalLandmarkCoordinateSystem != "ElektaNeuromag"
+
+DigitizedHeadPointsCoordinateSystemDeprecation:
+  $ref: rules.checks.deprecations.AnatomicalLandmarkCoordinateSystemDeprecation
+  selectors:
+    - sidecar.DigitizedHeadPointsCoordinateSystem
+  checks:
+    - sidecar.DigitizedHeadPointsCoordinateSystem != "ElektaNeuromag"
+
+EEGCoordinateSystemDeprecation:
+  $ref: rules.checks.deprecations.AnatomicalLandmarkCoordinateSystemDeprecation
+  selectors:
+    - sidecar.EEGCoordinateSystem
+  checks:
+    - sidecar.EEGCoordinateSystem != "ElektaNeuromag"
+
+FiducialsCoordinateSystemDeprecation:
+  $ref: rules.checks.deprecations.AnatomicalLandmarkCoordinateSystemDeprecation
+  selectors:
+    - sidecar.FiducialsCoordinateSystem
+  checks:
+    - sidecar.FiducialsCoordinateSystem != "ElektaNeuromag"
+
+HeadCoilCoordinateSystemDeprecation:
+  $ref: rules.checks.deprecations.AnatomicalLandmarkCoordinateSystemDeprecation
+  selectors:
+    - sidecar.HeadCoilCoordinateSystem
+  checks:
+    - sidecar.HeadCoilCoordinateSystem != "ElektaNeuromag"
+
+MEGCoordinateSystemDeprecation:
+  $ref: rules.checks.deprecations.AnatomicalLandmarkCoordinateSystemDeprecation
+  selectors:
+    - sidecar.MEGCoordinateSystem
+  checks:
+    - sidecar.MEGCoordinateSystem != "ElektaNeuromag"
+
+NIRSCoordinateSystemDeprecation:
+  $ref: rules.checks.deprecations.AnatomicalLandmarkCoordinateSystemDeprecation
+  selectors:
+    - sidecar.NIRSCoordinateSystem
+  checks:
+    - sidecar.NIRSCoordinateSystem != "ElektaNeuromag"

From 2f933e8ae9ba61a8277a7c22990784a1395b7f29 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 6 Jun 2024 14:19:27 +0200
Subject: [PATCH 27/74] [FIX] Consistently refer to Neuromag/Elekta/MEGIN
 (#1310)

* DRAFT: consistently refer to Neuromag/Elekta/MEGIN

* add deprecation notices

* add links to deprecation
---
 src/appendices/coordinate-systems.md |  5 +++--
 src/schema/objects/enums.yaml        | 10 +++++++++-
 src/schema/rules/sidecars/meg.yaml   |  5 ++++-
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/appendices/coordinate-systems.md b/src/appendices/coordinate-systems.md
index c5b44207bc..c3312a3e70 100644
--- a/src/appendices/coordinate-systems.md
+++ b/src/appendices/coordinate-systems.md
@@ -108,11 +108,12 @@ Restricted keywords for the `<CoordSysType>CoordinateSystem` field in the
 `coordinatesystem.json` file for MEG datasets:
 
 -   `CTF`: ALS orientation and the origin between the ears
--   `ElektaNeuromag`: RAS orientation and the origin between the ears
+-   `NeuromagElektaMEGIN`: RAS orientation and the origin between the ears
 -   `4DBti`: ALS orientation and the origin between the ears
 -   `KitYokogawa`: ALS orientation and the origin between the ears
 -   `ChietiItab`: RAS orientation and the origin between the ears
 -   Any keyword from the list of [Standard template identifiers](#standard-template-identifiers): RAS orientation and the origin at the center of the gradient coil for template NifTI images
+-   The use of `ElektaNeuromag` is [DEPRECATED][deprecated]. Dataset curators SHOULD use `NeuromagElektaMEGIN` instead.
 
 In the case that MEG was recorded simultaneously with EEG,
 the restricted keywords for
@@ -146,7 +147,7 @@ the restricted keywords for
 can also be applied to EEG:
 
 -   `CTF`
--   `ElektaNeuromag`
+-   `NeuromagElektaMEGIN`
 -   `4DBti`
 -   `KitYokogawa`
 -   `ChietiItab`
diff --git a/src/schema/objects/enums.yaml b/src/schema/objects/enums.yaml
index f01d16cdc6..2f63006460 100644
--- a/src/schema/objects/enums.yaml
+++ b/src/schema/objects/enums.yaml
@@ -20,7 +20,8 @@ _MEGCoordSys:
   type: string
   enum:
     - $ref: objects.enums.CTF.value
-    - $ref: objects.enums.ElektaNeuromag.value
+    - $ref: objects.enums.ElektaNeuromag.value # deprecated
+    - $ref: objects.enums.NeuromagElektaMEGIN.value
     - $ref: objects.enums.4DBti.value
     - $ref: objects.enums.KitYokogawa.value
     - $ref: objects.enums.ChietiItab.value
@@ -305,6 +306,13 @@ CTF:
 ElektaNeuromag:
   value: ElektaNeuromag
   display_name: Elekta Neuromag
+  description: |
+    RAS orientation and the origin between the ears.
+    [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
+    Dataset curators SHOULD use `NeuromagElektaMEGIN` instead.
+NeuromagElektaMEGIN:
+  value: NeuromagElektaMEGIN
+  display_name: Neuromag Elekta MEGIN
   description: |
     RAS orientation and the origin between the ears.
 4DBti:
diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index a989d40f9f..33d851f6af 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -20,8 +20,11 @@ MEGHardware:
       level: recommended
       description_addendum: |
         For MEG scanners, this must be one of:
-        `"CTF"`, `"Elekta/Neuromag"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
+        `"CTF"`, `"Neuromag/Elekta/MEGIN"`, `"BTi/4D"`, `"KIT/Yokogawa"`,
         `"ITAB"`, `"KRISS"`, `"Other"`.
+        The use of `"Elekta/Neuromag"` is
+        [DEPRECATED](SPEC_ROOT/common-principles.md#definitions).
+        Dataset curators SHOULD use `"Neuromag/Elekta/MEGIN"` instead.
         See the [MEG Systems Appendix](SPEC_ROOT/appendices/meg-systems.md) for
         preferred names.
     ManufacturersModelName:

From 4259163bc92b7da7771be8e8ded9cdc66d910ae0 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Fri, 7 Jun 2024 11:45:34 +0200
Subject: [PATCH 28/74] Update requirements.txt

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 25f0520a6a..81609f6b67 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,4 +1,4 @@
-mkdocs>=1.1
+mkdocs>=1.1.0
 mkdocs-material>=5.4
 pymdown-extensions>=7.0.0
 mkdocs-branchcustomization-plugin~=0.1.3

From eba3e08e2dbfd3ad2e57c2a52c3bda8c1961dc6c Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Fri, 7 Jun 2024 12:38:19 +0200
Subject: [PATCH 29/74] fix changelog generation [build changelog]

xref: https://github.com/bids-standard/bids-specification/pull/1850
---
 .github/workflows/changelog_generator.yml | 36 +++++++++++++----------
 1 file changed, 20 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/changelog_generator.yml b/.github/workflows/changelog_generator.yml
index 45d9948d32..7e0291b542 100644
--- a/.github/workflows/changelog_generator.yml
+++ b/.github/workflows/changelog_generator.yml
@@ -101,10 +101,11 @@ jobs:
 
     commit_generated_changelog:
         permissions:
-            # Give the default GITHUB_TOKEN write permission to commit and push the
-            # added or changed files to the repository.
             contents: write
+            pull-requests: write
         needs: lint_generated_changelog
+        # Run only if the head commit message contains "[build changelog]""
+        if: contains(github.event.head_commit.message, '[build changelog]')
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
@@ -113,18 +114,21 @@ jobs:
           with:
             name: changelog_post_lint
             path: ~/changelog_build
-        - name: Changelog deployment
+        - name: add changelog to git
           run: |
-            if (git log -1 --pretty=%s | grep Merge*) && (! git log -1 --pretty=%b | grep REL:) ; then
-              mv ~/changelog_build/CHANGES.md ${{ github.workspace }}/src/CHANGES.md
-              merge_message=$(git log -1 | grep Merge | grep "pull")
-              PR_number=$(echo $merge_message | cut -d ' ' -f 4)
-              git config credential.helper 'cache --timeout=120'
-              git config user.email "bids.maintenance@gmail.com"
-              git config user.name "bids-maintenance"
-              git add ${{ github.workspace }}/src/CHANGES.md
-              git commit -m "[DOC] Auto-generate changelog entry for PR ${PR_number}"
-              git push https://${{ secrets.GITHUB_TOKEN }}@github.com/bids-standard/bids-specification.git master
-            else
-              echo "Did not detect a "Merge commit" to master, or detected a Release ... doing nothing."
-            fi
+            mv ~/changelog_build/CHANGES.md ${{ github.workspace }}/src/CHANGES.md
+            git config credential.helper 'cache --timeout=120'
+            git config user.email "bids.maintenance@gmail.com"
+            git config user.name "bids-maintenance"
+            git add ${{ github.workspace }}/src/CHANGES.md
+            git commit -m "[DOC] Auto-generated changelog entry"
+        - name: Create Pull Request
+          uses: peter-evans/create-pull-request@v6
+          with:
+            token: ${{ secrets.GITHUB_TOKEN }}
+            branch: changelog_generator_update
+            delete-branch: true
+            title: '[DOC] Auto-generated changelog entry'
+            labels: |
+              exclude-from-changelog
+            draft: false

From b0cfe7b7bc7fc065cb8ab023cf0f60dd6ed3ce92 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Sun, 9 Jun 2024 22:28:29 -0400
Subject: [PATCH 30/74] schema: Add regression test to expression tests

---
 src/schema/meta/expression_tests.yaml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/src/schema/meta/expression_tests.yaml b/src/schema/meta/expression_tests.yaml
index 5ebb7dcec0..8ab60a28d4 100644
--- a/src/schema/meta/expression_tests.yaml
+++ b/src/schema/meta/expression_tests.yaml
@@ -112,6 +112,9 @@
   result: [1, 2, 3]
 - expression: allequal(sorted([3, 2, 1]), [1, 2, 3])
   result: true
+# Regression test. Javascript will sort lexically by default.
+- expression: sorted([9, 81, 729, 6561])
+  result: [9, 81, 729, 6561]
 - expression: min([-1, "n/a", 1])
   result: -1
 - expression: max([-1, "n/a", 1])

From a98153595e9ae653c4f87c5b6781e05291afbd37 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Thu, 13 Jun 2024 19:28:27 +0200
Subject: [PATCH 31/74] [DOC] Auto-generated changelog entry (#1852)

Co-authored-by: bids-maintenance <bids.maintenance@gmail.com>
---
 src/CHANGES.md | 145 ++++++++++++++++++++++++++++++++++---------------
 1 file changed, 102 insertions(+), 43 deletions(-)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index 087368ffea..106f7e1aa0 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -1,15 +1,50 @@
 # Changelog
 
+## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
+
+-   \[ENH] Add use of session entity as example of encoding multi-site studies in a single dataset [#1803](https://github.com/bids-standard/bids-specification/pull/1803) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Describe Inheritance Principle in Common Principles [#1807](https://github.com/bids-standard/bids-specification/pull/1807) ([Lestropie](https://github.com/Lestropie))
+-   \[ENH] Use deidentification consistently in place of anonymization [#1799](https://github.com/bids-standard/bids-specification/pull/1799) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   \[INFRA] Introduce metaschema [#1787](https://github.com/bids-standard/bids-specification/pull/1787) ([bendichter](https://github.com/bendichter))
+-   \[ENH] Add warning about deidentification when sharing sourcedata [#1769](https://github.com/bids-standard/bids-specification/pull/1769) ([Remi-Gau](https://github.com/Remi-Gau))
+-   ENH: Use "Tag XXXX, YYYY" not "Tag (XXXX,YYYY)" for DICOM Tags [#1758](https://github.com/bids-standard/bids-specification/pull/1758) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH]\[SCHEMA] Allow .bval and .bvec files for pepolar fmaps [#1754](https://github.com/bids-standard/bids-specification/pull/1754) ([mattcieslak](https://github.com/mattcieslak))
+-   FIX: Move `\_stim.\<ext\>` specification within the Task Events module [#1750](https://github.com/bids-standard/bids-specification/pull/1750) ([oesteban](https://github.com/oesteban))
+-   ENH: Add compressed TSV files to the common principles [#1749](https://github.com/bids-standard/bids-specification/pull/1749) ([oesteban](https://github.com/oesteban))
+-   \[MAINT] split physio metadata tables [#1746](https://github.com/bids-standard/bids-specification/pull/1746) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[FIX] Move `rawdata/` into `sourcedata/raw` in alternative structure example, clarify on naming of datasets themselves [#1741](https://github.com/bids-standard/bids-specification/pull/1741) ([yarikoptic](https://github.com/yarikoptic))
+-   \[FIX] Remove mentions of sourcedata in the datatype specific pages [#1737](https://github.com/bids-standard/bids-specification/pull/1737) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] events.tsv should be sorted by onset values [#1732](https://github.com/bids-standard/bids-specification/pull/1732) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[FIX] fix typo  in motion.md [#1731](https://github.com/bids-standard/bids-specification/pull/1731) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] Specify the naming of scanner-generated TRACE and ADC volumes [#1725](https://github.com/bids-standard/bids-specification/pull/1725) ([effigies](https://github.com/effigies))
+-   FIX: Re-add run entity to electrodes.tsv [#1722](https://github.com/bids-standard/bids-specification/pull/1722) ([effigies](https://github.com/effigies))
+-   \[FIX] Add misssing files in filename template for NIRS [#1716](https://github.com/bids-standard/bids-specification/pull/1716) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[FIX] Missing word in `genetic-descriptor.md` [#1715](https://github.com/bids-standard/bids-specification/pull/1715) ([markmikkelsen](https://github.com/markmikkelsen))
+-   Add `descriptions.tsv` to the schema [#1707](https://github.com/bids-standard/bids-specification/pull/1707) ([tsalo](https://github.com/tsalo))
+-   \[FIX] Remove task entity from DWI and PERF time series file templates [#1703](https://github.com/bids-standard/bids-specification/pull/1703) ([Remi-Gau](https://github.com/Remi-Gau))
+-   ENH: Clarify the relation of motion.tsv columns to channels.tsv rows [#1699](https://github.com/bids-standard/bids-specification/pull/1699) ([effigies](https://github.com/effigies))
+-   \[STY] apply black 24.1.0 [#1688](https://github.com/bids-standard/bids-specification/pull/1688) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] Describe parametric images above the suffix table, rather than below [#1687](https://github.com/bids-standard/bids-specification/pull/1687) ([CPernet](https://github.com/CPernet))
+-   \[ENH] Add support for HiP-CT [#1686](https://github.com/bids-standard/bids-specification/pull/1686) ([balbasty](https://github.com/balbasty))
+-   \[FIX] Add `part-<value>` to the PEPOLAR fieldmaps [#1685](https://github.com/bids-standard/bids-specification/pull/1685) ([oesteban](https://github.com/oesteban))
+-   \[MISC] Restructure MEG empty room example texts [#1677](https://github.com/bids-standard/bids-specification/pull/1677) ([guiomar](https://github.com/guiomar))
+-   ENH: Add sample metadata to MRI and PET [#1593](https://github.com/bids-standard/bids-specification/pull/1593) ([effigies](https://github.com/effigies))
+-   \[ENH] Add noRF suffix for MR excitation-free noise scans [#1451](https://github.com/bids-standard/bids-specification/pull/1451) ([tsalo](https://github.com/tsalo))
+-   \[ENH] Add generic metadata from BEP22 to MRI [#1396](https://github.com/bids-standard/bids-specification/pull/1396) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[FIX] Consistently refer to Neuromag/Elekta/MEGIN [#1310](https://github.com/bids-standard/bids-specification/pull/1310) ([sappelhoff](https://github.com/sappelhoff))
+
 ## [v1.9.0](https://github.com/bids-standard/bids-specification/tree/v1.9.0) (2023-11-20)
 
+-   \[ENH] Add `descriptions.tsv` file relating to the `desc-<label>` entity [#1613](https://github.com/bids-standard/bids-specification/pull/1613) ([CPernet](https://github.com/CPernet))
+-   \[INFRA] Publish schema tools API docs to additional ReadTheDocs site [#1491](https://github.com/bids-standard/bids-specification/pull/1491) ([bendhouseart](https://github.com/bendhouseart))
+-   \[ENH] Extend BIDS for Motion data (BEP029) [#981](https://github.com/bids-standard/bids-specification/pull/981) ([JuliusWelzel](https://github.com/JuliusWelzel))
 -   \[FIX] mention phenotype dir in folder structure [#1644](https://github.com/bids-standard/bids-specification/pull/1644) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[ENH] add `ElectricalStimulation` and `\*Parameters` metadata to MEEG jsons [#1638](https://github.com/bids-standard/bids-specification/pull/1638) ([sappelhoff](https://github.com/sappelhoff))
+-   \[ENH] add `ElectricalStimulation` and `*Parameters` metadata to MEEG jsons [#1638](https://github.com/bids-standard/bids-specification/pull/1638) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] years and degrees Units and unit to be singular to match the rest [#1631](https://github.com/bids-standard/bids-specification/pull/1631) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Hierarchical Event Descriptors (HED) page update [#1623](https://github.com/bids-standard/bids-specification/pull/1623) ([effigies](https://github.com/effigies))
--   \[ENH] Add `descriptions.tsv` file relating to the `desc-\<label\>` entity [#1613](https://github.com/bids-standard/bids-specification/pull/1613) ([CPernet](https://github.com/CPernet))
 -   \[FIX] Do not require notch frequencies to be parsed as numbers, accommodating multiples [#1605](https://github.com/bids-standard/bids-specification/pull/1605) ([effigies](https://github.com/effigies))
 -   \[ENH] Allow Levels field of column descriptions to be objects with TermURLs for each level [#1603](https://github.com/bids-standard/bids-specification/pull/1603) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[ENH] Add optional low_cutoff and high_cutoff columns for fnirs channels.tsv [#1597](https://github.com/bids-standard/bids-specification/pull/1597) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] Add optional low\_cutoff and high\_cutoff columns for fnirs channels.tsv [#1597](https://github.com/bids-standard/bids-specification/pull/1597) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] Recommend SliceTiming if MRAcquisitionType is "2D" [#1594](https://github.com/bids-standard/bids-specification/pull/1594) ([tsalo](https://github.com/tsalo))
 -   \[ENH] Add Level objects to channels.json for motion [#1591](https://github.com/bids-standard/bids-specification/pull/1591) ([effigies](https://github.com/effigies))
 -   \[ENH] Add "chunk" entity to MRI datatype [#1586](https://github.com/bids-standard/bids-specification/pull/1586) ([valosekj](https://github.com/valosekj))
@@ -27,24 +62,23 @@
 -   \[ENH] Clarify meaning of raw vs derivative datasets [#1537](https://github.com/bids-standard/bids-specification/pull/1537) ([CPernet](https://github.com/CPernet))
 -   \[FIX] match subject label in folder and filename in func example [#1536](https://github.com/bids-standard/bids-specification/pull/1536) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] Trail MEG directory formats with `/` [#1534](https://github.com/bids-standard/bids-specification/pull/1534) ([effigies](https://github.com/effigies))
--   \[ENH] Permit CITATION.cff as structured alternative to some dataset_description fields [#1525](https://github.com/bids-standard/bids-specification/pull/1525) ([effigies](https://github.com/effigies))
+-   \[ENH] Permit CITATION.cff as structured alternative to some dataset\_description fields [#1525](https://github.com/bids-standard/bids-specification/pull/1525) ([effigies](https://github.com/effigies))
 -   \[FIX] Add missing column description in physio example [#1514](https://github.com/bids-standard/bids-specification/pull/1514) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify that data files must be uniquely identified by entities/suffix [#1508](https://github.com/bids-standard/bids-specification/pull/1508) ([sappelhoff](https://github.com/sappelhoff))
--   \[INFRA] Publish schema tools API docs to additional ReadTheDocs site [#1491](https://github.com/bids-standard/bids-specification/pull/1491) ([bendhouseart](https://github.com/bendhouseart))
 -   \[FIX] Remove references to unspecified aslcontext.json [#1485](https://github.com/bids-standard/bids-specification/pull/1485) ([Remi-Gau](https://github.com/Remi-Gau))
 -   ENH: Define channel column for events and Delimiter field for column descriptions [#1483](https://github.com/bids-standard/bids-specification/pull/1483) ([effigies](https://github.com/effigies))
 -   \[FIX] Revert index (entity format) definition to be a non-negative number, permitting zero [#1482](https://github.com/bids-standard/bids-specification/pull/1482) ([TheChymera](https://github.com/TheChymera))
 -   \[FIX] Clean up qMRI RB1COR notes [#1465](https://github.com/bids-standard/bids-specification/pull/1465) ([lukeje](https://github.com/lukeje))
 -   \[ENH] Allow fractional seconds in StartTime [#1459](https://github.com/bids-standard/bids-specification/pull/1459) ([sappelhoff](https://github.com/sappelhoff))
--   \[MISC] consistently list filename templates; `ext` --> `extension`; `\_photo.jpg` --> `\_photo.\<extension\>` [#1458](https://github.com/bids-standard/bids-specification/pull/1458) ([sappelhoff](https://github.com/sappelhoff))
+-   \[MISC] consistently list filename templates; `ext` --> `extension`; `_photo.jpg` --> `_photo.<extension>` [#1458](https://github.com/bids-standard/bids-specification/pull/1458) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Demote `sample` and `value` columns in `events.tsv` from OPTIONAL to arbitrary [#1457](https://github.com/bids-standard/bids-specification/pull/1457) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify shape of PDT2 images and recommend acq entity for split PDw/T2w images [#1448](https://github.com/bids-standard/bids-specification/pull/1448) ([effigies](https://github.com/effigies))
 -   \[ENH] clarify guiding principles for requirement levels [#1444](https://github.com/bids-standard/bids-specification/pull/1444) ([sappelhoff](https://github.com/sappelhoff))
--   \[FIX] Clarify that dataset_description.Genetics object is required for genetics data [#1442](https://github.com/bids-standard/bids-specification/pull/1442) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Clarify that dataset\_description.Genetics object is required for genetics data [#1442](https://github.com/bids-standard/bids-specification/pull/1442) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify that BIDS specification is in American English [#1439](https://github.com/bids-standard/bids-specification/pull/1439) ([yarikoptic](https://github.com/yarikoptic))
 -   \[MISC] Link to new BEP guidelines. [#1426](https://github.com/bids-standard/bids-specification/pull/1426) ([arokem](https://github.com/arokem))
 -   \[FIX] reorganize anat filename templates [#1419](https://github.com/bids-standard/bids-specification/pull/1419) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[FIX] Rename `channels.tsv` column: `orientation\_component` to `component` [#1417](https://github.com/bids-standard/bids-specification/pull/1417) ([sjeung](https://github.com/sjeung))
+-   \[FIX] Rename `channels.tsv` column: `orientation_component` to `component` [#1417](https://github.com/bids-standard/bids-specification/pull/1417) ([sjeung](https://github.com/sjeung))
 -   \[ENH] Some missing docstrings for bidsschematools [#1413](https://github.com/bids-standard/bids-specification/pull/1413) ([anibalsolon](https://github.com/anibalsolon))
 -   \[FIX] fixing some minor issues introduced recently [#1411](https://github.com/bids-standard/bids-specification/pull/1411) ([yarikoptic](https://github.com/yarikoptic))
 -   \[ENH] Add paragraph about richness versus distinctness in filenames [#1392](https://github.com/bids-standard/bids-specification/pull/1392) ([CPernet](https://github.com/CPernet))
@@ -62,13 +96,14 @@
 -   \[ENH] Add qMRI fieldmap filename templates [#1336](https://github.com/bids-standard/bids-specification/pull/1336) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[ENH] Introduce GIFTI formats in derivatives [#1333](https://github.com/bids-standard/bids-specification/pull/1333) ([effigies](https://github.com/effigies))
 -   \[ENH] Add ParallelReductionFactorOutOfPlane to MRI metadata [#1221](https://github.com/bids-standard/bids-specification/pull/1221) ([lukeje](https://github.com/lukeje))
--   \[ENH]\[SCHEMA] Adding an OPTIONAL `\_task-\<label\>` to structural MRI acquisitions [#1185](https://github.com/bids-standard/bids-specification/pull/1185) ([melanieganz](https://github.com/melanieganz))
+-   \[ENH]\[SCHEMA] Adding an OPTIONAL `_task-<label>` to structural MRI acquisitions [#1185](https://github.com/bids-standard/bids-specification/pull/1185) ([melanieganz](https://github.com/melanieganz))
 -   \[INFRA] use tributors to list contributors and CITATION.cff for referencing [#1115](https://github.com/bids-standard/bids-specification/pull/1115) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[ENH] Extend BIDS for Motion data (BEP029) [#981](https://github.com/bids-standard/bids-specification/pull/981) ([JuliusWelzel](https://github.com/JuliusWelzel))
 -   \[SCHEMA] Add full object definitions for valid values in schema [#919](https://github.com/bids-standard/bids-specification/pull/919) ([tsalo](https://github.com/tsalo))
 
