fix several lints

pyproject.toml

@@ -93,9 +93,15 @@ indent-width = 4
 target-version = "py39"
 
 [tool.ruff.lint]
-#select = ["ANN", "BLE", "D103", "E", "F", "PLW", "PTH", "SIM", "UP", "TCH", "N"]
-select = ["PLW", "SIM", "UP", "EXE", "E701", "E702", "E703", "E711", "E713", "E714", "FA100", "FA102", "W191"]
-ignore = ["ANN101", "ANN102"]
+select = ["ANN", "BLE", "D103", "E", "EXE", "F", "N", "PLW", "PTH", "SIM", "TCH", "UP", "W191"]
+ignore = ["ANN101", "ANN102", "ANN401"]
+
+[tool.ruff.lint.per-file-ignores]
+"**/bfabric_scripts/**" = ["ALL"]
+"**/wrapper_creator/**" = ["ALL"]
+"**/examples/**" = ["ALL"]
+"**/tests/**" = ["ALL"]
+"noxfile.py" = ["ALL"]
 
 [tool.licensecheck]
 using = "PEP631"

src/bfabric/__init__.py

@@ -1,7 +1,7 @@
 import importlib.metadata
 
 from bfabric.bfabric import Bfabric, BfabricAPIEngineType
-from bfabric.config import BfabricAuth, BfabricClientConfig
+from bfabric.config.bfabric_auth import BfabricAuth
 from bfabric.config.bfabric_client_config import BfabricClientConfig
 
 __all__ = [
@@ -11,5 +11,4 @@
     "BfabricClientConfig",
 ]
 
-
 __version__ = importlib.metadata.version("bfabric")

src/bfabric/bfabric.py

@@ -22,8 +22,7 @@
 from functools import cached_property
 from pathlib import Path
 from pprint import pprint
-from typing import Literal, Any
-from collections.abc import Generator
+from typing import Literal, Any, TYPE_CHECKING
 
 from loguru import logger
 from rich.console import Console
@@ -37,6 +36,9 @@
 from bfabric.results.result_container import ResultContainer
 from bfabric.utils.paginator import compute_requested_pages, BFABRIC_QUERY_LIMIT
 
+if TYPE_CHECKING:
+    from collections.abc import Generator
+
 
 class BfabricAPIEngineType(Enum):
     """Choice of engine to use."""
@@ -277,15 +279,15 @@ def __repr__(self) -> str:
 
     __str__ = __repr__
 
-    def __getstate__(self):
+    def __getstate__(self) -> dict[str, Any]:
         return {
             "config": self._config,
             "auth": self._auth,
             "engine_type": self._engine_type,
             "query_counter": self.query_counter,
         }
 
-    def __setstate__(self, state):
+    def __setstate__(self, state: dict[str, Any]) -> None:
         self._config = state["config"]
         self._auth = state["auth"]
         self._engine_type = state["engine_type"]

src/bfabric/bfabric2.py

@@ -3,4 +3,3 @@
 
 warnings.warn("bfabric.bfabric2 module is deprecated, use bfabric instead", DeprecationWarning)
 # TODO deprecated - import from bfabric instead
-from bfabric.bfabric import Bfabric, BfabricAPIEngineType, get_system_auth

src/bfabric/config/bfabric_client_config.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Annotated
+from typing import Annotated, Any
 
 from pydantic import BaseModel, BeforeValidator, Field, TypeAdapter, AnyHttpUrl
 
@@ -25,7 +25,8 @@ class BfabricClientConfig(BaseModel):
     application_ids: Annotated[dict[str, int], Field(default_factory=dict)]
     job_notification_emails: Annotated[str, Field(default="")]
 
-    def __init__(self, **kwargs) -> None:
+    def __init__(self, **kwargs: Any) -> None:
+        # TODO remove this custom constructor (note that this is currently used in some places when "None" is passed)
         super().__init__(**{key: value for key, value in kwargs.items() if value is not None})
 
     def copy_with(

src/bfabric/config/config_file.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 import os
-from typing import Annotated
+from typing import Annotated, Any
 
 from loguru import logger
 from pydantic import BaseModel, Field, model_validator
@@ -21,14 +21,14 @@ class EnvironmentConfig(BaseModel):
 
