From b49cf5855ff4816f1fc646bf0e1ac65de8cc100d Mon Sep 17 00:00:00 2001
From: melanieganz <melanieganz@users.noreply.github.com>
Date: Thu, 10 Aug 2023 10:48:41 +0200
Subject: [PATCH 01/18] Update entities.yaml

Removed the atlas entity and added a seg (segmentation) entity instead.
---
 src/schema/objects/entities.yaml | 19 +++++++++----------
 1 file changed, 9 insertions(+), 10 deletions(-)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 3260b4a3d4..b2ea4647df 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -25,16 +25,6 @@ acquisition:
     remains at the discretion of the researcher.
   type: string
   format: label
-atlas:
-  name: atlas
-  display_name: Atlas
-  description: |
-    The `atlas-<label>` key/value pair corresponds to a custom label the user
-    MAY use to distinguish a different atlas used for similar type of data.
-
-    This entity is only applicable to derivative data.
-  type: string
-  format: label
 ceagent:
   name: ce
   display_name: Contrast Enhancing Agent
@@ -286,6 +276,15 @@ sample:
     The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
   type: string
   format: label
+seg:
+  name: seg
+  display_name: segmentation
+  description: |
+    The `seg-<label>` key/value pair corresponds to a custom label the user
+    MAY use to distinguish different segmentations.
+    This entity is only applicable to derivative data.
+  type: string
+  format: label
 session:
   name: ses
   display_name: Session

From e3ce5ffe7439477744ff41d862bd269f367aa9f1 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 10 Aug 2023 17:32:30 -0400
Subject: [PATCH 02/18] Move from atlas- to seg- in derivatives

---
 src/derivatives/imaging.md | 25 ++++++++++++-------------
 1 file changed, 12 insertions(+), 13 deletions(-)

diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index b802d6c309..bcd653da08 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -153,8 +153,8 @@ Template:
 
 A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../appendices/entities.md#space).
 If no transformation has taken place, the value of `space` SHOULD be set to `orig`.
-If the mask is an ROI mask derived from an atlas, then the [`label` entity](../appendices/entities.md#label)) SHOULD
-be used to specify the masked structure
+If the mask is an ROI mask derived from an atlas segmentation,
+then 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 `Atlas` metadata SHOULD be defined.
 
@@ -229,10 +229,10 @@ structure may be concatenated in a single file.
 Segmentations may be defined in a volume (labeled voxels), a surface (labeled
 vertices) or a combined volume/surface space.
 
-If the segmentation can be derived from different atlases,
-the [`atlas` entity](../appendices/entities.md#atlas) MAY be used to
-distinguish the different segmentations.
-If so, the `Atlas` metadata SHOULD also be defined.
+If the segmentation can be generated in different ways,
+for example, following an atlas segmentation,
+the [`seg` entity](../appendices/entities.md#atlas) MAY be used to
+distinguish the name of the segmentation used.
 
 The following section describes discrete and probabilistic segmentations of
 volumes, followed by discrete segmentations of surface/combined spaces.
@@ -268,7 +268,7 @@ Template:
 <pipeline_name>/
     sub-<label>/
         anat|func|dwi/
-            <source_entities>[_space-<space>][_atlas-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
+            <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.nii.gz
 ```
 
 Example:
@@ -296,8 +296,7 @@ In this case, the mask suffix MUST 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)),
-the [`atlas` entity](../appendices/entities.md#atlas) and the
-`Atlas` metadata SHOULD be defined.
+and the [`seg` entity](../appendices/entities.md#atlas) SHOULD be defined.
 
 For example:
 
@@ -310,8 +309,8 @@ A guide for using macros can be found at
     "pipeline": {
         "sub-001": {
             "anat": {
-                "sub-001_space-orig_atlas-Desikan_label-GM_mask.nii.gz": "",
-                "sub-001_space-orig_atlas-Desikan_label-GM_mask.json": "",
+                "sub-001_space-orig_seg-Desikan_label-GM_mask.nii.gz": "",
+                "sub-001_space-orig_seg-Desikan_label-GM_mask.json": "",
                 },
             },
         }
@@ -333,7 +332,7 @@ Template:
 <pipeline_name>/
     sub-<label>/
         func|anat|dwi/
-            <source_entities>[_space-<space>][_atlas-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
+            <source_entities>[_space-<space>][_seg-<label>][_res-<label>][_den-<label>][_label-<label>]_probseg.nii.gz
 ```
 