 ## [v1.8.0](https://github.com/bids-standard/bids-specification/tree/v1.8.0) (2022-10-29)
 
+-   \[ENH] allow for .png and .tif in eeg/ieeg/meg as allowed for micr [#1049](https://github.com/bids-standard/bids-specification/pull/1049) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Add BIDS URIs and deprecate relative paths, RawSources and (possibly unused) BasedOn [#918](https://github.com/bids-standard/bids-specification/pull/918) ([effigies](https://github.com/effigies))
 -   \[FIX] Drop the functional and f for NIRS [#1325](https://github.com/bids-standard/bids-specification/pull/1325) ([rob-luke](https://github.com/rob-luke))
 -   \[FIX]\[SCHEMA] Add conditionals for PET ReconMethod\* and ReconFilter [#1299](https://github.com/bids-standard/bids-specification/pull/1299) ([bendhouseart](https://github.com/bendhouseart))
 -   \[ENH] use schema to mention which "top directories" are allowed [#1289](https://github.com/bids-standard/bids-specification/pull/1289) ([Remi-Gau](https://github.com/Remi-Gau))
@@ -92,36 +127,50 @@
 -   \[ENH] Add Microscopy-BIDS citation [#1102](https://github.com/bids-standard/bids-specification/pull/1102) ([mariehbourget](https://github.com/mariehbourget))
 -   \[FIX] MEG link typo [#1100](https://github.com/bids-standard/bids-specification/pull/1100) ([xi](https://github.com/xi))
 -   \[FIX] IntendedFor in (i)EEG is dataset relative [#1093](https://github.com/bids-standard/bids-specification/pull/1093) ([sappelhoff](https://github.com/sappelhoff))
--   \[MISC] make dataset_description.Authors RECOMMENDED [#1092](https://github.com/bids-standard/bids-specification/pull/1092) ([sappelhoff](https://github.com/sappelhoff))
+-   \[MISC] make dataset\_description.Authors RECOMMENDED [#1092](https://github.com/bids-standard/bids-specification/pull/1092) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] adding optional \_rec-label to DWI [#1090](https://github.com/bids-standard/bids-specification/pull/1090) ([dorahermes](https://github.com/dorahermes))
+-   \[SCHEMA] Conform the schema/rules files consistently [#1078](https://github.com/bids-standard/bids-specification/pull/1078) ([ericearl](https://github.com/ericearl))
 -   \[ENH] State of the schema sprint [#1075](https://github.com/bids-standard/bids-specification/pull/1075) ([effigies](https://github.com/effigies))
+-   SCHEMA: Convert datatype lists to objects [#1074](https://github.com/bids-standard/bids-specification/pull/1074) ([effigies](https://github.com/effigies))
+-   \[SCHEMA] Define common derivatives rules [#1072](https://github.com/bids-standard/bids-specification/pull/1072) ([rwblair](https://github.com/rwblair))
+-   \[SCHEMA] Define blood.tsv columns [#1070](https://github.com/bids-standard/bids-specification/pull/1070) ([rwblair](https://github.com/rwblair))
+-   \[SCHEMA] Create context schema in meta/ [#1069](https://github.com/bids-standard/bids-specification/pull/1069) ([effigies](https://github.com/effigies))
+-   \[SCHEMA] Replace `addendum` with `description_addendum` [#1066](https://github.com/bids-standard/bids-specification/pull/1066) ([tsalo](https://github.com/tsalo))
+-   \[SCHEMA] Encode requirement levels for dataset\_description and genetic\_info [#1064](https://github.com/bids-standard/bids-specification/pull/1064) ([effigies](https://github.com/effigies))
+-   \[SCHEMA] Correlating existing validator issues to schema entries [#1063](https://github.com/bids-standard/bids-specification/pull/1063) ([bendhouseart](https://github.com/bendhouseart))
+-   \[SCHEMA] Specify column requirement levels for several tabular files [#1061](https://github.com/bids-standard/bids-specification/pull/1061) ([effigies](https://github.com/effigies))
+-   \[SCHEMA] Start drafting validation rules for ASL data [#1060](https://github.com/bids-standard/bids-specification/pull/1060) ([tsalo](https://github.com/tsalo))
+-   \[SCHEMA] Add MEG, func, and fmap metadata tables [#1054](https://github.com/bids-standard/bids-specification/pull/1054) ([tsalo](https://github.com/tsalo))
 -   \[MISC] Preface each macro call with comment [#1052](https://github.com/bids-standard/bids-specification/pull/1052) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[ENH] allow for .png and .tif in eeg/ieeg/meg as allowed for micr [#1049](https://github.com/bids-standard/bids-specification/pull/1049) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] typo in "rawdata" example [#1045](https://github.com/bids-standard/bids-specification/pull/1045) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] consistently use "directory" instead of "folder" as a term [#1044](https://github.com/bids-standard/bids-specification/pull/1044) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Update CODEOWNERS [#1040](https://github.com/bids-standard/bids-specification/pull/1040) ([erdalkaraca](https://github.com/erdalkaraca))
 -   \[ENH] Allow README file extensions. [#1033](https://github.com/bids-standard/bids-specification/pull/1033) ([mateuszpawlik](https://github.com/mateuszpawlik))
 -   \[MISC] Rewrite and update html build instructions [#1032](https://github.com/bids-standard/bids-specification/pull/1032) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Clarify that BIDS standard template data is to be in scanner coordinates (MEG, iEEG, EEG) [#1031](https://github.com/bids-standard/bids-specification/pull/1031) ([alexrockhill](https://github.com/alexrockhill))
+-   \[SCHEMA] Define YAML tables for DWI/ASL/(i)EEG/micr/beh metadata [#1029](https://github.com/bids-standard/bids-specification/pull/1029) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Add coordsystem-specific definition of DigitizedHeadPoints [#1023](https://github.com/bids-standard/bids-specification/pull/1023) ([tsalo](https://github.com/tsalo))
 -   \[FIX] PET Spec; added known DICOM tags, fixed tag error, updated citation, clarified scale factor. [#1021](https://github.com/bids-standard/bids-specification/pull/1021) ([bendhouseart](https://github.com/bendhouseart))
 -   \[MISC] clarify copyright for logo [#1019](https://github.com/bids-standard/bids-specification/pull/1019) ([sappelhoff](https://github.com/sappelhoff))
+-   \[SCHEMA] Define YAML tables for MRI common metadata fields and anatomy data [#1017](https://github.com/bids-standard/bids-specification/pull/1017) ([tsalo](https://github.com/tsalo))
+-   SCHEMA: Encode first two MR metadata tables as "sidecars.yml" [#1016](https://github.com/bids-standard/bids-specification/pull/1016) ([tsalo](https://github.com/tsalo))
+-   \[SCHEMA] Add datatypes field to datatype rule files [#1012](https://github.com/bids-standard/bids-specification/pull/1012) ([tsalo](https://github.com/tsalo))
 -   \[FIX] Change recording entity to REQUIRED for pet/blood modality [#1005](https://github.com/bids-standard/bids-specification/pull/1005) ([ghisvail](https://github.com/ghisvail))
 -   \[ENH] Microscopy: Add IntendedFor metadata field to photo files [#1000](https://github.com/bids-standard/bids-specification/pull/1000) ([mariehbourget](https://github.com/mariehbourget))
 -   \[ENH] Introduce the atlas entity for derivatives data [#997](https://github.com/bids-standard/bids-specification/pull/997) ([sebastientourbier](https://github.com/sebastientourbier))
 -   \[ENH] Clearly define "entity" in common principles [#947](https://github.com/bids-standard/bids-specification/pull/947) ([Lestropie](https://github.com/Lestropie))
--   \[ENH] Add BIDS URIs and deprecate relative paths, RawSources and (possibly unused) BasedOn [#918](https://github.com/bids-standard/bids-specification/pull/918) ([effigies](https://github.com/effigies))
 -   \[ENH] BEP030: Functional Near-Infrared Spectroscopy [#802](https://github.com/bids-standard/bids-specification/pull/802) ([rob-luke](https://github.com/rob-luke))
 -   \[FIX] Clarify run entity to accommodate multiple imaging modalities [#760](https://github.com/bids-standard/bids-specification/pull/760) ([yarikoptic](https://github.com/yarikoptic))
 
 ## [v1.7.0](https://github.com/bids-standard/bids-specification/tree/v1.7.0) (2022-02-15)
 
+-   \[ENH] add metadata to PET calibration factor: "DoseCalibrationFactor" [#825](https://github.com/bids-standard/bids-specification/pull/825) ([CPernet](https://github.com/CPernet))
 -   \[FIX] Use wikipedia for TIFF URL, adobe's page is 404ing now [#1007](https://github.com/bids-standard/bids-specification/pull/1007) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] update highlighting of examples, JSON keys and values, and TSV headers or values in the schema [#998](https://github.com/bids-standard/bids-specification/pull/998) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[MISC] minor wording and consistency improvements for channels.tsv in EEG, MEG, iEEG [#993](https://github.com/bids-standard/bids-specification/pull/993) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] typo: extra sentence in anat section [#991](https://github.com/bids-standard/bids-specification/pull/991) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] Optionally support echo entity for VFA suffix [#989](https://github.com/bids-standard/bids-specification/pull/989) ([TheChymera](https://github.com/TheChymera))
--   \[FIX] update definition acq_time for sessions.tsv [#986](https://github.com/bids-standard/bids-specification/pull/986) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[FIX] update definition acq\_time for sessions.tsv [#986](https://github.com/bids-standard/bids-specification/pull/986) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] add microscopy to modalities in schema [#984](https://github.com/bids-standard/bids-specification/pull/984) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[MISC] update steering group composition [#976](https://github.com/bids-standard/bids-specification/pull/976) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[MISC] customize footer on html spec [#975](https://github.com/bids-standard/bids-specification/pull/975) ([sappelhoff](https://github.com/sappelhoff))
@@ -134,7 +183,8 @@
 -   \[FIX] Spelling errors in appendices [#951](https://github.com/bids-standard/bids-specification/pull/951) ([Lestropie](https://github.com/Lestropie))
 -   \[FIX] Broken hyperlink in entity list file [#949](https://github.com/bids-standard/bids-specification/pull/949) ([Lestropie](https://github.com/Lestropie))
 -   \[FIX] Rewrite inheritance principle [#946](https://github.com/bids-standard/bids-specification/pull/946) ([Lestropie](https://github.com/Lestropie))
--   \[FIX] Typo: ECG_headshape [#942](https://github.com/bids-standard/bids-specification/pull/942) ([Moo-Marc](https://github.com/Moo-Marc))
+-   Address BEP031 macro requests [#945](https://github.com/bids-standard/bids-specification/pull/945) ([tsalo](https://github.com/tsalo))
+-   \[FIX] Typo: ECG\_headshape [#942](https://github.com/bids-standard/bids-specification/pull/942) ([Moo-Marc](https://github.com/Moo-Marc))
 -   \[FIX] description: dwi is specialized T2 weighting, not T2\* [#939](https://github.com/bids-standard/bids-specification/pull/939) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] relax unrealistically strict requirements with ieeg channels.tsv 'name' column [#938](https://github.com/bids-standard/bids-specification/pull/938) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Add links from derivatives section to entity list [#936](https://github.com/bids-standard/bids-specification/pull/936) ([sappelhoff](https://github.com/sappelhoff))
@@ -144,7 +194,7 @@
 -   \[ENH] Render valid value restrictions in tables based on object definitions in schema [#921](https://github.com/bids-standard/bids-specification/pull/921) ([tsalo](https://github.com/tsalo))
 -   \[ENH] add `hemi` entity to schema [#917](https://github.com/bids-standard/bids-specification/pull/917) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[ENH] update and reformat table for template in coordinate system page [#903](https://github.com/bids-standard/bids-specification/pull/903) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[ENH] add details for content of `\*\_beh.json` [#902](https://github.com/bids-standard/bids-specification/pull/902) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] add details for content of `*_beh.json` [#902](https://github.com/bids-standard/bids-specification/pull/902) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] small typo in json example [#897](https://github.com/bids-standard/bids-specification/pull/897) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[INFRA] Document \*.webm video files as binary [#895](https://github.com/bids-standard/bids-specification/pull/895) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[SCHEMA] Reorganize schema code into a package [#892](https://github.com/bids-standard/bids-specification/pull/892) ([tsalo](https://github.com/tsalo))
@@ -174,7 +224,6 @@
 -   \[FIX] Remove last hardcoded suffix table [#833](https://github.com/bids-standard/bids-specification/pull/833) ([tsalo](https://github.com/tsalo))
 -   \[MISC] make explicit that EDF+ (and for EEG: BDF+) are included in iEEG / EEG format requirements [#831](https://github.com/bids-standard/bids-specification/pull/831) ([sappelhoff](https://github.com/sappelhoff))
 -   \[SCHEMA] Add TSV column files [#827](https://github.com/bids-standard/bids-specification/pull/827) ([tsalo](https://github.com/tsalo))
--   \[ENH] add metadata to PET calibration factor: "DoseCalibrationFactor" [#825](https://github.com/bids-standard/bids-specification/pull/825) ([CPernet](https://github.com/CPernet))
 -   \[FIX] correct file location of scans.tsv file in example [#824](https://github.com/bids-standard/bids-specification/pull/824) ([ghisvail](https://github.com/ghisvail))
 -   \[MISC] update available datatypes in specification [#819](https://github.com/bids-standard/bids-specification/pull/819) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] document required column order MEG, EEG, iEEG, PET, and fix typo iEEG [#818](https://github.com/bids-standard/bids-specification/pull/818) ([sappelhoff](https://github.com/sappelhoff))
@@ -208,25 +257,25 @@
 
 ## [v1.6.0](https://github.com/bids-standard/bids-specification/tree/v1.6.0) (2021-04-22)
 
+-   \[ENH] Bep 009: Positron Emission Tomography [#633](https://github.com/bids-standard/bids-specification/pull/633) ([melanieganz](https://github.com/melanieganz))
 -   \[FIX] Typos discovered by codespell [#784](https://github.com/bids-standard/bids-specification/pull/784) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] Rename "Unit" metadata to "Units" for consistency with existing fields [#773](https://github.com/bids-standard/bids-specification/pull/773) ([effigies](https://github.com/effigies))
 -   \[FIX] typo in pet: institution -> institutional [#771](https://github.com/bids-standard/bids-specification/pull/771) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] install git in linkchecker job [#767](https://github.com/bids-standard/bids-specification/pull/767) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Fix CircleCI workflows [#764](https://github.com/bids-standard/bids-specification/pull/764) ([sappelhoff](https://github.com/sappelhoff))
--   \[INFRA] do not run remark on auto CHANGES [#755](https://github.com/bids-standard/bids-specification/pull/755) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Mix up (typo) between ficiduals and landmarks in EEG spec [#754](https://github.com/bids-standard/bids-specification/pull/754) ([rob-luke](https://github.com/rob-luke))
 -   \[INFRA] updating remark, CIs, contributor docs [#745](https://github.com/bids-standard/bids-specification/pull/745) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] schema for i/eeg coordsys+elecs: sub-ses-acq-space are allowed entities [#743](https://github.com/bids-standard/bids-specification/pull/743) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] move schema documentation into the schema directory [#740](https://github.com/bids-standard/bids-specification/pull/740) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[MISC] standardize string examples format in tables [#739](https://github.com/bids-standard/bids-specification/pull/739) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[MISC] Clarify participant_id in participants.tsv file if it exists [#738](https://github.com/bids-standard/bids-specification/pull/738) ([adam2392](https://github.com/adam2392))
+-   \[MISC] Clarify participant\_id in participants.tsv file if it exists [#738](https://github.com/bids-standard/bids-specification/pull/738) ([adam2392](https://github.com/adam2392))
 -   \[FIX] split MEG files should be listed separately in scans.tsv [#735](https://github.com/bids-standard/bids-specification/pull/735) ([eort](https://github.com/eort))
 -   \[FIX] 1) Clarify appropriate labels for space entity, 2) Clarify channels+electrodes do not have to match [#734](https://github.com/bids-standard/bids-specification/pull/734) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] refactor stimuli mentioning sections in the events page [#697](https://github.com/bids-standard/bids-specification/pull/697) ([Remi-Gau](https://github.com/Remi-Gau))
--   \[ENH] Bep 009: Positron Emission Tomography [#633](https://github.com/bids-standard/bids-specification/pull/633) ([melanieganz](https://github.com/melanieganz))
 
 ## [v1.5.0](https://github.com/bids-standard/bids-specification/tree/v1.5.0) (2021-02-23)
 
+-   \[ENH] Add "multipart DWI" acquisitions and refactor DWI specifications [#624](https://github.com/bids-standard/bids-specification/pull/624) ([oesteban](https://github.com/oesteban))
 -   \[MISC] Updated TotalAcquiredVolumes into TotalAcquiredPairs [#742](https://github.com/bids-standard/bids-specification/pull/742) ([effigies](https://github.com/effigies))
 -   \[SCHEMA] Update qMRI fieldmap schema [#728](https://github.com/bids-standard/bids-specification/pull/728) ([effigies](https://github.com/effigies))
 -   \[FIX] Add deprecated anatomical MRI suffixes back into schema [#725](https://github.com/bids-standard/bids-specification/pull/725) ([tsalo](https://github.com/tsalo))
@@ -259,12 +308,12 @@
 -   \[ENH] Update genetics-BIDS citation [#646](https://github.com/bids-standard/bids-specification/pull/646) ([effigies](https://github.com/effigies))
 -   \[SCHEMA] Add derivatives entities to the schema [#645](https://github.com/bids-standard/bids-specification/pull/645) ([tsalo](https://github.com/tsalo))
 -   \[MISC] add brief note that TSV example in the spec may currently use either tab or space characters [#643](https://github.com/bids-standard/bids-specification/pull/643) ([yarikoptic](https://github.com/yarikoptic))
--   \[ENH] Add "multipart DWI" acquisitions and refactor DWI specifications [#624](https://github.com/bids-standard/bids-specification/pull/624) ([oesteban](https://github.com/oesteban))
 -   \[SCHEMA] Render schema elements in text [#610](https://github.com/bids-standard/bids-specification/pull/610) ([tsalo](https://github.com/tsalo))
 -   \[ENH] Add part entity for complex-valued data [#424](https://github.com/bids-standard/bids-specification/pull/424) ([tsalo](https://github.com/tsalo))
 
 ## [v1.4.1](https://github.com/bids-standard/bids-specification/tree/v1.4.1) (2020-10-13)
 
+-   \[ENH] Extend date time information to include optional UTC syntax, warn about FIF requirements [#546](https://github.com/bids-standard/bids-specification/pull/546) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] minor robustness enhancements to pdf build shell script  [#642](https://github.com/bids-standard/bids-specification/pull/642) ([yarikoptic](https://github.com/yarikoptic))
 -   \[FIX] consistent CoordinateSystem fields for ephys [#641](https://github.com/bids-standard/bids-specification/pull/641) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] set up github action to detect latin phrases [#636](https://github.com/bids-standard/bids-specification/pull/636) ([Remi-Gau](https://github.com/Remi-Gau))
@@ -292,6 +341,7 @@
 -   \[FIX] Fix link in Common principles [#583](https://github.com/bids-standard/bids-specification/pull/583) ([tsalo](https://github.com/tsalo))
 -   \[ENH] Specify how to share cross-talk and fine-calibration for Neuromag/Elekta/MEGIN data [#581](https://github.com/bids-standard/bids-specification/pull/581) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Specify echo and run indices are nonnegative integers in schema [#578](https://github.com/bids-standard/bids-specification/pull/578) ([tsalo](https://github.com/tsalo))
+-   Updating the bep009 with the latest master branch updates [#576](https://github.com/bids-standard/bids-specification/pull/576) ([melanieganz](https://github.com/melanieganz))
 -   \[ENH] add optional presentation software name, version, OS, and code to events.json [#573](https://github.com/bids-standard/bids-specification/pull/573) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[ENH] added PPG as an accepted channel type for EEG, MEG and iEEG [#570](https://github.com/bids-standard/bids-specification/pull/570) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[INFRA] Move entity definitions to a separate page [#568](https://github.com/bids-standard/bids-specification/pull/568) ([tsalo](https://github.com/tsalo))
@@ -301,7 +351,6 @@
 -   \[FIX] Clarify requirement levels for TSV metadata fields [#555](https://github.com/bids-standard/bids-specification/pull/555) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Reorganize rec, ce entities, \_defacemask [#550](https://github.com/bids-standard/bids-specification/pull/550) ([emdupre](https://github.com/emdupre))
 -   \[FIX] Clarify Upper-casing of Channels.tsv Channel Type [#548](https://github.com/bids-standard/bids-specification/pull/548) ([adam2392](https://github.com/adam2392))
--   \[ENH] Extend date time information to include optional UTC syntax, warn about FIF requirements [#546](https://github.com/bids-standard/bids-specification/pull/546) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] clarify that \<physio|stim>.json is REQUIRED [#542](https://github.com/bids-standard/bids-specification/pull/542) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Replace all non-breaking spaces with vanilla spaces [#536](https://github.com/bids-standard/bids-specification/pull/536) ([nicholst](https://github.com/nicholst))
 -   \[FIX] Clarify indices are nonnegative integers. [#535](https://github.com/bids-standard/bids-specification/pull/535) ([nicholst](https://github.com/nicholst))
@@ -314,7 +363,7 @@
 -   \[FIX] restructure and clarify \*\_physio/\*\_stim section [#513](https://github.com/bids-standard/bids-specification/pull/513) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] clarify file formats in EEG, iEEG [#511](https://github.com/bids-standard/bids-specification/pull/511) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Add links and release dates to pre GH changelog, fix formatting [#509](https://github.com/bids-standard/bids-specification/pull/509) ([sappelhoff](https://github.com/sappelhoff))
--   \[FIX] Clarify that `acq\_time` in `scans.json` refers to first data point acquired [#506](https://github.com/bids-standard/bids-specification/pull/506) ([tsalo](https://github.com/tsalo))
+-   \[FIX] Clarify that `acq_time` in `scans.json` refers to first data point acquired [#506](https://github.com/bids-standard/bids-specification/pull/506) ([tsalo](https://github.com/tsalo))
 -   \[INFRA] make circle artifact link a GH action, point to pdf [#505](https://github.com/bids-standard/bids-specification/pull/505) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Typos in DECISION-MAKING file [#504](https://github.com/bids-standard/bids-specification/pull/504) ([tsalo](https://github.com/tsalo))
 -   \[ENH] Add `Commenting on a PR` to CONTRIBUTING.md [#490](https://github.com/bids-standard/bids-specification/pull/490) ([franklin-feingold](https://github.com/franklin-feingold))
@@ -324,31 +373,42 @@
 
 ## [v1.4.0](https://github.com/bids-standard/bids-specification/tree/v1.4.0) (2020-06-11)
 
+-   \[ENH] Derived (processed) MR data [#109](https://github.com/bids-standard/bids-specification/pull/109) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[FIX] Clarify language on unsetting a key/value pair [#495](https://github.com/bids-standard/bids-specification/pull/495) ([nicholst](https://github.com/nicholst))
+-   \[ENH] Add RECOMMENDED DatasetType key to dataset description [#494](https://github.com/bids-standard/bids-specification/pull/494) ([effigies](https://github.com/effigies))
+-   \[ENH] Clarify mask/dseg/probseg in common derivatives [#489](https://github.com/bids-standard/bids-specification/pull/489) ([effigies](https://github.com/effigies))
+-   \[ENH] Reorganize derivatives [#488](https://github.com/bids-standard/bids-specification/pull/488) ([effigies](https://github.com/effigies))
 -   \[ENH] optionally allow LICENSE file [#483](https://github.com/bids-standard/bids-specification/pull/483) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] linkchecker - ignore github pull and tree URLs [#477](https://github.com/bids-standard/bids-specification/pull/477) ([yarikoptic](https://github.com/yarikoptic))
 -   \[ENH] Allow fractional seconds in scans file datetimes [#470](https://github.com/bids-standard/bids-specification/pull/470) ([tsalo](https://github.com/tsalo))
 -   \[MISC] Maintainers - `Scope` responsibility [#467](https://github.com/bids-standard/bids-specification/pull/467) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] Align tables in MRI section [#465](https://github.com/bids-standard/bids-specification/pull/465) ([sappelhoff](https://github.com/sappelhoff))
--   \[FIX] Drop `\_part-` reference from example, introduce `\_split-` entity [#460](https://github.com/bids-standard/bids-specification/pull/460) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Drop `_part-` reference from example, introduce `_split-` entity [#460](https://github.com/bids-standard/bids-specification/pull/460) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] clarify participants tsv+json with examples and recommendations [#459](https://github.com/bids-standard/bids-specification/pull/459) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Remove BESA from list of restricted keywords of EEG coordsystems [#457](https://github.com/bids-standard/bids-specification/pull/457) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] add steps for release protocol (PDF upload) [#455](https://github.com/bids-standard/bids-specification/pull/455) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Add reference to PDF on front page of specification [#452](https://github.com/bids-standard/bids-specification/pull/452) ([nicholst](https://github.com/nicholst))
 -   \[INFRA] Add conditional for link-checking releases [#451](https://github.com/bids-standard/bids-specification/pull/451) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] unordered list formatting in BEP018 [#449](https://github.com/bids-standard/bids-specification/pull/449) ([sappelhoff](https://github.com/sappelhoff))
+-   \[INFRA] add zenodo badge to README [#447](https://github.com/bids-standard/bids-specification/pull/447) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] fix inconsistencies for task label between sections [#446](https://github.com/bids-standard/bids-specification/pull/446) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] update DECISION-MAKING.md document with new governance [#441](https://github.com/bids-standard/bids-specification/pull/441) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] specify the derivatives pipeline following #345 [#358](https://github.com/bids-standard/bids-specification/pull/358) ([CPernet](https://github.com/CPernet))
+-   ENH: Clarify the position toward non-compliant derivative datasets and files [#334](https://github.com/bids-standard/bids-specification/pull/334) ([effigies](https://github.com/effigies))
+-   \[FIX] Separate out imaging-specific "common derivatives" [#310](https://github.com/bids-standard/bids-specification/pull/310) ([effigies](https://github.com/effigies))
+-   \[FIX] Revise template-generated coordinate systems [#307](https://github.com/bids-standard/bids-specification/pull/307) ([oesteban](https://github.com/oesteban))
+-   \[ENH] Add `res` and `den` keywords to indicate resolution of resampled data [#301](https://github.com/bids-standard/bids-specification/pull/301) ([oesteban](https://github.com/oesteban))
 -   \[ENH] BEP 003: Common Derivatives [#265](https://github.com/bids-standard/bids-specification/pull/265) ([effigies](https://github.com/effigies))
+-   \[FIX] use \<label> for \_desc- - not some \<value> + clarify \<value> [#224](https://github.com/bids-standard/bids-specification/pull/224) ([yarikoptic](https://github.com/yarikoptic))
+-   \[ENH] Various proposed changes to diffusion derivatives [#205](https://github.com/bids-standard/bids-specification/pull/205) ([Lestropie](https://github.com/Lestropie))
 -   \[ENH] Add Glossary of terms/abbreviations used in the specification [#152](https://github.com/bids-standard/bids-specification/pull/152) ([yarikoptic](https://github.com/yarikoptic))
 
 ## [v1.3.0](https://github.com/bids-standard/bids-specification/tree/v1.3.0) (2020-04-14)
 
--   \[INFRA] add zenodo badge to README [#447](https://github.com/bids-standard/bids-specification/pull/447) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Added contributors from VisLab [#444](https://github.com/bids-standard/bids-specification/pull/444) ([VisLab](https://github.com/VisLab))
--   \[FIX] Clarify  snake_case+CamelCase in TSV+JSON [#442](https://github.com/bids-standard/bids-specification/pull/442) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Clarify  snake\_case+CamelCase in TSV+JSON [#442](https://github.com/bids-standard/bids-specification/pull/442) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Eliminate web/online-specific language [#437](https://github.com/bids-standard/bids-specification/pull/437) ([nicholst](https://github.com/nicholst))
--   \[INFRA] ensure build_docs_pdf CircleCI job runs last [#436](https://github.com/bids-standard/bids-specification/pull/436) ([sappelhoff](https://github.com/sappelhoff))
+-   \[INFRA] ensure build\_docs\_pdf CircleCI job runs last [#436](https://github.com/bids-standard/bids-specification/pull/436) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Add issue templates for GitHub [#434](https://github.com/bids-standard/bids-specification/pull/434) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Get latest PDF build from CircleCI artifacts [#433](https://github.com/bids-standard/bids-specification/pull/433) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Update release protocol [#432](https://github.com/bids-standard/bids-specification/pull/432) ([franklin-feingold](https://github.com/franklin-feingold))
@@ -359,19 +419,21 @@
 -   \[INFRA] add # before heading in CHANGES [#419](https://github.com/bids-standard/bids-specification/pull/419) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] fix heading of auto changelog to be a markdown header [#417](https://github.com/bids-standard/bids-specification/pull/417) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Add OPTIONAL EthicsApprovals field to dataset description [#412](https://github.com/bids-standard/bids-specification/pull/412) ([effigies](https://github.com/effigies))
+-   \[FIX] improve wording on data dictionaries [#410](https://github.com/bids-standard/bids-specification/pull/410) ([sappelhoff](https://github.com/sappelhoff))
+-   BEP 18 suggestions [#398](https://github.com/bids-standard/bids-specification/pull/398) ([effigies](https://github.com/effigies))
 -   \[ENH] BEP 018 - Genetic Information [#395](https://github.com/bids-standard/bids-specification/pull/395) ([effigies](https://github.com/effigies))
+-   \[FIX] consistent units description between EEG/MEG/iEEG. Clarify (derived) SI units + prefixes [#391](https://github.com/bids-standard/bids-specification/pull/391) ([sappelhoff](https://github.com/sappelhoff))
 
