Merge dev into main

.github/workflows/vr-foraging-cicd.yml

@@ -211,7 +211,7 @@ jobs:
           git config --global user.email "github-actions[bot]@users.noreply.github.com"
           git add .
           git commit -m "Release v${{ steps.get_version.outputs.version }} [skip ci]"
-          git tag -a "v${{ steps.get_version.outputs.version }}" -m "Release v${{ steps.get_version.outputs.version }}"
+          git tag -a "v${{ steps.get_version.outputs.version }}" -m "v${{ steps.get_version.outputs.version }}"
           git push origin main
           git push origin "v${{ steps.get_version.outputs.version }}"
 

pyproject.toml

@@ -28,7 +28,7 @@ Changelog = "https://github.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/rel
 
 [project.optional-dependencies]
 
-data = ["contraqctor<0.5.0"]
+data = ["contraqctor<0.6.0"]
 
 launcher = [
     "aind-clabe[aind-services]>=0.7",

src/DataSchemas/aind_behavior_vr_foraging.json

@@ -3,14 +3,14 @@
     "AindBehaviorSessionModel": {
       "properties": {
         "aind_behavior_services_pkg_version": {
-          "default": "0.12.2",
+          "default": "0.12.3",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"
         },
         "version": {
-          "const": "0.12.2",
-          "default": "0.12.2",
+          "const": "0.12.3",
+          "default": "0.12.3",
           "title": "Version",
           "type": "string"
         },
@@ -353,7 +353,7 @@
     "AindVrForagingRig": {
       "properties": {
         "aind_behavior_services_pkg_version": {
-          "default": "0.12.2",
+          "default": "0.12.3",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"
@@ -611,7 +611,7 @@
           "title": "Rng Seed"
         },
         "aind_behavior_services_pkg_version": {
-          "default": "0.12.2",
+          "default": "0.12.3",
           "pattern": "^(0|[1-9]\\d*)\\.(0|[1-9]\\d*)\\.(0|[1-9]\\d*)(?:-((?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*)(?:\\.(?:0|[1-9]\\d*|\\d*[a-zA-Z-][0-9a-zA-Z-]*))*))?(?:\\+([0-9a-zA-Z-]+(?:\\.[0-9a-zA-Z-]+)*))?$",
           "title": "aind_behavior_services package version",
           "type": "string"
@@ -4997,8 +4997,18 @@
       "type": "object"
     },
     "TruncationParameters": {
-      "description": "Parameters for truncating a distribution to a specified range. Truncation should\nbe applied after sampling and scaling.\n\nUsed to constrain sampled values within minimum and maximum bounds.",
+      "description": "Parameters for truncating a distribution to a specified range. Truncation should\nbe applied after sampling and scaling.\n\nThe truncation_mode determines how out-of-bounds values are handled:\n- \"exclude\": Resample until a value within [min, max] is obtained.\nIf after a certain number of attempts no valid value is found, it\nwill use the average of sampled values and pick the closest bound.\n- \"clamp\": Clamp values to the nearest bound within [min, max].\nUsed to constrain sampled values within minimum and maximum bounds.",
       "properties": {
+        "truncation_mode": {
+          "default": "exclude",
+          "description": "Mode of truncation to apply",
+          "enum": [
+            "exclude",
+            "clamp"
+          ],
+          "title": "Truncation Mode",
+          "type": "string"
+        },
         "min": {
           "default": 0,
           "description": "Minimum value of the sampled distribution",

