feat: expose json schema metadata to cat vrs models

pyproject.toml

@@ -1,54 +1,40 @@
 [project]
 name = "ga4gh.cat_vrs"
 authors = [
-    {name = "Larry Babb", email = "lbabb@broadinstitute.org"},
-    {name = "Alex Wagner", email = "alex.wagner@nationwidechildrens.org"},
-    {name = "Daniel Puthawala", email = "daniel.puthawala@nationwidechildrens.org"},
+  { name = "Larry Babb", email = "lbabb@broadinstitute.org" },
+  { name = "Alex Wagner", email = "alex.wagner@nationwidechildrens.org" },
+  { name = "Daniel Puthawala", email = "daniel.puthawala@nationwidechildrens.org" },
 ]
 readme = "README.md"
 description = "GA4GH Categorical Variation Representation (Cat-VRS) reference implementation"
-license = {file = "LICENSE"}
+license = { file = "LICENSE" }
 classifiers = [
-    "Development Status :: 3 - Alpha",
-    "Intended Audience :: Developers",
-    "Intended Audience :: Healthcare Industry",
-    "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: Apache Software License",
-    "Operating System :: OS Independent",
-    "Programming Language :: Python",
-    "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
-    "Programming Language :: Python :: 3.11",
-    "Programming Language :: Python :: 3.12",
-    "Topic :: Scientific/Engineering :: Bio-Informatics",
-    "Topic :: Scientific/Engineering :: Medical Science Apps.",
-]
-keywords = [
-    "bioinformatics",
-    "ga4gh",
-    "genomics",
-    "variation"
+  "Development Status :: 3 - Alpha",
+  "Intended Audience :: Developers",
+  "Intended Audience :: Healthcare Industry",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: Apache Software License",
+  "Operating System :: OS Independent",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Medical Science Apps.",
 ]
+keywords = ["bioinformatics", "ga4gh", "genomics", "variation"]
 requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
-    "ga4gh.vrs~=2.4.0a1",
-    "pydantic>=2.0,<3.0",
+  "ga4gh.vrs @ git+https://github.com/ga4gh/vrs-python.git@daceb0b6cd773f8c4c5b6dff560fb7f4a5ff7b34",
+  "pydantic>=2.0,<3.0",
 ]
 
 [project.optional-dependencies]
-dev = [
-    "pre-commit",
-    "ruff==0.4.9",
-]
-tests = [
-    "pytest",
-    "pytest-cov",
-    "pyyaml",
-]
-notebooks = [
-    "jupyter",
-]
+dev = ["pre-commit", "ruff==0.4.9"]
+tests = ["pytest", "pytest-cov", "pyyaml"]
+notebooks = ["jupyter"]
 
 [project.urls]
 Homepage = "https://github.com/ga4gh/cat-vrs-python"
@@ -63,53 +49,52 @@ build-backend = "setuptools.build_meta"
 
 [tool.ruff]
 src = ["src"]
-exclude = [
-    "submodules"
-]
+exclude = ["submodules"]
 