 ## [v1.2.2](https://github.com/bids-standard/bids-specification/tree/v1.2.2) (2020-02-12)
 
--   \[FIX] improve wording on data dictionaries [#410](https://github.com/bids-standard/bids-specification/pull/410) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Normalization of template-generated standard spaces [#306](https://github.com/bids-standard/bids-specification/pull/306) ([oesteban](https://github.com/oesteban))
 -   \[MISC] update contributions by CPernet [#409](https://github.com/bids-standard/bids-specification/pull/409) ([CPernet](https://github.com/CPernet))
 -   \[MISC] Add Sébastien Tourbier to contributors [#394](https://github.com/bids-standard/bids-specification/pull/394) ([sebastientourbier](https://github.com/sebastientourbier))
--   \[FIX] consistent units description between EEG/MEG/iEEG. Clarify (derived) SI units + prefixes [#391](https://github.com/bids-standard/bids-specification/pull/391) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] moved list of extension proposals to the main BIDS website [#389](https://github.com/bids-standard/bids-specification/pull/389) ([robertoostenveld](https://github.com/robertoostenveld))
 -   \[FIX] Typos and clarifications [#386](https://github.com/bids-standard/bids-specification/pull/386) ([apjanke](https://github.com/apjanke))
 -   \[INFRA] Add watermark to drafts [#383](https://github.com/bids-standard/bids-specification/pull/383) ([effigies](https://github.com/effigies))
 -   \[MISC] Teon Brooks retiring moderator duties for BEP021 [#381](https://github.com/bids-standard/bids-specification/pull/381) ([teonbrooks](https://github.com/teonbrooks))
--   \[FIX] clarify that string is expected for HowToAcknowledge field in dataset_description.json [#380](https://github.com/bids-standard/bids-specification/pull/380) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] clarify that string is expected for HowToAcknowledge field in dataset\_description.json [#380](https://github.com/bids-standard/bids-specification/pull/380) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Typo and style [#378](https://github.com/bids-standard/bids-specification/pull/378) ([TheChymera](https://github.com/TheChymera))
 -   \[FIX] divide readme into 3 parts [#374](https://github.com/bids-standard/bids-specification/pull/374) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Refer to BIDS consistently, instead of "\<Modality>-BIDS" [#366](https://github.com/bids-standard/bids-specification/pull/366) ([sappelhoff](https://github.com/sappelhoff))
@@ -393,7 +455,6 @@
 -   \[INFRA] Link to doc builds in CI checks [#315](https://github.com/bids-standard/bids-specification/pull/315) ([jasmainak](https://github.com/jasmainak))
 -   \[MISC] Add BEP027 - BIDS Execution to BEP list [#314](https://github.com/bids-standard/bids-specification/pull/314) ([effigies](https://github.com/effigies))
 -   \[FIX] Add CBV and phase to Entity table [#312](https://github.com/bids-standard/bids-specification/pull/312) ([tsalo](https://github.com/tsalo))
--   \[FIX] Normalization of template-generated standard spaces [#306](https://github.com/bids-standard/bids-specification/pull/306) ([oesteban](https://github.com/oesteban))
 -   \[ENH] Release protocol notes [#304](https://github.com/bids-standard/bids-specification/pull/304) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Adding contributor appendix sentence to PR template  [#299](https://github.com/bids-standard/bids-specification/pull/299) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[ENH] Added discontinuous datatype for EEG and iEEG [#286](https://github.com/bids-standard/bids-specification/pull/286) ([wouterpotters](https://github.com/wouterpotters))
@@ -401,6 +462,7 @@
 
 ## [v1.2.1](https://github.com/bids-standard/bids-specification/tree/v1.2.1) (2019-08-14)
 
+-   \[INFRA] Add clarification on merge methods to DECISION\_MAKING [#217](https://github.com/bids-standard/bids-specification/pull/217) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] repair link in anatomical MRI table [#297](https://github.com/bids-standard/bids-specification/pull/297) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] Clarify requirements in Release Protocol [#294](https://github.com/bids-standard/bids-specification/pull/294) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[INFRA] Use linkchecker (from a dedicated docker image) to check all URLs [#293](https://github.com/bids-standard/bids-specification/pull/293) ([yarikoptic](https://github.com/yarikoptic))
@@ -427,7 +489,6 @@
 -   \[INFRA] Enable version panel for quickly finding previous versions [#232](https://github.com/bids-standard/bids-specification/pull/232) ([effigies](https://github.com/effigies))
 -   \[FIX] Clarify Appendix II: The list of licenses only lists examples [#222](https://github.com/bids-standard/bids-specification/pull/222) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Trivial column header fix  [#220](https://github.com/bids-standard/bids-specification/pull/220) ([nicholst](https://github.com/nicholst))
--   \[INFRA] Add clarification on merge methods to DECISION_MAKING [#217](https://github.com/bids-standard/bids-specification/pull/217) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Enable permalink urls to appear at (sub)section headings [#214](https://github.com/bids-standard/bids-specification/pull/214) ([yarikoptic](https://github.com/yarikoptic))
 -   \[INFRA] bump up mkdocs-materials version [#211](https://github.com/bids-standard/bids-specification/pull/211) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Fix github username for @chrisgorgo [#204](https://github.com/bids-standard/bids-specification/pull/204) ([chrisgorgo](https://github.com/chrisgorgo))
@@ -450,36 +511,36 @@
 -   \[FIX] Clarify continuous recording metadata fields [#167](https://github.com/bids-standard/bids-specification/pull/167) ([effigies](https://github.com/effigies))
 -   \[FIX] changed reference of `dcm2nii` to `dcm2niix` [#166](https://github.com/bids-standard/bids-specification/pull/166) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
 -   \[FIX] Removing a leftover file [#162](https://github.com/bids-standard/bids-specification/pull/162) ([chrisgorgo](https://github.com/chrisgorgo))
+-   \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   \[FIX] use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic))
+-   \[FIX] Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   \[ENH] clarify decimal sep and numerical notation convention [#143](https://github.com/bids-standard/bids-specification/pull/143) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] Specify marker filenames for KIT data (MEG) [#62](https://github.com/bids-standard/bids-specification/pull/62) ([monkeyman192](https://github.com/monkeyman192))
 -   \[FIX] Remove father-level for meg filetypes other than BTi/4D data [#19](https://github.com/bids-standard/bids-specification/pull/19) ([teonbrooks](https://github.com/teonbrooks))
 
 ## [v1.2.0](https://github.com/bids-standard/bids-specification/tree/v1.2.0) (2019-03-04)
 
--   \[MISC] Adding Dimitri Papadopoulos Orfanos to the list of contributors [#157](https://github.com/bids-standard/bids-specification/pull/157) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
--   \[FIX] use "specification" not "protocol" to refer to BIDS [#156](https://github.com/bids-standard/bids-specification/pull/156) ([yarikoptic](https://github.com/yarikoptic))
--   \[FIX] Fix example misalignment [#155](https://github.com/bids-standard/bids-specification/pull/155) ([DimitriPapadopoulos](https://github.com/DimitriPapadopoulos))
+-   \[ENH] Merge bep006 and bep010 [#108](https://github.com/bids-standard/bids-specification/pull/108) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Update Pipfile.lock [#144](https://github.com/bids-standard/bids-specification/pull/144) ([franklin-feingold](https://github.com/franklin-feingold))
--   \[ENH] clarify decimal sep and numerical notation convention [#143](https://github.com/bids-standard/bids-specification/pull/143) ([sappelhoff](https://github.com/sappelhoff))
 -   \[ENH] clarify encoding of README, CHANGES, TSV, and JSON files [#140](https://github.com/bids-standard/bids-specification/pull/140) ([sappelhoff](https://github.com/sappelhoff))
--   \[MISC] Update site_name and release protocol [#137](https://github.com/bids-standard/bids-specification/pull/137) ([franklin-feingold](https://github.com/franklin-feingold))
+-   \[MISC] Update site\_name and release protocol [#137](https://github.com/bids-standard/bids-specification/pull/137) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[FIX] Example for IntendedFor was missing session indicator in the filename [#129](https://github.com/bids-standard/bids-specification/pull/129) ([yarikoptic](https://github.com/yarikoptic))
 -   \[ENH] Add "\_phase" suffix to func datatype for functional phase data [#128](https://github.com/bids-standard/bids-specification/pull/128) ([tsalo](https://github.com/tsalo))
--   \[MISC] Update to Release_Protocol.md [#126](https://github.com/bids-standard/bids-specification/pull/126) ([franklin-feingold](https://github.com/franklin-feingold))
+-   \[MISC] Update to Release\_Protocol.md [#126](https://github.com/bids-standard/bids-specification/pull/126) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] Update tag naming convention [#123](https://github.com/bids-standard/bids-specification/pull/123) ([chrisgorgo](https://github.com/chrisgorgo))
--   \[ENH] Merge bep006 and bep010 [#108](https://github.com/bids-standard/bids-specification/pull/108) ([sappelhoff](https://github.com/sappelhoff))
 -   \[MISC] Adding formal decision-making rules [#104](https://github.com/bids-standard/bids-specification/pull/104) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[FIX] number of small corrections to the specification [#98](https://github.com/bids-standard/bids-specification/pull/98) ([robertoostenveld](https://github.com/robertoostenveld))
 
 ## [v1.1.2](https://github.com/bids-standard/bids-specification/tree/v1.1.2) (2019-01-10)
 
 -   \[ENH] Global fields in data dictionaries [#117](https://github.com/bids-standard/bids-specification/pull/117) ([chrisgorgo](https://github.com/chrisgorgo))
+-   \[ENH] First(?) good practice recommendation. No excessive overrides in Inheritance principle [#99](https://github.com/bids-standard/bids-specification/pull/99) ([yarikoptic](https://github.com/yarikoptic))
 -   \[MISC] Propose BEP026 MER [#116](https://github.com/bids-standard/bids-specification/pull/116) ([greydongilmore](https://github.com/greydongilmore))
 -   \[FIX] Remove duplicate entries in MEG table [#113](https://github.com/bids-standard/bids-specification/pull/113) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] Propose BEP025 MIDS [#110](https://github.com/bids-standard/bids-specification/pull/110) ([josator2](https://github.com/josator2))
 -   \[FIX] repair links [#106](https://github.com/bids-standard/bids-specification/pull/106) ([sappelhoff](https://github.com/sappelhoff))
 -   \[INFRA] Autogenerate CHANGES.md [#103](https://github.com/bids-standard/bids-specification/pull/103) ([franklin-feingold](https://github.com/franklin-feingold))
 -   \[MISC] Added contributor information [#100](https://github.com/bids-standard/bids-specification/pull/100) ([jgrethe](https://github.com/jgrethe))
--   \[ENH] First(?) good practice recommendation. No excessive overrides in Inheritance principle [#99](https://github.com/bids-standard/bids-specification/pull/99) ([yarikoptic](https://github.com/yarikoptic))
 -   \[MISC] adding extensions page [#97](https://github.com/bids-standard/bids-specification/pull/97) ([choldgraf](https://github.com/choldgraf))
 -   \[FIX] fix some urls (as detected to be broken/inconsistent) [#95](https://github.com/bids-standard/bids-specification/pull/95) ([yarikoptic](https://github.com/yarikoptic))
 -   \[MISC] Change BEP numbers to include MRS [#94](https://github.com/bids-standard/bids-specification/pull/94) ([Hboni](https://github.com/Hboni))
@@ -496,7 +557,7 @@
 -   \[MISC] Updated my contributions [#75](https://github.com/bids-standard/bids-specification/pull/75) ([nicholst](https://github.com/nicholst))
 -   \[FIX] update HED appendix [#74](https://github.com/bids-standard/bids-specification/pull/74) ([sappelhoff](https://github.com/sappelhoff))
 -   \[FIX] unicode: replace greek mu and omega by micro and ohm signs [#73](https://github.com/bids-standard/bids-specification/pull/73) ([sappelhoff](https://github.com/sappelhoff))
--   \[ENH] add `ce-\<label\>` for fmri data [#70](https://github.com/bids-standard/bids-specification/pull/70) ([dasturge](https://github.com/dasturge))
+-   \[ENH] add `ce-<label>` for fmri data [#70](https://github.com/bids-standard/bids-specification/pull/70) ([dasturge](https://github.com/dasturge))
 -   \[INFRA] pin pip version [#68](https://github.com/bids-standard/bids-specification/pull/68) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] Fix link in index [#46](https://github.com/bids-standard/bids-specification/pull/46) ([chrisgorgo](https://github.com/chrisgorgo))
 -   \[MISC] edit contributing guide [#44](https://github.com/bids-standard/bids-specification/pull/44) ([patrick-g-h](https://github.com/patrick-g-h))
@@ -607,5 +668,3 @@
 ## 1.0.0-rc1
 
 -   Initial release
-
-\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*

From da7ee9e11433e0ad427b228f0cb1fbe2025b93e2 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 13 Jun 2024 19:28:54 +0200
Subject: [PATCH 32/74] DOC: Updates to how changelog generator is working
 (#1851)

---
 CONTRIBUTING.md     | 15 +++++----------
 Release_Protocol.md |  4 ----
 2 files changed, 5 insertions(+), 14 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 208d0bd43b..d16d54cdc5 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -721,17 +721,12 @@ The decision-making rules are outlined in
 
 The changelog (see `src/CHANGES.md`) is generated automatically using
 [github-changelog-generator](https://github.com/github-changelog-generator/github-changelog-generator).
-You can see the workflow in the CircleCI configuration file (`.circleci/config.yml`).
+You can see the workflow in the following GitHub Actions configuration file: `.github/workflows/changelog_generator.yml`.
 
-As it stands, the changelog is generated whenever a pull request is integrated into
-the `master` branch of the specification via a "Merge commit"
-(as opposed to "Squash and merge" or "Rebase and merge";
-see the [GitHub help page](https://help.github.com/en/articles/about-merge-methods-on-github)
-for more information on merge methods).
-
-![merge-commit](release_images/merge_commit.png "merge-commit")
-
-Note that for pull requests starting with `REL:`, no changelog is generated.
+This workflow is triggered for every commit to `master` that contains string `[build changelog]` in its commit message.
+If you push several commits at once, you need to make sure that the "youngest commit" (the HEAD commit) contains that string.
+The workflow will then open a Pull Request to incorporate the updated changelog.
+Check the proposed changes and merge the Pull Request at will.
 
 To exclude pull requests from showing up in the changelog, they have to be labeled with
 the "exclude-from-changelog" label.
diff --git a/Release_Protocol.md b/Release_Protocol.md
index c93c039a48..9e2f6292c6 100644
--- a/Release_Protocol.md
+++ b/Release_Protocol.md
@@ -12,10 +12,6 @@ your fork locally to a directory called `bids-specification`.
 
 Before you start a release, you have to ensure that the automatically generated changelog is **up to date**.
 See the relevant [section in CONTRIBUTING.md](CONTRIBUTING.md#how-is-the-changelog-generated) for further information.
-In practice this means ensuring that the most recently merged pull request
-was merged into the `master` branch using the "Merge commit" option.
-
-![merge-commit](release_images/merge_commit.png.png "merge-commit")
 
 ### 1. Fetch the latest version of the [master branch of the BIDS-specification](https://github.com/bids-standard/bids-specification/tree/master)
 

From 55e286981992021dcabb073af3a87a8336e489c5 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 13 Jun 2024 19:32:57 +0200
Subject: [PATCH 33/74] [DOC] add maintainers guide (#1770)

* add maintainers guide

* move file

* Apply suggestions from code review

Co-authored-by: Ariel Rokem <arokem@gmail.com>

* migrate info from DECISION_MAKING.md to maintainers guide

* streamlining and additions

* fix typo

---------

Co-authored-by: Ariel Rokem <arokem@gmail.com>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 DECISION-MAKING.md   |  45 ++++-----------
 Maintainers_Guide.md | 135 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 145 insertions(+), 35 deletions(-)
 create mode 100644 Maintainers_Guide.md

diff --git a/DECISION-MAKING.md b/DECISION-MAKING.md
index f31b2eacbf..cbf7946af4 100644
--- a/DECISION-MAKING.md
+++ b/DECISION-MAKING.md
@@ -14,40 +14,15 @@ BIDS governance.
 
 ### Steering Group
 
-Current and past members of the steering group can be found
-[here](https://bids.neuroimaging.io/governance.html#bids-steering-group).
+Current and past members of the steering group can be found in the
+[BIDS governance](https://bids.neuroimaging.io/governance.html#bids-steering-group).
 
 ### Maintainers Group
 
-| Name                                                                      | Time commitment | Scope                                 | Joined   |
-| ------------------------------------------------------------------------- | --------------- | ------------------------------------- | -------- |
-| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff))           | 1h/week         |                                       | Mar 2020 |
-| Chris Markiewicz ([@effigies](https://github.com/effigies))               | 5h/week         |                                       | Mar 2020 |
-| Ross Blair ([@rwblair](https://github.com/rwblair))                       |                 | Maintainer of the bids-validator      | Mar 2020 |
-| Taylor Salo ([@tsalo](https://github.com/tsalo))                          | 3h/week         | MRI                                   | Sep 2020 |
-| Remi Gau ([@Remi-Gau](https://github.com/Remi-Gau))                       | 3h/week         | Community development, MRI            | Oct 2020 |
-| Anthony Galassi  ([@bendhouseart](https://github.com/bendhouseart))       | 3h/week         | PET, Community development            | Sep 2021 |
-| Eric Earl ([@ericearl](https://github.com/ericearl))                      | 2h/week         |                                       | Dec 2021 |
-| Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/month        | Interoperability, EEG and multi-modal | Apr 2023 |
-| Nell Hardcastle ([@nellh](https://github.com/nellh))                      | 2h/week         |                                       | Jul 2023 |
-| Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay))           | 1h/week         |                                       | Nov 2022 |
-
-In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
-classification of a maintainer, maintainers may declare a limited scope of responsibility.
-Such a scope can range from maintaining a modality supported in the specification to nurturing a
-welcoming BIDS community.
-Any number of scopes can be chosen by the maintainer and agreed upon by the Maintainers Group.
-A maintainer is primarily responsible for issues within their chosen scope(s), although
-contributions elsewhere are welcome, as well.
-
-The role of the "lead maintainer", that is, the BIDS maintainer currently representing the maintainers group,
-is rotating among current maintainers.
-
-#### Past maintainers group members
-
-| Name                                                                           | Duration            |
-| ------------------------------------------------------------------------------ | ------------------- |
-| Franklin Feingold ([@franklin-feingold](https://github.com/franklin-feingold)) | Mar 2020 - Jul 2022 |
+Current and past members of the maintainers group can be found in the
+[BIDS governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group),
+and in the
+[Maintainers Guide](Maintainers_Guide.md).
 
 ### BEP Leads Group
 
@@ -65,8 +40,9 @@ according to the instructions listed there.
 
 ### Other groups
 
-The following groups not listed in detail. Please learn more about these groups
-from the [governance document](https://bids.neuroimaging.io/governance.html).
+The following groups are not described in detail.
+Please learn more about these groups from the
+[BIDS governance](https://bids.neuroimaging.io/governance.html).
 
 - BEP working groups
 - Advisory Group
@@ -82,8 +58,7 @@ following rules with the intention to:
 - Minimize the administrative burden.
 - Provide a path for when consensus cannot be made.
 - Grow the community.
-- Maximize the [bus factor](https://en.wikipedia.org/wiki/Bus_factor) of the
-  project.
+- Maximize the [bus factor](https://en.wikipedia.org/wiki/Bus_factor) of the project.
 
 The rules outlined below are inspired by the [lazy consensus system used in the Apache Foundation](https://www.apache.org/foundation/voting.html)
 and heavily depends on [GitHub Pull Request Review system](https://help.github.com/articles/about-pull-requests/).
diff --git a/Maintainers_Guide.md b/Maintainers_Guide.md
new file mode 100644
index 0000000000..1c668ec382
--- /dev/null
+++ b/Maintainers_Guide.md
@@ -0,0 +1,135 @@
+# BIDS Maintainers Group Guide
+
+The BIDS Maintainers are a key group of members that ensure that the BIDS infrastructure is kept up.
+The maintainers have wide-ranging responsibilities that enable BIDS to continue to grow and succeed.
+As furthermore detailed in the [DECISION-MAKING document](DECISION-MAKING.md),
+maintainers have a set of rights that go beyond those of a contributor.
+
+The following guide draws heavily on a related [blog post](https://matthewrocklin.com/blog/2019/05/18/maintainer)
+on "The Role of a Maintainer" by Matthew Rocklin,
+which is a recommended reading in conjunction with this guide.
+
+## Current BIDS Maintainers
+
+See also: [BIDS governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
+
+| Name                                                                      | Time commitment | Scope                                 | Joined   |
+| ------------------------------------------------------------------------- | --------------- | ------------------------------------- | -------- |
+| Stefan Appelhoff ([@sappelhoff](https://github.com/sappelhoff))           | 1h/week         |                                       | Mar 2020 |
+| Chris Markiewicz ([@effigies](https://github.com/effigies))               | 5h/week         |                                       | Mar 2020 |
+| Ross Blair ([@rwblair](https://github.com/rwblair))                       |                 | Maintainer of the bids-validator      | Mar 2020 |
+| Taylor Salo ([@tsalo](https://github.com/tsalo))                          | 3h/week         | MRI                                   | Sep 2020 |
+| Remi Gau ([@Remi-Gau](https://github.com/Remi-Gau))                       | 3h/week         | Community development, MRI            | Oct 2020 |
+| Anthony Galassi  ([@bendhouseart](https://github.com/bendhouseart))       | 3h/week         | PET, Community development            | Sep 2021 |
+| Eric Earl ([@ericearl](https://github.com/ericearl))                      | 2h/week         |                                       | Dec 2021 |
+| Christine Rogers ([@christinerogers](https://github.com/christinerogers)) | 2h/month        | Interoperability, EEG and multi-modal | Apr 2023 |
+| Nell Hardcastle ([@nellh](https://github.com/nellh))                      | 2h/week         |                                       | Jul 2023 |
+| Kimberly Ray ([@KimberlyLRay](https://github.com/KimberlyLRay))           | 1h/week         |                                       | Nov 2022 |
+
+In addition to the [BIDS Governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
+classification of a maintainer, maintainers may declare a limited scope of responsibility.
+Such a scope can range from maintaining a modality supported in the specification to nurturing a
+welcoming BIDS community.
+Any number of scopes can be chosen by the maintainer and agreed upon by the Maintainers Group.
+A maintainer is primarily responsible for issues within their chosen scope(s), although
+contributions elsewhere are welcome, as well.
+
+### Lead Maintainer
+
+The role of the "lead maintainer", that is, the BIDS maintainer currently representing the maintainers group,
+is rotating among current maintainers.
+
+## Past BIDS Maintainers
+
+See also: [BIDS governance](https://bids.neuroimaging.io/governance.html#bids-maintainers-group)
+
+| Name                                                                           | Duration            |
+| ------------------------------------------------------------------------------ | ------------------- |
+| Franklin Feingold ([@franklin-feingold](https://github.com/franklin-feingold)) | Mar 2020 - Jul 2022 |
+
+## Why become a maintainer?
+
+As a BIDS maintainer you may get the chance to:
+
+* Learn to work as a team
+* Bring your expertise to the BIDS maintainers group and cover technical blind spots it may have
+* Improving your technical writing skills (for example documentation)
+* Learn to work with continuous integration and deployment
+* Advise and participate in the development of BIDS extensions that are most commonly associated with a publication
+
+## Responsibilities
+
+* Maintainers need to be loosely aware of the entire project
+  and use their knowledge to facilitate and initiate interactions
+  between different nodes of the project
+  and determine a reasonable and timely order for features to be added and issues to be resolved.
+* Maintainers direct other BIDS contributors in reviewing PRs,
+  writing clarifications to the specification, or other contributions.
+* Maintainers ensure that all contributors maintain a friendly and welcoming tone
+  to encourage productive conversations.
+* If no work team is suitable or available,
+  the final responsibility of getting the work done lies with the maintainers.
+* The development of each BIDS extension proposal should be "followed"
+  by at least one maintainer who acts as a preferential point of contact
+  between the BIDS maintainers and the BEP leads.
+
+Apart from these abstract and general responsibilities,
+maintainers within the BIDS community also need to ensure that the following tasks get done:
+
+* Keeping the
+  [Contributors wiki](https://github.com/bids-standard/bids-specification/wiki/Recent-Contributors)
+  up to date and assisting new contributors with adding their credits,
+  and performing community inquiries to ensure contributors are credited in the
+  [Contributors appendix](https://bids-specification.readthedocs.io/en/stable/appendices/contributors.html)
+    * Deciding what constitutes a contribution worth adding to the "Contributors list"
+* Preparing a monthly report to the BIDS Steering Group.
+  The monthly report is in the form of milestones, issues addressed,
+  and open issues raised in the past month and goals/plans for the next month.
+  The BIDS Steering Group may ask for additional information or propose a meeting to further discuss report items.
+  The report format and meetings are at the discretion of the BIDS Steering Group.
+
+Maintainers are not expected to individually be responsible for all the responsibilities listed.
+Rather, the responsibilities are distributed amongst the entire group.
+
+## Organization
+
+* The group of maintainers are a group of people with the above mentioned responsibilities,
+  who commit to convene bi-weekly meetings to discuss the project.
+* One lead maintainer represents the group to other BIDS Groups, mediates disagreement among members,
+  and casts deciding votes when needed (tie break).
+  Note that the maintainers will always strive for consensus decision making, and will try to avoid resorting to voting.
+    * The lead maintainer may delegate any of their duties to another maintainer.
+    * The lead maintainer is appointed collectively by the group of maintainers, preferably through consensus.
+    * If no one else does, the lead maintainer sets the schedule for the maintainers meeting.
+* Additions to and departures from the group are negotiated collectively between the lead maintainer
+  and the new/departing members, as they involve the redistribution of duties.
+    * If a maintainer wishes to serve for a limited term, that can be arranged at the start. Otherwise, due notice is expected.
+    * See also "How to become a maintainer?" below
+
+## How to become a maintainer?
+
+If you are interested in becoming a BIDS maintainer,
+please get in contact with an active BIDS maintainer
+(for example via opening a GitHub issue on bids-standard/bids-specification and tagging `@bids-standard/maintainers`).
+In that initial contact, it would be great if you could outline previous experience with BIDS (if any)
+and your motivation to become a maintainer, as well as particular interests for work that you would like to do.
+The BIDS maintainers will then invite you to one of the biweekly maintainers meetings (online)
+to discuss further steps and point you to the onboarding documentation (things to do).
+
+We would be happy to hear from you!
+
+## Crediting BIDS maintainers in work submissions
+
+If you prepare a submission of work related to BIDS, and would like to credit the BIDS maintainers
+in that submission, please get in touch.
+
+It is for example possible to include BIDS maintainers as a consortium author,
+through using the following OSF account: [https://osf.io/y48x9/](https://osf.io/y48x9/)
+
+We are furthermore preparing more guidelines on this topic, see this work in progress:
+https://docs.google.com/document/d/1yQdYOw7WMpkcFgT4tNalOjKuH34nhmRqg4luI4V9uhE/
+
+## Notes
+
+As detailed in the [BIDS governance](https://bids.neuroimaging.io/governance.html),
+this guide is subject to change and to amendment by the BIDS Steering Group.

From 63ef0412f237db71e5ed1be71dc01d435b3a3014 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 13 Jun 2024 15:55:16 -0400
Subject: [PATCH 34/74] fix(schema): Bad README path check. Sorry.

