update SM & MSP to bring forward useful changes for all repos. (#72)

ga4gh · Nov 7, 2024 · 3b3d9be · 3b3d9be
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diff --git a/.requirements.txt b/.requirements.txt
@@ -2,6 +2,6 @@ pytest
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2
 pyyaml
-ga4gh.gks.metaschema==0.3.0b14
+ga4gh.gks.metaschema==0.3.0b16
 jsonschema
 referencing
diff --git a/schema/cat-vrs/def/CanonicalAllele.rst b/schema/cat-vrs/def/CanonicalAllele.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#>`_ that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.
@@ -18,6 +16,7 @@ A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.x/concep
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
diff --git a/schema/cat-vrs/def/CategoricalCnv.rst b/schema/cat-vrs/def/CategoricalCnv.rst
@@ -1,9 +1,7 @@
-
 .. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
+    significantly in future releases. Maturity levels are described in
     the :ref:`maturity-model`.
-
-
+
 **Computational Definition**
 
 A representation of the constraints for matching knowledge about CNVs.
@@ -18,6 +16,7 @@ A representation of the constraints for matching knowledge about CNVs.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
diff --git a/schema/cat-vrs/def/CategoricalVariant.rst b/schema/cat-vrs/def/CategoricalVariant.rst
@@ -1,8 +1,7 @@
-
 .. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 A representation of a categorically-defined domain for variation, in which individual Constraintual variation instances may be members of the domain.
@@ -18,42 +17,67 @@ Some CategoricalVariant attributes are inherited from :ref:`gks-core:Entity`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - id
+      - 
       - string
       - 0..1
       - The 'logical' identifier of the Entity in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "CategoricalVariant"
    *  - members
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Variation` | :ref:`iriReference`
       - 0..m
       - A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant.
    *  - constraints
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Constraint`
       - 0..m
       - 
    *  - mappings
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`ConceptMapping`
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
diff --git a/schema/cat-vrs/def/Constraint.rst b/schema/cat-vrs/def/Constraint.rst
@@ -1,8 +1,7 @@
-
 .. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 Constraints are used to construct an intensional semantics of categorical variant types.
@@ -17,10 +16,12 @@ Constraints are used to construct an intensional semantics of categorical varian
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - type
+      - 
       - string
       - 1..1
       - 
diff --git a/schema/cat-vrs/def/CopyChangeConstraint.rst b/schema/cat-vrs/def/CopyChangeConstraint.rst
@@ -1,8 +1,7 @@
-
 .. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 The relative assessment of the change in copies that members of this categorical variant satisfies.
@@ -18,14 +17,17 @@ Some CopyChangeConstraint attributes are inherited from :ref:`Constraint`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "CopyChangeConstraint"
    *  - copyChange
+      - 
       - string
       - 1..1
       - The relative assessment of the change in copies that members of this categorical variant satisfies.
diff --git a/schema/cat-vrs/def/CopyCountConstraint.rst b/schema/cat-vrs/def/CopyCountConstraint.rst
@@ -1,8 +1,7 @@
-
 .. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 The exact or range of copies that members of this categorical variant must satisfy.
@@ -18,14 +17,17 @@ Some CopyCountConstraint attributes are inherited from :ref:`Constraint`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "CopyCountConstraint"
    *  - copies
+      - 
       - integer | :ref:`Range`
       - 1..1
       - The precise value or range of copies members of this categorical variant must satisfy.
diff --git a/schema/cat-vrs/def/DefiningAlleleConstraint.rst b/schema/cat-vrs/def/DefiningAlleleConstraint.rst
@@ -1,8 +1,7 @@
-
 .. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 The defining allele and its associated relationships that are congruent with member variants.
@@ -18,18 +17,25 @@ Some DefiningAlleleConstraint attributes are inherited from :ref:`Constraint`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "DefiningAlleleConstraint"
    *  - allele
+      - 
       - :ref:`Allele` | :ref:`iriReference`
       - 1..1
       - 
    *  - relations
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Defined relationships from which members relate to the defining allele. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept.
diff --git a/schema/cat-vrs/def/DefiningLocationConstraint.rst b/schema/cat-vrs/def/DefiningLocationConstraint.rst
@@ -1,8 +1,7 @@
-
 .. note:: This data class is at a **trial use** maturity level and may change
-    in future releases. Maturity levels are described in the :ref:`maturity-model`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 The defining location and its associated relationships that are congruent with member locations.
@@ -18,22 +17,30 @@ Some DefiningLocationConstraint attributes are inherited from :ref:`Constraint`.
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "DefiningLocationConstraint"
    *  - location
+      - 
       - :ref:`SequenceLocation` | :ref:`iriReference`
       - 1..1
       - 
    *  - relations
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Defined relationships from which members relate to the defining location. ``sequence_liftover`` refers to variants or locations that represent a congruent concept on a differing assembly of a human genome (e.g. "GRCh37" and "GRCh38") or gene (e.g. Locus Reference Genomic) sequence. ``transcript_projection`` refers to variants or locations that occur on transcripts projected from the defined genomic concept. ``codon_translation`` refers to variants or locations that translate from the codon(s) represented by the defined concept.
    *  - matchCharacteristic
+      - 
       - string
       - 1..1
       - A characteristic of the location that is used to match the defining location to member locations. 
diff --git a/schema/cat-vrs/def/ProteinSequenceConsequence.rst b/schema/cat-vrs/def/ProteinSequenceConsequence.rst
@@ -12,6 +12,7 @@ A change that occurs in a protein sequence as a result of genomic changes. Due t
    :widths: auto
 
    *  - Field
+      - Flags
       - Type
       - Limits
       - Description
diff --git a/submodules/vrs b/submodules/vrs