test: add typing tests (#178)

* test: adding typesafety

* fix manifest

* add test dep

.github/workflows/test.yml

@@ -56,6 +56,23 @@ jobs:
 
       - uses: codecov/codecov-action@v2
 
+  test-types:
+    name: Typesafety
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.11"
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install pytest pytest-mypy-plugins
+          python -m pip install .
+
+      - name: Test
+        run: pytest typesafety -v
+
   deploy:
     name: Deploy
     runs-on: ubuntu-latest

.pre-commit-config.yaml

@@ -29,3 +29,7 @@ repos:
     hooks:
       - id: mypy
         exclude: ^tests|^docs|_napari_plugin|widgets
+        additional_dependencies:
+          - pydantic<2
+          - Pint
+          - types-lxml

pyproject.toml

@@ -40,15 +40,21 @@ ome-types = "ome_types._napari_plugin"
 # extras
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
-dev = ["black", "ruff", "xsdata[cli]>=23.6", "mypy"]
+dev = ["black", "ruff", "xsdata[cli]>=23.6", "mypy", "pre-commit", "types-lxml"]
 docs = [
   "numpydoc",
   "pygments",
   "sphinx==5.3.0",
   "sphinx-rtd-theme==1.1.1",
   "ipython",
 ]
-test = ["pytest", "pytest-cov", "xmlschema"]
+test = [
+  "pytest",
+  "pytest-cov",
+  "xmlschema",
+  "pytest-mypy-plugins",
+  "types-lxml",
+]
 
 # https://hatch.pypa.io/latest/plugins/build-hook/custom/
 [tool.hatch.build.targets.wheel.hooks.custom]
@@ -128,6 +134,7 @@ ignore = [
   ".readthedocs.yml",
   "docs/**/*",
   "tests/**/*",
+  "typesafety/**/*",
 ]
 
 
@@ -144,6 +151,7 @@ target-version = ['py38']
 [tool.pytest.ini_options]
 minversion = "6.0"
 testpaths = ["tests"]
+addopts = '--mypy-only-local-stub'
 filterwarnings = [
   "error",
   "ignore:Casting invalid AnnotationID:UserWarning",
@@ -159,10 +167,16 @@ files = "src/**/*/*.py"
 follow_imports = 'silent'
 strict_optional = true
 warn_redundant_casts = true
+warn_unused_ignores = true
 disallow_any_generics = false
 no_implicit_reexport = true
 ignore_missing_imports = true
 disallow_untyped_defs = true
+plugins = "pydantic.mypy"
+
+[tool.pydantic-mypy]
+init_forbid_extra = true
+init_typed = false       # allow parsing Any
 
 [[tool.mypy.overrides]]
 module = ['ome_types._autogenerated.ome_2016_06.structured_annotations']

src/ome_types/_conversion.py

@@ -14,7 +14,7 @@
 try:
     from lxml import etree as ET
 except ImportError:  # pragma: no cover
-    from xml.etree import ElementTree as ET
+    from xml.etree import ElementTree as ET  # type: ignore[no-redef]
 
 from xsdata.formats.dataclass.parsers.config import ParserConfig
 
@@ -57,8 +57,8 @@ def _get_ome_type(xml: str | bytes) -> type[OMEType]:
             xml = xml.encode("utf-8")
         root = ET.fromstring(xml)  # noqa: S314
 
-    *ns, localname = root.tag[1:].split("}", 1)
-    ns = next(iter(ns), None)
+    *_ns, localname = root.tag[1:].split("}", 1)
+    ns = next(iter(_ns), None)
 
     if not ns or ns not in MODULES:
         raise ValueError(f"Unsupported OME schema tag {root.tag!r} in namespace {ns!r}")

src/ome_types/_mixins/_base_type.py

@@ -4,7 +4,7 @@
 from textwrap import indent
 from typing import TYPE_CHECKING, Any, ClassVar, Optional, Sequence, Set, cast
 
-from pydantic import BaseModel, PrivateAttr, validator
+from pydantic import BaseModel, validator
 
 from ome_types._mixins._ids import validate_id
 from ome_types.units import ureg
@@ -57,11 +57,9 @@ class Config:
         underscore_attrs_are_private = True
         use_enum_values = False
         validate_all = True
-        validation_mode: str = "strict"
 
     # allow use with weakref
     __slots__: ClassVar[Set[str]] = {"__weakref__"}  # type: ignore
-    _validation_mode: str = PrivateAttr("strict")
 
     def __init__(__pydantic_self__, **data: Any) -> None:
         if "id" in __pydantic_self__.__fields__:

src/ome_types/_mixins/_ome.py

@@ -24,7 +24,7 @@ def _link_refs(self) -> None:
         for ref in collect_references(self):
             # all reference subclasses do actually have an 'id' field
             # but it's not declared in the base class
-            ref._ref = weakref.ref(ids[ref.id])  # type: ignore [attr-defined]
+            ref._ref = weakref.ref(ids[ref.id])
 
     def __setstate__(self, state: dict[str, Any]) -> None:
         """Support unpickle of our weakref references."""
@@ -66,7 +66,7 @@ def collect_ids(value: Any) -> dict[str, OMEType]:
             if f == "id" and not isinstance(value, Reference):
                 # We don't need to recurse on the id string, so just record it
                 # and move on.
-                ids[value.id] = value  # type: ignore
+                ids[value.id] = value
             else:
                 ids.update(collect_ids(getattr(value, f)))
     # Do nothing for uninteresting types.

src/xsdata_pydantic_basemodel/compat.py

@@ -76,7 +76,7 @@ def derived_element(self) -> Type:
     def is_model(self, obj: Any) -> bool:
         clazz = obj if isinstance(obj, type) else type(obj)
         if issubclass(clazz, BaseModel):
-            clazz.update_forward_refs()  # type: ignore
+            clazz.update_forward_refs()
             return True
 
         return False

typesafety/test_type_inits.yml

@@ -0,0 +1,25 @@
+- case: types_requiring_no_arguments
+  main: |
+    import ome_types.model as m
+
+    m.OME()
+    m.Annotation()
+    m.BasicAnnotation()
+    m.Dataset()
+    m.Arc()
+    m.Microscope()
+    ch = m.Channel()
+    reveal_type(ch.id)  # N: Revealed type is "builtins.str"
+
+- case: types_requiring_arguments
+  main: |
+    import ome_types.model as m
+
+    m.BinData(value=b'213', length=1)  # ER: Missing named argument "big_endian" .*
+    m.Image()  # ER: Missing named argument "pixels" .*
+
+- case: extra_arguments
+  main: |
+    import ome_types.model as m
+
+    m.Channel(idd='123')  # ER: Unexpected keyword argument "idd" .*