---
 src/schema/rules/checks/hints.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/checks/hints.yaml b/src/schema/rules/checks/hints.yaml
index 55b63c4784..50cc0f05dc 100644
--- a/src/schema/rules/checks/hints.yaml
+++ b/src/schema/rules/checks/hints.yaml
@@ -17,7 +17,7 @@ ReadmeFileMissing:
   selectors:
     - path == '/dataset_description.json'
   checks:
-    - exists(["/README", "/README.txt", "/README.md", "/README.rst"], "dataset") > 0
+    - exists(["README", "README.txt", "README.md", "README.rst"], "dataset") > 0
 
 # 102
 TooFewAuthors:

From 9d7c1eda618bf4b7978e23a05a6a44c6e59b8e95 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 13 Jun 2024 18:55:22 -0400
Subject: [PATCH 35/74] [FIX] Update links to moved RRID site (#1857)

sed -i'' -e 's#https://scicrunch.org/resources#https://rrid.site#' src/**/*.{md,yaml}
---
 src/introduction.md                       |  2 +-
 src/modality-specific-files/microscopy.md |  2 +-
 src/schema/objects/columns.yaml           |  2 +-
 src/schema/objects/formats.yaml           |  2 +-
 src/schema/objects/metadata.yaml          | 10 +++++-----
 5 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/src/introduction.md b/src/introduction.md
index e56f6ddef7..4315720e3a 100644
--- a/src/introduction.md
+++ b/src/introduction.md
@@ -190,4 +190,4 @@ BIDS has also a
 [Research Resource Identifier (RRID)](https://force11.org/group/resource-identification-initiative),
 which you can also include in your citations in addition to relevant publications (see above):
 
