style: configure src for ruff to ensure correct isort

Author: jsstevenson

pyproject.toml

@@ -62,6 +62,7 @@ requires = ["setuptools>=65.3", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [tool.ruff]
+src = ["src"]
 exclude = [
     "submodules"
 ]

src/ga4gh/va_spec/aac_2017/models.py

@@ -6,6 +6,11 @@
 
 from enum import Enum
 
+from pydantic import (
+    Field,
+    field_validator,
+)
+
 from ga4gh.core.models import MappableConcept, iriReference
 from ga4gh.va_spec.base.core import (
     Method,
@@ -16,10 +21,6 @@
 )
 from ga4gh.va_spec.base.enums import System
 from ga4gh.va_spec.base.validators import validate_mappable_concept
-from pydantic import (
-    Field,
-    field_validator,
-)
 
 
 class Strength(str, Enum):

src/ga4gh/va_spec/acmg_2015/models.py

@@ -5,6 +5,8 @@
 
 from enum import Enum
 
+from pydantic import Field, field_validator, model_validator
+
 from ga4gh.core.models import MappableConcept, iriReference
 from ga4gh.va_spec.base.core import (
     EvidenceLine,
@@ -21,7 +23,6 @@
 from ga4gh.va_spec.base.validators import (
     validate_mappable_concept,
 )
-from pydantic import Field, field_validator, model_validator
 
 
 class AcmgClassification(str, Enum):

src/ga4gh/va_spec/base/core.py

@@ -9,6 +9,15 @@
 from enum import Enum
 from typing import Annotated, Literal, TypeVar
 
+from pydantic import (
+    ConfigDict,
+    Field,
+    RootModel,
+    StringConstraints,
+    ValidationError,
+    field_validator,
+)
+
 from ga4gh.cat_vrs.models import CategoricalVariant
 from ga4gh.core.models import (
     BaseModelForbidExtra,
@@ -25,14 +34,6 @@
 )
 from ga4gh.va_spec.base.validators import validate_mappable_concept
 from ga4gh.vrs.models import Allele, MolecularVariation
-from pydantic import (
-    ConfigDict,
-    Field,
-    RootModel,
-    StringConstraints,
-    ValidationError,
-    field_validator,
-)
 
 StatementType = TypeVar("StatementType")
 EvidenceLineType = TypeVar("EvidenceLineType")

src/ga4gh/va_spec/base/domain_entities.py

@@ -2,9 +2,10 @@
 
 from __future__ import annotations
 
+from pydantic import ConfigDict, Field, RootModel
+
 from ga4gh.core.models import BaseModelForbidExtra, Element, MappableConcept
 from ga4gh.va_spec.base.enums import MembershipOperator
-from pydantic import ConfigDict, Field, RootModel
 
 
 class ConditionSet(Element, BaseModelForbidExtra):

src/ga4gh/va_spec/ccv_2022/models.py

@@ -5,6 +5,8 @@
 
 from enum import Enum
 
+from pydantic import Field, field_validator, model_validator
+
 from ga4gh.core.models import MappableConcept, iriReference
 from ga4gh.va_spec.base.core import (
     EvidenceLine,
@@ -19,7 +21,6 @@
     System,
 )
 from ga4gh.va_spec.base.validators import validate_mappable_concept
-from pydantic import Field, field_validator, model_validator
 
 
 class VariantOncogenicityEvidenceLine(EvidenceLine):

tests/validation/test_va_spec_fixtures_validation.py

@@ -1,10 +1,10 @@
 """Ensure that VA-Spec test fixtures validate against Pydantic models"""
 
 import yaml
-from ga4gh.va_spec import aac_2017, acmg_2015, base, ccv_2022
-
 from tests.conftest import SUBMODULES_DIR, VaSpecSchema, get_va_spec_schema
 
+from ga4gh.va_spec import aac_2017, acmg_2015, base, ccv_2022
+
 VA_SPEC_TESTS_DIR = SUBMODULES_DIR / "tests"
 
 

tests/validation/test_va_spec_models.py

@@ -5,6 +5,9 @@
 
 import pytest
 import yaml
+from pydantic import ValidationError
+from tests.conftest import SUBMODULES_DIR
+
 from ga4gh.core.models import Coding, MappableConcept, code, iriReference
 from ga4gh.va_spec import acmg_2015, base, ccv_2022
 from ga4gh.va_spec.aac_2017.models import VariantTherapeuticResponseStudyStatement
@@ -23,9 +26,6 @@
     VariantOncogenicityEvidenceLine,
     VariantOncogenicityStudyStatement,
 )
-from pydantic import ValidationError
-
-from tests.conftest import SUBMODULES_DIR
 
 VA_SPEC_TESTS_DIR = SUBMODULES_DIR / "tests"
 VA_SPEC_TEST_FIXTURES = VA_SPEC_TESTS_DIR / "fixtures"

tests/validation/test_va_spec_schema.py

@@ -4,15 +4,15 @@
 from pathlib import Path
 
 import pytest
-from ga4gh.va_spec import aac_2017, acmg_2015, base, ccv_2022
 from pydantic import BaseModel
-
 from tests.conftest import (
     SUBMODULES_DIR,
     VaSpecSchema,
     get_va_spec_schema,
 )
 
+from ga4gh.va_spec import aac_2017, acmg_2015, base, ccv_2022
+
 VA_SCHEMA_DIR = SUBMODULES_DIR / "schema" / "va-spec"