Merge branch 'master' into enh/1748

Author: Remi-Gau

.pre-commit-config.yaml

@@ -47,7 +47,7 @@ repos:
         files: tools/schemacode
         args: ["--settings-file", "tools/schemacode/pyproject.toml"]
   - repo: https://github.com/pyCQA/flake8
-    rev: 7.1.1
+    rev: 7.1.2
     hooks:
       - id: flake8
         args: [--config=tools/schemacode/.flake8]

CONTRIBUTING.md

@@ -9,7 +9,7 @@ If you have any questions that aren't discussed below, please let us know
 by [opening an issue](https://github.com/bids-standard/bids-specification/issues/new).
 
 If you are not familiar with Git and GitHub,
-check our [generic contributing guidelines](https://bids-website.readthedocs.io/en/latest/collaboration/bids_github/CONTRIBUTING.html).
+check our [generic contributing guidelines](https://bids.neuroimaging.io/collaboration/bids_github/CONTRIBUTING.html).
 
 If you want to contribute to the BIDS specification,
 make sure you also read the instructions below.

src/appendices/entity-table.md

@@ -12,7 +12,7 @@ For example, if a file has an acquisition and reconstruction label, the
 acquisition entity must precede the reconstruction entity.
 REQUIRED and OPTIONAL entities for a given file type are denoted;
 empty cells imply that entities MUST NOT be specified.
-Entity formats indicate whether the value is alphanumeric
+Entity formats indicate whether the value is alphanumeric (and possibly including `+` character(s))
 (`<label>`) or numeric (`<index>`).
 
 A general introduction to entities is given in the section on

src/common-principles.md

@@ -49,7 +49,7 @@ Each entity has the following attributes:
     1.  *Index*: A non-negative integer, potentially zero-padded for
         consistent width.
 
-    1.  *Label*: An alphanumeric string.
+    1.  *Label*: An alphanumeric (and possibly including `+` character(s)) string.
         Note that labels MUST not collide when casing is ignored
         (see [Case collision intolerance](#case-collision-intolerance)).
 
@@ -1120,7 +1120,7 @@ A guide for using macros can be found at
 Additional files and directories containing raw data MAY be added as needed for
 special cases.
 All non-standard file entities SHOULD conform to BIDS-style naming conventions, including
-alphabetic entities and suffixes and alphanumeric labels/indices.
+alphabetic entities and suffixes and alphanumeric (and possibly including `+` character(s)) labels/indices.
 Non-standard suffixes SHOULD reflect the nature of the data, and existing
 entities SHOULD be used when appropriate.
 For example, an ASSET calibration scan might be named

src/schema/objects/columns.yaml

@@ -110,7 +110,7 @@ derived_from:
     `sample-<label>` entity from which a sample is derived,
     for example a slice of tissue (`sample-02`) derived from a block of tissue (`sample-01`).
   type: string
-  pattern: ^sample-[0-9a-zA-Z]+$
+  pattern: ^sample-[0-9a-zA-Z+]+$
 desc_id:
   name: desc_id
   display_name: Description Label
@@ -125,7 +125,7 @@ desc_id:
     its `desc_id` column SHOULD contain all labels of the `desc` entity)
     used across the entire derivative dataset.
   type: string
-  pattern: ^desc-[0-9a-zA-Z]+$
+  pattern: ^desc-[0-9a-zA-Z+]+$
 description:
   name: description
   display_name: Description
@@ -371,7 +371,7 @@ participant_id:
     A participant identifier of the form `sub-<label>`,
     matching a participant entity found in the dataset.
   type: string
-  pattern: ^sub-[0-9a-zA-Z]+$
+  pattern: ^sub-[0-9a-zA-Z+]+$
 placement__motion:
   name: placement
   display_name: Placement
@@ -436,7 +436,7 @@ sample_id:
     A sample identifier of the form `sample-<label>`,
     matching a sample entity found in the dataset.
   type: string
-  pattern: ^sample-[0-9a-zA-Z]+$
+  pattern: ^sample-[0-9a-zA-Z+]+$
 sample_type:
   name: sample_type
   display_name: Sample type
@@ -468,7 +468,7 @@ session_id:
     A session identifier of the form `ses-<label>`,
     matching a session found in the dataset.
   type: string
-  pattern: ^ses-[0-9a-zA-Z]+$
+  pattern: ^ses-[0-9a-zA-Z+]+$
 sex:
   name: sex
   display_name: Sex

src/schema/objects/common_principles.yaml

@@ -86,7 +86,8 @@ index:
 label:
   display_name: label
   description: |
-    An alphanumeric value, possibly prefixed with arbitrary number of 0s for consistent indentation,
+    An alphanumeric (and possibly including `+` character(s)) value, possibly prefixed with arbitrary
+    number of 0s for consistent indentation,
     for example, it is `rest` in `task-rest` following `task-<label>` specification.
     Note that labels MUST not collide when casing is ignored
     (see [Case collision intolerance](SPEC_ROOT/common-principles.md#case-collision-intolerance)).

src/schema/objects/entities.yaml

@@ -76,7 +76,7 @@ direction:
   name: dir
   display_name: Phase-Encoding Direction
   description: |
-    The `dir-<label>` entity can be set to an arbitrary alphanumeric label
+    The `dir-<label>` entity can be set to an arbitrary legitimate label
     (for example, `dir-LR` or `dir-AP`)
     to distinguish different phase-encoding directions.
 