 [tool.ruff.lint]
 select = [
-    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
-    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
-    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
-    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
-    "D",  # https://docs.astral.sh/ruff/rules/#pydocstyle-d
-    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
-    "ANN",  # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
-    "ASYNC",  # https://docs.astral.sh/ruff/rules/#flake8-async-async
-    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
-    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
-    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
-    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
-    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-    "T10",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
-    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
-    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
-    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
-    "T20",  # https://docs.astral.sh/ruff/rules/#flake8-print-t20
-    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
-    "Q",  # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
-    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
-    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
-    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
-    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
-    "PGH",  # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
-    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
+  "F",     # https://docs.astral.sh/ruff/rules/#pyflakes-f
+  "E",
+  "W",     # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
+  "I",     # https://docs.astral.sh/ruff/rules/#isort-i
+  "N",     # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+  "D",     # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+  "UP",    # https://docs.astral.sh/ruff/rules/#pyupgrade-up
+  "ANN",   # https://docs.astral.sh/ruff/rules/#flake8-annotations-ann
+  "ASYNC", # https://docs.astral.sh/ruff/rules/#flake8-async-async
+  "S",     # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
+  "B",     # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
+  "A",     # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
+  "C4",    # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
+  "DTZ",   # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  "T10",   # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
+  "EM",    # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  "G",     # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
+  "PIE",   # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
+  "T20",   # https://docs.astral.sh/ruff/rules/#flake8-print-t20
+  "PT",    # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
+  "Q",     # https://docs.astral.sh/ruff/rules/#flake8-quotes-q
+  "RSE",   # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
+  "RET",   # https://docs.astral.sh/ruff/rules/#flake8-return-ret
+  "SIM",   # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
+  "PTH",   # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
+  "PGH",   # https://docs.astral.sh/ruff/rules/#pygrep-hooks-pgh
+  "RUF",   # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
 ]
 fixable = [
-    "I",
-    "F401",
-    "D",
-    "UP",
-    "ANN",
-    "B",
-    "C4",
-    "G",
-    "PIE",
-    "PT",
-    "RSE",
-    "SIM",
-    "RUF"
+  "I",
+  "F401",
+  "D",
+  "UP",
+  "ANN",
+  "B",
+  "C4",
+  "G",
+  "PIE",
+  "PT",
+  "RSE",
+  "SIM",
+  "RUF",
 ]
 # ANN101 - missing-type-self
 # ANN003 - missing-type-kwargs
@@ -128,11 +113,21 @@ fixable = [
 # S321 - suspicious-ftp-lib-usage
 # *ignored for compatibility with formatter
 ignore = [
-    "ANN101", "ANN003",
-    "D203", "D205", "D206", "D213", "D300", "D400", "D415",
-    "E111", "E114", "E117", "E501",
-    "W191",
-    "S321",
+  "ANN101",
+  "ANN003",
+  "D203",
+  "D205",
+  "D206",
+  "D213",
+  "D300",
+  "D400",
+  "D415",
+  "E111",
+  "E114",
+  "E117",
+  "E501",
+  "W191",
+  "S321",
 ]
 
 [tool.ruff.lint.per-file-ignores]

src/ga4gh/cat_vrs/__init__.py

@@ -1,21 +1,23 @@
 """Package for Cat-VRS Python implementation"""
 
-from importlib.metadata import PackageNotFoundError, version
+from importlib.metadata import PackageNotFoundError
+from importlib.metadata import version as package_version
 
 from . import models, recipes
+from .metadata import CatVRSMetadataMixin
+from .version import CATVRS_VERSION
 
 try:
-    __version__ = version(__name__)
+    __version__ = package_version(__name__)
 except PackageNotFoundError:  # pragma: nocover
     __version__ = "unknown"
 finally:
-    del version, PackageNotFoundError
+    del package_version, PackageNotFoundError
 
 
-CATVRS_VERSION = "1.1.0-snapshot.2026-02.3"
-
 __all__ = [
     "CATVRS_VERSION",
+    "CatVRSMetadataMixin",
     "__version__",
     "models",
     "recipes",

src/ga4gh/cat_vrs/metadata.py

@@ -0,0 +1,11 @@
+"""Provide metadata mixins for Cat-VRS models."""
+
+from ga4gh.cat_vrs.version import CATVRS_VERSION
+from ga4gh.core.metadata import GKSMetadataMixin
+
+
+class CatVRSMetadataMixin(GKSMetadataMixin):
+    """Provide metadata for a concrete Cat-VRS model."""
+
+    _product_name = "cat-vrs"
+    _product_version = CATVRS_VERSION

src/ga4gh/cat_vrs/models.py

@@ -4,10 +4,12 @@
 the GA4GH website for more information.
 """
 
-from typing import Literal
+from typing import ClassVar, Literal
 
 from pydantic import Field, RootModel
 
+from ga4gh.cat_vrs.metadata import CatVRSMetadataMixin
+from ga4gh.core.metadata import Maturity
 from ga4gh.core.models import (
     BaseModelForbidExtra,
     ConceptMapping,
@@ -18,11 +20,13 @@
 from ga4gh.vrs.models import Allele, CopyChange, Range, SequenceLocation, Variation
 