 Example:
@@ -407,7 +406,7 @@ Template:
 <pipeline_name>/
     sub-<label>/
         anat/
-            <source_entities>[_hemi-{L|R}][_space-<space>][_atlas-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
+            <source_entities>[_hemi-{L|R}][_space-<space>][_seg-<label>][_res-<label>][_den-<label>]_dseg.{label.gii|dlabel.nii}
 ```
 
 The [`hemi-<label>`](../appendices/entities.md#hemi) entity is REQUIRED for GIFTI files storing information about

From 9c7ca6d5cc690f829b15f8c2e4851ca58fa2aba8 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 10 Aug 2023 17:33:25 -0400
Subject: [PATCH 03/18] Remove Atlas metadata object/rule

---
 src/schema/objects/metadata.yaml                       |  6 ------
 .../rules/sidecars/derivatives/common_derivatives.yaml | 10 ----------
 2 files changed, 16 deletions(-)

diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 0e1fe96916..7171581ad3 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -177,12 +177,6 @@ AssociatedEmptyRoom:
       format: dataset_relative
     - type: string
       format: bids_uri
-Atlas:
-  name: Atlas
-  display_name: Atlas
-  description: |
-    Which atlas (if any) was used to generate the mask.
-  type: string
 AttenuationCorrection:
   name: AttenuationCorrection
   display_name: Attenuation Correction
diff --git a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
index 5982b2e01d..301dac44ea 100644
--- a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
@@ -55,16 +55,6 @@ SegmentationCommon:
   fields:
     Manual: optional
 
-SegmentationCommonAtlas:
-  selectors:
-    - dataset.dataset_description.DatasetType == "derivative"
-    - 'intersects([suffix], ["dseg", "probseg"])'
-    - '"atlas" in entities'
-  fields:
-    Atlas:
-      level: recommended
-      level_addendum: if `atlas` is present
-
 # Derivatives -> Imaging data types
 ImageDerivatives:
   selectors:

From a014ae6247c895a2137e931d0d54bc3441cfbde2 Mon Sep 17 00:00:00 2001
From: melanieganz <melanieganz@users.noreply.github.com>
Date: Tue, 15 Aug 2023 17:50:14 +0200
Subject: [PATCH 04/18] Update src/schema/objects/entities.yaml

The object key should be the long version of the name. name is what is seen in the entity _<name>-<value>_. And display_name is generally capitalized, imagining someone might write a GUI with a drop-down menu in it.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/objects/entities.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index b2ea4647df..7085145dce 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -276,9 +276,9 @@ sample:
     The label MUST be unique per subject and is RECOMMENDED to be unique throughout the dataset.
   type: string
   format: label
-seg:
+segmentation:
   name: seg
-  display_name: segmentation
+  display_name: Segmentation
   description: |
     The `seg-<label>` key/value pair corresponds to a custom label the user
     MAY use to distinguish different segmentations.

From d3a093a100b87869c6ad0243fb57883977c7d3f7 Mon Sep 17 00:00:00 2001
From: melanieganz <melanieganz@users.noreply.github.com>
Date: Tue, 15 Aug 2023 17:51:06 +0200
Subject: [PATCH 05/18] Update src/schema/objects/entities.yaml

The double-newline ensures that a newline is rendered.

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 src/schema/objects/entities.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/schema/objects/entities.yaml b/src/schema/objects/entities.yaml
index 7085145dce..bd946f3abb 100644
--- a/src/schema/objects/entities.yaml
+++ b/src/schema/objects/entities.yaml
@@ -282,6 +282,7 @@ segmentation:
   description: |
     The `seg-<label>` key/value pair corresponds to a custom label the user
     MAY use to distinguish different segmentations.
+
     This entity is only applicable to derivative data.
   type: string
   format: label

From 6bfb81612c2c5a5c50acf2cc7e3327caa85a0604 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 17 Aug 2023 16:30:57 -0400
Subject: [PATCH 06/18] fix validation

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

diff --git a/src/schema/rules/entities.yaml b/src/schema/rules/entities.yaml
index 09f240510b..2194a61a92 100644
--- a/src/schema/rules/entities.yaml
+++ b/src/schema/rules/entities.yaml
@@ -25,7 +25,7 @@
 - split
 - recording
 - chunk
-- atlas
+- segmentation
 - resolution
 - density
 - label

From 24becf6ffbf713a4c49e2857de647907a7a98b8d Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 17 Aug 2023 16:36:27 -0400
Subject: [PATCH 07/18] rm metadata mention of atlas for mask

---
 .../rules/sidecars/derivatives/common_derivatives.yaml | 10 ----------
 1 file changed, 10 deletions(-)

diff --git a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
index 301dac44ea..fbc05937bc 100644
--- a/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
+++ b/src/schema/rules/sidecars/derivatives/common_derivatives.yaml
@@ -38,16 +38,6 @@ MaskDerivatives:
     Sources: recommended
     RawSources: deprecated
 
-MaskDerivativesAtlas:
-  selectors:
-    - dataset.dataset_description.DatasetType == "derivative"
-    - suffix == "mask"
-    - '"label" in entities'
-  fields:
-    Atlas:
-      level: recommended
-      level_addendum: if `label` entity is defined
-
 SegmentationCommon:
   selectors:
     - dataset.dataset_description.DatasetType == "derivative"

From 4b4d87e14cc9a46fc0306928f251b7ec76182e98 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Thu, 17 Aug 2023 16:42:28 -0400
Subject: [PATCH 08/18] fix macro

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

diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index bcd653da08..61e1dfd1cd 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -170,7 +170,6 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table([
        "derivatives.common_derivatives.MaskDerivatives",
-       "derivatives.common_derivatives.MaskDerivativesAtlas",
        "derivatives.common_derivatives.ImageDerivativeResEntity",
        "derivatives.common_derivatives.ImageDerivativeDenEntity",
    ]) }}

From 39e28058c079b31024a6d32cbedad2b08a5edfaf Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 17 Aug 2023 16:47:43 -0400
Subject: [PATCH 09/18] One more macro

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

diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index 61e1dfd1cd..2dd1f22fc3 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -249,7 +249,6 @@ A guide for using macros can be found at
 -->
 {{ MACROS___make_sidecar_table([
        "derivatives.common_derivatives.SegmentationCommon",
-       "derivatives.common_derivatives.SegmentationCommonAtlas",
        "derivatives.common_derivatives.ImageDerivativeResEntity",
        "derivatives.common_derivatives.ImageDerivativeDenEntity",
    ]) }}

From 29c05e0e1f97534cdbf6e4a227c42da0cdb1d9e0 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 17 Aug 2023 16:49:34 -0400
Subject: [PATCH 10/18] FIX: Drop remaining reference to Atlas

---
 src/derivatives/imaging.md | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index 2dd1f22fc3..382cdd6074 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -155,8 +155,7 @@ A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` ent
 If no transformation has taken place, the value of `space` SHOULD be set to `orig`.
 If the mask is an ROI mask derived from an atlas segmentation,
 then 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 `Atlas` metadata SHOULD be defined.
+(see [Common image-derived labels](#common-image-derived-labels)).
 
 JSON metadata fields:
 

From 84ed83759fb15266d284c6b50128fe4d32b30e14 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Thu, 17 Aug 2023 16:50:22 -0400
Subject: [PATCH 11/18] FIX: Links to segmentation entity

---
 src/derivatives/imaging.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/derivatives/imaging.md b/src/derivatives/imaging.md
index 382cdd6074..1a8fa2b9f7 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -229,7 +229,7 @@ vertices) or a combined volume/surface space.
 
 If the segmentation can be generated in different ways,
 for example, following an atlas segmentation,
-the [`seg` entity](../appendices/entities.md#atlas) MAY be used to
+the [`seg` entity](../appendices/entities.md#segmentation) MAY be used to
 distinguish the name of the segmentation used.
 
 The following section describes discrete and probabilistic segmentations of
@@ -293,7 +293,7 @@ In this case, the mask suffix MUST 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#atlas) SHOULD be defined.
+and the [`seg` entity](../appendices/entities.md#segmentation) SHOULD be defined.
 
 For example:
 

From 3d299fdc3fcbb58a43cea7551077b44a0c1352f7 Mon Sep 17 00:00:00 2001
From: melanieganz <melanieganz@users.noreply.github.com>
Date: Thu, 31 Aug 2023 12:52:48 +0200
Subject: [PATCH 12/18] Update src/derivatives/imaging.md

Co-authored-by: Robert Smith <robert.smith@florey.edu.au>
---
 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 1a8fa2b9f7..aea21dbaad 100644
--- a/src/derivatives/imaging.md
+++ b/src/derivatives/imaging.md
@@ -154,7 +154,7 @@ Template:
 A binary (1 - inside, 0 - outside) mask in the space defined by the [`space` entity](../appendices/entities.md#space).
 If no transformation has taken place, the value of `space` SHOULD be set to `orig`.
 If the mask is an ROI mask derived from an atlas segmentation,
-then the [`label` entity](../appendices/entities.md#label)) SHOULD be used to specify the masked structure
+then the [`label` entity](../appendices/entities.md#label) SHOULD be used to specify the masked structure
 (see [Common image-derived labels](#common-image-derived-labels)).
 
 JSON metadata fields:

From 064e142e0b306f077751076f133d7c720006c200 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <markiewicz@stanford.edu>
Date: Fri, 8 Sep 2023 10:51:48 -0400
Subject: [PATCH 13/18] SCHEMA: Ignore n/a entries in stim_file columns when
 checking existence (#1608)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Fixes the following failures in bids-examples:

```
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ eeg_ds003645s_hed                                                                                                                 │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    STIMULUS_FILE_MISSING                      sub-002_task-FacePerception_run-3_events   schema.rules.checks.events.StimulusFileM
                                               .tsv                                       issing
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ eeg_ds003645s_hed_inheritance                                                                                                     │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    STIMULUS_FILE_MISSING                      sub-002_task-FacePerception_run-3_events   schema.rules.checks.events.StimulusFileM
                                               .tsv                                       issing
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ eeg_ds003645s_hed_library                                                                                                         │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    STIMULUS_FILE_MISSING                      sub-002_task-FacePerception_run-3_events   schema.rules.checks.events.StimulusFileM
                                               .tsv                                       issing
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ eeg_ds003645s_hed_longform                                                                                                        │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    STIMULUS_FILE_MISSING                      sub-002_task-FacePerception_run-3_events   schema.rules.checks.events.StimulusFileM
                                               .tsv                                       issing
  ┌───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┐
  │ ieeg_filtered_speech                                                                                                              │
  └───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────┘
    STIMULUS_FILE_MISSING                      sub-cm8_task-FilteredSpeech_events.tsv     schema.rules.checks.events.StimulusFileM
                                                                                          issing

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

diff --git a/src/schema/rules/checks/events.yaml b/src/schema/rules/checks/events.yaml
index 458e60d408..cd8fd414bd 100644
--- a/src/schema/rules/checks/events.yaml
+++ b/src/schema/rules/checks/events.yaml
@@ -26,4 +26,4 @@ StimulusFileMissing:
     - suffix == "events"
     - columns.stim_file != null
   checks:
-    - exists(columns.stim_file, "stimuli") == length(columns.stim_file)
+    - exists(columns.stim_file, "stimuli") == length(columns.stim_file) - count(columns.stim_file, "n/a")

From 76db9aa8fbdc32ed1b5f073a5617407112b23ea6 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 11 Sep 2023 12:12:05 +0200
Subject: [PATCH 14/18] Bump actions/checkout from 3 to 4 (#1610)