--   [`RRID:SCR_016124`](https://scicrunch.org/resources/data/record/nlx_144509-1/SCR_016124/resolver?q=SCR_016124)
+-   [`RRID:SCR_016124`](https://rrid.site/data/record/nlx_144509-1/SCR_016124/resolver?q=SCR_016124)
diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md
index 1b813f9eb2..998e463886 100644
--- a/src/modality-specific-files/microscopy.md
+++ b/src/modality-specific-files/microscopy.md
@@ -434,7 +434,7 @@ sub-02 mus musculus C57BL/6J RRID:IMSR_JAX:000664
         "Description": "name of the strain of the species"
     },
     "strain_rrid": {
-        "Description": "research resource identifier (RRID) of the strain (https://scicrunch.org/resources/data/source/nlx_154697-1/search)"
+        "Description": "research resource identifier (RRID) of the strain (https://rrid.site/data/source/nlx_154697-1/search)"
     }
 }
 ```
diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 5ca387a007..9128a235ba 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -615,7 +615,7 @@ strain_rrid:
   display_name: Strain RRID
   description: |
     For species different from `homo sapiens`, research resource identifier
-    ([RRID](https://scicrunch.org/resources/data/source/nlx_154697-1/search))
+    ([RRID](https://rrid.site/data/source/nlx_154697-1/search))
     of the strain of the species, for example: `RRID:IMSR_JAX:000664`.
   type: string
   format: rrid
diff --git a/src/schema/objects/formats.yaml b/src/schema/objects/formats.yaml
index 804dfda885..7de4345b2d 100644
--- a/src/schema/objects/formats.yaml
+++ b/src/schema/objects/formats.yaml
@@ -95,7 +95,7 @@ participant_relative:
 rrid:
   display_name: Research resource identifier
   description: |
-    A [research resource identifier](https://scicrunch.org/resources).
+    A [research resource identifier](https://rrid.site).
   pattern: 'RRID:.+_.+'
 stimuli_relative:
   display_name: Path relative to the stimuli directory
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 1b13a6a614..051a990470 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -2850,9 +2850,9 @@ SamplePrimaryAntibody:
   display_name: Sample Primary Antibody
   description: |
     Description(s) of the primary antibody used for immunostaining.
-    Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalog
+    Either an [RRID](https://rrid.site) or the name, supplier and catalog
     number of a commercial antibody.
-    For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the
+    For non-commercial antibodies either an [RRID](https://rrid.site) or the
     host-animal and immunogen used (for examples: `"RRID:AB_2122563"` or
     `"Rabbit anti-Human HTR5A Polyclonal Antibody, Invitrogen, Catalog # PA1-2453"`).
     MAY be an array of strings if different antibodies are used in each channel of the file.
@@ -2866,9 +2866,9 @@ SampleSecondaryAntibody:
   display_name: Sample Secondary Antibody
   description: |
     Description(s) of the secondary antibody used for immunostaining.
-    Either an [RRID](https://scicrunch.org/resources) or the name, supplier and catalog
+    Either an [RRID](https://rrid.site) or the name, supplier and catalog
     number of a commercial antibody.
-    For non-commercial antibodies either an [RRID](https://scicrunch.org/resources) or the
+    For non-commercial antibodies either an [RRID](https://rrid.site) or the
     host-animal and immunogen used (for examples: `"RRID:AB_228322"` or
     `"Goat anti-Mouse IgM Secondary Antibody, Invitrogen, Catalog # 31172"`).
     MAY be an array of strings if different antibodies are used in each channel of the file.
@@ -3148,7 +3148,7 @@ SoftwareRRID:
   name: SoftwareRRID
   display_name: SoftwareRRID
   description: |
-    [Research Resource Identifier](https://scicrunch.org/resources) of the
+    [Research Resource Identifier](https://rrid.site) of the
     software that was used to present the stimuli.
     Examples: The RRID for Psychtoolbox is 'SCR_002881',
     and that of PsychoPy is 'SCR_006571'.

From d8397a3b85cd568ae8e1b351fdfb4e6b41a2373b Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 17 Jun 2024 15:59:40 -0400
Subject: [PATCH 36/74] Units is not for the entire file, but rather a variable
 (column or a field in sidecar) (#1849)

---
 src/schema/objects/metadata.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 051a990470..70926904fc 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -3561,7 +3561,7 @@ Units:
   name: Units
   display_name: Units
   description: |
-    Measurement units for the associated file.
+    Measurement units for the associated variable.
     SI units in CMIXF formatting are RECOMMENDED
     (see [Units](SPEC_ROOT/common-principles.md#units)).
   type: string

From d25a3fd5ad431b2fd853c300c68caa8eb539dadf Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 17 Jun 2024 16:01:16 -0400
Subject: [PATCH 37/74] [ENH] Add explicit wording on DICOM terms
 correspondence (#1450)

* Add explicit wording on DICOM terms correspondence

* Extend to Based on for DICOM

* Update src/common-principles.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* Update avoiding "instructions to spec authors" language

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

---------

Co-authored-by: Remi Gau <remi_gau@hotmail.com>
Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/common-principles.md | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/common-principles.md b/src/common-principles.md
index 08ef8e6a4f..da87a35e06 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -449,6 +449,11 @@ possible. Since the NIfTI standard offers limited support for the various image
 acquisition parameters available in DICOM files, we RECOMMEND that users provide
 additional meta information extracted from DICOM files in a sidecar JSON file
 (with the same filename as the `.nii[.gz]` file, but with a `.json` extension).
+Currently defined metadata fields are listed in the [Glossary](./glossary.md).
+Where possible, DICOM Tags are adopted directly as BIDS metadata terms and
+indicated with "**Corresponds to** DICOM Tag ID1, ID2 `DICOM Tag Name`.".
+When harmonization has been deemed necessary, this is indicated in the
+BIDS term description with "**Based on** DICOM Tag ID1, ID2 `DICOM Tag Name`.".
 Extraction of BIDS compatible metadata can be performed using [dcm2niix](https://github.com/rordenlab/dcm2niix)
 and [dicm2nii](https://www.mathworks.com/matlabcentral/fileexchange/42997-xiangruili-dicm2nii)
 DICOM to NIfTI converters. The [BIDS-validator](https://github.com/bids-standard/bids-validator)

From 1fb7a154bba3258133e02481b4dc4cbdf94ea73f Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 17 Jun 2024 21:01:17 +0000
Subject: [PATCH 38/74] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pyCQA/flake8: 7.0.0 → 7.1.0](https://github.com/pyCQA/flake8/compare/7.0.0...7.1.0)
---
 .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 d6b5c19929..f7bd4f01c6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -35,7 +35,7 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 7.0.0
+    rev: 7.1.0
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]

From 1a3317aa1d2d962867c1ec8d04696fb83e385ee4 Mon Sep 17 00:00:00 2001
From: Matthieu Chourrout <83714683+chourroutm@users.noreply.github.com>
Date: Thu, 20 Jun 2024 05:28:05 +0100
Subject: [PATCH 39/74] Changed hipCT microscopy suffix to XPCT (#1822)

---
 src/modality-specific-files/microscopy.md | 4 ++--
 src/schema/objects/suffixes.yaml          | 8 ++++----
 src/schema/rules/files/raw/micr.yaml      | 2 +-
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md
index 998e463886..d095a7bb4d 100644
--- a/src/modality-specific-files/microscopy.md
+++ b/src/modality-specific-files/microscopy.md
@@ -28,7 +28,7 @@ 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", "hipCT"], n_dupes_to_combine=4) }}
+"PC", "DIC", "FLUO", "CONF", "PLI", "CARS", "2PE", "MPE", "SR", "NLO", "OCT", "SPIM", "XPCT"], n_dupes_to_combine=4) }}
 
 Microscopy data MUST be stored in the `micr` directory.
 
@@ -88,7 +88,7 @@ and a guide for using macros can be found at
          "NLO",
          "OCT",
          "SPIM",
-         "hipCT",
+         "XPCT",
       ]
    )
 }}
diff --git a/src/schema/objects/suffixes.yaml b/src/schema/objects/suffixes.yaml
index 5f57b28ba8..b370ef646a 100644
--- a/src/schema/objects/suffixes.yaml
+++ b/src/schema/objects/suffixes.yaml
@@ -617,11 +617,11 @@ 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
+XPCT:
+  value: XPCT
+  display_name: X-ray Phase-Contrast Tomography
   description: |
-    Hierarchical Phase-Contrast Tomography imaging data
+    X-ray phase-contrast tomography imaging data
 ieeg:
   value: ieeg
   display_name: Intracranial Electroencephalography
diff --git a/src/schema/rules/files/raw/micr.yaml b/src/schema/rules/files/raw/micr.yaml
index 52d1adb74f..b256033ce9 100644
--- a/src/schema/rules/files/raw/micr.yaml
+++ b/src/schema/rules/files/raw/micr.yaml
@@ -18,7 +18,7 @@ microscopy:
     - NLO
     - OCT
     - SPIM
-    - hipCT
+    - XPCT
   extensions:
     - .ome.tif
     - .ome.btf

From e738e35cae2c66a6acb74bc813947d1e4940b33b Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Thu, 20 Jun 2024 03:28:21 -0400
Subject: [PATCH 40/74] Correct mistyped name of "dataset_description.json"
 (#1860)

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

diff --git a/src/common-principles.md b/src/common-principles.md
index da87a35e06..0a42e4a885 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -351,7 +351,7 @@ Derivatives can be stored/distributed in two ways:
     it is anticipated that the same pipeline will output more than one variant
     (for example, `AFNI-blurring` and `AFNI-noblurring`).
     For the sake of consistency, the subdirectory name SHOULD be
-    the `GeneratedBy.Name` field in `data_description.json`,
+    the `GeneratedBy.Name` field in `dataset_description.json`,
     optionally followed by a hyphen and a suffix (see
     [Derived dataset and pipeline description][derived-dataset-description]).
 

From 69f37f122e642f49154079cdc8d59be340c656bc Mon Sep 17 00:00:00 2001
From: Yaroslav Halchenko <debian@onerussian.com>
Date: Mon, 24 Jun 2024 17:31:14 +0900
Subject: [PATCH 41/74] Make two Dimitis into one
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Before:

    ❯ git shortlog -sn 598a6c0749aef0180143b92937d079d9883b9c2e..
         ...
         3  Ben Dichter
         2  Dimitri Papadopoulos Orfanos
         2  Teon L Brooks
         1  Ariel Rokem
         1  Dimitri Papadopoulos

After:

    ❯ git shortlog -sn 598a6c0749aef0180143b92937d079d9883b9c2e.. | grep -v bot
         ...
         3	Ben Dichter
         3	Dimitri Papadopoulos Orfanos
         2	Teon L Brooks
---
 .mailmap | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.mailmap b/.mailmap
index 066e8097c5..087f292a4f 100644
--- a/.mailmap
+++ b/.mailmap
@@ -64,3 +64,5 @@ Patrick Park <parkpatrickj@gmail.com>
 Ezequiel Mikulan <e.mikulan@gmail.com>
 
 Guillaume Flandin <gllmflndn@users.noreply.github.com>
+
+Dimitri Papadopoulos Orfanos <3234522+DimitriPapadopoulos@users.noreply.github.com>

From 9cc8b70d8592919ccbf3e414811aeb22d3993443 Mon Sep 17 00:00:00 2001
From: Kabilar Gunalan <kabi@mit.edu>
Date: Fri, 28 Jun 2024 12:28:58 -0500
Subject: [PATCH 42/74] Remove extra bracket

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

diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index aea21dbaad..4ba975824f 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -290,7 +290,7 @@ A guide for using macros can be found at
 A segmentation can be used to generate a binary mask that functions as a
 discrete "label" for a single structure.
 In this case, the mask suffix MUST be used,
-the [`label` entity](../appendices/entities.md#label)) SHOULD be used
+the [`label` entity](../appendices/entities.md#label) SHOULD be used
 to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)),
 and the [`seg` entity](../appendices/entities.md#segmentation) SHOULD be defined.

From 555f46127044b829cd26fcc65f3ee49c8a0985c2 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 1 Jul 2024 22:11:37 +0000
Subject: [PATCH 43/74] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/mirrors-mypy: v1.10.0 → v1.10.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.10.0...v1.10.1)
---
 .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 f7bd4f01c6..5e1ed3b234 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -57,7 +57,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.0
+    rev: v1.10.1
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

From 9f2a7a839a8bd67da28d582cd4ce9ff32db858dc Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 11 Jul 2024 15:08:04 -0400
Subject: [PATCH 44/74] FIX: Declare context definition to be JSON schema, fix
 validation errors (#1867)

* fix(schema): Use integer instead of int for type definitions

* fix(schema): Use number instead of float for type definitions

* feat(metaschema): Declare meta.context.context to be JSON schema

* rf(schema): Remove indirection in context description

* chore(schema): Bump schema minor version
---
 src/metaschema.json               |   3 +-
 src/schema/README.md              |   2 +-
 src/schema/SCHEMA_VERSION         |   2 +-
 src/schema/meta/associations.yaml |   2 +-
 src/schema/meta/context.yaml      | 673 +++++++++++++++---------------
 5 files changed, 341 insertions(+), 341 deletions(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index 5d01c8862f..7e7baaf0ee 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -51,7 +51,8 @@
           "additionalProperties": false
         },
         "context": {
-          "type": "object"
+          "description": "The context object is itself JSON schema",
+          "$ref": "http://json-schema.org/draft-07/schema#"
         },
         "expression_tests": {
           "type": "array",
diff --git a/src/schema/README.md b/src/schema/README.md
index 5f1abb4595..14290337c1 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -215,7 +215,7 @@ We see expressions may contain:
 -   Comparison operators such as `==` (equality) or `in` (subfield exists in field)
 -   Functions such as `intersects()`
 
-In fact, the full list of fields is defined in the `meta.context.context` object,
+In fact, the full list of fields is defined in the `meta.context` object,
 which (currently) contains at the top level:
 
 -   `schema`: access to the schema itself
diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index dc9bff91aa..29b2d3ea50 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.9.1-dev
+0.10.0-dev
diff --git a/src/schema/meta/associations.yaml b/src/schema/meta/associations.yaml
index b55f746bf3..503fa728c1 100644
--- a/src/schema/meta/associations.yaml
+++ b/src/schema/meta/associations.yaml
@@ -1,4 +1,4 @@
-# These rules indicate whether an association (defined in meta.context.context.associations)
+# These rules indicate whether an association (defined in meta.context.associations)
 # applies to a given file. These are hints to allow implementations to avoid unnecessary
 # directory and file reads.
 #
diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 7f9ca1259c..280ae7b933 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -17,353 +17,352 @@
 # principle.
 #
 ---
-context:
-  type: object
-  properties:
-    schema:
-      description: 'The BIDS specification schema'
-      type: object
-    dataset:
-      description: 'Properties and contents of the entire dataset'
-      type: object
-      properties:
-        dataset_description:
-          description: 'Contents of /dataset_description.json'
-          type: object
-        files:
-          description: 'List of all files in dataset'
-          type: array
-        tree:
-          description: 'Tree view of all files in dataset'
-          type: object
-        ignored:
-          description: 'Set of ignored files'
-          type: array
-        datatypes:
-          description: 'Data types present in the dataset'
-          type: array
-        modalities:
-          description: 'Modalities present in the dataset'
-          type: array
-        subjects:
-          description: 'Collections of subjects in dataset'
-          type: object
-          properties:
-            sub_dirs:
-              description: 'Subjects as determined by sub-*/ directories'
-              type: array
-              items:
-                type: string
-            participant_id:
-              description: 'The participant_id column of participants.tsv'
-              type: array
-              items:
-                type: string
-            phenotype:
-              description: 'The union of participant_id columns in phenotype files'
-              type: array
-              items:
-                type: string
-    subject:
-      description: 'Properties and contents of the current subject'
-      type: object
-      properties:
-        sessions:
-          description: 'Collections of sessions in subject'
-          type: object
-          properties:
-            ses_dirs:
-              description: 'Sessions as determined by ses-*/ directories'
-              type: array
-              items:
-                type: string
-            session_id:
-              description: 'The session_id column of sessions.tsv'
-              type: array
-              items:
-                type: string
-            phenotype:
-              description: 'The union of session_id columns in phenotype files'
-              type: array
-              items:
-                type: string
-
-    # Properties of the current file
-    path:
-      description: 'Path of the current file'
-      type: string
-    size:
-      description: 'Length of the current file in bytes'
-      type: int
-    entities:
-      description: 'Entities parsed from the current filename'
-      type: object
-    datatype:
-      description: 'Datatype of current file, for examples, anat'
-      type: string
-    suffix:
-      description: 'Suffix of current file'
-      type: string
-    extension:
-      description: 'Extension of current file including initial dot'
-      type: string
-    modality:
-      description: 'Modality of current file, for examples, MRI'
-      type: string
-
-    sidecar:
-      description: 'Sidecar metadata constructed via the inheritance principle'
-      type: object
-    associations:
-      # Note that this is not intended to be an exhaustive list of associated files
-      # or to expose every attribute of those files. It is specifically those files
-      # and attributes for which a rule needs to be applied from an originating file.
-      description: |
-        Associated files, indexed by suffix, selected according to the inheritance principle
-      type: object
-      properties:
-        events:
-          description: 'Events file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated events file'
-              type: string
-            onset:
-              description: 'Contents of the onset column'
-              type: array
-              items:
-                type: string
-        aslcontext:
-          description: 'ASL context file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated aslcontext file'
+type: object
+properties:
+  schema:
+    description: 'The BIDS specification schema'
+    type: object
+  dataset:
+    description: 'Properties and contents of the entire dataset'
+    type: object
+    properties:
+      dataset_description:
+        description: 'Contents of /dataset_description.json'
+        type: object
+      files:
+        description: 'List of all files in dataset'
+        type: array
+      tree:
+        description: 'Tree view of all files in dataset'
+        type: object
+      ignored:
+        description: 'Set of ignored files'
+        type: array
+      datatypes:
+        description: 'Data types present in the dataset'
+        type: array
+      modalities:
+        description: 'Modalities present in the dataset'
+        type: array
+      subjects:
+        description: 'Collections of subjects in dataset'
+        type: object
+        properties:
+          sub_dirs:
+            description: 'Subjects as determined by sub-*/ directories'
+            type: array
+            items:
               type: string
-            n_rows:
-              description: 'Number of rows in aslcontext.tsv'
-              type: integer
-            volume_type:
-              description: 'Contents of the volume_type column'
-              type: array
-              items:
-                type: string
-        m0scan:
-          description: 'M0 scan file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated M0 scan file'
+          participant_id:
+            description: 'The participant_id column of participants.tsv'
+            type: array
+            items:
               type: string
-        magnitude:
-          description: 'Magnitude image file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated magnitude file'
+          phenotype:
+            description: 'The union of participant_id columns in phenotype files'
+            type: array
+            items:
               type: string
-        magnitude1:
-          description: 'Magnitude1 image file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated magnitude1 file'
+  subject:
+    description: 'Properties and contents of the current subject'
+    type: object
+    properties:
+      sessions:
+        description: 'Collections of sessions in subject'
+        type: object
+        properties:
+          ses_dirs:
+            description: 'Sessions as determined by ses-*/ directories'
+            type: array
+            items:
               type: string
-        bval:
-          description: 'B value file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated bval file'
+          session_id:
+            description: 'The session_id column of sessions.tsv'
+            type: array
+            items:
               type: string
-            n_cols:
-              description: 'Number of columns in bval file'
-              type: integer
-            n_rows:
-              description: 'Number of rows in bval file'
-              type: integer
-            values:
-              description: 'B-values contained in bval file'
-              type: array
-              items:
-                type: number
-        bvec:
-          description: 'B vector file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated bvec file'
+          phenotype:
+            description: 'The union of session_id columns in phenotype files'
+            type: array
+            items:
               type: string
-            n_cols:
-              description: 'Number of columns in bvec file'
-              type: integer
-            n_rows:
-              description: 'Number of rows in bvec file'
-              type: integer
-        channels:
-          description: 'Channels file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated channels file'
+
+  # Properties of the current file
+  path:
+    description: 'Path of the current file'
+    type: string
+  size:
+    description: 'Length of the current file in bytes'
+    type: integer
+  entities:
+    description: 'Entities parsed from the current filename'
+    type: object
+  datatype:
+    description: 'Datatype of current file, for examples, anat'
+    type: string
+  suffix:
+    description: 'Suffix of current file'
+    type: string
+  extension:
+    description: 'Extension of current file including initial dot'
+    type: string
+  modality:
+    description: 'Modality of current file, for examples, MRI'
+    type: string
+
+  sidecar:
+    description: 'Sidecar metadata constructed via the inheritance principle'
+    type: object
+  associations:
+    # Note that this is not intended to be an exhaustive list of associated files
+    # or to expose every attribute of those files. It is specifically those files
+    # and attributes for which a rule needs to be applied from an originating file.
+    description: |
+      Associated files, indexed by suffix, selected according to the inheritance principle
+    type: object
+    properties:
+      events:
+        description: 'Events file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated events file'
+            type: string
+          onset:
+            description: 'Contents of the onset column'
+            type: array
+            items:
               type: string
-            type:
-              description: 'Contents of the type column'
-              type: array
-              items:
-                type: string
-        coordsystem:
-          description: 'Coordinate system file'
-          type: object
-          properties:
-            path:
-              description: 'Path to associated coordsystem file'
+      aslcontext:
+        description: 'ASL context file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated aslcontext file'
+            type: string
+          n_rows:
+            description: 'Number of rows in aslcontext.tsv'
+            type: integer
+          volume_type:
+            description: 'Contents of the volume_type column'
+            type: array
+            items:
               type: string
-    # The following properties are populated if the current file is of an appropriate type
-    columns:
-      description: 'TSV columns, indexed by column header, values are arrays with column contents'
-      type: object
-      additionalProperties:
-        type: array
-    json:
-      description: 'Contents of the current JSON file'
-      type: object
-    gzip:
-      description: 'Parsed contents of gzip header'
-      type: object
-      properties:
-        timestamp:
-          description: 'Modification time, unix timestamp'
-          type: number
-        filename:
-          description: 'Filename'
-          type: string
-        comment:
-          description: 'Comment'
-          type: string
-    nifti_header:
-      name: 'NIfTI Header'
-      description: 'Parsed contents of NIfTI header referenced elsewhere in schema.'
-      type: object
-      properties:
-        dim_info:
-          name: 'Dimension Information'
-          description: 'Metadata about dimensions data.'
-          type: object
-          properties:
-            freq:
-              name: 'Frequency'
-              description: 'These fields encode which spatial dimension (1, 2, or 3).'
-              type: integer
-            phase:
-              name: 'Phase'
-              description: 'Corresponds to which acquisition dimension for MRI data.'
-              type: integer
-            slice:
-              name: 'Slice'
-              description: 'Slice dimensions.'
-              type: integer
-        dim:
-          name: 'Data Dimensions'
-          description: 'Data seq dimensions.'
-          type: array
-          minItems: 8
-          maxItems: 8
-          items:
+      m0scan:
+        description: 'M0 scan file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated M0 scan file'
+            type: string
+      magnitude:
+        description: 'Magnitude image file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated magnitude file'
+            type: string
+      magnitude1:
+        description: 'Magnitude1 image file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated magnitude1 file'
+            type: string
+      bval:
+        description: 'B value file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated bval file'
+            type: string
+          n_cols:
+            description: 'Number of columns in bval file'
             type: integer
-        pixdim:
-          name: 'Pixel Dimension'
-          description: 'Grid spacings (unit per dimension).'
-          type: array
-          minItems: 8
-          maxItems: 8
-          items:
-            type: number
-        shape:
-          name: 'Data shape'
-          description: 'Data array shape, equal to dim[1:dim[0] + 1]'
-          type: array
-          minItems: 0
-          maxItems: 7
-          items:
+          n_rows:
+            description: 'Number of rows in bval file'
             type: integer
-        voxel_sizes:
-          name: 'Voxel sizes'
-          description: 'Voxel sizes, equal to pixdim[1:dim[0] + 1]'
-          type: array
-          minItems: 0
-          maxItems: 7
-          items:
-            type: number
-        xyzt_units:
-          name: 'XYZT Units'
-          description: 'Units of pixdim[1..4]'
-          type: object
-          properties:
-            xyz:
-              name: 'XYZ Units'
-              description: 'String representing the unit of voxel spacing.'
-              type: string
-              enum:
-                - $ref: objects.enums.unknown.value
-                # TODO: Add definitions for these values. (perhaps don't specify)
-                - 'meter'
-                - 'mm'
-                - 'um'
-            t:
-              name: 'Time Unit'
-              description: 'String representing the unit of inter-volume intervals.'
+          values:
+            description: 'B-values contained in bval file'
+            type: array
+            items:
+              type: number
+      bvec:
+        description: 'B vector file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated bvec file'
+            type: string
+          n_cols:
+            description: 'Number of columns in bvec file'
+            type: integer
+          n_rows:
+            description: 'Number of rows in bvec file'
+            type: integer
+      channels:
+        description: 'Channels file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated channels file'
+            type: string
+          type:
+            description: 'Contents of the type column'
+            type: array
+            items:
               type: string
-              enum:
-                - $ref: objects.enums.unknown.value
-                # TODO: Add definitions for these values. (perhaps don't specify)
-                - 'sec'
-                - 'msec'
-                - 'usec'
-        qform_code:
-          name: 'qform code'
-          description: 'Use of the quaternion fields.'
+      coordsystem:
+        description: 'Coordinate system file'
+        type: object
+        properties:
+          path:
+            description: 'Path to associated coordsystem file'
+            type: string
+  # The following properties are populated if the current file is of an appropriate type
+  columns:
+    description: 'TSV columns, indexed by column header, values are arrays with column contents'
+    type: object
+    additionalProperties:
+      type: array
+  json:
+    description: 'Contents of the current JSON file'
+    type: object
+  gzip:
+    description: 'Parsed contents of gzip header'
+    type: object
+    properties:
+      timestamp:
+        description: 'Modification time, unix timestamp'
+        type: number
+      filename:
+        description: 'Filename'
+        type: string
+      comment:
+        description: 'Comment'
+        type: string
+  nifti_header:
+    name: 'NIfTI Header'
+    description: 'Parsed contents of NIfTI header referenced elsewhere in schema.'
+    type: object
+    properties:
+      dim_info:
+        name: 'Dimension Information'
+        description: 'Metadata about dimensions data.'
+        type: object
+        properties:
+          freq:
+            name: 'Frequency'
+            description: 'These fields encode which spatial dimension (1, 2, or 3).'
+            type: integer
+          phase:
+            name: 'Phase'
+            description: 'Corresponds to which acquisition dimension for MRI data.'
+            type: integer
+          slice:
+            name: 'Slice'
+            description: 'Slice dimensions.'
+            type: integer
+      dim:
+        name: 'Data Dimensions'
+        description: 'Data seq dimensions.'
+        type: array
+        minItems: 8
+        maxItems: 8
+        items:
           type: integer
-        sform_code:
-          name: 'sform code'
-          description: 'Use of the affine fields.'
+      pixdim:
+        name: 'Pixel Dimension'
+        description: 'Grid spacings (unit per dimension).'
+        type: array
+        minItems: 8
+        maxItems: 8
+        items:
+          type: number
+      shape:
+        name: 'Data shape'
+        description: 'Data array shape, equal to dim[1:dim[0] + 1]'
+        type: array
+        minItems: 0
+        maxItems: 7
+        items:
           type: integer
-    ome:
-      name: 'Open Microscopy Environment fields'
-      description: 'Parsed contents of OME-XML header, which may be found in OME-TIFF or OME-ZARR files'
-      type: object
-      properties:
-        PhysicalSizeX:
-          name: 'PhysicalSizeX'
-          description: 'Pixels / @PhysicalSizeX'
-          type: float
-        PhysicalSizeY:
-          name: 'PhysicalSizeY'
-          description: 'Pixels / @PhysicalSizeY'
-          type: float
-        PhysicalSizeZ:
-          name: 'PhysicalSizeZ'
-          description: 'Pixels / @PhysicalSizeZ'
-          type: float
-        PhysicalSizeXUnit:
-          name: 'PhysicalSizeXUnit'
-          description: 'Pixels / @PhysicalSizeXUnit'
-          type: string
-        PhysicalSizeYUnit:
-          name: 'PhysicalSizeYUnit'
-          description: 'Pixels / @PhysicalSizeYUnit'
-          type: string
-        PhysicalSizeZUnit:
-          name: 'PhysicalSizeZUnit'
-          description: 'Pixels / @PhysicalSizeZUnit'
-          type: string
-    tiff:
-      name: 'TIFF'
-      description: 'TIFF file format metadata'
-      type: object
-      properties:
-        version:
-          name: 'Version'
-          description: 'TIFF file format version (the second 2-byte block)'
-          type: int
+      voxel_sizes:
+        name: 'Voxel sizes'
+        description: 'Voxel sizes, equal to pixdim[1:dim[0] + 1]'
+        type: array
+        minItems: 0
+        maxItems: 7
+        items:
+          type: number
+      xyzt_units:
+        name: 'XYZT Units'
+        description: 'Units of pixdim[1..4]'
+        type: object
+        properties:
+          xyz:
+            name: 'XYZ Units'
+            description: 'String representing the unit of voxel spacing.'
+            type: string
+            enum:
+              - $ref: objects.enums.unknown.value
+              # TODO: Add definitions for these values. (perhaps don't specify)
+              - 'meter'
+              - 'mm'
+              - 'um'
+          t:
+            name: 'Time Unit'
+            description: 'String representing the unit of inter-volume intervals.'
+            type: string
+            enum:
+              - $ref: objects.enums.unknown.value
+              # TODO: Add definitions for these values. (perhaps don't specify)
+              - 'sec'
+              - 'msec'
+              - 'usec'
+      qform_code:
+        name: 'qform code'
+        description: 'Use of the quaternion fields.'
+        type: integer
+      sform_code:
+        name: 'sform code'
+        description: 'Use of the affine fields.'
+        type: integer
+  ome:
+    name: 'Open Microscopy Environment fields'
+    description: 'Parsed contents of OME-XML header, which may be found in OME-TIFF or OME-ZARR files'
+    type: object
+    properties:
+      PhysicalSizeX:
+        name: 'PhysicalSizeX'
+        description: 'Pixels / @PhysicalSizeX'
+        type: number
+      PhysicalSizeY:
+        name: 'PhysicalSizeY'
+        description: 'Pixels / @PhysicalSizeY'
+        type: number
+      PhysicalSizeZ:
+        name: 'PhysicalSizeZ'
+        description: 'Pixels / @PhysicalSizeZ'
+        type: number
+      PhysicalSizeXUnit:
+        name: 'PhysicalSizeXUnit'
+        description: 'Pixels / @PhysicalSizeXUnit'
+        type: string
+      PhysicalSizeYUnit:
+        name: 'PhysicalSizeYUnit'
+        description: 'Pixels / @PhysicalSizeYUnit'
+        type: string
+      PhysicalSizeZUnit:
+        name: 'PhysicalSizeZUnit'
+        description: 'Pixels / @PhysicalSizeZUnit'
+        type: string
+  tiff:
+    name: 'TIFF'
+    description: 'TIFF file format metadata'
+    type: object
+    properties:
+      version:
+        name: 'Version'
+        description: 'TIFF file format version (the second 2-byte block)'
+        type: integer

From c2995f243ecf6a6ca386c0e127dd49b26dbe526d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 11 Jul 2024 15:19:22 -0400
Subject: [PATCH 45/74] schema-0.10.0

---
 src/schema/SCHEMA_VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index 29b2d3ea50..78bc1abd14 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.10.0-dev
+0.10.0

From 6beec139d14d8ce9335e1c25bd5e5833ec61ca9a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 11 Jul 2024 15:20:48 -0400
Subject: [PATCH 46/74] schema-0.10.1-dev

---
 src/schema/SCHEMA_VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index 78bc1abd14..539f9fc668 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.10.0
+0.10.1-dev

From daf2ec8e999cd9ced44b6e89196917f38729eb27 Mon Sep 17 00:00:00 2001
From: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
Date: Thu, 18 Jul 2024 08:00:13 +0200
Subject: [PATCH 47/74] Add ephys channel count rules to schema (#1319)

* schema: add EEG channel count rules

* Update src/schema/rules/checks/eeg.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* add issues

* add missing quotation mark

* fix again

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/checks/eeg.yaml | 79 ++++++++++++++++++++++++++++++++
 1 file changed, 79 insertions(+)
 create mode 100644 src/schema/rules/checks/eeg.yaml

diff --git a/src/schema/rules/checks/eeg.yaml b/src/schema/rules/checks/eeg.yaml
new file mode 100644
index 0000000000..b0b0dfd2bc
--- /dev/null
+++ b/src/schema/rules/checks/eeg.yaml
@@ -0,0 +1,79 @@
+---
+EEGChannelCountReq:
+  issue:
+    code: EEG_CHANNEL_COUNT_MISMATCH
+    message: |
+      The EEGChannelCount metadata does not match the number of channels
+      with type EEG in the associated channels.tsv file.
+    level: warning
+  selectors:
+    - suffix == "eeg"
+    - type(sidecar.EEGChannelCount) != "null"
+    - associations.channels.type
+  checks:
+    - sidecar.EEGChannelCount == count(associations.channels.type, "EEG")
+ECGChannelCountReq:
+  issue:
+    code: ECG_CHANNEL_COUNT_MISMATCH
+    message: |
+      The ECGChannelCount metadata does not match the number of channels
+      with type ECG in the associated channels.tsv file.
+    level: warning
+  selectors:
+    - suffix == "eeg"
+    - type(sidecar.ECGChannelCount) != "null"
+    - associations.channels.type
+  checks:
+    - sidecar.ECGChannelCount == count(associations.channels.type, "ECG")
+EMGChannelCountReq:
+  issue:
+    code: EMG_CHANNEL_COUNT_MISMATCH
+    message: |
+      The EMGChannelCount metadata does not match the number of channels
+      with type EMG in the associated channels.tsv file.
+    level: warning
+  selectors:
+    - suffix == "eeg"
+    - type(sidecar.EMGChannelCount) != "null"
+    - associations.channels.type
+  checks:
+    - sidecar.EMGChannelCount == count(associations.channels.type, "EMG")
+EOGChannelCountReq:
+  issue:
+    code: EOG_CHANNEL_COUNT_MISMATCH
+    message: |
+      The EOGChannelCount metadata does not match the number of channels
+      with type EOG in the associated channels.tsv file.
+    level: warning
+  selectors:
+    - suffix == "eeg"
+    - type(sidecar.EOGChannelCount) != "null"
+    - associations.channels.type
+  checks:
+    - sidecar.EOGChannelCount == count(associations.channels.type, "EOG")
+MiscChannelCountReq:
+  issue:
+    code: MISC_CHANNEL_COUNT_MISMATCH
+    message: |
+      The MiscChannelCount metadata does not match the number of channels
+      with type MISC in the associated channels.tsv file.
+    level: warning
+  selectors:
+    - suffix == "eeg"
+    - type(sidecar.MiscChannelCount) != "null"
+    - associations.channels.type
+  checks:
+    - sidecar.MiscChannelCount == count(associations.channels.type, "MISC")
+TriggerChannelCountReq:
+  issue:
+    code: TRIGGER_CHANNEL_COUNT_MISMATCH
+    message: |
+      The TriggerChannelCount metadata does not match the number of channels
+      with type TRIG in the associated channels.tsv file.
+    level: warning
+  selectors:
+    - suffix == "eeg"
+    - type(sidecar.TriggerChannelCount) != "null"
+    - associations.channels.type
+  checks:
+    - sidecar.TriggerChannelCount == count(associations.channels.type, "TRIG")

From 1418ce8d8eb8dd94c153d2c1cd87b9e3df34eecf Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 18 Jul 2024 15:28:28 -0400
Subject: [PATCH 48/74] rf(metaschema): Validate object definitions that are
 JSON schema (#1869)

---
 .pre-commit-config.yaml                       |  12 +
 src/metaschema.json                           | 346 ++++++++----------
 src/schema/objects/metadata.yaml              |  10 +-
 .../bidsschematools/render/tables.py          |   4 +-
 4 files changed, 167 insertions(+), 205 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 5e1ed3b234..886c93bce6 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -14,6 +14,16 @@ repos:
       - id: check-ast
       - id: check-added-large-files
       - id: check-case-conflict
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.29.0
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+        args: ["--verbose"]
+      - id: check-metaschema
+        files: src/metaschema.json
+      - id: check-readthedocs
+        files: readthedocs.yml
   - repo: https://github.com/psf/black
     rev: 24.4.2
     hooks:
@@ -71,6 +81,8 @@ repos:
           - types-PyYAML
           - types-tabulate
           - types-jsonschema
+          - jsonschema
+          - httpx
         args: ["tools/schemacode/bidsschematools"]
         pass_filenames: false
   - repo: https://github.com/koalaman/shellcheck-precommit
diff --git a/src/metaschema.json b/src/metaschema.json
index 7e7baaf0ee..dd1a3fcb91 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -1,5 +1,5 @@
 {
-  "$schema": "http://json-schema.org/draft-07/schema#",
+  "$schema": "https://json-schema.org/draft/2020-12/schema#",
   "type": "object",
   "properties": {
     "meta": {
@@ -52,7 +52,7 @@
         },
         "context": {
           "description": "The context object is itself JSON schema",
-          "$ref": "http://json-schema.org/draft-07/schema#"
+          "$ref": "https://json-schema.org/draft/2020-12/schema#"
         },
         "expression_tests": {
           "type": "array",
@@ -84,44 +84,19 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "name": {
-                  "type": "string"
-                },
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                },
-                "type": {
-                  "$ref": "http://json-schema.org/draft-07/schema#/properties/type"
-                },
-                "format": {
-                  "type": "string"
-                },
-                "pattern": {
-                  "type": "string"
-                },
-                "unit": {
-                  "type": "string"
-                },
-                "enum": {
-                  "type": "array"
-                },
-                "anyOf": {
-                  "$ref": "http://json-schema.org/draft-07/schema#/properties/anyOf"
-                },
-                "maximum": {
-                  "type": "number"
-                },
-                "minimum": {
-                  "type": "number"
+              "allOf": [
+                { "$ref": "#/definitions/schemaTerm" },
+                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/nameValueTerm" },
+                {
+                  "type": "object",
+                  "properties": {
+                    "format": { "$ref": "#/definitions/formats" },
+                    "unit": { "type": "string" }
+                  }
                 }
-              },
-              "required": ["name", "display_name"],
-              "additionalProperties": false
+              ],
+              "unevaluatedProperties": false
             }
           },
           "additionalProperties": false
@@ -130,17 +105,8 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                }
-              },
-              "required": ["display_name", "description"],
-              "additionalProperties": false
+              "$ref": "#/definitions/generalTerm",
+              "unevaluatedProperties": false
             },
             "additionalProperties": false
           }
@@ -149,20 +115,11 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "value": {
-                  "type": "string"
-                },
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                }
-              },
-              "required": ["value", "display_name", "description"],
-              "additionalProperties": false
+              "allOf": [
+                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/valueTerm" }
+              ],
+              "unevaluatedProperties": false
             }
           },
           "additionalProperties": false
@@ -171,35 +128,19 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "name": {
-                  "type": "string"
-                },
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                },
-                "type": {
-                  "$ref": "http://json-schema.org/draft-07/schema#/properties/type"
-                },
-                "format": {
-                  "type": "string"
-                },
-                "enum": {
-                  "type": "array"
+              "allOf": [
+                { "$ref": "#/definitions/schemaTerm" },
+                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/nameValueTerm" },
+                {
+                  "type": "object",
+                  "properties": {
+                    "format": { "$ref": "#/definitions/formats" }
+                  },
+                  "required": ["format"]
                 }
-              },
-              "required": [
-                "name",
-                "display_name",
-                "description",
-                "type",
-                "format"
               ],
-              "additionalProperties": false
+              "unevaluatedProperties": false
             }
           },
           "additionalProperties": false
@@ -207,30 +148,18 @@
         "enums": {
           "type": "object",
           "patternProperties": {
-            "^[a-zA-Z0-9_-]+$": {
-              "type": "object",
-              "properties": {
-                "type": {
-                  "$ref": "http://json-schema.org/draft-07/schema#/properties/type"
-                },
-                "enum": {
-                  "type": "array"
-                },
-                "value": {
-                  "type": "string"
-                },
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                },
-                "tags": {
-                  "type": "array"
-                }
-              },
-              "additionalProperties": false
-            }
+            "^[a-zA-Z0-9][a-zA-Z0-9_-]*$": {
+              "allOf": [
+                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/valueTerm" },
+                { "properties": { "tags": { "type": "array" } } }
+              ]
+            },
+            "^_[a-zA-Z0-9_-]+$": {
+              "$ref": "https://json-schema.org/draft/2020-12/schema#",
+              "required": ["type", "enum"]
+            },
+            "unevaluatedProperties": false
           },
           "additionalProperties": false
         },
@@ -238,20 +167,11 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "value": {
-                  "type": "string"
-                },
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                }
-              },
-              "required": ["display_name", "description", "value"],
-              "additionalProperties": false
+              "allOf": [
+                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/valueTerm" }
+              ],
+              "unevaluatedProperties": false
             }
           },
           "additionalProperties": false
@@ -260,66 +180,56 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "display_name": {
-                  "type": "string"
-                },
-                "file_type": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
+              "allOf": [
+                { "$ref": "#/definitions/generalTerm" },
+                {
+                  "properties": { "file_type": { "type": "string" } },
+                  "required": ["file_type"]
                 }
-              },
-              "required": ["display_name", "file_type", "description"],
-              "additionalProperties": false
+              ],
+              "unevaluatedProperties": false
             }
           },
           "additionalProperties": false
         },
         "formats": {
           "type": "object",
-          "patternProperties": {
-            "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
+          "propertyNames": { "$ref": "#/definitions/formats" },
+          "additionalProperties": {
+            "allOf": [
+              { "$ref": "#/definitions/generalTerm" },
+              {
+                "type": "object",
+                "properties": {
+                  "pattern": {
+                    "$ref": "https://json-schema.org/draft/2020-12/meta/validation#/properties/pattern"
+                  }
                 },
-                "pattern": {
-                  "format": "regex"
-                }
-              },
-              "required": ["display_name", "description", "pattern"],
-              "additionalProperties": false
-            }
-          },
-          "additionalProperties": false
+                "required": ["pattern"]
+              }
+            ],
+            "unevaluatedProperties": false
+          }
         },
         "metadata": {
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "name": {
-                  "type": "string"
-                },
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                },
-                "type": {
-                  "$ref": "http://json-schema.org/draft-07/schema#/properties/type"
+              "allOf": [
+                { "$ref": "#/definitions/schemaTerm" },
+                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/nameValueTerm" },
+                {
+                  "type": "object",
+                  "properties": {