src/schema/objects/formats.yaml

@@ -9,8 +9,16 @@ index:
 label:
   display_name: Label
   description: |
-    Freeform labels without special characters.
-  pattern: '[0-9a-zA-Z]+'
+    Free-form labels with alphanumeric and plus (+) characters.
+
+    Plus signs MAY be used to concatenate multiple applicable labels,
+    but no relationship is established by a partial match.
+    In particular, the inheritance principle does not connect files
+    containing entities such as `<name>-x+y` with either `<name>-x` or `<name>-y`.
+    For example, metadata stored in a file at the root of the dataset with name `/acq-6p_T2w.json`
+    does not apply to files with partially matching "acquisition" entity values
+    such as `/sub-1/anat/sub-1_acq-6p+s2_T2w.nii`.
+  pattern: '[0-9a-zA-Z+]+'
 # Metadata types
 boolean:
   display_name: Boolean
@@ -59,7 +67,7 @@ dataset_relative:
     The validation for this format is minimal.
     It simply ensures that the value is a string with any characters that may appear in a valid path,
     without starting with "/" (an absolute path).
-  pattern: '(?!/)[0-9a-zA-Z/\_\-\.]+'
+  pattern: '(?!/)[0-9a-zA-Z+/\_\-\.]+'
 date:
   display_name: Date
   description: |
@@ -90,7 +98,7 @@ file_relative:
     The validation for this format is minimal.
     It simply ensures that the value is a string with any characters that may appear in a valid path,
     without starting with "/" (an absolute path).
-  pattern: '(?!/)[0-9a-zA-Z/\_\-\.]+'
+  pattern: '(?!/)[0-9a-zA-Z+/\_\-\.]+'
 participant_relative:
   display_name: Path relative to the participant directory
   description: |
@@ -100,7 +108,7 @@ participant_relative:
     It simply ensures that the value is a string with any characters that may appear in a valid path,
     without starting with "/" (an absolute path) or "sub/"
     (a relative path starting with the participant directory, rather than relative to that directory).
-  pattern: '(?!/)(?!sub-)[0-9a-zA-Z/\_\-\.]+'
+  pattern: '(?!/)(?!sub-)[0-9a-zA-Z+/\_\-\.]+'
 rrid:
   display_name: Research resource identifier
   description: |
@@ -115,7 +123,7 @@ stimuli_relative:
     It simply ensures that the value is a string with any characters that may appear in a valid path,
     without starting with "/" (an absolute path) or "stimuli/"
     (a relative path starting with the stimuli directory, rather than relative to that directory).
-  pattern: '(?!/)(?!stimuli/)[0-9a-zA-Z/\_\-\.]+'
+  pattern: '(?!/)(?!stimuli/)[0-9a-zA-Z+/\_\-\.]+'
 time:
   display_name: Time
   description: |

src/schema/objects/metadata.yaml

@@ -3245,8 +3245,8 @@ ScreenResolution:
     - type: array
       items:
         type: integer
-        minItems: 2
-        maxItems: 2
+      minItems: 2
+      maxItems: 2
     - type: string
       enum:
         - n/a
@@ -3262,8 +3262,8 @@ ScreenSize:
       items:
         type: number
         unit: m
-        minItems: 2
-        maxItems: 2
+      minItems: 2
+      maxItems: 2
     - type: string
       enum:
         - n/a
@@ -3683,9 +3683,10 @@ TaskName:
     Name of the task.
     No two tasks should have the same name.
     The task label included in the filename is derived from this `"TaskName"` field
-    by removing all non-alphanumeric characters (that is, all except those matching `[0-9a-zA-Z]`).
-    For example `"TaskName"` `"faces n-back"` or `"head nodding"` will correspond to task labels
-    `facesnback` and `headnodding`, respectively.
+    by removing all non-alphanumeric or `+` characters (that is, all except those matching `[0-9a-zA-Z+]`),
+    and potentially replacing spaces with `+` to ease readability.
+    For example `"TaskName"` `"faces n-back"` or `"head nodding"` could correspond to task labels
+    `faces+n+back` or `facesnback` and `head+nodding` or `headnodding`, respectively.
   type: string
 TermURL:
   name: TermURL

tools/schemacode/pyproject.toml

@@ -103,6 +103,8 @@ markers = [
 minversion = "6.0"
 xfail_strict = true
 
+[tool.coverage]
+
 [tool.coverage.paths]
 source = [
     "src/bidsschematools",
@@ -112,10 +114,32 @@ source = [
 [tool.coverage.run]
 parallel = true
 
-[tool.bumpver]
+# Release process:
+# cd tools/schemacode
+# uvx bump-my-version bump pre_label --tag
+# [inspect result]
+# git push upstream <current-branch> --tags
+# uvx bump-my-version bump <patch|minor|major>
+# git push upstream <current-branch>
+[tool.bumpversion]
 current_version = "1.1.0-dev"
-version_pattern = "MAJOR.MINOR.PATCH[-TAG]"
-commit = false
+parse = """(?x)
+    (?P<major>[0-9]+)
+    \\.(?P<minor>[0-9]+)
+    \\.(?P<patch>[0-9]+)
+    (?:-(?P<pre_label>dev))?
+"""
+serialize = ["{major}.{minor}.{patch}-{pre_label}", "{major}.{minor}.{patch}"]
+commit = true
+message = "chore: Bump schema package to {new_version}"
+# Use --tag on releases
+tag = false
+tag_name = "schema-{new_version}"
+tag_message = "Schema release {new_version}"
+
+[tool.bumpversion.parts.pre_label]
+values = ["dev", "final"]
+optional_value = "final"
 
-[tool.bumpver.file_patterns]
-"src/bidsschematools/data/schema/SCHEMA_VERSION" = ['{version}']
+[[tool.bumpversion.files]]
+filename = "../../src/schema/SCHEMA_VERSION"