refactor: lint

Author: harryle95

pyproject.toml

@@ -37,7 +37,7 @@ analysis = [
 ]
 
 [tool.codespell]
-ignore-words-list = "selectin"
+ignore-words-list = "selectin,UE,ue"
 skip = 'pdm.lock,./assets/'
 
 [tool.coverage.run]

src/helpers.py

@@ -14,7 +14,7 @@
 
 from src.model.base import Base
 
-sqlalchemy_log._add_default_handler = lambda x: None  # Patch to avoid duplicate logging
+sqlalchemy_log._add_default_handler = lambda x: None  # type: ignore[assignment]
 
 __all__ = ("create_db_config", "provide_transaction", "set_sqlite_pragma")
 

src/model/event.py

@@ -1,21 +1,14 @@
 import datetime
-from typing import TYPE_CHECKING, Optional
 from uuid import UUID
 
-from litestar.dto import dto_field
 from sqlalchemy import ForeignKey
-from sqlalchemy.orm import Mapped, mapped_column, relationship
+from sqlalchemy.orm import Mapped, mapped_column
 
 from src.model import Base
 
 __all__ = ("Event",)
 
 
-if TYPE_CHECKING:
-    from src.model.observation_unit import ObservationUnit
-    from src.model.vocabulary import Vocabulary
-
-
 class Event(Base):
     __tablename__ = "event_table"  # type: ignore[assignment]
     event_date: Mapped[datetime.datetime | None]

src/model/facility.py

@@ -13,7 +13,6 @@
 if TYPE_CHECKING:
     from src.model.experiment import Experiment
     from src.model.institution import Institution
-    from src.model.observation_unit import ObservationUnit
     from src.model.vocabulary import Vocabulary
 
 

src/model/method.py

@@ -11,7 +11,6 @@
 
 
 if TYPE_CHECKING:
-    from src.model.biological_material import BiologicalMaterial
     from src.model.device import Device
     from src.model.observed_variable import ObservedVariable
     from src.model.vocabulary import Vocabulary

src/model/observation_unit.py

@@ -1,24 +1,14 @@
-from typing import TYPE_CHECKING, Optional
 from uuid import UUID
 
-from litestar.dto import dto_field
 from sqlalchemy import UUID as UUID_SQL
 from sqlalchemy import Column, ForeignKey, Table
-from sqlalchemy.orm import Mapped, mapped_column, relationship
+from sqlalchemy.orm import Mapped, mapped_column
 
 from src.model import Base
 
 __all__ = ("ObservationUnit",)
 
 
-if TYPE_CHECKING:
-    from src.model.event import Event
-    from src.model.facility import Facility
-    from src.model.sample import Sample
-    from src.model.study import Study
-    from src.model.variable import Variable
-    from src.model.vocabulary import Vocabulary
-
 ob_unit_to_ob_unit_table = Table(
     "ob_unit_to_ob_unit_table",
     Base.metadata,

src/model/sample.py

@@ -1,21 +1,14 @@
 import datetime
-from typing import TYPE_CHECKING, Optional
 from uuid import UUID
 
-from litestar.dto import dto_field
 from sqlalchemy import ForeignKey
-from sqlalchemy.orm import Mapped, mapped_column, relationship
+from sqlalchemy.orm import Mapped, mapped_column
 
 from src.model import Base
 
 __all__ = ("Sample",)
 
 
-if TYPE_CHECKING:
-    from src.model.observation_unit import ObservationUnit
-    from src.model.vocabulary import Vocabulary
-
-
 class Sample(Base):
     __tablename__ = "sample_table"  # type: ignore[assignment]
 

src/model/variable.py

@@ -14,7 +14,6 @@
 
 if TYPE_CHECKING:
     from src.model.device import Device
-    from src.model.facility import Facility
     from src.model.study import Study
 
     # from src.model.observation_unit import ObservationUnit
@@ -29,7 +28,7 @@
 
 
 class Variable(Base):
-    __tablename__: str = "variable_table"  # type: ignore[assignment]
+    __tablename__: str = "variable_table"
     __mapper_args__ = {
         "polymorphic_identity": "variable",
         "polymorphic_on": "type",

src/model/vocabulary.py

@@ -25,7 +25,7 @@
 
 
 class Vocabulary(Base):
-    __tablename__: str = "vocabulary_table"  # type: ignore[assignment]
+    __tablename__: str = "vocabulary_table"
     title: Mapped[str]
     # Todo: use the same terminologies as PHIS - extract, widening, narrowing?
     relationship_type: Mapped[str | None]

src/router/base.py

@@ -107,7 +107,7 @@ async def get_items(
         title: str | None,
         id: UUID | list[UUID] | None = None,
         **kwargs: Any,
-    ) -> Sequence[T.__name__]:
+    ) -> Sequence[T.__name__]:  # type: ignore[name-defined]
         return cast(
             Sequence[T],
             await read_items_by_attrs(transaction, table, title=title, id=id, **kwargs),
@@ -119,7 +119,7 @@ async def get_item_by_id(
         table: Any,
         transaction: "AsyncSession",
         id: UUID,
-    ) -> T.__name__:
+    ) -> T.__name__:  # type: ignore[name-defined]
         return cast(
             T,
             await read_item_by_id(session=transaction, table=table, id=id),
@@ -171,7 +171,7 @@ async def get_items(
         title: str | None,
         id: UUID | list[UUID] | None = None,
         **kwargs: Any,
-    ) -> Sequence[V.__name__]:
+    ) -> Sequence[V.__name__]:  # type: ignore[name-defined]
         return cast(
             Sequence[V],
             await read_items_by_attrs(
@@ -180,7 +180,7 @@ async def get_items(
         )
 
     @get("/{id:uuid}")
-    async def get_item_by_id(self, table: Any, transaction: AsyncSession, id: UUID) -> V.__name__:
+    async def get_item_by_id(self, table: Any, transaction: AsyncSession, id: UUID) -> V.__name__:  # type: ignore[name-defined]
         data = await read_item_by_id(transaction, table, id, self.selectinload_attrs)
         return cast(V, self.dataclass.from_orm(data))
 
@@ -193,7 +193,7 @@ async def create_item(self, table: Any, transaction: AsyncSession, data: V.__nam
         return cast(V, self.dataclass.from_orm(table_data))
 
     @put("{id:uuid}")
-    async def update_item(self, table: Any, transaction: AsyncSession, data: V.__name__, id: UUID) -> V.__name__:
+    async def update_item(self, table: Any, transaction: AsyncSession, data: V.__name__, id: UUID) -> V.__name__:  # type: ignore[name-defined]
         # Fetch item
         item = cast(
             T,