+                    "recommended": {
+                      "$ref": "https://json-schema.org/draft/2020-12/meta/validation#/properties/required"
+                    },
+                    "unit": { "type": "string" }
+                  }
                 }
-              },
-              "required": ["name", "display_name", "description"]
+              ],
+              "unevaluatedProperties": false
             }
           },
           "additionalProperties": false
@@ -328,17 +238,8 @@
           "type": "object",
           "patternProperties": {
             "^[a-z]+$": {
-              "type": "object",
-              "properties": {
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
-                }
-              },
-              "required": ["display_name", "description"],
-              "additionalProperties": false
+              "$ref": "#/definitions/generalTerm",
+              "unevaluatedProperties": false
             }
           },
           "additionalProperties": false
@@ -347,19 +248,22 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "type": "object",
-              "properties": {
-                "value": {
-                  "type": "string"
-                },
-                "display_name": {
-                  "type": "string"
-                },
-                "description": {
-                  "type": "string"
+              "allOf": [
+                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/valueTerm" },
+                {
+                  "type": "object",
+                  "properties": {
+                    "unit": { "type": "string" },
+                    "anyOf": {
+                      "$ref": "https://json-schema.org/draft/2020-12/meta/applicator#/properties/anyOf"
+                    },
+                    "maxValue": { "type": "number" },
+                    "minValue": { "type": "number" }
+                  }
                 }
-              },
-              "required": ["value", "display_name", "description"]
+              ],
+              "unevaluatedProperties": false
             },
             "additionalProperties": false
           }
@@ -605,6 +509,52 @@
   "required": ["meta", "objects", "rules", "bids_version", "schema_version"],
   "additionalProperties": false,
   "definitions": {
+    "formats": {
+      "$comment": "Formats whose patterns are defined in BIDS schema",
+      "type": "string",
+      "enum": [
+        "index",
+        "label",
+        "boolean",
+        "integer",
+        "number",
+        "string",
+        "hed_version",
+        "bids_uri",
+        "dataset_relative",
+        "date",
+        "datetime",
+        "file_relative",
+        "participant_relative",
+        "rrid",
+        "stimuli_relative",
+        "time",
+        "unit",
+        "uri"
+      ]
+    },
+    "generalTerm": {
+      "type": "object",
+      "properties": {
+        "display_name": { "type": "string" },
+        "description": { "type": "string" }
+      },
+      "required": ["display_name", "description"]
+    },
+    "schemaTerm": {
+      "$ref": "https://json-schema.org/draft/2020-12/schema#",
+      "anyOf": [{ "required": ["type"] }, { "required": ["anyOf"] }]
+    },
+    "nameValueTerm": {
+      "type": "object",
+      "properties": { "name": { "type": "string" } },
+      "required": ["name"]
+    },
+    "valueTerm": {
+      "type": "object",
+      "properties": { "value": { "type": "string" } },
+      "required": ["value"]
+    },
     "entities": {
       "type": "object",
       "patternProperties": {
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 70926904fc..5614a37c3f 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -1104,8 +1104,8 @@ GeneratedBy:
   minItems: 1
   items:
     type: object
-    required_fields: [Name]
-    recommended_fields: [Version]
+    required: [Name]
+    recommended: [Version]
     properties:
       Name:
         name: Name
@@ -1136,7 +1136,7 @@ GeneratedBy:
           used to produce the dataset. Valid keys in this object include `Type`, `Tag` and
           [`URI`][uri] with [string][] values.
         type: object
-        recommended_fields:
+        recommended:
           - Type
           - Tag
           - URI
@@ -1170,7 +1170,7 @@ Genetics:
   description: |
     An object containing information about the genetics descriptor.
   type: object
-  required_fields: [Dataset]
+  required: [Dataset]
   properties:
     Dataset:
       name: Dataset
@@ -3353,7 +3353,7 @@ StimulusPresentation:
     Object containing key-value pairs related to the software used to present
     the stimuli during the experiment.
   type: object
-  recommended_fields:
+  recommended:
     - OperatingSystem
     - ScreenDistance
     - ScreenRefreshRate
diff --git a/tools/schemacode/bidsschematools/render/tables.py b/tools/schemacode/bidsschematools/render/tables.py
index b32e982e52..9366ae5725 100644
--- a/tools/schemacode/bidsschematools/render/tables.py
+++ b/tools/schemacode/bidsschematools/render/tables.py
@@ -528,8 +528,8 @@ def make_subobject_table(
         The tabulated table as a Markdown string.
     """
     obj = schema.objects[object_name]
-    required_fields = set(obj.get("required_fields", ()))
-    recommended_fields = set(obj.get("recommended_fields", ()))
+    required_fields = set(obj.get("required", ()))
+    recommended_fields = set(obj.get("recommended", ()))
 
     field_info = {}
     for field in obj.properties:

From 3a636a1f11bc2549ee97dd7d7d2e1813d21814a8 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 18 Jul 2024 17:28:46 -0400
Subject: [PATCH 49/74] fix(checks): Sort columns.onset numerically (#1871)

* enh(expressions): Allow numeric or lexical sorting

* fix(checks): Sort columns.onset numerically

* enh(expressions): Test behavior of numerically sorting n/a
---
 src/schema/README.md                  |  2 +-
 src/schema/meta/expression_tests.yaml | 10 ++++++++++
 src/schema/rules/checks/events.yaml   |  2 +-
 3 files changed, 12 insertions(+), 2 deletions(-)

diff --git a/src/schema/README.md b/src/schema/README.md
index 14290337c1..68be4f2a9b 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -270,7 +270,7 @@ The following functions should be defined by an interpreter:
 | `match(arg: str, pattern: str) -> bool`         | `true` if `arg` matches the regular expression `pattern` (anywhere in string)                                                                              | `match(extension, ".gz$")`                             | True if the file extension ends with `.gz`                                     |
 | `max(arg: array) -> number`                     | The largest non-`n/a` value in an array                                                                                                                    | `max(columns.onset)`                                   | The time of the last onset in an events.tsv file                               |
 | `min(arg: array) -> number`                     | The smallest non-`n/a` value in an array                                                                                                                   | `min(sidecar.SliceTiming) == 0`                        | A check that the onset of the first slice is 0s                                |
-| `sorted(arg: array) -> array`                   | The sorted values of the input array                                                                                                                       | `sorted(sidecar.VolumeTiming) == sidecar.VolumeTiming` | True if `sidecar.VolumeTiming` is sorted                                       |
+| `sorted(arg: array, method: str) -> array`      | The sorted values of the input array; defaults to type-determined sort. If method is "lexical", or "numeric" use lexical or numeric sort.                  | `sorted(sidecar.VolumeTiming) == sidecar.VolumeTiming` | True if `sidecar.VolumeTiming` is sorted                                       |
 | `substr(arg: str, start: int, end: int) -> str` | The portion of the input string spanning from start position to end position                                                                               | `substr(path, 0, length(path) - 3)`                    | `path` with the last three characters dropped                                  |
 | `type(arg: Any) -> str`                         | The name of the type, including `"array"`, `"object"`, `"null"`                                                                                            | `type(datatypes)`                                      | Returns `"array"`                                                              |
 
diff --git a/src/schema/meta/expression_tests.yaml b/src/schema/meta/expression_tests.yaml
index 8ab60a28d4..0d5d54a1f2 100644
--- a/src/schema/meta/expression_tests.yaml
+++ b/src/schema/meta/expression_tests.yaml
@@ -110,6 +110,16 @@
   result: null
 - expression: sorted([3, 2, 1])
   result: [1, 2, 3]
+- expression: sorted([1, 2, 5, 10], "lexical")
+  result: [1, 10, 2, 5]
+- expression: sorted(["1", "2", "5", "10"])
+  result: ["1", "10", "2", "5"]
+- expression: sorted(["1", "2", "5", "10"], "numeric")
+  result: ["1", "2", "5", "10"]
+- expression: sorted(["1", "2", "n/a"], "numeric")
+  result: ["1", "2", "n/a"]
+- expression: sorted(["n/a", "2", "1"], "numeric")
+  result: ["n/a", "1", "2"]
 - expression: allequal(sorted([3, 2, 1]), [1, 2, 3])
   result: true
 # Regression test. Javascript will sort lexically by default.
diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index 234b9d078d..1f0f57a123 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -39,4 +39,4 @@ SortedOnsets:
     - extension == ".tsv"
   checks:
     # n/a values will likely cause false alarms if encountered. Consider alternatives.
-    - allequal(sorted(columns.onset), columns.onset)
+    - allequal(sorted(columns.onset, "numeric"), columns.onset)

From c0917c337413df39cf73db73f120d1db9b7a6e83 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 18 Jul 2024 17:31:51 -0400
Subject: [PATCH 50/74] fix(schema): metaschema cleanup, schema bugs caught
 (#1870)

* chore(metaschema): Organize enums and termTypes in definitions

* fix(metaschema): Improve definitions of requirement levels, fields and issues

* fix(schema): Inconsistencies caught by improved metaschema

* rf(metaschema): Define and use expressionList

* fix(metaschema): Remove unused README property

* rf(metaschema): Move single-use definition back inline

* fix(metaschema): Unify derivative and raw file rules
---
 src/metaschema.json                 | 332 ++++++++++++----------------
 src/schema/rules/sidecars/func.yaml |   2 +-
 src/schema/rules/sidecars/mri.yaml  |  13 +-
 3 files changed, 154 insertions(+), 193 deletions(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index dd1a3fcb91..ce500d6418 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -12,10 +12,7 @@
               "type": "object",
               "properties": {
                 "selectors": {
-                  "type": "array",
-                  "items": {
-                    "type": "string"
-                  }
+                  "$ref": "#/definitions/ruleTypes/expressionList"
                 },
                 "target": {
                   "type": "object",
@@ -85,13 +82,13 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/schemaTerm" },
-                { "$ref": "#/definitions/generalTerm" },
-                { "$ref": "#/definitions/nameValueTerm" },
+                { "$ref": "#/definitions/termTypes/JSONSchema" },
+                { "$ref": "#/definitions/termTypes/general" },
+                { "$ref": "#/definitions/termTypes/nameValue" },
                 {
                   "type": "object",
                   "properties": {
-                    "format": { "$ref": "#/definitions/formats" },
+                    "format": { "$ref": "#/definitions/enums/formats" },
                     "unit": { "type": "string" }
                   }
                 }
@@ -105,7 +102,7 @@
           "type": "object",
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
-              "$ref": "#/definitions/generalTerm",
+              "$ref": "#/definitions/termTypes/general",
               "unevaluatedProperties": false
             },
             "additionalProperties": false
@@ -116,8 +113,8 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/generalTerm" },
-                { "$ref": "#/definitions/valueTerm" }
+                { "$ref": "#/definitions/termTypes/general" },
+                { "$ref": "#/definitions/termTypes/value" }
               ],
               "unevaluatedProperties": false
             }
@@ -129,13 +126,13 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/schemaTerm" },
-                { "$ref": "#/definitions/generalTerm" },
-                { "$ref": "#/definitions/nameValueTerm" },
+                { "$ref": "#/definitions/termTypes/JSONSchema" },
+                { "$ref": "#/definitions/termTypes/general" },
+                { "$ref": "#/definitions/termTypes/nameValue" },
                 {
                   "type": "object",
                   "properties": {
-                    "format": { "$ref": "#/definitions/formats" }
+                    "format": { "$ref": "#/definitions/enums/formats" }
                   },
                   "required": ["format"]
                 }
@@ -150,8 +147,8 @@
           "patternProperties": {
             "^[a-zA-Z0-9][a-zA-Z0-9_-]*$": {
               "allOf": [
-                { "$ref": "#/definitions/generalTerm" },
-                { "$ref": "#/definitions/valueTerm" },
+                { "$ref": "#/definitions/termTypes/general" },
+                { "$ref": "#/definitions/termTypes/value" },
                 { "properties": { "tags": { "type": "array" } } }
               ]
             },
@@ -168,8 +165,8 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/generalTerm" },
-                { "$ref": "#/definitions/valueTerm" }
+                { "$ref": "#/definitions/termTypes/general" },
+                { "$ref": "#/definitions/termTypes/value" }
               ],
               "unevaluatedProperties": false
             }
@@ -181,7 +178,7 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/generalTerm" },
+                { "$ref": "#/definitions/termTypes/general" },
                 {
                   "properties": { "file_type": { "type": "string" } },
                   "required": ["file_type"]
@@ -194,10 +191,10 @@
         },
         "formats": {
           "type": "object",
-          "propertyNames": { "$ref": "#/definitions/formats" },
+          "propertyNames": { "$ref": "#/definitions/enums/formats" },
           "additionalProperties": {
             "allOf": [
-              { "$ref": "#/definitions/generalTerm" },
+              { "$ref": "#/definitions/termTypes/general" },
               {
                 "type": "object",
                 "properties": {
@@ -216,9 +213,9 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/schemaTerm" },
-                { "$ref": "#/definitions/generalTerm" },
-                { "$ref": "#/definitions/nameValueTerm" },
+                { "$ref": "#/definitions/termTypes/JSONSchema" },
+                { "$ref": "#/definitions/termTypes/general" },
+                { "$ref": "#/definitions/termTypes/nameValue" },
                 {
                   "type": "object",
                   "properties": {
@@ -238,7 +235,7 @@
           "type": "object",
           "patternProperties": {
             "^[a-z]+$": {
-              "$ref": "#/definitions/generalTerm",
+              "$ref": "#/definitions/termTypes/general",
               "unevaluatedProperties": false
             }
           },
@@ -249,8 +246,8 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/generalTerm" },
-                { "$ref": "#/definitions/valueTerm" },
+                { "$ref": "#/definitions/termTypes/general" },
+                { "$ref": "#/definitions/termTypes/value" },
                 {
                   "type": "object",
                   "properties": {
@@ -296,26 +293,19 @@
                 "^[a-zA-Z0-9_]+$": {
                   "type": "object",
                   "properties": {
-                    "issues": {
-                      "type": "object",
-                      "properties": {
-                        "code": { "type": "string" },
-                        "message": { "type": "string" },
-                        "level": { "enum": ["error", "warning"] }
-                      },
-                      "required": ["code", "message", "level"],
-                      "additionalProperties": false
+                    "issue": {
+                      "allOf": [{ "$ref": "#/definitions/ruleTypes/issue" }],
+                      "required": ["level"]
                     },
                     "selectors": {
-                      "type": "array",
-                      "items": { "type": "string" }
+                      "$ref": "#/definitions/ruleTypes/expressionList"
                     },
                     "checks": {
-                      "type": "array",
-                      "items": { "type": "string" }
+                      "$ref": "#/definitions/ruleTypes/expressionList"
                     }
                   },
-                  "required": ["checks", "selectors"]
+                  "required": ["checks", "selectors"],
+                  "additionalProperties": false
                 }
               }
             }
@@ -359,18 +349,10 @@
             "deriv": {
               "type": "object",
               "patternProperties": {
-                "^[a-zA-Z0-9_]+$": {
+                "^[a-z_]+$": {
                   "type": "object",
                   "patternProperties": {
-                    "^[a-zA-Z0-9_]+$": {
-                      "type": "object",
-                      "properties": {
-                        "entities": {
-                          "$ref": "#/definitions/entities"
-                        }
-                      }
-                    },
-                    "additionalProperties": false
+                    "^[a-zA-Z0-9_]+$": { "$ref": "#/definitions/suffixRule" }
                   }
                 }
               },
@@ -454,10 +436,7 @@
                 "message": { "type": "string" },
                 "level": { "enum": ["error", "warning"] },
                 "selectors": {
-                  "type": "array",
-                  "items": {
-                    "type": "string"
-                  }
+                  "$ref": "#/definitions/ruleTypes/expressionList"
                 }
               },
               "required": ["message", "level"],
@@ -501,81 +480,100 @@
     },
     "schema_version": {
       "type": "string"
-    },
-    "README": {
-      "type": "string"
     }
   },
   "required": ["meta", "objects", "rules", "bids_version", "schema_version"],
   "additionalProperties": false,
   "definitions": {
-    "formats": {
-      "$comment": "Formats whose patterns are defined in BIDS schema",
-      "type": "string",
-      "enum": [
-        "index",
-        "label",
-        "boolean",
-        "integer",
-        "number",
-        "string",
-        "hed_version",
-        "bids_uri",
-        "dataset_relative",
-        "date",
-        "datetime",
-        "file_relative",
-        "participant_relative",
-        "rrid",
-        "stimuli_relative",
-        "time",
-        "unit",
-        "uri"
-      ]
-    },
-    "generalTerm": {
-      "type": "object",
-      "properties": {
-        "display_name": { "type": "string" },
-        "description": { "type": "string" }
+    "enums": {
+      "formats": {
+        "$comment": "Formats whose patterns are defined in BIDS schema",
+        "type": "string",
+        "enum": [
+          "index",
+          "label",
+          "boolean",
+          "integer",
+          "number",
+          "string",
+          "hed_version",
+          "bids_uri",
+          "dataset_relative",
+          "date",
+          "datetime",
+          "file_relative",
+          "participant_relative",
+          "rrid",
+          "stimuli_relative",
+          "time",
+          "unit",
+          "uri"
+        ]
       },
-      "required": ["display_name", "description"]
-    },
-    "schemaTerm": {
-      "$ref": "https://json-schema.org/draft/2020-12/schema#",
-      "anyOf": [{ "required": ["type"] }, { "required": ["anyOf"] }]
-    },
-    "nameValueTerm": {
-      "type": "object",
-      "properties": { "name": { "type": "string" } },
-      "required": ["name"]
+      "requirement_level": {
+        "$comment": "Requirement levels that may apply to terms",
+        "type": "string",
+        "enum": ["required", "recommended", "optional", "deprecated"]
+      }
     },
-    "valueTerm": {
-      "type": "object",
-      "properties": { "value": { "type": "string" } },
-      "required": ["value"]
+    "termTypes": {
+      "general": {
+        "type": "object",
+        "properties": {
+          "display_name": { "type": "string" },
+          "description": { "type": "string" }
+        },
+        "required": ["display_name", "description"]
+      },
+      "JSONSchema": {
+        "$ref": "https://json-schema.org/draft/2020-12/schema#",
+        "anyOf": [{ "required": ["type"] }, { "required": ["anyOf"] }]
+      },
+      "nameValue": {
+        "type": "object",
+        "properties": { "name": { "type": "string" } },
+        "required": ["name"]
+      },
+      "value": {
+        "type": "object",
+        "properties": { "value": { "type": "string" } },
+        "required": ["value"]
+      }
     },
-    "entities": {
-      "type": "object",
-      "patternProperties": {
-        "^[a-z]+$": {
-          "anyOf": [
-            { "enum": ["optional", "required"] },
-            {
-              "type": "object",
-              "properties": {
-                "level": { "enum": ["optional", "required"] },
-                "enum": {
-                  "type": "array",
-                  "items": { "type": "string" }
-                }
-              },
-              "required": ["level", "enum"]
-            }
-          ]
-        }
+    "ruleTypes": {
+      "field": {
+        "anyOf": [
+          { "$ref": "#/definitions/enums/requirement_level" },
+          {
+            "type": "object",
+            "properties": {
+              "level": { "$ref": "#/definitions/enums/requirement_level" },
+              "level_addendum": { "type": "string" },
+              "description_addendum": { "type": "string" },
+              "issue": { "$ref": "#/definitions/ruleTypes/issue" }
+            },
+            "required": ["level"],
+            "additionalProperties": false
+          },
+          { "type": "string", "pattern": "recommended.*" }
+        ]
       },
-      "additionalProperties": false
+      "issue": {
+        "type": "object",
+        "properties": {
+          "code": { "type": "string" },
+          "message": { "type": "string" },
+          "level": { "enum": ["error", "warning"] }
+        },
+        "required": ["code", "message"],
+        "additionalProperties": false
+      },
+      "expressionList": {
+        "type": "array",
+        "items": {
+          "type": "string"
+        }
+      }
     },
     "sidecar": {
       "type": "object",
@@ -583,41 +581,12 @@
         "^[a-zA-Z0-9_]+$": {
           "type": "object",
           "properties": {
-            "selectors": {
-              "type": "array",
-              "items": { "type": "string" }
-            },
+            "selectors": { "$ref": "#/definitions/ruleTypes/expressionList" },
             "fields": {
               "type": "object",
               "patternProperties": {
                 "^[a-zA-Z0-9_]+$": {
-                  "anyOf": [
-                    {
-                      "enum": [
-                        "recommended",
-                        "optional",
-                        "required",
-                        "deprecated"
-                      ]
-                    },
-                    {
-                      "type": "object",
-                      "properties": {
-                        "level": {
-                          "enum": [
-                            "recommended",
-                            "optional",
-                            "required",
-                            "deprecated"
-                          ]
-                        },
-                        "level_addendum": { "type": "string" }
-                      },
-                      "required": ["level", "level_addendum"],
-                      "additionalProperties": false
-                    },
-                    { "pattern": "recommended.*" }
-                  ]
+                  "$ref": "#/definitions/ruleTypes/field"
                 }
               },
               "additionalProperties": false
@@ -635,42 +604,12 @@
         "^[a-zA-Z0-9_]+$": {
           "type": "object",
           "properties": {
-            "selectors": {
-              "type": "array",
-              "items": { "type": "string" }
-            },
+            "selectors": { "$ref": "#/definitions/ruleTypes/expressionList" },
             "columns": {
               "type": "object",
               "patternProperties": {
                 "^[a-zA-Z0-9_]+$": {
-                  "anyOf": [
-                    {
-                      "enum": [
-                        "recommended",
-                        "optional",
-                        "required",
-                        "deprecated"
-                      ]
-                    },
-                    {
-                      "type": "object",
-                      "properties": {
-                        "level": {
-                          "enum": [
-                            "recommended",
-                            "optional",
-                            "required",
-                            "deprecated"
-                          ]
-                        },
-                        "level_addendum": { "type": "string" },
-                        "description_addendum": { "type": "string" }
-                      },
-                      "required": ["level"],
-                      "additionalProperties": false
-                    },
-                    { "pattern": "recommended.*" }
-                  ]
+                  "$ref": "#/definitions/ruleTypes/field"
                 }
               },
               "additionalProperties": false
@@ -725,7 +664,28 @@
           "items": { "pattern": "^[a-zA-Z0-9]+$" }
         },
         "extensions": { "type": "array", "items": { "type": "string" } },
-        "entities": { "$ref": "#/definitions/entities" }
+        "entities": {
+          "type": "object",
+          "patternProperties": {
+            "^[a-z]+$": {
+              "anyOf": [
+                { "enum": ["optional", "required"] },
+                {
+                  "type": "object",
+                  "properties": {
+                    "level": { "enum": ["optional", "required"] },
+                    "enum": {
+                      "type": "array",
+                      "items": { "type": "string" }
+                    }
+                  },
+                  "required": ["level", "enum"]
+                }
+              ]
+            }
+          },
+          "additionalProperties": false
+        }
       },
       "required": ["suffixes", "extensions", "entities"],
       "additionalProperties": false
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index f3b7e70b69..dbb4d714e0 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -58,7 +58,7 @@ MRIFuncTimingParameters:
         field and that do not have the `SliceTiming` field set to allow for
         accurate calculation of "acquisition time"
       issue:
-        name: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
+        code: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
         message: |
           The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
     DelayAfterTrigger: recommended
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index cc27d676be..c9b94ec83b 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -27,7 +27,8 @@ MRIHardware:
       description_addendum: Corresponds to DICOM Tag 0018, 1020 `Software Versions`.
     HardcopyDeviceSoftwareVersion: deprecated
     MagneticFieldStrength:
-      level: recommended, but required for Arterial Spin Labeling
+      level: recommended
+      level_addendum: required for Arterial Spin Labeling
     ReceiveCoilName: recommended
     ReceiveCoilActiveElements: recommended
     NumberReceiveCoilActiveElements: optional
@@ -170,14 +171,14 @@ PhaseEncodingDirectionReq:
     PhaseEncodingDirection:
       level: required
       issue:
-        name: PHASE_ENCODING_DIRECTION_MUST_DEFINE
-        issue: |
+        code: PHASE_ENCODING_DIRECTION_MUST_DEFINE
+        message: |
           You have to define 'PhaseEncodingDirection' for this file.
     TotalReadoutTime:
       level: required
       description_addendum: <sup>3</sup>
       issue:
-        name: TOTAL_READOUT_TIME_MUST_DEFINE
+        code: TOTAL_READOUT_TIME_MUST_DEFINE
         message: |
           You have to define 'TotalReadoutTime' for this file.
 
@@ -191,7 +192,7 @@ MRITimingParameters:
         required if corresponding fieldmap data is present,
         or the data comes from a multi-echo sequence or Arterial Spin Labeling.
       issue:
-        name: ECHO_TIME_NOT_DEFINED
+        code: ECHO_TIME_NOT_DEFINED
         message: |
           You must define 'EchoTime' for this file. 'EchoTime' is the echo time (TE)
           for the acquisition, specified in seconds. Corresponds to DICOM Tag
@@ -273,7 +274,7 @@ MRIFlipAngleLookLockerTrue:
     FlipAngle:
       level: required
       issue:
-        name: LOOK_LOCKER_FLIP_ANGLE_MISSING
+        code: LOOK_LOCKER_FLIP_ANGLE_MISSING
         message: |
           You should define 'FlipAngle' for this file, in
           case of a LookLocker acquisition. 'FlipAngle' is the

From 65ca8ddc6d897246c1f820edb3b135662e1bda2d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 18 Jul 2024 17:34:55 -0400
Subject: [PATCH 51/74] fix(schema): Deduplicate enum values constructed from
 anyOfs (#1872)

---
 tools/schemacode/bidsschematools/schema.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/tools/schemacode/bidsschematools/schema.py b/tools/schemacode/bidsschematools/schema.py
index ed6b5da5f3..a00eaddac9 100644
--- a/tools/schemacode/bidsschematools/schema.py
+++ b/tools/schemacode/bidsschematools/schema.py
@@ -164,7 +164,10 @@ def flatten_enums(namespace, inplace=True):
         namespace = deepcopy(namespace)
     for struct in _find(namespace, lambda obj: "anyOf" in obj):
         try:
-            all_enum = [val for item in struct["anyOf"] for val in item["enum"]]
+            # Deduplicate because JSON schema validators may not like duplicates
+            # Long run, we should get rid of this function and have the rendering
+            # code handle anyOfs
+            all_enum = list(dict.fromkeys(val for item in struct["anyOf"] for val in item["enum"]))
         except KeyError:
             continue
 

From 5cac7c5a9c19869c546af3ed585ad7c1e9402f4b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 22 Jul 2024 21:09:49 +0000
Subject: [PATCH 52/74] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/pre-commit/mirrors-mypy: v1.10.1 → v1.11.0](https://github.com/pre-commit/mirrors-mypy/compare/v1.10.1...v1.11.0)
---
 .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 886c93bce6..c59c7ce96a 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -67,7 +67,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.10.1
+    rev: v1.11.0
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

From 74eda56cc7c4483e6516963659c192389f09a825 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 25 Jul 2024 12:52:11 -0400
Subject: [PATCH 53/74] feat(metaschema): Allow column definition object as an
 alternative to JSON Schema

---
 src/metaschema.json | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index ce500d6418..c0462edcaf 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -82,7 +82,18 @@
           "patternProperties": {
             "^[a-zA-Z0-9_]+$": {
               "allOf": [
-                { "$ref": "#/definitions/termTypes/JSONSchema" },
+                {
+                  "anyOf": [
+                    { "$ref": "#/definitions/termTypes/JSONSchema" },
+                    {
+                      "type": "object",
+                      "properties": {
+                        "definition": { "type": "object" }
+                      },
+                      "required": ["definition"]
+                    }
+                  ]
+                },
                 { "$ref": "#/definitions/termTypes/general" },
                 { "$ref": "#/definitions/termTypes/nameValue" },
                 {

From 8fdfdb98745194215964811bc554f4fb3260b4f4 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 25 Jul 2024 12:53:14 -0400
Subject: [PATCH 54/74] feat(schema): Provide default JSON column definitions

---
 src/schema/objects/columns.yaml | 115 +++++++++++++++++++-------------
 1 file changed, 69 insertions(+), 46 deletions(-)

diff --git a/src/schema/objects/columns.yaml b/src/schema/objects/columns.yaml
index 9128a235ba..d93145430e 100644
--- a/src/schema/objects/columns.yaml
+++ b/src/schema/objects/columns.yaml
@@ -40,14 +40,20 @@ age:
 
     It is recommended to tag participant ages that are 89 or higher as 89+,
     for privacy purposes.
-  type: number
-  unit: year
+  definition: {
+    "LongName": "Subject age",
+    "Description": "Subject age in postnatal years",
+    "Units": "year",
+  }
 cardiac:
   name: cardiac
   display_name: Cardiac measurement
   description: |
     continuous pulse measurement
-  type: number
+  definition: {
+    "Description": "continuous pulse measurement",
+    "Units": "mV"
+  }
 channel:
   name: channel
   display_name: Channel
@@ -185,6 +191,27 @@ group__channel:
 handedness:
   name: handedness
   display_name: Subject handedness
+  definition: {
+    "LongName": "Subject handedness",
+    "Description": "String value indicating one of \"left\", \"right\", or \"ambidextrous\".",
+    "Levels": {
+      "left": "Left-handed",
+      "l": "Left-handed",
+      "L": "Left-handed",
+      "LEFT": "Left-handed",
+      "Left": "Left-handed",
+      "right": "Right-handed",
+      "r": "Right-handed",
+      "R": "Right-handed",
+      "RIGHT": "Right-handed",
+      "Right": "Right-handed",
+      "ambidextrous": "Ambidextrous",
+      "a": "Ambidextrous",
+      "A": "Ambidextrous",
+      "AMBIDEXTROUS": "Ambidextrous",
+      "Ambidextrous": "Ambidextrous",
+    }
+  }
   description: |
     String value indicating one of "left", "right", "ambidextrous".
 
@@ -194,25 +221,6 @@ handedness:
 
     For "ambidextrous", use one of these values: `ambidextrous`, `a`, `A`, `AMBIDEXTROUS`,
     `Ambidextrous`.
-  type: string
-  # TODO: Add definitions for these values. (perhaps don't specify)
-  enum:
-    - left
-    - l
-    - L
-    - LEFT
-    - Left
-    - right
-    - r
-    - R
-    - RIGHT
-    - Right
-    - ambidextrous
-    - a
-    - A
-    - AMBIDEXTROUS
-    - Ambidextrous
-    - n/a
 hemisphere:
   name: hemisphere
   display_name: Electrode hemisphere
@@ -368,7 +376,9 @@ pathology:
     When different from `healthy`, pathology SHOULD be specified.
     The pathology may be specified in either `samples.tsv` or
     `sessions.tsv`, depending on whether the pathology changes over time.
-  type: string
+  definition: {
+    "Description": "Description of the pathology of the sample or type of control."
+  }
 participant_id:
   name: participant_id
   display_name: Participant ID
@@ -429,7 +439,10 @@ respiratory:
   display_name: Respiratory measurement
   description: |
     continuous breathing measurement
-  type: number
+  definition: {
+    "Description": "continuous measurements by respiration belt",
+    "Units": "mV"
+  }
 response_time:
   name: response_time
   display_name: Response time
@@ -494,25 +507,27 @@ sex:
     For "female", use one of these values: `female`, `f`, `F`, `FEMALE`, `Female`.
 
     For "other", use one of these values: `other`, `o`, `O`, `OTHER`, `Other`.
-  type: string
-  # TODO: Add definitions for these values. (perhaps don't specify)
-  enum:
-    - male
-    - m
-    - M
-    - MALE
-    - Male
-    - female
-    - f
-    - F
-    - FEMALE
-    - Female
-    - other
-    - o
-    - O
-    - OTHER
-    - Other
-    - n/a
+  definition: {
+    "LongName": "sex",
+    "Description": "String value indicating phenotypical sex.",
+    "Levels": {
+      "F": "Female",
+      "FEMALE": "Female",
+      "Female": "Female",
+      "f": "Female",
+      "female": "Female",
+      "M": "Male",
+      "MALE": "Male",
+      "Male": "Male",
+      "m": "Male",
+      "male": "Male",
+      "O": "Other",
+      "OTHER": "Other",
+      "Other": "Other",
+      "o": "Other",
+      "other": "Other",
+    }
+  }
 short_channel:
   name: short_channel
   display_name: Short Channel
@@ -568,7 +583,10 @@ species:
     (for example, `homo sapiens`, `mus musculus`, `rattus norvegicus`).
     For backwards compatibility, if `species` is absent, the participant is assumed to be
     `homo sapiens`.
-  type: string
+  definition: {
+    "Description":
+      "binomial species name from the NCBI Taxonomy (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi)"
+  }
 status:
   name: status
   display_name: Channel status
@@ -609,7 +627,9 @@ strain:
   description: |
     For species different from `homo sapiens`, string value indicating
     the strain of the species, for example: `C57BL/6J`.
-  type: string
+  definition: {
+    "Description": "name of the strain of the species"
+  }
 strain_rrid:
   name: strain_rrid
   display_name: Strain RRID
@@ -649,7 +669,10 @@ trigger:
   display_name: Trigger
   description: |
     continuous measurement of the scanner trigger signal
-  type: number
+  definition: {
+    "Description": "continuous measurement of the scanner trigger signal",
+    "Units": "arbitrary"
+  }
 # type column in channels.tsv files
 type__channels:
   name: type

From 40ca7bbd2f9bd2d981df29707d8ff9f3e9ab78de Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 25 Jul 2024 12:54:32 -0400
Subject: [PATCH 55/74] feat(spec): Render definition and enum columns alike

---
 .../bidsschematools/render/tables.py          | 16 ++++++------
 .../schemacode/bidsschematools/render/text.py | 24 ++++++++++--------
 .../bidsschematools/render/utils.py           | 25 ++++++++++++++++++-
 3 files changed, 45 insertions(+), 20 deletions(-)

diff --git a/tools/schemacode/bidsschematools/render/tables.py b/tools/schemacode/bidsschematools/render/tables.py
index 9366ae5725..31b6e13fd0 100644
--- a/tools/schemacode/bidsschematools/render/tables.py
+++ b/tools/schemacode/bidsschematools/render/tables.py
@@ -74,8 +74,8 @@ def _make_object_table(
         "columns": "column",
     }.get(table_type)
 
-    for element in subschema.keys():
-        field_name = subschema[element]["name"]
+    for element, field in subschema.items():
+        field_name = field["name"]
         # NOTE: Link to the glossary entry,
         # except for subobjects (if table_type) and
         # "additional columns" (field_name.startswith("**"))
@@ -90,19 +90,19 @@ def _make_object_table(
             "[DEPRECATED](SPEC_ROOT/common-principles.md#definitions)",
         )
 
-        type_string = utils.resolve_metadata_type(subschema[element])
+        type_string = utils.resolve_metadata_type(field)
 
         description = utils.normalize_requirements(
-            subschema[element]["description"] + " " + description_addendum
+            f"{field['description']} {description_addendum}".strip()
         )
 
         # Append a list of valid values, if provided, to the description.
         # If there are a lot of valid values, this will add a link to the description linking to
         # the associated glossary entry.
-        if (
-            "enum" in subschema[element].keys()
-            and len(subschema[element]["enum"]) >= n_values_to_combine
-        ):
+        levels = subschema[element].get("enum", []) or subschema[element].get(
+            "definition", {}
+        ).get("Levels", [])
+        if len(levels) >= n_values_to_combine:
             glossary_entry = f"{GLOSSARY_PATH}.md#objects.{table_type}.{element}"
             valid_values_str = (
                 f"For a list of valid values for this {element_type}, see the "
diff --git a/tools/schemacode/bidsschematools/render/text.py b/tools/schemacode/bidsschematools/render/text.py
index f26ba73204..ce70ae0ded 100644
--- a/tools/schemacode/bidsschematools/render/text.py
+++ b/tools/schemacode/bidsschematools/render/text.py
@@ -175,17 +175,19 @@ def make_glossary(schema, src_path=None):
         elif obj["type"] == "format":
             text += f"**Regular expression**: `{obj_def['pattern']}`\n\n"
 
-        keys_to_drop = ["description", "display_name", "name", "value", "pattern"]
-        if "enum" in obj_def.keys():
-            allowed_values = []
-            keys_to_drop.append("enum")
-            for value in obj_def["enum"]:
-                if isinstance(value, str):
-                    allowed_values.append(value)
-                else:
-                    allowed_values.append(value["name"])
-
-            text += f"**Allowed values**: `{'`, `'.join(allowed_values)}`\n\n"
+        keys_to_drop = [
+            "description",
+            "display_name",
+            "name",
+            "value",
+            "pattern",
+            "enum",
+            "definition",
+        ]
+        levels = list(obj_def.get("enum", []) or obj_def.get("definition", {}).get("Levels", {}))
+        if levels:
+            levels = [level["name"] if isinstance(level, dict) else level for level in levels]
+            text += f"**Allowed values**: `{'`, `'.join(levels)}`\n\n"
 
         text += f"**Description**:\n{obj_desc}\n\n"
 
diff --git a/tools/schemacode/bidsschematools/render/utils.py b/tools/schemacode/bidsschematools/render/utils.py
index 873699058e..97b3eefa0f 100644
--- a/tools/schemacode/bidsschematools/render/utils.py
+++ b/tools/schemacode/bidsschematools/render/utils.py
@@ -222,6 +222,21 @@ def resolve_metadata_type(definition):
 
         string = " or ".join(substrings)
 
+    elif "definition" in definition:
+        json_def = definition["definition"]
+
+        if "Delimiter" in json_def:
+            # Delimiter indicates the value must be parsed. For BIDS purposes,
+            # this is a string, even if the parsed array is of numbers.
+            string = "string"
+        elif "Levels" in json_def:
+            # JSON keys are always strings.
+            string = "string"
+        elif "Units" in json_def:
+            # Values with units are always (any exceptions?) numbers.
+            string = "number"
+        else:
+            string = "string or number"
     else:
         # This clause should only catch $refs.
         # The schema should be deferenced by this point, so $refs should not exist.
@@ -246,7 +261,15 @@ def describe_valid_values(definition):
     str : A sentence describing valid values for the object.
     """
     description = ""
-    if "anyOf" in definition.keys():
+    if "anyOf" in definition:
+        return description
+
+    if "definition" in definition:
+        levels = definition["definition"].get("Levels")
+        if levels:
+            description = (
+                f"Unless redefined in a sidecar file, must be one of: {', '.join(levels)}."
+            )
         return description
 
     if definition["type"] == "boolean":

From 439736145afb70ea8c59b92a2aa70140b4bfd71a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 25 Jul 2024 20:29:21 +0200
Subject: [PATCH 56/74] [ENH] Add admonitions to task and beh pages (#1735)

* update task and beh pages

* update doc

* apply suggestions from review

* Update CONTRIBUTING.md

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>

* typo

* semantic line break

---------

Co-authored-by: Stefan Appelhoff <stefan.appelhoff@mailbox.org>
---
 CONTRIBUTING.md                               |  3 +
 .../behavioral-experiments.md                 | 25 ++++--
 src/modality-specific-files/task-events.md    | 84 ++++++++++---------
 3 files changed, 64 insertions(+), 48 deletions(-)

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index d16d54cdc5..adae5e2cba 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -257,6 +257,9 @@ The keyword for the heading must be one of the following:
 - example
 - quote
 
+Do not put [macros](#using-macros) in admonitions,
+as this will likely not give the output you expect.
+
 ## Using macros
 
 We use [mkdocs-macros](https://mkdocs-macros-plugin.readthedocs.io/en/latest/)
diff --git a/src/modality-specific-files/behavioral-experiments.md b/src/modality-specific-files/behavioral-experiments.md
index aa17cc3757..b27592cad4 100644
--- a/src/modality-specific-files/behavioral-experiments.md
+++ b/src/modality-specific-files/behavioral-experiments.md
@@ -1,5 +1,11 @@
 # Behavioral experiments (with no neural recordings)
 
+!!! example "Example datasets"
+
+    Datasets containing behavioral data can be found
+    in the [BIDS examples repository](https://bids-standard.github.io/bids-examples/#behavioral)
+    and can be used as helpful guidance when curating new datasets.
+
 <!--
 This block generates a filename templates.
 The inputs for this macro can be found in the directory
@@ -9,17 +15,20 @@ and a guide for using macros can be found at
 -->
 {{ MACROS___make_filename_template("raw", datatypes=["beh"]) }}
 
-In addition to logs from behavioral experiments performed alongside imaging data
-acquisitions, one can also include data from experiments performed with no neural
-recordings.
-The results of those experiments can be stored in the `beh` directory using the same
-formats for event timing (`_events.tsv`), metadata (`_events.json`),
+In addition to logs from behavioral experiments
+performed alongside imaging data acquisitions,
+one MAY also include data from experiments
+performed with no neural recordings.
+The results of those experiments MAY be stored in the `beh` directory
+using the same formats for event timing (`_events.tsv`),
+metadata (`_events.json`),
 physiological (`_physio.tsv.gz`, `_physio.json`)
 and other continuous recordings (`_stim.tsv.gz`, `_stim.json`)
 as for tasks performed during MRI, electrophysiological or other neural recordings.
-Additionally, events files that do not include the mandatory `onset` and
-`duration` columns can still be included, but should be labeled `_beh.tsv`
-rather than `_events.tsv`.
+Additionally, events files
+that do not include the mandatory `onset` and `duration` columns
+MAY be included,
+but MUST be labeled `_beh.tsv` rather than `_events.tsv`.
 
 ## Sidecar JSON (`*_beh.json`)
 
diff --git a/src/modality-specific-files/task-events.md b/src/modality-specific-files/task-events.md
index ca5925909d..7dd53428a6 100644
--- a/src/modality-specific-files/task-events.md
+++ b/src/modality-specific-files/task-events.md
@@ -27,9 +27,9 @@ Each task events file REQUIRES a corresponding task data file.
 It is also possible to have a single `events.tsv` file describing events
 for all participants and runs (see
 [Inheritance Principle](../common-principles.md#the-inheritance-principle)).
-As with all other tabular data, `events.tsv` files MAY be accompanied by a JSON
-file describing the columns in detail (see
-[Tabular Files](../common-principles.md#tabular-files)).
+As with all other tabular data, `events.tsv` files MAY be accompanied
+by a JSON file describing the columns in detail
+(see [Tabular Files](../common-principles.md#tabular-files)).
 
 The tabular files consists of one row per event and a set of REQUIRED
 and OPTIONAL columns:
@@ -44,26 +44,30 @@ and a guide for using macros can be found at
 
 The content of  `events.tsv` files SHOULD be sorted by values in the `onset` column.
 
-Note for MRI data:
-If any acquired scans have been discarded before forming the imaging data file,
-ensure that an `onset` of 0 corresponds to the time the first image was stored.
-For example in case there is an in scanner training phase that
-begins before the scanning sequence has started events from this sequence should
-have negative onset time counting down to the beginning of the acquisition of
-the first volume.
-
-Note regarding the precision of numeric metadata:
-It is RECOMMENDENDED that dataset curators specify numeric metadata like `onset` and
-`duration` with as much decimal precision as is reasonable in the context of the experiment.
-For example in an EEG experiment with devices operating at 1000 Hz sampling frequency,
-dataset curators SHOULD specify **at least** 3 figures after the decimal point.
-
-An arbitrary number of additional columns can be added. Those allow describing
-other properties of events that could be later referenced in modeling and
+An arbitrary number of additional columns can be added.
+Those allow describing other properties of events that could be later referenced in modeling and
 hypothesis extensions of BIDS.
 Note that the `trial_type` and any additional columns in a TSV file
 SHOULD be documented in an accompanying JSON sidecar file.
 
+!!! note "Regarding the precision of numeric metadata"
+
+    For the precision of numeric metadata,
+    it is RECOMMENDENDED that dataset curators specify numeric metadata like `onset` and
+    `duration` with as much decimal precision as is reasonable in the context of the experiment.
+    For example in an EEG experiment with devices operating at 1000 Hz sampling frequency,
+    dataset curators SHOULD specify **at least** 3 figures after the decimal point.
+
+!!! note "For fMRI data"
+
+    For fMRI data
+    if any acquired scans have been discarded before forming the imaging data file,
+    ensure that an `onset` of 0 corresponds to the time the first image was stored.
+    For example in case there is an in scanner training phase that
+    begins before the scanning sequence has started events from this sequence should
+    have negative onset time counting down to the beginning of the acquisition of
+    the first volume.
+
 Example:
 
 <!-- This block generates a file tree.
@@ -119,24 +123,26 @@ In the accompanying JSON sidecar, the `trial_type` column might look as follows:
 }
 ```
 
