Fix spine annotation schema (#102)

* fix spine annotation schema

* formatting

* fix tests

Author: bdpedigo

emannotationschemas/schemas/postsynaptic_compartment.py

@@ -1,7 +1,11 @@
 import marshmallow as mm
 from marshmallow.validate import OneOf
 
-from emannotationschemas.schemas.base import BoundSpatialPoint, ReferenceAnnotation
+from emannotationschemas.schemas.base import (
+    AnnotationSchema,
+    BoundSpatialPoint,
+    ReferenceAnnotation,
+)
 
 allowed_compartments = [
     "soma",
@@ -32,7 +36,13 @@ class PostsynapticCompartment(ReferenceAnnotation):
     )
 
 
-class SpineWithInfo(BoundSpatialPoint):
+class SpineWithInfo(AnnotationSchema):
+    pt = mm.fields.Nested(
+        BoundSpatialPoint,
+        required=True,
+        description="Spatial point representing the location of the spine",
+    )
+
     volume = mm.fields.Float(
         required=False, description="Estimated volume of the spine"
     )

tests/test_spine.py

@@ -1,9 +1,7 @@
 from emannotationschemas.schemas.postsynaptic_compartment import SpineWithInfo
 
 good_spine_with_info = {
-    "position": [100, 200, 300],
-    "supervoxel_id": 50,
-    "root_id": 10,
+    "pt": {"position": [100, 200, 300], "supervoxel_id": 50, "root_id": 10},
     "volume": 1.5,
     "n_inputs": 3,
 }
@@ -12,9 +10,9 @@
 def test_spine_with_info_schema():
     schema = SpineWithInfo()
     result = schema.load(good_spine_with_info)
-    assert result["position"] == [100, 200, 300]
-    assert result["supervoxel_id"] == 50
-    assert result["root_id"] == 10
+    assert result['pt']["position"] == [100, 200, 300]
+    assert result['pt']["supervoxel_id"] == 50
+    assert result['pt']["root_id"] == 10
     assert result["volume"] == 1.5
     assert result["n_inputs"] == 3
 
@@ -23,13 +21,11 @@ def test_spine_with_info_optional():
     schema = SpineWithInfo()
     result = schema.load(
         {
-            "position": [100, 200, 300],
-            "supervoxel_id": 50,
-            "root_id": 10,
+            "pt": {"position": [100, 200, 300], "supervoxel_id": 50, "root_id": 10},
         }
     )
-    assert result["position"] == [100, 200, 300]
-    assert result["supervoxel_id"] == 50
-    assert result["root_id"] == 10
+    assert result['pt']["position"] == [100, 200, 300]
+    assert result['pt']["supervoxel_id"] == 50
+    assert result['pt']["root_id"] == 10
     assert "volume" not in result
     assert "n_inputs" not in result