Merge branch 'main' of https://github.com/VirtualBrainLab/vbl-aquarium

models/schemas/urchin/LineModel.json

@@ -1 +1 @@
-{"$defs": {"Color": {"properties": {"r": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "title": "Color", "type": "object"}, "Vector3": {"properties": {"x": {"default": 0.0, "title": "X", "type": "number"}, "y": {"default": 0.0, "title": "Y", "type": "number"}, "z": {"default": 0.0, "title": "Z", "type": "number"}}, "title": "Vector3", "type": "object"}}, "properties": {"ID": {"title": "Id", "type": "string"}, "Positions": {"default": [], "items": {"$ref": "#/$defs/Vector3"}, "title": "Positions", "type": "array"}, "Color": {"allOf": [{"$ref": "#/$defs/Color"}], "default": {"r": 1.0, "g": 1.0, "b": 1.0, "a": 1.0}}}, "required": ["ID"], "title": "LineModel", "type": "object"}
+{"$defs": {"Color": {"properties": {"r": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "title": "Color", "type": "object"}, "Vector3": {"properties": {"x": {"default": 0.0, "title": "X", "type": "number"}, "y": {"default": 0.0, "title": "Y", "type": "number"}, "z": {"default": 0.0, "title": "Z", "type": "number"}}, "title": "Vector3", "type": "object"}}, "properties": {"ID": {"title": "Id", "type": "string"}, "Positions": {"items": {"$ref": "#/$defs/Vector3"}, "title": "Positions", "type": "array"}, "Color": {"allOf": [{"$ref": "#/$defs/Color"}], "default": {"r": 1.0, "g": 1.0, "b": 1.0, "a": 1.0}}}, "required": ["ID"], "title": "LineModel", "type": "object"}

models/schemas/urchin/ParticleSystemModel.json

@@ -1 +1 @@
-{"$defs": {"Color": {"properties": {"r": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "title": "Color", "type": "object"}, "Vector3": {"properties": {"x": {"default": 0.0, "title": "X", "type": "number"}, "y": {"default": 0.0, "title": "Y", "type": "number"}, "z": {"default": 0.0, "title": "Z", "type": "number"}}, "title": "Vector3", "type": "object"}}, "properties": {"ID": {"title": "Id", "type": "string"}, "N": {"title": "N", "type": "integer"}, "Material": {"default": "circle", "title": "Material", "type": "string"}, "Positions": {"default": [], "items": {"$ref": "#/$defs/Vector3"}, "title": "Positions", "type": "array"}, "Sizes": {"default": [], "items": {"type": "number"}, "title": "Sizes", "type": "array"}, "Colors": {"default": [], "items": {"$ref": "#/$defs/Color"}, "title": "Colors", "type": "array"}}, "required": ["ID", "N"], "title": "ParticleSystemModel", "type": "object"}
+{"$defs": {"Color": {"properties": {"r": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "R", "type": "number"}, "g": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "G", "type": "number"}, "b": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "B", "type": "number"}, "a": {"default": 1, "maximum": 1.0, "minimum": 0.0, "title": "A", "type": "number"}}, "title": "Color", "type": "object"}, "Vector3": {"properties": {"x": {"default": 0.0, "title": "X", "type": "number"}, "y": {"default": 0.0, "title": "Y", "type": "number"}, "z": {"default": 0.0, "title": "Z", "type": "number"}}, "title": "Vector3", "type": "object"}}, "properties": {"ID": {"title": "Id", "type": "string"}, "N": {"title": "N", "type": "integer"}, "Material": {"default": "circle", "title": "Material", "type": "string"}, "Positions": {"items": {"$ref": "#/$defs/Vector3"}, "title": "Positions", "type": "array"}, "Sizes": {"items": {"type": "number"}, "title": "Sizes", "type": "array"}, "Colors": {"items": {"$ref": "#/$defs/Color"}, "title": "Colors", "type": "array"}}, "required": ["ID", "N"], "title": "ParticleSystemModel", "type": "object"}

src/vbl_aquarium/build.py

@@ -57,7 +57,7 @@ def remove_ignored_classes(module):
 
         # Move using statement to top
         output = "using System;\n" + output
-        
+
         if "using UnityEngine;" in output:
             output = "using UnityEngine;\n" + output.replace("using UnityEngine;", "")
 

src/vbl_aquarium/models/generic.py

@@ -10,10 +10,12 @@
 class IDData(VBLBaseModel):
     id: str = Field(..., alias="ID")
 
+
 class Vector2Data(VBLBaseModel):
-    id: str = Field(alias= "ID")
+    id: str = Field(alias="ID")
     value: Vector2
 
+
 class Vector3Data(VBLBaseModel):
     id: str = Field(..., alias="ID")
     value: Vector3
@@ -80,14 +82,17 @@ class BoolList(VBLBaseModel):
 class IDList(VBLBaseModel):
     ids: list[str] = Field(..., alias="IDs")
 
+
 class IDListVector2Data(VBLBaseModel):
     ids: list[str] = Field(..., alias="IDs")
     value: Vector2
 
+
 class IDListVector2List(VBLBaseModel):
     ids: list[str] = Field(..., alias="IDs")
     values: list[Vector2]
 
+
 class IDListVector3Data(VBLBaseModel):
     ids: list[str] = Field(..., alias="IDs")
     value: Vector3

src/vbl_aquarium/models/urchin.py

@@ -72,14 +72,16 @@ class CameraMode(str, Enum):
     zoom: float = 16
     pan: Vector2 = Vector2()
     mode: CameraMode = CameraMode.orthographic
-    background_color: Color = Color() # white by default
+    background_color: Color = Color()  # white by default
     controllable: bool = True
     main: bool = False
 
+
 class CameraRotationModel(VBLBaseModel):
     start_rotation: Vector3
     end_rotation: Vector3
 
+
 # Individual mesh neuron
 
 
@@ -96,15 +98,19 @@ class MeshModel(VBLBaseModel):
     material: str
     interactive: bool
 
+
 # Lines
-
+
+
 class LineModel(VBLBaseModel):
     id: str = Field(alias="ID")
-    positions: list[Vector3] = []
+    positions: list[Vector3] = Field(default_factory=list)
     color: Color = Color()
 
+
 # Probes
-
+
+
 class ProbeModel(VBLBaseModel):
     id: str = Field(alias="ID")
     position: Vector3
@@ -113,30 +119,35 @@ class ProbeModel(VBLBaseModel):
     style: str
     scale: Vector3
 
+
 # Particle group
 
 
 class ParticleSystemModel(VBLBaseModel):
     id: str = Field(alias="ID")
     n: int
-    material: str = 'circle'
+    material: str = "circle"
+
+    positions: list[Vector3] = Field(default_factory=list)
+    sizes: list[float] = Field(default_factory=list)
+    colors: list[Color] = Field(default_factory=list)
 
-    positions: list[Vector3] = []
-    sizes: list[float] = []
-    colors: list[Color] = []
 
 # Text
-
+
+
 class TextModel(VBLBaseModel):
     id: str = Field(alias="ID")
     text: str
-    color: Color = Color(r = 0, g = 0, b = 0)
+    color: Color = Color(r=0, g=0, b=0)
     font_size: int = 12
     position: Vector2 = Vector2()
 
+
 # Utilities
-
+
+
 class ColormapModel(VBLBaseModel):
-    name: str = ''
+    name: str = ""
     min: float = 0
-    max: float = 1
+    max: float = 1