-Note that in the example above:
+!!! note
 
-1.  Only a subset of columns are described for the sake of brevity.
-    In a real dataset, all other columns SHOULD also be described.
+    In the example above:
 
-1.  The `channel` column contains a list of values that are separated
-    by a delimiter (`|`), as is declared in the `Delimiter` metadata
-    field of the `events.json` file.
-    Thus, the channels related to the event in the third row of the example
-    are called `F,1`, `F,2`, and `Cz`.
+    1.  Only a subset of columns are described for the sake of brevity.
+        In a real dataset, all other columns SHOULD also be described.
 
-1.  The example contains a column called `annots`.
-    This column is not defined in BIDS, and constitutes additional, arbitrary
-    (that is, unofficial) metadata.
-    In the present case, it is used to describe artifacts in the data,
-    in reference to the `channel` column.
-    The `annots` column is making
-    use of the powerful HED system for documenting events, see below.
+    1.  The `channel` column contains a list of values that are separated
+        by a delimiter (`|`), as is declared in the `Delimiter` metadata field
+        of the `events.json` file.
+        Thus, the channels related to the event in the third row of the example
+        are called `F,1`, `F,2`, and `Cz`.
+
+    1.  The example contains a column called `annots`.
+        This column is not defined in BIDS, and constitutes additional,
+        arbitrary (that is, unofficial) metadata.
+        In the present case, it is used to describe artifacts in the data,
+        in reference to the `channel` column.
+        The `annots` column is making use of the powerful HED system
+        for documenting events, see below.
 
 Events MAY also be documented in machine-actionable form
 using HED (Hierarchical Event Descriptor) tags.
@@ -145,8 +151,8 @@ in event-related analyses.
 See [Hierarchical Event Descriptors](../appendices/hed.md)
 for additional information and examples.
 
-For multi-echo files, the `events.tsv` file is applicable to all echos of
-a particular run:
+For multi-echo files, the `events.tsv` file is applicable
+to all echos of a particular run:
 
 <!-- This block generates a file tree.
 A guide for using macros can be found at
@@ -188,8 +194,6 @@ References to existing databases can also be encoded using additional columns.
 The following example includes references to the
 [Karolinska Directed Emotional Faces (KDEF) database](https://www.kdef.se/).
 
