Merge pull request #15 from BioImageTools/feat/pydantic

Feat/pydantic

pyproject.toml

@@ -38,8 +38,12 @@ dev = [
     "pytest>=8.3.3",
 ]
 
+test = ["pytest"]
+
+pydantic=["pydantic"]
+
 [tool.uv]
-default-groups = ["docs", "dev"]
+default-groups = ["docs", "dev", "pydantic", "test"]
 
 # Ruff configuration for linting and formatting
 # https://docs.astral.sh/ruff

src/ome_zarr_models/base.py

@@ -0,0 +1,7 @@
+import pydantic
+
+
+class Base(pydantic.BaseModel):
+    """
+    The base pydantic model for all metadata classes 
+    """

src/ome_zarr_models/utils.py

@@ -1,9 +1,15 @@
-"""Utility functions."""
-from dataclasses import MISSING, fields, is_dataclass
-
 import pydantic
+from dataclasses import MISSING, fields, is_dataclass
 from pydantic import create_model
 
+from typing import TypeVar
+T = TypeVar("T")
+
+def _unique_items_validator(values: list[T]) -> list[T]:
+    for ind, value in enumerate(values, start=1):
+        if value in values[ind:]:
+            raise ValueError(f"Non-unique values in {values}.")
+    return values
 
 def dataclass_to_pydantic(dataclass_type: type) -> type[pydantic.BaseModel]:
     """Convert a dataclass to a Pydantic model.
@@ -32,4 +38,8 @@ def dataclass_to_pydantic(dataclass_type: type) -> type[pydantic.BaseModel]:
             # No default value
             field_definitions[_field.name] = (_field.type, Ellipsis)
 
+<<<<<<< HEAD
+    return create_model(dataclass_type.__name__, **field_definitions)
+=======
     return create_model(dataclass_type.__name__, **field_definitions)
+>>>>>>> 470f4f1a33aef4ecf2ebf0906c912a3621c8957b

src/ome_zarr_models/v04/models/__init__.py

@@ -0,0 +1,3 @@
+from ome_zarr_models.v04.models.axes import Axis
+from ome_zarr_models.v04.models.coordinate_transformations import PathScale, PathTranslation, VectorScale, VectorTranslation
+from ome_zarr_models.v04.models.multiscales import Dataset, Multiscale, MultiscaleGroupAttrs

src/ome_zarr_models/v04/models/axes.py

@@ -0,0 +1,13 @@
+from ome_zarr_models.base import Base
+
+
+class Axis(Base):
+    """
+    Model for an element of `Multiscale.axes`.
+
+    See https://ngff.openmicroscopy.org/0.4/#axes-md.
+    """
+
+    name: str
+    type: str | None = None
+    unit: str | None = None