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

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/schemacode_ci.yml |  8 ++++----
 .github/workflows/validation.yml    | 12 ++++++------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/schemacode_ci.yml b/.github/workflows/schemacode_ci.yml
index 8188370cdd..e888fb06ad 100644
--- a/.github/workflows/schemacode_ci.yml
+++ b/.github/workflows/schemacode_ci.yml
@@ -26,7 +26,7 @@ jobs:
         os: ["ubuntu-latest"]
         python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
@@ -64,7 +64,7 @@ jobs:
             python-version: 3
     name: ${{ matrix.os }} with Python ${{ matrix.python-version }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: "Set up Python"
         uses: actions/setup-python@v4
@@ -129,7 +129,7 @@ jobs:
     runs-on: ubuntu-latest
     name: Validate schema
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set Up Python environment
         uses: actions/setup-python@v4
@@ -157,7 +157,7 @@ jobs:
     needs: [test, validate_schema]
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Download artifacts
         uses: actions/download-artifact@v3
diff --git a/.github/workflows/validation.yml b/.github/workflows/validation.yml
index 8e48d85bb6..aea69e6e93 100644
--- a/.github/workflows/validation.yml
+++ b/.github/workflows/validation.yml
@@ -16,14 +16,14 @@ jobs:
   codespell:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: codespell-project/actions-codespell@master
 
   # Markdown formatting
   remark:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-node@v3
         with:
           node-version: 14
@@ -36,7 +36,7 @@ jobs:
   yamllint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3
@@ -49,7 +49,7 @@ jobs:
   python-style:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3
@@ -63,7 +63,7 @@ jobs:
   latin-phrases:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3
@@ -86,7 +86,7 @@ jobs:
   validate_cff:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: actions/setup-python@v4
       with:
         python-version: 3

From 36e2e3c923f6460eb7351ea17201749c4a801771 Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Mon, 11 Sep 2023 10:18:07 -0400
Subject: [PATCH 15/18] [ENH] allow Levels values to be objects (#1603)