-Example:
-
 <!-- 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
@@ -235,8 +239,8 @@ in the accompanying JSON sidecar as follows:
 }
 ```
 
-Note that all other columns SHOULD also be described but are omitted for the
-sake of brevity.
+Note that all other columns SHOULD also be described but are omitted
+for the sake of brevity.
 
 ### Stimulus presentation details
 

From 7a33d51484305ad1d50051899451b0f1dd0a8028 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Mon, 29 Jul 2024 16:36:40 -0400
Subject: [PATCH 57/74] fix(schema): Point to correct DigitizedHeadPoints
 definition for MEG coordsystem (#1876)

---
 src/schema/rules/sidecars/meg.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/rules/sidecars/meg.yaml b/src/schema/rules/sidecars/meg.yaml
index 33d851f6af..2390766900 100644
--- a/src/schema/rules/sidecars/meg.yaml
+++ b/src/schema/rules/sidecars/meg.yaml
@@ -205,7 +205,7 @@ MEGCoordsystemDigitizedHeadPoints:
     - datatype == "meg"
     - suffix == "coordsystem"
   fields:
-    DigitizedHeadPoints: optional
+    DigitizedHeadPoints__coordsystem: optional
     DigitizedHeadPointsCoordinateSystem: optional
     DigitizedHeadPointsCoordinateUnits: optional
     DigitizedHeadPointsCoordinateSystemDescription:

From 6bd4458f050d758be04baf0a8374933676e513bf Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 29 Jul 2024 18:32:30 -0400
Subject: [PATCH 58/74] [pre-commit.ci] pre-commit autoupdate (#1877)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/python-jsonschema/check-jsonschema: 0.29.0 → 0.29.1](https://github.com/python-jsonschema/check-jsonschema/compare/0.29.0...0.29.1)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .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 c59c7ce96a..82122e77c7 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -15,7 +15,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.0
+    rev: 0.29.1
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

From b1be6768a7476ad746eb6f905347638c83816333 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Tue, 30 Jul 2024 10:31:12 -0400
Subject: [PATCH 59/74] fix(schema): Fix checks to reduce false positives
 (#1878)

* fix(schema): Limit EVENTS_TSV_MISSING to data files

* fix(schema): Move VolumeTiming check into checks

* fix(schema): Associated file checks only apply to data files

* fix(schema): Improve targeting of B0Field* recommendations

* fix(schema): Improve targeting of MRIAnatomicalLandmarks

* fix(schema): Check sidecars of data files only

* fix(schema): NIRS SamplingFrequency check should look in sidecar
---
 .../magnetic-resonance-imaging-data.md             |  6 +++++-
 src/schema/rules/checks/events.yaml                |  1 +
 src/schema/rules/checks/fmap.yaml                  |  3 +++
 src/schema/rules/checks/func.yaml                  | 11 +++++++++++
 src/schema/rules/checks/nirs.yaml                  |  3 ++-
 src/schema/rules/sidecars/func.yaml                |  4 ----
 src/schema/rules/sidecars/mri.yaml                 | 14 +++++++++++---
 7 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/src/modality-specific-files/magnetic-resonance-imaging-data.md b/src/modality-specific-files/magnetic-resonance-imaging-data.md
index d5e8e6abc9..a4e6c1fc7a 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -160,7 +160,11 @@ The definitions of the fields specified in these tables may be found in
 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.MRIEchoPlanarImagingAndB0Mapping") }}
+{{ MACROS___make_sidecar_table([
+     "mri.MRIB0FieldIdentifier",
+     "mri.MRIEchoPlanarImagingAndB0FieldSource",
+   ])
+}}
 
 #### Tissue description
 
diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index 1f0f57a123..a5fa9ac5fd 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -13,6 +13,7 @@ EventsMissing:
     - '"task" in entities'
     - '!match(entities.task, "rest")'
     - suffix != "events"
+    - extension != ".json"
   checks:
     - '"events" in associations'
 
diff --git a/src/schema/rules/checks/fmap.yaml b/src/schema/rules/checks/fmap.yaml
index b6e8e621cc..199b6e44b3 100644
--- a/src/schema/rules/checks/fmap.yaml
+++ b/src/schema/rules/checks/fmap.yaml
@@ -9,6 +9,7 @@ EchoTime12DifferenceUnreasonable:
     level: error
   selectors:
     - suffix == "phasediff"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - sidecar.EchoTime2 - sidecar.EchoTime1 >= 0.0001
     - sidecar.EchoTime2 - sidecar.EchoTime1 <= 0.01
@@ -22,6 +23,7 @@ FmapFieldmapWithoutMagnitude:
     level: error
   selectors:
     - suffix == "fieldmap"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - '"magnitude" in associations'
 
@@ -34,6 +36,7 @@ FmapPhasediffWithoutMagnitude:
     level: warning
   selectors:
     - suffix == "phasediff"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - '"magnitude1" in associations'
 
diff --git a/src/schema/rules/checks/func.yaml b/src/schema/rules/checks/func.yaml
index cce740a1ec..a908bfa345 100644
--- a/src/schema/rules/checks/func.yaml
+++ b/src/schema/rules/checks/func.yaml
@@ -127,3 +127,14 @@ SliceTimingAcquisitionDurationMutex:
   checks:
     - type(sidecar.AcquisitionDuration) == "null"
     - type(sidecar.DelayTime) == "null"
+
+VolumeTimingMissingAcquisitionDuration:
+  issue:
+    code: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
+    message: |
+      The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
+    level: error
+  selectors:
+    - type(sidecar.VolumeTiming) != "null"
+  checks:
+    - '"SliceTiming" in sidecar || "AcquisitionDuration" in sidecar'
diff --git a/src/schema/rules/checks/nirs.yaml b/src/schema/rules/checks/nirs.yaml
index 3ec07ce1d2..e4cabe3291 100644
--- a/src/schema/rules/checks/nirs.yaml
+++ b/src/schema/rules/checks/nirs.yaml
@@ -2,7 +2,7 @@
 NASamplingFreq:
   selectors:
     - suffix == "nirs"
-    - samplingFrequency == "n/a"
+    - sidecar.SamplingFrequency == "n/a"
   checks:
     - associations.channels.sampling_frequency != null
 
@@ -10,6 +10,7 @@ NIRSChannelCount:
   selectors:
     - datatype == "nirs"
     - suffix == "nirs"
+    - match(extension, '\.nii(\.gz)?$')
   checks:
     - |
       sidecar.NIRSChannelCount
diff --git a/src/schema/rules/sidecars/func.yaml b/src/schema/rules/sidecars/func.yaml
index dbb4d714e0..7192886407 100644
--- a/src/schema/rules/sidecars/func.yaml
+++ b/src/schema/rules/sidecars/func.yaml
@@ -57,10 +57,6 @@ MRIFuncTimingParameters:
         required for sequences that are described with the `VolumeTiming`
         field and that do not have the `SliceTiming` field set to allow for
         accurate calculation of "acquisition time"
-      issue:
-        code: VOLUME_TIMING_MISSING_ACQUISITION_DURATION
-        message: |
-          The field 'VolumeTiming' requires 'AcquisitionDuration' or 'SliceTiming' to be defined.
     DelayAfterTrigger: recommended
 
 # fMRI task information
diff --git a/src/schema/rules/sidecars/mri.yaml b/src/schema/rules/sidecars/mri.yaml
index c9b94ec83b..1dce5f67af 100644
--- a/src/schema/rules/sidecars/mri.yaml
+++ b/src/schema/rules/sidecars/mri.yaml
@@ -296,15 +296,23 @@ MRISliceAcceleration:
 
 MRIAnatomicalLandmarks:
   selectors:
-    - modality == "mri"
+    - datatype == "anat"
+    - intersects(dataset.datatypes, ["meg"])
   fields:
     AnatomicalLandmarkCoordinates__mri: recommended
 
-MRIEchoPlanarImagingAndB0Mapping:
+MRIB0FieldIdentifier:
   selectors:
-    - modality == "mri"
+    - datatype == 'fmap'
+    - match(extension, '\.nii(\.gz)?$')
   fields:
     B0FieldIdentifier: recommended
+
+MRIEchoPlanarImagingAndB0FieldSource:
+  selectors:
+    - intersects(datatype, ['dwi', 'func', 'perf'])
+    - intersects(dataset.datatypes, ['fmap'])
+  fields:
     B0FieldSource: recommended
 
 MRIInstitutionInformation:

From fdca7ec3885045319e32dbd04e14389f49544948 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Thu, 1 Aug 2024 09:14:34 -0500
Subject: [PATCH 60/74] fix(schema): Add hint to see if dataset name contains a
 visible character (#1879)

* add check to see if dataset name contains a visible character

* Update src/schema/rules/checks/hints.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

* js regex expects double slash for character classes in strings

* Revert "js regex expects double slash for character classes in strings"

This reverts commit 156960770ffc4a65bbff37315f202c3fa0c03f0e.

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/checks/hints.yaml | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/src/schema/rules/checks/hints.yaml b/src/schema/rules/checks/hints.yaml
index 50cc0f05dc..6efaf4ecdc 100644
--- a/src/schema/rules/checks/hints.yaml
+++ b/src/schema/rules/checks/hints.yaml
@@ -34,6 +34,19 @@ TooFewAuthors:
   checks:
     - length(json.Authors) > 1
 
+# 115
+EmptyDatasetName:
+  issue:
+    code: EMPTY_DATASET_NAME
+    message: |
+      The Name field of dataset_description.json is present but empty of visible characters.
+    level: warning
+  selectors:
+    - path == '/dataset_description.json'
+    - type(json.Name) != 'null'
+  checks:
+    - match(json.Name, '\S')
+
 ### Functional files
 
 # 85

From d2557e3c28f20515d3ac0520bb521818fee63c45 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Mon, 5 Aug 2024 12:02:34 -0400
Subject: [PATCH 61/74] [FIX] Replace defunct awaresystems.be and fslwiki links
 (#1874)

* [FIX] Replace defunct awaresystems.be link with Wayback machine link

* [FIX] fslwiki is redirecting to fsl/docs
---
 src/modality-specific-files/magnetic-resonance-imaging-data.md | 2 +-
 src/modality-specific-files/microscopy.md                      | 2 +-
 2 files 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 a4e6c1fc7a..5e4528aca5 100644
--- a/src/modality-specific-files/magnetic-resonance-imaging-data.md
+++ b/src/modality-specific-files/magnetic-resonance-imaging-data.md
@@ -721,7 +721,7 @@ within the `[*_]dwi.bval` and `[*_]dwi.bvec` files) MAY change across DWI runs.
 
 **Gradient orientation file formats**.
 The `[*_]dwi.bval` and `[*_]dwi.bvec` files MUST follow the
-[FSL format](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide#DTIFIT):
+[FSL format](https://fsl.fmrib.ox.ac.uk/fsl/docs/#/diffusion/index?id=diffusion-data-in-fsl):
 The `[*_]dwi.bvec` file contains 3 rows with *N* space-delimited floating-point numbers
 (corresponding to the *N* volumes in the corresponding NIfTI file.)
 The first row contains the *x* elements, the second row contains the *y* elements and
diff --git a/src/modality-specific-files/microscopy.md b/src/modality-specific-files/microscopy.md
index d095a7bb4d..569e6a5245 100644
--- a/src/modality-specific-files/microscopy.md
+++ b/src/modality-specific-files/microscopy.md
@@ -55,7 +55,7 @@ Microscopy raw data MUST be stored in one of the following formats:
 
 -   [OME-TIFF](https://docs.openmicroscopy.org/ome-model/6.1.2/ome-tiff/specification.html#)
     (`.ome.tif` for standard TIFF files or `.ome.btf` for
-    [BigTIFF](https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
+    [BigTIFF](https://web.archive.org/web/20240706160214/https://www.awaresystems.be/imaging/tiff/bigtiff.html) files)
 
 -   [OME-ZARR/NGFF](https://ngff.openmicroscopy.org/latest/) (`.ome.zarr` directories)
 

From 7f63953f6b9b84aeb811352d1d1b03eb514ff3e7 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Aug 2024 23:25:11 -0400
Subject: [PATCH 62/74] fix(metaschema): Require issues for checks

---
 src/metaschema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index c0462edcaf..f6e5a62d25 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -315,7 +315,7 @@
                       "$ref": "#/definitions/ruleTypes/expressionList"
                     }
                   },
-                  "required": ["checks", "selectors"],
+                  "required": ["checks", "selectors", "issue"],
                   "additionalProperties": false
                 }
               }

From e23714770c88590fffdb699eca599e3dd84d127d Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Aug 2024 23:26:07 -0400
Subject: [PATCH 63/74] fix(schema): Add issues for file reference checks

---
 src/schema/rules/checks/references.yaml | 42 +++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/src/schema/rules/checks/references.yaml b/src/schema/rules/checks/references.yaml
index b0f1dd6e9d..191dcb6d4f 100644
--- a/src/schema/rules/checks/references.yaml
+++ b/src/schema/rules/checks/references.yaml
@@ -1,5 +1,11 @@
 ---
 SubjectRelativeIntendedForString:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be subject-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype != "ieeg"
     - type(sidecar.IntendedFor) == "string"
@@ -7,6 +13,12 @@ SubjectRelativeIntendedForString:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "subject") == 1
 
 SubjectRelativeIntendedForArray:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be subject-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype != "ieeg"
     - type(sidecar.IntendedFor) == "array"
@@ -14,6 +26,12 @@ SubjectRelativeIntendedForArray:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "subject") == length(sidecar.IntendedFor)
 
 DatasetRelativeIntendedForString:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "ieeg"
     - type(sidecar.IntendedFor) == "string"
@@ -21,6 +39,12 @@ DatasetRelativeIntendedForString:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "dataset") == 1
 
 DatasetRelativeIntendedForArray:
+  issue:
+    code: INTENDED_FOR
+    message: |
+      'IntendedFor' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "ieeg"
     - type(sidecar.IntendedFor) == "array"
@@ -28,6 +52,12 @@ DatasetRelativeIntendedForArray:
     - exists(sidecar.IntendedFor, "bids-uri") + exists(sidecar.IntendedFor, "dataset") == length(sidecar.IntendedFor)
 
 AssociatedEmptyRoomString:
+  issue:
+    code: ASSOCIATED_EMPTY_ROOM
+    message: |
+      'AssociatedEmptyRoom' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "meg"
     - type(sidecar.AssociatedEmptyRoom) == "string"
@@ -35,6 +65,12 @@ AssociatedEmptyRoomString:
     - exists(sidecar.AssociatedEmptyRoom, "bids-uri") + exists(sidecar.AssociatedEmptyRoom, "dataset") == 1
 
 AssociatedEmptyRoomArray:
+  issue:
+    code: ASSOCIATED_EMPTY_ROOM
+    message: |
+      'AssociatedEmptyRoom' field needs to point to an existing file.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - datatype == "meg"
     - type(sidecar.AssociatedEmptyRoom) == "array"
@@ -44,6 +80,12 @@ AssociatedEmptyRoomArray:
       == length(sidecar.AssociatedEmptyRoom)
 
 Sources:
+  issue:
+    code: SOURCE_FILE_EXIST
+    message: |
+      'Sources' field needs to point to existing files.
+      Files must be dataset-relative paths or BIDS URIs.
+    level: error
   selectors:
     - dataset.dataset_description.DatasetType == "derivatives"
     - type(sidecar.Sources) != "null"

From c5cb8eed6ef6179cc239a960d0fdf20f5c0d02f1 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 1 Aug 2024 23:47:19 -0400
Subject: [PATCH 64/74] fix(schema): Add issues for resolution/density object
 checks

---
 src/schema/rules/checks/common_derivatives.yaml | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/src/schema/rules/checks/common_derivatives.yaml b/src/schema/rules/checks/common_derivatives.yaml
index 723ddf0e59..6d9cd2eda7 100644
--- a/src/schema/rules/checks/common_derivatives.yaml
+++ b/src/schema/rules/checks/common_derivatives.yaml
@@ -1,18 +1,32 @@
 ---
 ResInSidecar:
+  issue:
+    code: MISSING_RESOLUTION_DESCRIPTION
+    message: |
+      The Resolution metadata object does not contain an entry for the file's
+      res-<label> entity.
+    level: error
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
     - intersects([modality], ["mri", "pet"])
     - match(extension, '^\.nii(\.gz)?$')
+    - type(entities.resolution) != 'null'
     - type(sidecar.Resolution) == "object"
   checks:
     - entities.resolution in sidecar.Resolution
 
 DenInSidecar:
+  issue:
+    code: MISSING_DENSITY_DESCRIPTION
+    message: |
+      The Density metadata object does not contain an entry for the file's
+      res-<label> entity.
+    level: error
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"
     - intersects([modality], ["mri", "pet"])
     - match(extension, '^\.nii(\.gz)?$')
+    - type(entities.density) != 'null'
     - type(sidecar.Density) == "object"
   checks:
     - entities.density in sidecar.Density

From 02049c56bc5dfff6b09f5792ebc7cc540dc0d910 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Fri, 2 Aug 2024 00:23:38 -0400
Subject: [PATCH 65/74] fix(schema): Add issues for NIRS checks

---
 src/schema/meta/context.yaml      | 10 +++++
 src/schema/rules/checks/nirs.yaml | 62 +++++++++++++++++++++++++++++++
 2 files changed, 72 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 280ae7b933..a1881df37b 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -212,6 +212,16 @@ properties:
             type: array
             items:
               type: string
+          short_channel:
+            description: 'Contents of the short_channel column'
+            type: array
+            items:
+              type: string
+          sampling_frequency:
+            description: 'Contents of the sampling_frequency column'
+            type: array
+            items:
+              type: string
       coordsystem:
         description: 'Coordinate system file'
         type: object
diff --git a/src/schema/rules/checks/nirs.yaml b/src/schema/rules/checks/nirs.yaml
index e4cabe3291..b4038b9d34 100644
--- a/src/schema/rules/checks/nirs.yaml
+++ b/src/schema/rules/checks/nirs.yaml
@@ -1,5 +1,11 @@
 ---
 NASamplingFreq:
+  issue:
+    code: NIRS_SAMPLING_FREQUENCY
+    message: |
+      Sampling frequency must be defined in the sidecar, or else as a sampling_frequency
+      column of channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - sidecar.SamplingFrequency == "n/a"
@@ -7,10 +13,17 @@ NASamplingFreq:
     - associations.channels.sampling_frequency != null
 
 NIRSChannelCount:
+  issue:
+    code: NIRS_CHANNEL_COUNT
+    message: |
+      NIRSChannelCount metadata must equal the number of channels with type NIRS*,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "nirs"
     - match(extension, '\.nii(\.gz)?$')
+    - type(sidecar.NIRSChannelCount) != 'null'
   checks:
     - |
       sidecar.NIRSChannelCount
@@ -22,6 +35,12 @@ NIRSChannelCount:
       +  count(associations.channels.type, "NIRSCWMUA")
 
 ACCELChannelCountReq:
+  issue:
+    code: ACCEL_CHANNEL_COUNT
+    message: |
+      ACCELChannelCount metadata must equal the number of channels with type ACCEL,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - count(associations.channels.type, "ACCEL") > 0
@@ -29,6 +48,12 @@ ACCELChannelCountReq:
     - sidecar.ACCELChannelCount == count(associations.channels.type, "ACCEL")
 
 GYROChannelCountReq:
+  issue:
+    code: GYRO_CHANNEL_COUNT
+    message: |
+      GYROChannelCount metadata must equal the number of channels with type GYRO,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - count(associations.channels.type, "GYRO") > 0
@@ -36,6 +61,12 @@ GYROChannelCountReq:
     - sidecar.GYROChannelCount == count(associations.channels.type, "GYRO")
 
 MAGNChannelCountReq:
+  issue:
+    code: MAGN_CHANNEL_COUNT
+    message: |
+      MAGNChannelCount metadata must equal the number of channels with type MAGN,
+      as listed in channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - count(associations.channels.type, "MAGN") > 0
@@ -43,6 +74,12 @@ MAGNChannelCountReq:
     - sidecar.MAGNChannelCount == count(associations.channels.type, "MAGN")
 
 ShortChannelCountReq:
+  issue:
+    code: SHORT_CHANNEL_COUNT
+    message: |
+      ShortChannelCount metadata must equal the number of channels with the value `true`
+      in the `short_channel` column of channels.tsv.
+    level: error
   selectors:
     - suffix == "nirs"
     - '"ShortChannelCount" in sidecar'
@@ -50,6 +87,11 @@ ShortChannelCountReq:
     - sidecar.ShortChannelCount == count(associations.channels.short_channel, "true")
 
 Component:
+  issue:
+    code: COMPONENT_COLUMN_REQUIRED
+    message: |
+      ACCEL, GYRO, and MAGN columns require a `component` column in channels.tsv.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "channels"
@@ -71,6 +113,11 @@ RecommendedChannels:
     - associations.channels != null
 
 RequiredTemplateX:
+  issue:
+    code: REQUIRED_TEMPLATE_X
+    message: |
+      The `template_x` column MUST be defined if the `x` column is `n/a`.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"
@@ -80,6 +127,11 @@ RequiredTemplateX:
     - columns.template_x != null
 
 RequiredTemplateY:
+  issue:
+    code: REQUIRED_TEMPLATE_Y
+    message: |
+      The `template_y` column MUST be defined if the `y` column is `n/a`.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"
@@ -89,6 +141,11 @@ RequiredTemplateY:
     - columns.template_y != null
 
 RequiredTemplateZ:
+  issue:
+    code: REQUIRED_TEMPLATE_Z
+    message: |
+      The `template_z` column MUST be defined if the `z` column is `n/a`.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"
@@ -98,6 +155,11 @@ RequiredTemplateZ:
     - columns.template_z != null
 
 RequiredCoordsystem:
+  issue:
+    code: REQUIRED_COORDSYSTEM
+    message: |
+      If an optodes.tsv file is provided, an associated coordsystem.json must also be present.
+    level: error
   selectors:
     - datatype == "nirs"
     - suffix == "optodes"

From d3485762f1844e5b94f05fc2032a62e73647d681 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 5 Aug 2024 21:42:05 +0000
Subject: [PATCH 66/74] [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: 24.4.2 → 24.8.0](https://github.com/psf/black/compare/24.4.2...24.8.0)
- [github.com/pyCQA/flake8: 7.1.0 → 7.1.1](https://github.com/pyCQA/flake8/compare/7.1.0...7.1.1)
- [github.com/pre-commit/mirrors-mypy: v1.11.0 → v1.11.1](https://github.com/pre-commit/mirrors-mypy/compare/v1.11.0...v1.11.1)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 82122e77c7..5f2ddc1b5e 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -25,7 +25,7 @@ repos:
       - id: check-readthedocs
         files: readthedocs.yml
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
         files: ^tools/(?!schemacode)
@@ -45,7 +45,7 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 7.1.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/setup.cfg]
@@ -67,7 +67,7 @@ repos:
       - id: codespell
         args: ["--config=.codespellrc", "--dictionary=-", "--dictionary=.codespell_dict"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.0
+    rev: v1.11.1
     hooks:
       - id: mypy
         # Sync with project.optional-dependencies.typing

From 3892f8e5839e4ee3bae0a4f1879668b815ebd4cc Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Mon, 5 Aug 2024 19:51:36 -0400
Subject: [PATCH 67/74] rf(schema): Drop context.dataset.files (#1883)

* fix(schema): Use exists() function instead of comparing to dataset.files

* rf(schema): Drop context.dataset.files; exists() is cleaner

* schema: Bump schema minor version
---
 src/schema/SCHEMA_VERSION              | 2 +-
 src/schema/meta/context.yaml           | 3 ---
 src/schema/rules/checks/dataset.yaml   | 2 +-
 src/schema/rules/dataset_metadata.yaml | 2 +-
 4 files changed, 3 insertions(+), 6 deletions(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index 539f9fc668..eb1336c84d 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.10.1-dev
+0.11.0-dev
diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 280ae7b933..3001292586 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -29,9 +29,6 @@ properties:
       dataset_description:
         description: 'Contents of /dataset_description.json'
         type: object
-      files:
-        description: 'List of all files in dataset'
-        type: array
       tree:
         description: 'Tree view of all files in dataset'
         type: object
diff --git a/src/schema/rules/checks/dataset.yaml b/src/schema/rules/checks/dataset.yaml
index 91704d32e4..f3967ba266 100644
--- a/src/schema/rules/checks/dataset.yaml
+++ b/src/schema/rules/checks/dataset.yaml
@@ -51,7 +51,7 @@ SamplesTSVMissing:
     - path == '/dataset_description.json'
     - '"micr" in dataset.modalities'
   checks:
-    - "'samples.tsv' in dataset.files"
+    - exists('samples.tsv', 'dataset')
 
 UnknownVersion:
   issue:
diff --git a/src/schema/rules/dataset_metadata.yaml b/src/schema/rules/dataset_metadata.yaml
index d0a92081a0..1a702baa37 100644
--- a/src/schema/rules/dataset_metadata.yaml
+++ b/src/schema/rules/dataset_metadata.yaml
@@ -34,7 +34,7 @@ derivative_description:
 dataset_description_with_genetics:
   selectors:
     - path == "/dataset_description.json"
-    - intersects(dataset.files, ["/genetic_info.json"])
+    - exists('genetic_info.json', 'dataset')
   fields:
     Genetics: required
 

From cb00fd6791ac1474a92c0a2d30a525de7bba57f8 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Thu, 8 Aug 2024 12:40:58 -0400
Subject: [PATCH 68/74] feat(schema): Add rule to check files listed in
 scans.tsv exist (#1881)

* feat(schema): Update README with detail on exists(), add file-relative paths

* doc: Add return types to count() and index()

* feat(schema): Add check for the filename column of scans.tsv
---
 src/schema/README.md                 | 44 +++++++++++++++++++---------
 src/schema/rules/checks/dataset.yaml | 12 ++++++++
 2 files changed, 42 insertions(+), 14 deletions(-)

diff --git a/src/schema/README.md b/src/schema/README.md
index 68be4f2a9b..6d2225bf69 100644
--- a/src/schema/README.md
+++ b/src/schema/README.md
@@ -259,20 +259,36 @@ The following operators should be defined by an interpreter:
 
 The following functions should be defined by an interpreter:
 
-| Function                                        | Definition                                                                                                                                                 | Example                                                | Note                                                                           |
-| ----------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------ | ------------------------------------------------------------------------------ |
-| `count(arg: array, val: any)`                   | Number of elements in an array equal to `val`                                                                                                              | `count(columns.type, "EEG")`                           | The number of times "EEG" appears in the column "type" of the current TSV file |
-| `exists(arg: str \| array, rule: str) -> int`   | Count of files in an array that exist in the dataset. String is array with length 1. Rules include `"bids-uri"`, `"dataset"`, `"subject"` and `"stimuli"`. | `exists(sidecar.IntendedFor, "subject")`               | True if all files in `IntendedFor` exist, relative to the subject directory.   |
-| `index(arg: array, val: any)`                   | Index of first element in an array equal to `val`, `null` if not found                                                                                     | `index(["i", "j", "k"], axis)`                         | The number, from 0-2 corresponding to the string `axis`                        |
-| `intersects(a: array, b: array) -> bool`        | `true` if arguments contain any shared elements                                                                                                            | `intersects(dataset.modalities, ["pet", "mri"])`       | True if either PET or MRI data is found in dataset                             |
-| `allequal(a: array, b: array) -> bool`          | `true` if arrays have the same length and paired elements are equal                                                                                        | `intersects(dataset.modalities, ["pet", "mri"])`       | True if either PET or MRI data is found in dataset                             |
-| `length(arg: array) -> int`                     | Number of elements in an array                                                                                                                             | `length(columns.onset) > 0`                            | True if there is at least one value in the onset column                        |
-| `match(arg: str, pattern: str) -> bool`         | `true` if `arg` matches the regular expression `pattern` (anywhere in string)                                                                              | `match(extension, ".gz$")`                             | True if the file extension ends with `.gz`                                     |
-| `max(arg: array) -> number`                     | The largest non-`n/a` value in an array                                                                                                                    | `max(columns.onset)`                                   | The time of the last onset in an events.tsv file                               |
-| `min(arg: array) -> number`                     | The smallest non-`n/a` value in an array                                                                                                                   | `min(sidecar.SliceTiming) == 0`                        | A check that the onset of the first slice is 0s                                |
-| `sorted(arg: array, method: str) -> array`      | The sorted values of the input array; defaults to type-determined sort. If method is "lexical", or "numeric" use lexical or numeric sort.                  | `sorted(sidecar.VolumeTiming) == sidecar.VolumeTiming` | True if `sidecar.VolumeTiming` is sorted                                       |
-| `substr(arg: str, start: int, end: int) -> str` | The portion of the input string spanning from start position to end position                                                                               | `substr(path, 0, length(path) - 3)`                    | `path` with the last three characters dropped                                  |
-| `type(arg: Any) -> str`                         | The name of the type, including `"array"`, `"object"`, `"null"`                                                                                            | `type(datatypes)`                                      | Returns `"array"`                                                              |
+| Function                                        | Definition                                                                                                                                | Example                                                | Note                                                                           |
+| ----------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------ | ------------------------------------------------------------------------------ |
+| `count(arg: array, val: any) -> int`            | Number of elements in an array equal to `val`                                                                                             | `count(columns.type, "EEG")`                           | The number of times "EEG" appears in the column "type" of the current TSV file |
+| `exists(arg: str \| array, rule: str) -> int`   | Count of files in an array that exist in the dataset. String is array with length 1. See following section for the meanings of rules.     | `exists(sidecar.IntendedFor, "subject")`               | True if all files in `IntendedFor` exist, relative to the subject directory.   |
+| `index(arg: array, val: any) -> int`            | Index of first element in an array equal to `val`, `null` if not found                                                                    | `index(["i", "j", "k"], axis)`                         | The number, from 0-2 corresponding to the string `axis`                        |
+| `intersects(a: array, b: array) -> bool`        | `true` if arguments contain any shared elements                                                                                           | `intersects(dataset.modalities, ["pet", "mri"])`       | True if either PET or MRI data is found in dataset                             |
+| `allequal(a: array, b: array) -> bool`          | `true` if arrays have the same length and paired elements are equal                                                                       | `intersects(dataset.modalities, ["pet", "mri"])`       | True if either PET or MRI data is found in dataset                             |
+| `length(arg: array) -> int`                     | Number of elements in an array                                                                                                            | `length(columns.onset) > 0`                            | True if there is at least one value in the onset column                        |
+| `match(arg: str, pattern: str) -> bool`         | `true` if `arg` matches the regular expression `pattern` (anywhere in string)                                                             | `match(extension, ".gz$")`                             | True if the file extension ends with `.gz`                                     |
+| `max(arg: array) -> number`                     | The largest non-`n/a` value in an array                                                                                                   | `max(columns.onset)`                                   | The time of the last onset in an events.tsv file                               |
+| `min(arg: array) -> number`                     | The smallest non-`n/a` value in an array                                                                                                  | `min(sidecar.SliceTiming) == 0`                        | A check that the onset of the first slice is 0s                                |
+| `sorted(arg: array, method: str) -> array`      | The sorted values of the input array; defaults to type-determined sort. If method is "lexical", or "numeric" use lexical or numeric sort. | `sorted(sidecar.VolumeTiming) == sidecar.VolumeTiming` | True if `sidecar.VolumeTiming` is sorted                                       |
+| `substr(arg: str, start: int, end: int) -> str` | The portion of the input string spanning from start position to end position                                                              | `substr(path, 0, length(path) - 3)`                    | `path` with the last three characters dropped                                  |
+| `type(arg: Any) -> str`                         | The name of the type, including `"array"`, `"object"`, `"null"`                                                                           | `type(datatypes)`                                      | Returns `"array"`                                                              |
+
+#### The `exists()` function
+
+In various places, BIDS datasets may declare links between files.
+In order to validate these links,
+the `exists()` function returns a count of files that can be found within the dataset.
+To accommodate the various ways of declaring these links,
+the following rules are defined:
+
+| `rule`       | Definition                                                                                                | Example                                                                               |
+| ------------ | --------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------- |
+| `"dataset"`  | A path relative to the root of the dataset.                                                               | `exists('participants.tsv', 'dataset')`                                               |
+| `"subject"`  | A path relative to the current subject directory.                                                         | `exists('ses-1/anat/sub-01_ses-1_T1w.nii.gz', 'subject')`                             |
+| `"stimuli"`  | A path relative to the `/stimuli` directory.                                                              | For `events.tsv`: `exists(columns.stim_file, 'stimuli') == length(columns.stim_file)` |
+| `"file"`     | A path relative to the directory containing the current file.                                             | For `scans.tsv`: `exists(columns.filename, 'file') == length(columns.stim_file)`      |
+| `"bids-uri"` | A URI of the form `bids:<dataset>:<relative-path>`. If `<dataset>` is empty, the current dataset is used. | `exists('bids::participants.tsv', 'bids-uri')`                                        |
 
 #### The special value `null`
 
diff --git a/src/schema/rules/checks/dataset.yaml b/src/schema/rules/checks/dataset.yaml
index f3967ba266..69444aed9e 100644
--- a/src/schema/rules/checks/dataset.yaml
+++ b/src/schema/rules/checks/dataset.yaml
@@ -91,3 +91,15 @@ SingleSourceCitationFields:
     - '!("HowToAcknowledge" in dataset.dataset_description)'
     - '!("License" in dataset.dataset_description)'
     - '!("ReferencesAndLinks" in dataset.dataset_description)'
+
+ScansTSVScans:
+  issue:
+    code: SCANS_FILENAME_NOT_MATCH_DATASET
+    level: error
+    message: |
+      Filenames in scans.tsv file do not match what is present in the BIDS dataset.
+  selectors:
+    - suffix == 'scans'
+    - extension == '.tsv'
+  checks:
+    - exists(columns.filename, "file") == length(columns.filename)

From 0e506f08de3a1f22b14b6c96067b050bddc28364 Mon Sep 17 00:00:00 2001
From: Ross Blair <rosswilsonblair@gmail.com>
Date: Mon, 12 Aug 2024 14:16:22 -0500
Subject: [PATCH 69/74] [SCHEMA] add non behavioral datatype assertion for
 warning about missing events.tsv (#1887)

* add non behavioral datatype assertion for warning about missing events.tsv

* should not apply to behaviorally suffixed files either.

* Update src/schema/rules/checks/events.yaml

Co-authored-by: Chris Markiewicz <effigies@gmail.com>

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/rules/checks/events.yaml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index a5fa9ac5fd..4c4e143afd 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -10,9 +10,10 @@ EventsMissing:
     level: warning # could be an error with the proper selectors, I think
   selectors:
     - dataset.dataset_description.DatasetType == "raw"
+    - datatype != "beh"
     - '"task" in entities'
     - '!match(entities.task, "rest")'
-    - suffix != "events"
+    - '!intersects([suffix], ["events", "beh"])'
     - extension != ".json"
   checks:
     - '"events" in associations'

From 58e236e3acb5152b170bd9ce5fa7ef6bd4acbfa9 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Wed, 14 Aug 2024 17:00:57 -0400
Subject: [PATCH 70/74] fix(regex): Construct backreferences to ensure entity
 consistency (#1889)

* fix(regex): Construct backreferences to ensure entity consistency

* test(regex): Test the regexes more thoroughly
---
 tools/schemacode/bidsschematools/rules.py     | 10 +++++
 .../bidsschematools/tests/test_rules.py       | 37 ++++++++++++++++---
 .../bidsschematools/tests/test_validator.py   | 36 ++++++++++++++++++
 3 files changed, 77 insertions(+), 6 deletions(-)

diff --git a/tools/schemacode/bidsschematools/rules.py b/tools/schemacode/bidsschematools/rules.py
index 6004b0363b..ea4b054ded 100644
--- a/tools/schemacode/bidsschematools/rules.py
+++ b/tools/schemacode/bidsschematools/rules.py
@@ -69,6 +69,16 @@ def _format_entity(entity, name, pattern, level, directory=False):
     if directory and entity not in DIR_ENTITIES:
         return ""
 
+    # For a directory entity appearing in a filename, match the value
+    # found in the directory name
+    # Note that this makes it impossible to do something like
+    # /ses-1_dwi.json instead of /sub-??/ses-1/sub-??_ses-1_dwi.json
+    # We'll assume this is a negligible use case.
+    # It is possible to create such a regular expression, but doing it
+    # in a piecewise fashion is difficult.
+    if not directory and entity in DIR_ENTITIES:
+        return rf"(?({entity}){name}-(?P={entity})_)"
+
     label = _capture_regex(entity, pattern, not directory and entity in DIR_ENTITIES)
     post = "/" if directory else "_"
 
diff --git a/tools/schemacode/bidsschematools/tests/test_rules.py b/tools/schemacode/bidsschematools/tests/test_rules.py
index 35b167e199..ca2c5b920e 100644
--- a/tools/schemacode/bidsschematools/tests/test_rules.py
+++ b/tools/schemacode/bidsschematools/tests/test_rules.py
@@ -1,3 +1,5 @@
+import re
+
 from bidsschematools import rules
 
 from ..types import Namespace
@@ -13,19 +15,29 @@ def test_entity_rule(schema_obj):
             "extensions": [".nii"],
         }
     )
-    assert rules._entity_rule(rule, schema_obj) == {
+    nii_rule = rules._entity_rule(rule, schema_obj)
+    assert nii_rule == {
         "regex": (
             r"sub-(?P<subject>[0-9a-zA-Z]+)/"
             r"(?:ses-(?P<session>[0-9a-zA-Z]+)/)?"
             r"(?P<datatype>anat)/"
-            r"sub-(?P=subject)_"
-            r"(?:ses-(?P=session)_)?"
+            r"(?(subject)sub-(?P=subject)_)"
+            r"(?(session)ses-(?P=session)_)"
             r"(?P<suffix>T1w)"
             r"(?P<extension>\.nii)\Z"
         ),
         "mandatory": False,
     }
 
+    assert re.match(nii_rule["regex"], "sub-01/anat/sub-01_T1w.nii")
+    assert re.match(nii_rule["regex"], "sub-01/ses-01/anat/sub-01_ses-01_T1w.nii")
+    assert not re.match(nii_rule["regex"], "sub-01/anat/sub-02_T1w.nii")
+    assert not re.match(nii_rule["regex"], "sub-01/sub-01_T1w.nii")
+    assert not re.match(nii_rule["regex"], "sub-01_T1w.nii")
+    assert not re.match(nii_rule["regex"], "sub-01/ses-01/anat/sub-01_T1w.nii")
+    assert not re.match(nii_rule["regex"], "sub-01/anat/sub-01_ses-01_T1w.nii")
+    assert not re.match(nii_rule["regex"], "sub-01/ses-01/anat/sub-01_ses-02_T1w.nii")
+
     # Sidecar entities are optional
     rule = Namespace.build(
         {
@@ -35,18 +47,31 @@ def test_entity_rule(schema_obj):
             "extensions": [".json"],
         }
     )
-    assert rules._entity_rule(rule, schema_obj) == {
+    json_rule = rules._entity_rule(rule, schema_obj)
+    assert json_rule == {
         "regex": (
             r"(?:sub-(?P<subject>[0-9a-zA-Z]+)/)?"
             r"(?:ses-(?P<session>[0-9a-zA-Z]+)/)?"
             r"(?:(?P<datatype>anat)/)?"
-            r"(?:sub-(?P=subject)_)?"
-            r"(?:ses-(?P=session)_)?"
+            r"(?(subject)sub-(?P=subject)_)"
+            r"(?(session)ses-(?P=session)_)"
             r"(?P<suffix>T1w)"
             r"(?P<extension>\.json)\Z"
         ),
         "mandatory": False,
     }
+    assert re.match(json_rule["regex"], "sub-01/anat/sub-01_T1w.json")
+    assert re.match(json_rule["regex"], "sub-01/sub-01_T1w.json")
+    assert re.match(json_rule["regex"], "T1w.json")
+    assert re.match(json_rule["regex"], "sub-01/ses-01/anat/sub-01_ses-01_T1w.json")
+    assert re.match(json_rule["regex"], "sub-01/ses-01/sub-01_ses-01_T1w.json")
+    assert not re.match(json_rule["regex"], "sub-01/anat/sub-02_T1w.json")
+    assert not re.match(json_rule["regex"], "sub-01_T1w.json")
+    assert not re.match(json_rule["regex"], "ses-01_T1w.json")
+    assert not re.match(json_rule["regex"], "sub-01/ses-01/anat/sub-01_T1w.json")
+    assert not re.match(json_rule["regex"], "sub-01/anat/sub-01_ses-01_T1w.json")
+    assert not re.match(json_rule["regex"], "sub-01/ses-01/ses-01_T1w.json")
+    assert not re.match(json_rule["regex"], "sub-01/ses-01/anat/sub-01_ses-02_T1w.json")
 
 
 def test_split_inheritance_rules():
diff --git a/tools/schemacode/bidsschematools/tests/test_validator.py b/tools/schemacode/bidsschematools/tests/test_validator.py
index abd11737f0..90f0695308 100644
--- a/tools/schemacode/bidsschematools/tests/test_validator.py
+++ b/tools/schemacode/bidsschematools/tests/test_validator.py
@@ -29,6 +29,42 @@ def test_inheritance_examples():
     assert result["path_tracking"] == incorrect_inheritance
 
 
+def test_regression_examples():
+    """Tests that failed on pybids when switching to bst-regex-based validation"""
+    examples = [
+        "/sub-01/ses-ses/sub-01_dwi.bval",  # redundant dir /ses-ses/
+        "/sub-01/01_dwi.bvec",  # missed subject suffix
+        "/sub-01/sub_dwi.json",  # missed subject id
+        "/sub-01/sub-01_23_run-01_dwi.bval",  # wrong _23_
+        "/sub-01/sub-01_run-01_dwi.vec",  # wrong extension
+        "/sub-01/sub-01_run-01_dwi.jsn",  # wrong extension
+        "/sub-01/sub-01_acq_dwi.bval",  # missed suffix value
+        "/sub-01/sub-01_acq-23-singleband_dwi.bvec",  # redundant -23-
+        "/sub-01/anat/sub-01_acq-singleband_dwi.json",  # redundant /anat/
+        "/sub-01/sub-01_recrod-record_acq-singleband_run-01_dwi.bval",  # redundant record-record_
+        "/sub_01/sub-01_acq-singleband_run-01_dwi.bvec",  # wrong /sub_01/
+        "/sub-01/sub-01_acq-singleband__run-01_dwi.json",  # wrong __
+        "/sub-01/ses-test/sub-01_ses_test_dwi.bval",  # wrong ses_test
+        "/sub-01/ses-test/sb-01_ses-test_dwi.bvec",  # wrong sb-01
+        "/sub-01/ses-test/sub-01_ses-test_dw.json",  # wrong modality
+        "/sub-01/ses-test/sub-01_ses-test_run-01_dwi.val",  # wrong extension
+        "/sub-01/ses-test/sub-01_run-01_dwi.bvec",  # missed session in the filename
+        # This validator adds a .*/ to the regex, so this will be a false negative
+        # If I cared about this validator, I would dig into it, but it doesn't seem worth it.
+        # -cjm 2024.08.14
+        # "/sub-01/ses-test/ses-test_run-01_dwi.json",  # missed subject in the filename
+        "/sub-01/ses-test/sub-01_ses-test_acq-singleband.bval",  # missed modality
+        "/sub-01/ses-test/sub-01_ses-test_acq-singleband_dwi",  # missed extension
+        "/ses-test/sub-01/sub-01_ses-test_acq-singleband_dwi.json",  # wrong dirs order
+        "/sub-01/ses-test/sub-02_ses-test_acq-singleband_run-01_dwi.bval",  # wrong sub id
+        "/sub-01/sub-01_ses-test_acq-singleband_run-01_dwi.bvec",  # ses dir missed
+        "/ses-test/sub-01_ses-test_acq-singleband_run-01_dwi.json",  # sub id dir missed
+    ]
+
+    result = validate_bids(examples, dummy_paths=True)
+    assert result["path_tracking"] == examples
+
+
 def test_write_report(tmp_path):
     from bidsschematools.validator import write_report
 

From 98645a1643f3b9ce37675eed102a624f9700828a Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Wed, 14 Aug 2024 17:05:26 -0400
Subject: [PATCH 71/74] feat(schema): Improve type annotations of
 schema.context (#1886)

* feat(schema): Add additionalProperties=false to context objects

This is intended to give better guidance to tooling that would
auto-generate classes or interfaces for the validation context.

* feat(schema): Set requirement levels for context properties

* feat(schema): Type more array/object values in context

* fix(schema): Not all files have a subject
---
 src/schema/meta/context.yaml | 74 ++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

diff --git a/src/schema/meta/context.yaml b/src/schema/meta/context.yaml
index 5e33df0f66..ef35475238 100644
--- a/src/schema/meta/context.yaml
+++ b/src/schema/meta/context.yaml
@@ -18,6 +18,14 @@
 #
 ---
 type: object
+required:
+  - schema
+  - dataset
+  - path
+  - size
+  - sidecar
+  - associations
+additionalProperties: false
 properties:
   schema:
     description: 'The BIDS specification schema'
@@ -25,6 +33,14 @@ properties:
   dataset:
     description: 'Properties and contents of the entire dataset'
     type: object
+    required:
+      - dataset_description
+      - tree
+      - ignored
+      - datatypes
+      - modalities
+      - subjects
+    additionalProperties: false
     properties:
       dataset_description:
         description: 'Contents of /dataset_description.json'
@@ -35,15 +51,24 @@ properties:
       ignored:
         description: 'Set of ignored files'
         type: array
+        items:
+          type: string
       datatypes:
         description: 'Data types present in the dataset'
         type: array
+        items:
+          type: string
       modalities:
         description: 'Modalities present in the dataset'
         type: array
+        items:
+          type: string
       subjects:
         description: 'Collections of subjects in dataset'
         type: object
+        required:
+          - sub_dirs
+        additionalProperties: false
         properties:
           sub_dirs:
             description: 'Subjects as determined by sub-*/ directories'
@@ -63,10 +88,16 @@ properties:
   subject:
     description: 'Properties and contents of the current subject'
     type: object
+    required:
+      - sessions
+    additionalProperties: false
     properties:
       sessions:
         description: 'Collections of sessions in subject'
         type: object
+        required:
+          - ses_dirs
+        additionalProperties: false
         properties:
           ses_dirs:
             description: 'Sessions as determined by ses-*/ directories'
@@ -94,6 +125,8 @@ properties:
   entities:
     description: 'Entities parsed from the current filename'
     type: object
+    additionalProperties:
+      type: string
   datatype:
     description: 'Datatype of current file, for examples, anat'
     type: string
@@ -117,10 +150,13 @@ properties:
     description: |
       Associated files, indexed by suffix, selected according to the inheritance principle
     type: object
+    additionalProperties: false
     properties:
       events:
         description: 'Events file'
         type: object
+        required: [path, onset]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated events file'
@@ -133,6 +169,8 @@ properties:
       aslcontext:
         description: 'ASL context file'
         type: object
+        required: [path, n_rows, volume_type]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated aslcontext file'
@@ -148,6 +186,8 @@ properties:
       m0scan:
         description: 'M0 scan file'
         type: object
+        required: [path]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated M0 scan file'
@@ -155,6 +195,8 @@ properties:
       magnitude:
         description: 'Magnitude image file'
         type: object
+        required: [path]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated magnitude file'
@@ -162,6 +204,8 @@ properties:
       magnitude1:
         description: 'Magnitude1 image file'
         type: object
+        required: [path]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated magnitude1 file'
@@ -169,6 +213,8 @@ properties:
       bval:
         description: 'B value file'
         type: object
+        required: [path, n_cols, n_rows, values]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated bval file'
@@ -187,6 +233,8 @@ properties:
       bvec:
         description: 'B vector file'
         type: object
+        required: [path, n_cols, n_rows]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated bvec file'
@@ -200,6 +248,8 @@ properties:
       channels:
         description: 'Channels file'
         type: object
+        required: [path, type]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated channels file'
@@ -222,6 +272,8 @@ properties:
       coordsystem:
         description: 'Coordinate system file'
         type: object
+        required: [path]
+        additionalProperties: false
         properties:
           path:
             description: 'Path to associated coordsystem file'
@@ -232,12 +284,16 @@ properties:
     type: object
     additionalProperties:
       type: array
+      items:
+        type: string
   json:
     description: 'Contents of the current JSON file'
     type: object
   gzip:
     description: 'Parsed contents of gzip header'
     type: object
+    required: [timestamp, filename]
+    additionalProperties: false
     properties:
       timestamp:
         description: 'Modification time, unix timestamp'
@@ -252,11 +308,23 @@ properties:
     name: 'NIfTI Header'
     description: 'Parsed contents of NIfTI header referenced elsewhere in schema.'
     type: object
+    required:
+      - dim_info
+      - dim
+      - pixdim
+      - shape
+      - voxel_sizes
+      - xyzt_units
+      - qform_code
+      - sform_code
+    additionalProperties: false
     properties:
       dim_info:
         name: 'Dimension Information'
         description: 'Metadata about dimensions data.'
         type: object
+        required: [freq, phase, slice]
+        additionalProperties: false
         properties:
           freq:
             name: 'Frequency'
@@ -306,6 +374,8 @@ properties:
         name: 'XYZT Units'
         description: 'Units of pixdim[1..4]'
         type: object
+        required: [xyz, t]
+        additionalProperties: false
         properties:
           xyz:
             name: 'XYZ Units'
@@ -339,6 +409,7 @@ properties:
     name: 'Open Microscopy Environment fields'
     description: 'Parsed contents of OME-XML header, which may be found in OME-TIFF or OME-ZARR files'
     type: object
+    additionalProperties: false
     properties:
       PhysicalSizeX:
         name: 'PhysicalSizeX'
@@ -368,6 +439,9 @@ properties:
     name: 'TIFF'
     description: 'TIFF file format metadata'
     type: object
+    required:
+      - version
+    additionalProperties: false
     properties:
       version:
         name: 'Version'

From 2887f8baebda676d9b248302e0703e0c86e6766c Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 14 Aug 2024 17:06:58 -0400
Subject: [PATCH 72/74] schema-0.11.0

---
 src/schema/SCHEMA_VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index eb1336c84d..d9df1bbc0c 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.11.0-dev
+0.11.0

From 71ae45bfa8b02388fb8feb3e4cbb969ef70880ae Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 14 Aug 2024 17:07:56 -0400
Subject: [PATCH 73/74] schema-0.11.1-dev

---
 src/schema/SCHEMA_VERSION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/schema/SCHEMA_VERSION b/src/schema/SCHEMA_VERSION
index d9df1bbc0c..72ab694d37 100644
--- a/src/schema/SCHEMA_VERSION
+++ b/src/schema/SCHEMA_VERSION
@@ -1 +1 @@
-0.11.0
+0.11.1-dev

From 0de4c9c11c72676033a466b320e8a00f5890724e Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Wed, 14 Aug 2024 17:10:50 -0400
Subject: [PATCH 74/74] chore(ci): Fix installation step

---
 .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 14746534db..46c437826c 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -33,7 +33,7 @@ jobs:
       - name: "Install build dependencies"
         run: pip install --upgrade build twine
       - name: "Install test dependencies on tag"
-        run: pip install --upgrade tools/schemacode[test]
+        run: pip install --upgrade tools/schemacode[tests]
         if: ${{ startsWith(github.ref, 'refs/tags/schema-') }}
       - name: "Build archive on tag"
         run: pytest tools/schemacode/bidsschematools -k make_archive