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 01/11] [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 02/11] [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 03/11] [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 04/11] 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 05/11] 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 06/11] 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 07/11] 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 08/11] 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 09/11] 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 10/11] 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 11/11] 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 ---