     @model_validator(mode="before")
     @classmethod
-    def gather_config(cls, values):
+    def gather_config(cls, values: dict[str, Any]) -> dict[str, Any]:
         """Gathers all configs into the config field."""
         values["config"] = {key: value for key, value in values.items() if key not in ["login", "password"]}
         return values
 
     @model_validator(mode="before")
     @classmethod
-    def gather_auth(cls, values):
+    def gather_auth(cls, values: dict[str, Any]) -> dict[str, Any]:
         if "login" in values:
             values["auth"] = BfabricAuth.model_validate(values)
         return values
@@ -40,7 +40,7 @@ class ConfigFile(BaseModel):
 
     @model_validator(mode="before")
     @classmethod
-    def gather_configs(cls, values):
+    def gather_configs(cls, values: dict[str, Any]) -> dict[str, Any]:
         """Gathers all configs into the configs field."""
         configs = {}
         for key, value in values.items():

src/bfabric/engine/response_format_suds.py

@@ -22,7 +22,7 @@ def convert_suds_type(item: Any) -> int | str | Any:
     return item
 
 
-def suds_asdict_recursive(d, convert_types: bool = False) -> dict[str, Value]:
+def suds_asdict_recursive(d: Any, convert_types: bool = False) -> dict[str, Value]:
     """Convert Suds object into serializable format.
     https://stackoverflow.com/a/15678861
     :param d: The input suds object

src/bfabric/entities/application.py

@@ -2,11 +2,11 @@
 
 from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 from bfabric.entities.core.has_one import HasOne
 
 if TYPE_CHECKING:
+    from bfabric import Bfabric
     from bfabric.entities.executable import Executable
     from bfabric.entities.storage import Storage
 

src/bfabric/entities/core/entity.py

@@ -1,15 +1,15 @@
 from __future__ import annotations
 
-from collections.abc import Iterable
 from typing import TYPE_CHECKING
 
 from loguru import logger
 
-from bfabric import Bfabric
 from bfabric.experimental import MultiQuery
 from bfabric.experimental.entity_lookup_cache import EntityLookupCache
 
 if TYPE_CHECKING:
+    from collections.abc import Iterable
+    from bfabric import Bfabric
     from typing import Any, Self
 
 
@@ -101,7 +101,7 @@ def __repr__(self) -> str:
     __str__ = __repr__
 
     @classmethod
-    def __check_ids_list(cls, ids) -> list[int]:
+    def __check_ids_list(cls, ids: list[int]) -> list[int]:
         """Converts the ids to a list of integers (if they are not already) and raises an error if this fails or
         there are duplicates."""
         ids_requested = [int(id) for id in ids]

src/bfabric/entities/core/has_many.py

@@ -1,15 +1,18 @@
 from __future__ import annotations
 
-from typing import Generic, TypeVar
-from collections.abc import Iterator
-
+from typing import Generic, TypeVar, TYPE_CHECKING
+from bfabric.entities.core.relationship import Relationship
 from polars import DataFrame
 
-from bfabric import Bfabric
-from bfabric.entities.core.entity import Entity  # type: ignore
-from bfabric.entities.core.relationship import Relationship
+if TYPE_CHECKING:
+    from collections.abc import Iterator
+    from bfabric import Bfabric
+
+    # noinspection PyUnresolvedReferences
+    from bfabric.entities.core.entity import Entity
 
 E = TypeVar("E", bound="Entity")
+T = TypeVar("T")
 
 
 class HasMany(Relationship[E]):
@@ -28,15 +31,17 @@ def __init__(
         self._client_property = client_property
         self._optional = optional
 
-    def __get__(self, obj, objtype=None) -> _HasManyProxy:
+    def __get__(self, obj: T | None, objtype: type[T] | None = None) -> _HasManyProxy:
         cache_attr = f"_HasMany__{self._ids_property or self._bfabric_field}_cache"
+        if obj is None:
+            raise ValueError("Cannot access HasMany relationship on class")
         if not hasattr(obj, cache_attr):
             ids = self._get_ids(obj)
             client = getattr(obj, self._client_property)
             setattr(obj, cache_attr, _HasManyProxy(entity_type=self._entity_type, ids=ids, client=client))
         return getattr(obj, cache_attr)
 