src/Extensions.csproj

@@ -1,23 +1,25 @@
 <Project Sdk="Microsoft.NET.Sdk">
   <PropertyGroup>
-    <TargetFramework>net48</TargetFramework>
+    <!-- <OutputType>Exe</OutputType> -->
+    <!--<TargetFramework>net8.0-windows</TargetFramework>-->
+    <TargetFramework>net480</TargetFramework>
     <UseWindowsForms>true</UseWindowsForms>
-	<AllowUnsafeBlocks>true</AllowUnsafeBlocks>
+    <AllowUnsafeBlocks>true</AllowUnsafeBlocks>
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="Bonsai.Core" Version="2.9.0" />
-	<PackageReference Include="AllenNeuralDynamics.Core.Design" Version="0.3.0" />
+    <PackageReference Include="AllenNeuralDynamics.Core.Design" Version="0.3.0" />
     <PackageReference Include="OpenCV.Net" Version="3.4.2" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
-    <PackageReference Include="Bonsai.Harp" Version="3.5.0" />
+    <PackageReference Include="Bonsai.Harp" Version="3.5.2" />
     <PackageReference Include="MathNet.Numerics" Version="4.15.0" />
     <PackageReference Include="Harp.Olfactometer" Version="0.1.0-build231127" />
     <PackageReference Include="AllenNeuralDynamics.AindManipulator" Version="0.1.6" />
-	<PackageReference Include="Hexa.NET.ImGui" Version="2.2.8.4" />
-    <PackageReference Include="Hexa.NET.ImPlot" Version="2.2.8.4" />
+    <PackageReference Include="Hexa.NET.ImGui" Version="2.2.9" />
+    <PackageReference Include="Hexa.NET.ImPlot" Version="2.2.9" />
     <PackageReference Include="OpenTK.GLControl" Version="3.1.0" />
     <PackageReference Include="Bonsai.Dsp.Design" Version="2.9.0" />
-    <PackageReference Include="Hexa.NET.ImGui.Backends" Version="1.0.17" />
+    <PackageReference Include="Hexa.NET.ImGui.Backends" Version="1.0.17.4" />
     <PackageReference Include="AllenNeuralDynamics.AindBehaviorServices" Version="0.12.0" />
   </ItemGroup>
 </Project>

src/Extensions/AddRewardSite.bonsai

@@ -1,10 +1,11 @@
 <?xml version="1.0" encoding="utf-8"?>
-<WorkflowBuilder Version="2.8.2"
+<WorkflowBuilder Version="2.9.0"
                  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                  xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
                  xmlns:p1="clr-namespace:AindVrForagingDataSchema;assembly=Extensions"
                  xmlns:sys="clr-namespace:System;assembly=mscorlib"
                  xmlns:num="clr-namespace:Bonsai.Numerics;assembly=Bonsai.Numerics"
+                 xmlns:p2="clr-namespace:;assembly=Extensions"
                  xmlns="https://bonsai-rx.org/2018/workflow">
   <Workflow>
     <Nodes>
@@ -180,6 +181,16 @@
                       <Property Name="OperantLogic" />
                     </PropertyMappings>
                   </Expression>
+                  <Expression xsi:type="Combinator">
+                    <Combinator xsi:type="p2:NullDistribution" />
+                  </Expression>
+                  <Expression xsi:type="PropertyMapping">
+                    <PropertyMappings>
+                      <Property Name="Amount" />
+                      <Property Name="Probability" />
+                      <Property Name="Available" />
+                    </PropertyMappings>
+                  </Expression>
                   <Expression xsi:type="Combinator">
                     <Combinator xsi:type="p1:RewardSpecification" />
                   </Expression>
@@ -188,7 +199,7 @@
                 <Edges>
                   <Edge From="0" To="1" Label="Source1" />
                   <Edge From="1" To="2" Label="Source1" />
-                  <Edge From="2" To="16" Label="Source1" />
+                  <Edge From="2" To="18" Label="Source1" />
                   <Edge From="3" To="4" Label="Source1" />
                   <Edge From="4" To="5" Label="Source1" />
                   <Edge From="5" To="6" Label="Source1" />
@@ -201,8 +212,10 @@
                   <Edge From="12" To="13" Label="Source1" />
                   <Edge From="13" To="14" Label="Source2" />
                   <Edge From="14" To="15" Label="Source1" />
-                  <Edge From="15" To="16" Label="Source2" />
+                  <Edge From="15" To="18" Label="Source2" />
                   <Edge From="16" To="17" Label="Source1" />
+                  <Edge From="17" To="18" Label="Source3" />
+                  <Edge From="18" To="19" Label="Source1" />
                 </Edges>
               </Workflow>
             </Expression>

src/Extensions/AindBehaviorVrForaging.Generated.cs

@@ -43,8 +43,8 @@ public partial class AindBehaviorSessionModel
 
         public AindBehaviorSessionModel()
         {
-            _aindBehaviorServicesPkgVersion = "0.12.2";
-            _version = "0.12.2";
+            _aindBehaviorServicesPkgVersion = "0.12.3";
+            _version = "0.12.3";
             _experimenter = new System.Collections.Generic.List<string>();
             _experimentVersion = "";
             _allowDirtyRepo = false;
@@ -954,7 +954,7 @@ public partial class AindVrForagingRig
 