* update level description

* Apply suggestions from code review

Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>

* add link to glossary

* rm weird file

* fix path

---------

Co-authored-by: Sebastian Urchs <surchs@users.noreply.github.com>
---
 src/common-principles.md         | 23 +++++++++++++++++++++++
 src/schema/objects/metadata.yaml |  5 +++--
 2 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/src/common-principles.md b/src/common-principles.md
index c268e19203..2dc9905d9a 100644
--- a/src/common-principles.md
+++ b/src/common-principles.md
@@ -513,6 +513,29 @@ Example:
 }
 ```
 
+Each level can be described with a string as in the example above,
+or with an object containing the fields [`Description`](./glossary.md#description-metadata)
+and [`TermURL`](./glossary.md#termurl-metadata)
+like in the example below.
+
+```JSON
+{
+    "sex": {
+        "Description": "sex of the participant as reported by the participant",
+        "Levels": {
+            "M": {
+                "Description": "Male",
+                "TermURL": "https://www.ncbi.nlm.nih.gov/mesh/68008297"
+            },
+            "F": {
+                "Description": "Female",
+                "TermURL": "https://www.ncbi.nlm.nih.gov/mesh/68005260"
+            },
+        }
+    }
+}
+```
+
 ### Key-value files (dictionaries)
 
 JavaScript Object Notation (JSON) files MUST be used for storing key-value
diff --git a/src/schema/objects/metadata.yaml b/src/schema/objects/metadata.yaml
index 5347a5d5b5..f39d0d0465 100644
--- a/src/schema/objects/metadata.yaml
+++ b/src/schema/objects/metadata.yaml
@@ -3371,9 +3371,10 @@ TermURL:
   name: TermURL
   display_name: TermURL
   description: |
-    URL pointing to a formal definition of this type of data in an ontology
-    available on the web.
+    URL pointing to a formal definition of this type of data in an ontology available on the web.
+    For example: https://www.ncbi.nlm.nih.gov/mesh/68008297 for "male".
   type: string
+  format: uri
 TimeZero:
   name: TimeZero
   display_name: Time Zero

From e7d25de61a4cc379da1db7bd9dbf985b8af9e71c Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 12 Sep 2023 04:01:02 -0400
Subject: [PATCH 16/18] [pre-commit.ci] pre-commit autoupdate (#1611)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/psf/black: 23.7.0 → 23.9.1](https://github.com/psf/black/compare/23.7.0...23.9.1)

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 fa428cfd96..bd4d16ba06 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -13,7 +13,7 @@ repos:
       - id: check-added-large-files
       - id: check-case-conflict
   - repo: https://github.com/psf/black
-    rev: 23.7.0
+    rev: 23.9.1
     hooks:
       - id: black
         files: ^tools/(?!schemacode)

From 18837afe2909090811a49f019d55de6f0a47241a Mon Sep 17 00:00:00 2001
From: Remi Gau <remi_gau@hotmail.com>
Date: Tue, 12 Sep 2023 16:42:06 -0400
Subject: [PATCH 17/18] [MAINT] add mastodon badge (#1612)

* add mastodon badge

* add link to badge

* Update README.md

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

---------

Co-authored-by: Chris Markiewicz <effigies@gmail.com>
---
 README.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/README.md b/README.md
index 54b7bd11d7..f5c548feca 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,6 @@
 [![Validation](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml/badge.svg)](https://github.com/bids-standard/bids-specification/actions/workflows/validation.yml)
 [![CircleCI](https://circleci.com/gh/bids-standard/bids-specification.svg?style=shield)](https://circleci.com/gh/bids-standard/bids-specification)
+[![Mastodon Follow](https://img.shields.io/mastodon/follow/109520103085644521?domain=https%3A%2F%2Ffosstodon.org%2F)](https://fosstodon.org/@bidsstandard)
 [![@BIDSstandard](http://img.shields.io/twitter/follow/bidsstandard.svg?style=social)](https://twitter.com/BIDSstandard)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3686061.svg)](https://doi.org/10.5281/zenodo.3686061)
 

From d56b6892948fb9d0ce2685a48490fa00ce870126 Mon Sep 17 00:00:00 2001
From: bids-maintenance <bids.maintenance@gmail.com>
Date: Mon, 18 Sep 2023 13:58:34 +0000
Subject: [PATCH 18/18] [DOC] Auto-generate changelog entry for PR #1579

---
 src/CHANGES.md | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/src/CHANGES.md b/src/CHANGES.md
index f6b0a97cd4..8c55dcd092 100644
--- a/src/CHANGES.md
+++ b/src/CHANGES.md
@@ -2,7 +2,18 @@
 
 ## [Unreleased](https://github.com/bids-standard/bids-specification/tree/HEAD)
 
+-   \[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))
+-   \[SCHEMA]\[ENH] Remove atlas entity and replace it with seg in prep of BEP038 [#1579](https://github.com/bids-standard/bids-specification/pull/1579) ([melanieganz](https://github.com/melanieganz))
+-   \[FIX] improve longitudinal example [#1576](https://github.com/bids-standard/bids-specification/pull/1576) ([Remi-Gau](https://github.com/Remi-Gau))
+-   Adds Kim Ray as maintainer. [#1571](https://github.com/bids-standard/bids-specification/pull/1571) ([arokem](https://github.com/arokem))
+-   \[ENH] Allow for "echo" entity to be used with T1w and other nonparametric anatomical suffixes [#1570](https://github.com/bids-standard/bids-specification/pull/1570) ([yarikoptic](https://github.com/yarikoptic))
+-   Update `templates` in modality-agnostic-files [#1564](https://github.com/bids-standard/bids-specification/pull/1564) ([sappelhoff](https://github.com/sappelhoff))
+-   \[FIX] Clarify that electrodes.tsv is optional for MEG, for use with simultaneous (i)EEG [#1555](https://github.com/bids-standard/bids-specification/pull/1555) ([effigies](https://github.com/effigies))
+-   \[ENH] Allow UNKNOWN and NONE ContrastBolusIngredients [#1547](https://github.com/bids-standard/bids-specification/pull/1547) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[FIX] Update links to BIDS examples [#1545](https://github.com/bids-standard/bids-specification/pull/1545) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] add schema in appendix [#1543](https://github.com/bids-standard/bids-specification/pull/1543) ([Remi-Gau](https://github.com/Remi-Gau))
+-   \[ENH] add "visual correction" and "head stabilization" metadata [#1539](https://github.com/bids-standard/bids-specification/pull/1539) ([Remi-Gau](https://github.com/Remi-Gau))
 -   \[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))