misc

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
         exclude: ^tests|^docs
 
   - repo: https://github.com/charliermarsh/ruff-pre-commit
-    rev: v0.0.270
+    rev: v0.0.275
     hooks:
       - id: ruff
         args: [--fix]
@@ -25,7 +25,7 @@ repos:
         exclude: ^docs
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.4.1
     hooks:
       - id: mypy
         exclude: ^tests|^docs|_napari_plugin|widgets

pyproject.toml

@@ -54,7 +54,13 @@ dev = [
   "xsdata-pydantic-basemodel @ git+https://github.com/tlambert03/xsdata-pydantic-basemodel",
   "mypy",
 ]
-docs = ["numpydoc", "pygments", "sphinx==5.3.0", "sphinx-rtd-theme==1.1.1", "ipython"]
+docs = [
+  "numpydoc",
+  "pygments",
+  "sphinx==5.3.0",
+  "sphinx-rtd-theme==1.1.1",
+  "ipython",
+]
 test = ["pytest", "pytest-cov", "pytest-benchmark", "xmlschema"]
 
 
@@ -93,13 +99,14 @@ select = [
   "E",    # style errors
   "F",    # flakes
   "D",    # pydocstyle
-  "I001", # isort
+  "I",    # isort
   "UP",   # pyupgrade
-  # "N",  # pep8-naming
   "S",    # bandit
-  "C",    # flake8-comprehensions
+  "C4",   # flake8-comprehensions
   "B",    # flake8-bugbear
   "A001", # flake8-builtins
+  "TID",  # tidy
+  "TCH",  # typechecking
   "RUF",  # ruff-specific rules
 ]
 ignore = [

src/ome_autogen/__main__.py

@@ -1,3 +1,3 @@
-from .main import build_model
+from ome_autogen.main import build_model
 
 build_model()

src/ome_autogen/main.py

@@ -1,13 +1,14 @@
 import os
 import subprocess
+import sys
 from pathlib import Path
 
 from xsdata.codegen.transformer import SchemaTransformer
 
 from ome_autogen import _util
 from ome_autogen._config import OUTPUT_PACKAGE, get_config
 
-DO_MYPY = os.environ.get("OME_AUTOGEN_MYPY", "0") == "1"
+DO_MYPY = os.environ.get("OME_AUTOGEN_MYPY", "0") == "1" or "--mypy" in sys.argv
 SRC_PATH = Path(__file__).parent.parent
 SCHEMA_FILE = SRC_PATH / "ome_types" / "ome-2016-06.xsd"
 RUFF_IGNORE: list[str] = [

src/ome_types/_conversion.py

@@ -1,6 +1,5 @@
 from __future__ import annotations
 
-import io
 from dataclasses import is_dataclass
 from pathlib import Path
 from struct import Struct
@@ -12,6 +11,7 @@
 from xsdata_pydantic_basemodel.bindings import XmlParser, XmlSerializer
 
 if TYPE_CHECKING:
+    import io
     from typing import TypedDict
 
     from xsdata.formats.dataclass.parsers.mixins import XmlHandler
@@ -53,7 +53,7 @@ def to_dict(source: OME | Path | str | bytes) -> dict[str, Any]:
     )
 
 
-def _class_factory(cls: type, kwargs: Any):
+def _class_factory(cls: type, kwargs: Any) -> Any:
     kwargs.setdefault("validation", "strict")
     return cls(**kwargs)
 

src/ome_types/_mixins/_base_type.py

@@ -114,7 +114,7 @@ def __repr__(self) -> str:
 
     @validator("id", pre=True, always=True, check_fields=False)
     @classmethod
-    def _validate_id(cls, value: Any, values=None, config=None) -> Any:
+    def _validate_id(cls, value: Any) -> Any:
         """Pydantic validator for ID fields in OME models.
 
         If no value is provided, this validator provides and integer ID, and stores the

src/ome_types/_mixins/_ome.py

@@ -1,12 +1,13 @@
 from __future__ import annotations
 
 import weakref
-from pathlib import Path
 from typing import TYPE_CHECKING, Any, cast
 
 from ._base_type import OMEType
 
 if TYPE_CHECKING:
+    from pathlib import Path
+
     from ome_types.model import OME, Reference
 
 

src/ome_types/_mixins/_structured_annotations.py

@@ -1,14 +1,12 @@
-from typing import Iterable, Sequence, TypeVar, overload
+from typing import Iterator, Sequence, overload
 
 from ome_types.model.ome_2016_06 import Annotation
 
 from ._base_type import OMEType
 
-_T_co = TypeVar("_T_co", covariant=True)  # Any type covariant containers.
 
-
-class StructuredAnnotationsMixin(OMEType, Sequence[Annotation]):  # type: ignore
-    def _iter_annotations(self) -> Iterable[Annotation]:
+class StructuredAnnotationsMixin(OMEType, Sequence[Annotation]):
+    def _iter_annotations(self) -> Iterator[Annotation]:
         for x in self.__fields__.values():
             if issubclass(x.type_, Annotation):
                 yield from getattr(self, x.name)
@@ -26,3 +24,6 @@ def __getitem__(self, key: int | slice) -> Annotation | Sequence[Annotation]:
 
     def __len__(self) -> int:
         return len(list(self._iter_annotations()))
+
+    def __iter__(self) -> Iterator[Annotation]:
+        return self._iter_annotations()