ci: coverage changes (#195)

* ci: coverage changes

* import or skip lxml

* add badge

README.md

@@ -7,7 +7,8 @@
 Version](https://img.shields.io/pypi/pyversions/ome-types.svg)](https://python.org)
 [![Tests](https://github.com/tlambert03/ome-types/workflows/tests/badge.svg)](https://github.com/tlambert03/ome-types/actions)
 [![Docs](https://readthedocs.org/projects/ome-types/badge/?version=latest)](https://ome-types.readthedocs.io/en/latest/?badge=latest)
-<!-- [![conda-forge](https://img.shields.io/conda/vn/conda-forge/ome-types)](https://anaconda.org/conda-forge/ome-types) -->
+[![codecov](https://codecov.io/gh/tlambert03/ome-types/branch/master/graph/badge.svg?token=GocY9y8A32)](https://codecov.io/gh/tlambert03/ome-types)
+
 
 ## A pure-python implementation of the OME data model
 

pyproject.toml

@@ -201,6 +201,7 @@ exclude_lines = [
 
 [tool.coverage.run]
 source = ["src/ome_types", "src/ome_autogen"]
+omit = ["src/ome_types/_autogenerated/*"]
 
 
 # Entry points -- REMOVE ONCE XSDATA-PYDANTIC-BASEMODEL IS SEPARATE

src/ome_autogen/__main__.py

@@ -1,3 +1,4 @@
+# pragma: no cover
 from ome_autogen.main import build_model
 
 build_model()

src/ome_autogen/_generator.py

@@ -125,7 +125,7 @@ def class_params(self, obj: Class) -> Iterator[tuple[str, str, str]]:
         # to fixup the numpy docstring format.
         # https://github.com/tefra/xsdata/issues/818
 
-        if sys.version_info < (3, 8):
+        if sys.version_info < (3, 8):  # pragma: no cover
             # i don't know why, but in python 3.7, it's not picking up our
             # template ... so this method yields too many values to unpack
             # xsdata/formats/dataclass/templates/docstrings.numpy.jinja2", line 6

src/ome_autogen/_transformer.py

@@ -17,7 +17,7 @@
 
 # we don't need RenameDuplicateAttributes because we inject
 # proper enum names in our _generator.py
-UNWANTED_HANDLERS = [(RenameDuplicateAttributes, None)]
+UNWANTED_HANDLERS = [RenameDuplicateAttributes]
 
 
 def display_help(self: Attribute) -> str | None:
@@ -63,12 +63,10 @@ def analyze_classes(self, classes: list[Class]) -> list[Class]:
         container = ClassContainer(config=self.config)
 
         for handlers in container.processors.values():
-            for idx, h in enumerate(list(handlers)):
-                for unwanted, wanted in UNWANTED_HANDLERS:
+            for h in list(handlers):
+                for unwanted in UNWANTED_HANDLERS:
                     if isinstance(h, unwanted):
                         handlers.remove(h)
-                        if wanted is not None:
-                            handlers.insert(idx, wanted(container))
 
         container.extend(classes)
 

src/ome_autogen/main.py

@@ -71,7 +71,7 @@ def _check_mypy(package_dir: str) -> None:
     mypy = ["mypy", package_dir, "--strict"]
     try:
         subprocess.check_output(mypy, stderr=subprocess.STDOUT)  # noqa S
-    except subprocess.CalledProcessError as e:
+    except subprocess.CalledProcessError as e:  # pragma: no cover
         raise RuntimeError(f"mypy errors:\n\n{e.output.decode()}") from e
 
 

src/ome_types/__init__.py

@@ -5,7 +5,7 @@
 
 try:
     __version__ = version("ome-types")
-except PackageNotFoundError:
+except PackageNotFoundError:  # pragma: no cover
     __version__ = "unknown"
 
 from ome_types import model

src/ome_types/_mixins/_base_type.py

@@ -130,7 +130,7 @@ def _quantity_property(field_name: str) -> property:
 
     def quantity(self: Any) -> Optional["pint.Quantity"]:
         value = getattr(self, field_name)
-        if value is None:
+        if value is None:  # pragma: no cover
             return None
 
         unit = cast("Enum", getattr(self, _UNIT_FIELD.format(field_name)))

src/ome_types/_mixins/_bin_data.py

@@ -14,7 +14,7 @@ def _v(cls, values: dict) -> Dict[str, Any]:
         # seems like it could be done in a default_factory, but that would
         # require more modification of xsdata I think
         if "value" not in values:
-            if values.get("length") != 0:
+            if values.get("length") != 0:  # pragma: no cover
                 warnings.warn(
                     "BinData length is non-zero but value is missing", stacklevel=2
                 )

src/ome_types/_mixins/_ids.py

@@ -77,7 +77,7 @@ def validate_id(cls: type[BaseModel], value: int | str) -> Any:
         msg = f"Casting invalid {id_name}ID {value!r} to {newname!r}"
         warnings.warn(msg, stacklevel=2)
         return newname
-    elif not isinstance(value, int):
+    elif not isinstance(value, int):  # pragma: no cover
         raise ValueError(f"Invalid ID value: {value!r}, {type(value)}")
 
     # update the counter to be at least this value

src/ome_types/_mixins/_instrument.py

@@ -18,6 +18,7 @@
 class InstrumentMixin:
     @property
     def light_source_group(self) -> List["LightSource"]:
+        # here for backwards compatibility
         slf = cast("Instrument", self)
         return [
             *slf.arcs,

src/ome_types/model/_shape_union.py

@@ -71,7 +71,7 @@ def _validate_root(cls, v: ShapeType) -> ShapeType:
             for cls_ in _ShapeCls:
                 with suppress(ValidationError):
                     return cls_(**v)
-        raise ValueError(f"Invalid shape: {v}")
+        raise ValueError(f"Invalid shape: {v}")  # pragma: no cover
 
     def __repr__(self) -> str:
         return f"{self.__class__.__name__}({self.__root__!r})"

tests/test_serialization.py

@@ -18,6 +18,7 @@
 if TYPE_CHECKING:
     import xmlschema
 
+DATA = Path(__file__).parent / "data"
 SKIP_ROUNDTRIP = {
     # These have XMLAnnotations with extra namespaces and mixed content, which
     # the automated round-trip test code doesn't properly verify yet. So even
@@ -154,3 +155,9 @@ def _sort_elements(element: ET.Element, recursive: bool = True) -> None:
         # Recursively sort child elements for each subelement
         for child in element:
             _sort_elements(child)
+
+
+def test_canonicalize() -> None:
+    pytest.importorskip("lxml")
+    ome = from_xml(DATA / "example.ome.xml", validate=True)
+    _ = to_xml(ome, validate=True, canonicalize=True)