Implement bioformats2raw structure

src/ome_zarr_models/base.py

@@ -13,3 +13,9 @@ class Config:
 
         validate_assignment = True
         extra = "allow"
+        # This allows fields with aliases to be populated by either
+        # their alias or class attribute name
+        #
+        # We use this so we can handle (at least) the "bioformats2raw.version"
+        # key - attributes in Python can't contain a "."
+        populate_by_name = True

src/ome_zarr_models/v04/bioformats2raw.py

@@ -0,0 +1,16 @@
+from typing import Any, Literal
+
+from pydantic import Field
+
+from ome_zarr_models.base import Base
+from ome_zarr_models.v04.plate import Plate
+
+
+class BioFormats2RawAttrs(Base):
+    """
+    A bioformats2raw zarr group.
+    """
+
+    bioformats2raw_layout: Literal[3] = Field(..., alias="bioformats2raw.layout")
+    plate: Plate | None = None
+    series: Any | None = None

tests/v04/data/bioformats2raw_example.json

@@ -0,0 +1,30 @@
+{
+  "bioformats2raw.layout": 3,
+  "plate": {
+    "columns": [
+      {
+        "name": "1"
+      }
+    ],
+    "name": "Plate Name 0",
+    "wells": [
+      {
+        "path": "A/1",
+        "rowIndex": 0,
+        "columnIndex": 0
+      }
+    ],
+    "field_count": 1,
+    "rows": [
+      {
+        "name": "A"
+      }
+    ],
+    "acquisitions": [
+      {
+        "id": 0
+      }
+    ],
+    "version": "0.4"
+  }
+}

tests/v04/test_bioformats2raw.py

@@ -0,0 +1,33 @@
+from pathlib import Path
+
+from ome_zarr_models.v04.bioformats2raw import BioFormats2RawAttrs
+from ome_zarr_models.v04.plate import (
+    AcquisitionInPlate,
+    ColumnInPlate,
+    Plate,
+    RowInPlate,
+    WellInPlate,
+)
+
+
+def test_bioformats2raw_exmaple_json():
+    with open(Path(__file__).parent / "data" / "bioformats2raw_example.json") as f:
+        model = BioFormats2RawAttrs.model_validate_json(f.read())
+
+    assert model == BioFormats2RawAttrs(
+        bioformats2raw_layout=3,
+        plate=Plate(
+            acquisitions=[
+                AcquisitionInPlate(
+                    id=0, maximumfieldcount=None, name=None, description=None
+                )
+            ],
+            columns=[ColumnInPlate(name="1")],
+            field_count=1,
+            name="Plate Name 0",
+            rows=[RowInPlate(name="A")],
+            version="0.4",
+            wells=[WellInPlate(path="A/1", rowIndex=0, columnIndex=0)],
+        ),
+        series=None,
+    )