feat!: update models to cat-vrs 1.0.0 trial review ballot

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "submodules/cat_vrs"]
 	path = submodules/cat_vrs
 	url = https://github.com/ga4gh/cat-vrs
-	branch = 1.x
+	branch = 1.0.0-ballot.2024-11

pyproject.toml

@@ -32,7 +32,7 @@ keywords = [
 requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
-    "ga4gh.vrs~=2.0.0a12",
+    "ga4gh.vrs==2.0.0a13",
     "pydantic==2.*",
 ]
 
@@ -137,7 +137,8 @@ ignore = [
 # S101 - assert
 # B011 - assert-false
 "tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011"]
-"src/ga4gh/cat_vrs/*models.py" = ["ANN102"]
+"src/ga4gh/cat_vrs/models.py" = ["ANN102", "N815"]
+"src/ga4gh/cat_vrs/recipes.py" = ["ANN102", "N815"]
 
 [tool.setuptools.packages.find]
 where = ["src"]

src/ga4gh/cat_vrs/__init__.py

@@ -1,5 +1,5 @@
 """Package for Cat-VRS Python implementation"""
 
-from . import profile_models as cat_vrs_models
+from . import models, recipes
 
-__all__ = ["cat_vrs_models"]
+__all__ = ["models", "recipes"]

src/ga4gh/cat_vrs/models.py

@@ -0,0 +1,133 @@
+"""Define Pydantic models for GA4GH categorical variation objects.
+
+See the `CatVar page <https://www.ga4gh.org/product/categorical-variation-catvar/>`_ on
+the GA4GH website for more information.
+"""
+
+from enum import Enum
+from typing import Literal
+
+from ga4gh.core.models import (
+    ConceptMapping,
+    Entity,
+    MappableConcept,
+    iriReference,
+)
+from ga4gh.vrs.models import Allele, CopyChange, Range, SequenceLocation, Variation
+from pydantic import BaseModel, Field, RootModel, field_validator
+
+
+class Relation(str, Enum):
+    """Defined relationships between members of the categorical variant and the defining
+    context.
+    """
+
+    TRANSLATES_FROM = "translates_from"
+    LIFTOVER_TO = "liftover_to"
+    TRANSCRIBES_TO = "transcribes_to"
+
+
+class DefiningAlleleConstraint(BaseModel):
+    """The defining allele and its associated relationships that are congruent with
+    member variants.
+    """
+
+    type: Literal["DefiningAlleleConstraint"] = Field(
+        "DefiningAlleleConstraint", description="MUST be 'DefiningAlleleConstraint'"
+    )
+    allele: Allele | iriReference
+    relations: list[MappableConcept] | None = Field(
+        None,
+        description="Defined relationships from which members relate to the defining allele.",
+    )
+
+
+class DefiningLocationConstraint(BaseModel):
+    """The defining location and its associated relationships that are congruent with
+    member locations.
+    """
+
+    type: Literal["DefiningLocationConstraint"] = Field(
+        "DefiningLocationConstraint", description="MUST be 'DefiningLocationConstraint'"
+    )
+    location: SequenceLocation | iriReference
+    relations: list[MappableConcept] | None = Field(
+        None,
+        description="Defined relationships from which members relate to the defining location.",
+    )
+    matchCharacteristic: MappableConcept = Field(
+        ...,
+        description="A characteristic of the location that is used to match the defining location to member locations.",
+    )
+
+
+class CopyCountConstraint(BaseModel):
+    """The exact or range of copies that members of this categorical variant must
+    satisfy.
+    """
+
+    type: Literal["CopyCountConstraint"] = Field(
+        "CopyCountConstraint", description="MUST be 'CopyCountConstraint'"
+    )
+    copies: int | Range = Field(
+        ...,
+        description="The precise value or range of copies members of this categorical variant must satisfy.",
+    )
+
+
+class CopyChangeConstraint(BaseModel):
+    """A representation of copy number change"""
+
+    type: Literal["CopyChangeConstraint"] = Field(
+        "CopyChangeConstraint", description="MUST be 'CopyChangeConstraint'"
+    )
+    copyChange: str = Field(
+        ...,
+        description="The relative assessment of the change in copies that members of this categorical variant satisfies.",
+    )
+
+    @field_validator("copyChange")
+    @classmethod
+    def validate_copy_change(cls, v: str) -> str:
+        """Validate copyChange property
+
+        :param v: copyChange value
+        :raises ValueError: If ``copyChange.code`` is not a valid CopyChange
+        :return: copyChange property
+        """
+        try:
+            CopyChange(v)
+        except ValueError as e:
+            err_msg = f"copyChange, {v}, not one of {[cc.value for cc in CopyChange]}"
+            raise ValueError(err_msg) from e
+        return v
+
+
+class Constraint(RootModel):
+    """Constraints are used to construct an intensional semantics of categorical variant types."""
+
+    root: (
+        DefiningAlleleConstraint
+        | DefiningLocationConstraint
+        | CopyCountConstraint
+        | CopyChangeConstraint
+    ) = Field(..., discriminator="type")
+
+
+class CategoricalVariant(Entity):
+    """A representation of a categorically-defined domain for variation, in which
+    individual Constraintual variation instances may be members of the domain.
+    """
+
+    type: Literal["CategoricalVariant"] = Field(
+        "CategoricalVariant", description="MUST be 'CategoricalVariant'"
+    )
+    members: list[Variation | iriReference] | None = Field(
+        None,
+        description="A non-exhaustive list of VRS variation Constraints that satisfy the constraints of this categorical variant.",
+    )
+    constraints: list[Constraint] | None = None
+    mappings: list[ConceptMapping] | None = Field(
+        None,
+        description="A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.",
+    )