-    def _get_ids(self, obj) -> list[int]:
+    def _get_ids(self, obj: T) -> list[int]:
         if self._bfabric_field is not None:
             if self._ids_property is not None:
                 raise ValueError("Exactly one of bfabric_field and ids_property must be set, but both are set")

src/bfabric/entities/core/has_one.py

@@ -1,11 +1,15 @@
 from __future__ import annotations
 
-from typing import TypeVar
+from typing import TypeVar, TYPE_CHECKING
 
-from bfabric.entities.core.entity import Entity  # type: ignore
 from bfabric.entities.core.relationship import Relationship
 
+if TYPE_CHECKING:
+    # noinspection PyUnresolvedReferences
+    from bfabric.entities.core.entity import Entity
+
 E = TypeVar("E", bound="Entity")
+T = TypeVar("T")
 
 
 class HasOne(Relationship[E]):
@@ -14,13 +18,13 @@ def __init__(self, entity: str, *, bfabric_field: str, optional: bool = False) -
         self._bfabric_field = bfabric_field
         self._optional = optional
 
-    def __get__(self, obj, objtype=None) -> E | None:
+    def __get__(self, obj: T | None, objtype: type[T] | None = None) -> E | None:
         cache_attr = f"_HasOne__{self._bfabric_field}_cache"
         if not hasattr(obj, cache_attr):
             setattr(obj, cache_attr, self._load_entity(obj=obj))
         return getattr(obj, cache_attr)
 
-    def _load_entity(self, obj) -> E | None:
+    def _load_entity(self, obj: T) -> E | None:
         client = obj._client
         entity_data = obj.data_dict.get(self._bfabric_field)
         if self._optional and entity_data is None:

src/bfabric/entities/core/relationship.py

@@ -2,9 +2,11 @@
 
 import importlib
 from functools import cached_property
-from typing import TypeVar, Generic
+from typing import TypeVar, Generic, TYPE_CHECKING
 
-from bfabric.entities.core.entity import Entity  # type: ignore
+
+if TYPE_CHECKING:
+    from bfabric.entities.core.entity import Entity
 
 E = TypeVar("E", bound="Entity")
 

src/bfabric/entities/dataset.py

@@ -2,13 +2,15 @@
 
 import tempfile
 from pathlib import Path
-from typing import Any
+from typing import Any, TYPE_CHECKING
 
 from polars import DataFrame
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 
+if TYPE_CHECKING:
+    from bfabric import Bfabric
+
 
 class Dataset(Entity):
     """Immutable representation of a single dataset in B-Fabric.

src/bfabric/entities/executable.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
-from typing import Any
+from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 
+if TYPE_CHECKING:
+    from bfabric import Bfabric
+
 
 class Executable(Entity):
     ENDPOINT = "executable"

src/bfabric/entities/externaljob.py

@@ -3,11 +3,11 @@
 from functools import cached_property
 from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 from bfabric.entities.core.has_one import HasOne
 
 if TYPE_CHECKING:
+    from bfabric import Bfabric
     from bfabric.entities.workunit import Workunit
     from bfabric.entities.executable import Executable
 

src/bfabric/entities/multiplexid.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
-from typing import Any
+from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 
+if TYPE_CHECKING:
+    from bfabric import Bfabric
+
 
 class MultiplexId(Entity):
     ENDPOINT = "multiplexid"

src/bfabric/entities/multiplexkit.py

@@ -3,12 +3,12 @@
 from functools import cached_property
 from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 from bfabric.entities.core.has_many import HasMany
 
 
 if TYPE_CHECKING:
+    from bfabric import Bfabric
     from bfabric.entities.multiplexid import MultiplexId
 
 

src/bfabric/entities/order.py

@@ -2,11 +2,11 @@
 
 from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 from bfabric.entities.core.has_one import HasOne
 
 if TYPE_CHECKING:
+    from bfabric import Bfabric
     from bfabric.entities.project import Project
 
 

src/bfabric/entities/parameter.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
-from typing import Any
+from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 
+if TYPE_CHECKING:
+    from bfabric import Bfabric
+
 
 class Parameter(Entity):
     ENDPOINT = "parameter"

src/bfabric/entities/project.py

@@ -1,10 +1,12 @@
 from __future__ import annotations
 
-from typing import Any
+from typing import Any, TYPE_CHECKING
 
-from bfabric import Bfabric
 from bfabric.entities.core.entity import Entity
 
+if TYPE_CHECKING:
+    from bfabric import Bfabric
+
 
 class Project(Entity):
     ENDPOINT = "project"