 
-class DefiningAlleleConstraint(BaseModelForbidExtra):
+class DefiningAlleleConstraint(CatVRSMetadataMixin, BaseModelForbidExtra):
     """The defining allele and its associated relationships that are congruent with
     member variants.
     """
 
+    _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE
+
     type: Literal["DefiningAlleleConstraint"] = Field(
         default="DefiningAlleleConstraint",
         description="MUST be 'DefiningAlleleConstraint'",
@@ -34,11 +38,13 @@ class DefiningAlleleConstraint(BaseModelForbidExtra):
     )
 
 
-class DefiningLocationConstraint(BaseModelForbidExtra):
+class DefiningLocationConstraint(CatVRSMetadataMixin, BaseModelForbidExtra):
     """The defining location and its associated relationships that are congruent with
     member locations.
     """
 
+    _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE
+
     type: Literal["DefiningLocationConstraint"] = Field(
         default="DefiningLocationConstraint",
         description="MUST be 'DefiningLocationConstraint'",
@@ -54,11 +60,13 @@ class DefiningLocationConstraint(BaseModelForbidExtra):
     )
 
 
-class CopyCountConstraint(BaseModelForbidExtra):
+class CopyCountConstraint(CatVRSMetadataMixin, BaseModelForbidExtra):
     """The exact or range of copies that members of this categorical variant must
     satisfy.
     """
 
+    _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE
+
     type: Literal["CopyCountConstraint"] = Field(
         default="CopyCountConstraint", description="MUST be 'CopyCountConstraint'"
     )
@@ -68,11 +76,13 @@ class CopyCountConstraint(BaseModelForbidExtra):
     )
 
 
-class CopyChangeConstraint(BaseModelForbidExtra):
+class CopyChangeConstraint(CatVRSMetadataMixin, BaseModelForbidExtra):
     """The relative assessment of the change in copies that members of this categorical
     variant satisfy.
     """
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
     type: Literal["CopyChangeConstraint"] = Field(
         default="CopyChangeConstraint", description="MUST be 'CopyChangeConstraint'"
     )
@@ -82,19 +92,23 @@ class CopyChangeConstraint(BaseModelForbidExtra):
     )
 
 
-class FeatureContextConstraint(BaseModelForbidExtra):
+class FeatureContextConstraint(CatVRSMetadataMixin, BaseModelForbidExtra):
     """The feature that members of this categorical variant are associated with."""
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
     type: Literal["FeatureContextConstraint"] = Field(
         default="FeatureContextConstraint",
         description="MUST be 'FeatureContextConstraint'",
     )
     featureContext: MappableConcept = Field(..., description="A feature identifier.")
 
 
-class FunctionConstraint(BaseModelForbidExtra):
+class FunctionConstraint(CatVRSMetadataMixin, BaseModelForbidExtra):
     """A classification of the protein functional consequence that characterizes members of this categorical variant."""
 
+    _maturity: ClassVar[Maturity] = Maturity.DRAFT
+
     type: Literal["FunctionConstraint"] = Field(
         default="FunctionConstraint",
         description='MUST be "FunctionConstraint"',
@@ -108,9 +122,11 @@ class FunctionConstraint(BaseModelForbidExtra):
     )
 
 
-class Constraint(RootModel):
+class Constraint(CatVRSMetadataMixin, RootModel):
     """Constraints are used to construct an intensional semantics of categorical variant types."""
 
+    _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE
+
     root: (
         DefiningAlleleConstraint
         | DefiningLocationConstraint
@@ -121,11 +137,13 @@ class Constraint(RootModel):
     ) = Field(..., discriminator="type")
 
 
-class CategoricalVariant(Entity, BaseModelForbidExtra):
+class CategoricalVariant(CatVRSMetadataMixin, Entity, BaseModelForbidExtra):
     """A representation of a categorically-defined domain for variation, in which
     individual Constraintual variation instances may be members of the domain.
     """
 
+    _maturity: ClassVar[Maturity] = Maturity.TRIAL_USE
+
     type: Literal["CategoricalVariant"] = Field(
         default="CategoricalVariant", description="MUST be 'CategoricalVariant'"
     )