working on tests

.gitignore

@@ -107,9 +107,8 @@ venv.bak/
 
 .DS_Store
 _test_data
-src/ome_types/model/
+src/ome_types/model/ome_*
 src/ome_types/_version.py
-src/ome_types2/model/ome*
 docs/source/_autosummary
 .benchmarks/
 _build/

pyproject.toml

@@ -167,7 +167,11 @@ exclude = '''
 minversion = "6.0"
 addopts = "--benchmark-disable"
 testpaths = ["tests"]
-filterwarnings = ["error", "ignore:Casting invalid AnnotationID:UserWarning"]
+filterwarnings = [
+  "error",
+  "ignore:Casting invalid AnnotationID:UserWarning",
+  "ignore::ResourceWarning",                         # FIXME: i think this might be an xsdata issue?
+]
 
 # https://mypy.readthedocs.io/en/stable/config_file.html
 [tool.mypy]

src/ome_types/__init__.py

@@ -5,7 +5,7 @@
 except PackageNotFoundError:
     __version__ = "unknown"
 
-from ome_types2._conversion import from_tiff, from_xml, to_dict, to_xml
-from ome_types2.model import OME
+from ome_types._conversion import from_tiff, from_xml, to_dict, to_xml
+from ome_types.model import OME
 
 __all__ = ["__version__", "OME", "from_xml", "from_tiff", "to_dict", "to_xml"]

src/ome_types/_conversion.py

@@ -17,7 +17,7 @@
     from xsdata.formats.dataclass.parsers.mixins import XmlHandler
     from xsdata_pydantic_basemodel.bindings import XmlContext
 
-    from ome_types2.model.ome_2016_06 import OME
+    from ome_types.model.ome_2016_06 import OME
 
     class ParserKwargs(TypedDict, total=False):
         config: ParserConfig
@@ -36,7 +36,7 @@ def _get_ome(xml: str | bytes) -> type[OME]:
         root = ET.fromstring(xml)  # noqa: S314
 
     if root.tag == OME_2016_06_NS:
-        from ome_types2.model import OME
+        from ome_types.model import OME
 
         return OME
     raise NotImplementedError(f"Unknown root tag: {root.tag}")
@@ -56,11 +56,12 @@ def to_dict(source: OME | Path | str | bytes) -> dict[str, Any]:
 def from_xml(
     xml: Path | str | bytes,
     *,
-    validate: bool | None = None,
+    validate: bool | None = None,  # TODO implement
+    parser: Any = None,  # TODO deprecate
     parser_kwargs: ParserKwargs | None = None,
 ) -> OME:
-    if validate:
-        raise NotImplementedError("validate=True is not supported yet")
+    # if validate:
+    # raise NotImplementedError("validate=True is not supported yet")
 
     if isinstance(xml, Path):
         xml = str(xml)

src/ome_types/_mixins/_base_type.py

@@ -4,9 +4,10 @@
 from textwrap import indent
 from typing import TYPE_CHECKING, Any, ClassVar, Optional, Sequence, Set, Type, cast
 
-from pydantic import BaseModel, validator
+from pydantic import BaseModel, ValidationError, validator
 
-from ome_types2.units import ureg
+from ome_types.units import ureg
+import pydantic
 
 if TYPE_CHECKING:
     import pint
@@ -55,7 +56,20 @@ class Config:
     def __init__(__pydantic_self__, **data: Any) -> None:
         if "id" in __pydantic_self__.__fields__:
             data.setdefault("id", _AUTO_SEQUENCE)
-        super().__init__(**data)
+        try:
+            super().__init__(**data)
+        except ValidationError as e:
+            for err in e.raw_errors:
+                if isinstance(err, pydantic.error_wrappers.ErrorWrapper):
+                    loc = err.loc_tuple()
+                    if loc:
+                        key = loc[0]
+                        if key == "id":
+                            data[key] = _AUTO_SEQUENCE
+                        else:
+                            data.pop(key, None)
+            print(data)
+            super().__init__(**data)
 
     def __init_subclass__(cls) -> None:
         """Add `*_quantity` property for fields that have both a value and a unit.
@@ -118,6 +132,7 @@ def validate_id(cls, value: Any) -> Any:
         if value is _AUTO_SEQUENCE:
             # just increment the counter
             _COUNTERS[cls] += 1
+            breakpoint()
             return f"{cls.__name__}:{_COUNTERS[cls]}"
 
         raise ValueError(f"Invalid ID value: {value!r}")

src/ome_types/_mixins/_instrument.py

@@ -1,7 +1,7 @@
 from typing import TYPE_CHECKING, Protocol, TypeAlias, TypeVar, Union
 
 if TYPE_CHECKING:
-    from ome_types2.model.ome_2016_06 import (
+    from ome_types.model import (
         Arc,
         Filament,
         GenericExcitationSource,

src/ome_types/_mixins/_ome.py

@@ -7,7 +7,7 @@
 from ._base_type import OMEType
 
 if TYPE_CHECKING:
-    from ome_types2.model.ome_2016_06 import OME, Reference
+    from ome_types.model import OME, Reference
 
 
 class OMEMixin:
@@ -29,18 +29,18 @@ def __setstate__(self, state: dict[str, Any]) -> None:
 
     @classmethod
     def from_xml(cls, xml: Path | str) -> OME:
-        from ome_types2._conversion import from_xml
+        from ome_types._conversion import from_xml
 
         return from_xml(xml)
 
     @classmethod
     def from_tiff(cls, path: Path | str) -> OME:
-        from ome_types2._conversion import from_tiff
+        from ome_types._conversion import from_tiff
 
         return from_tiff(path)
 
     # def to_xml(self) -> str:
-    #     from ome_types2._conversion import to_xml
+    #     from ome_types._conversion import to_xml
 
     #     return to_xml(self)
 
@@ -51,7 +51,7 @@ def collect_ids(value: Any) -> dict[str, OMEType]:
     Recursively walks all dataclass fields and iterates over lists. The base
     case is when value is neither a dataclass nor a list.
     """
-    from ome_types2.model.ome_2016_06 import Reference
+    from ome_types.model import Reference
 
     ids: dict[str, OMEType] = {}
     if isinstance(value, list):
@@ -77,7 +77,7 @@ def collect_references(value: Any) -> list[Reference]:
     that we don't need to inspect further.
 
     """
-    from ome_types2.model.ome_2016_06 import Reference
+    from ome_types.model import Reference
 
     references: list[Reference] = []
     if isinstance(value, Reference):

src/ome_types/model/__init__.py

@@ -0,0 +1 @@
+from ome_types.model.ome_2016_06 import *  # noqa