         public AindVrForagingRig()
         {
-            _aindBehaviorServicesPkgVersion = "0.12.2";
+            _aindBehaviorServicesPkgVersion = "0.12.3";
             _version = "0.6.0-rc13";
             _triggeredCameraController = new CameraControllerSpinnakerCamera();
             _harpBehavior = new HarpBehavior();
@@ -1521,7 +1521,7 @@ public partial class AindVrForagingTaskParameters
 
         public AindVrForagingTaskParameters()
         {
-            _aindBehaviorServicesPkgVersion = "0.12.2";
+            _aindBehaviorServicesPkgVersion = "0.12.3";
             _environment = new BlockStructure();
             _operationControl = new OperationControl();
         }
@@ -13113,33 +13113,66 @@ public override string ToString()
     /// Parameters for truncating a distribution to a specified range. Truncation should
     ///be applied after sampling and scaling.
     ///
+    ///The truncation_mode determines how out-of-bounds values are handled:
+    ///- "exclude": Resample until a value within [min, max] is obtained.
+    ///If after a certain number of attempts no valid value is found, it
+    ///will use the average of sampled values and pick the closest bound.
+    ///- "clamp": Clamp values to the nearest bound within [min, max].
     ///Used to constrain sampled values within minimum and maximum bounds.
     /// </summary>
     [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
-    [System.ComponentModel.DescriptionAttribute("Parameters for truncating a distribution to a specified range. Truncation should\n" +
-        "be applied after sampling and scaling.\n\nUsed to constrain sampled values within " +
-        "minimum and maximum bounds.")]
+    [System.ComponentModel.DescriptionAttribute(@"Parameters for truncating a distribution to a specified range. Truncation should
+    be applied after sampling and scaling.
+
+    The truncation_mode determines how out-of-bounds values are handled:
+    - ""exclude"": Resample until a value within [min, max] is obtained.
+    If after a certain number of attempts no valid value is found, it
+    will use the average of sampled values and pick the closest bound.
+    - ""clamp"": Clamp values to the nearest bound within [min, max].
+    Used to constrain sampled values within minimum and maximum bounds.")]
     [Bonsai.WorkflowElementCategoryAttribute(Bonsai.ElementCategory.Source)]
     [Bonsai.CombinatorAttribute(MethodName="Generate")]
     public partial class TruncationParameters
     {
 
+        private TruncationParametersTruncationMode _truncationMode;
+
         private double _min;
 
         private double _max;
 
         public TruncationParameters()
         {
+            _truncationMode = AindVrForagingDataSchema.TruncationParametersTruncationMode.Exclude;
             _min = 0D;
             _max = 0D;
         }
 
         protected TruncationParameters(TruncationParameters other)
         {
+            _truncationMode = other._truncationMode;
             _min = other._min;
             _max = other._max;
         }
 
+        /// <summary>
+        /// Mode of truncation to apply
+        /// </summary>
+        [System.Xml.Serialization.XmlIgnoreAttribute()]
+        [Newtonsoft.Json.JsonPropertyAttribute("truncation_mode")]
+        [System.ComponentModel.DescriptionAttribute("Mode of truncation to apply")]
+        public TruncationParametersTruncationMode TruncationMode
+        {
+            get
+            {
+                return _truncationMode;
+            }
+            set
+            {
+                _truncationMode = value;
+            }
+        }
+
         /// <summary>
         /// Minimum value of the sampled distribution
         /// </summary>
@@ -13186,6 +13219,7 @@ public System.IObservable<TruncationParameters> Generate<TSource>(System.IObserv
 
         protected virtual bool PrintMembers(System.Text.StringBuilder stringBuilder)
         {
+            stringBuilder.Append("TruncationMode = " + _truncationMode + ", ");
             stringBuilder.Append("Min = " + _min + ", ");
             stringBuilder.Append("Max = " + _max);
             return true;
@@ -15768,6 +15802,19 @@ public enum SpinnakerCameraColorProcessing
     }
 
 
+    [System.CodeDom.Compiler.GeneratedCodeAttribute("Bonsai.Sgen", "0.6.1.0 (Newtonsoft.Json v13.0.0.0)")]
+    [Newtonsoft.Json.JsonConverter(typeof(Newtonsoft.Json.Converters.StringEnumConverter))]
+    public enum TruncationParametersTruncationMode
+    {
+
+        [System.Runtime.Serialization.EnumMemberAttribute(Value="exclude")]
+        Exclude = 0,
+
+        [System.Runtime.Serialization.EnumMemberAttribute(Value="clamp")]
+        Clamp = 1,
+    }
+
+
     [System.CodeDom.Compiler.GeneratedCode("NJsonSchema", "10.9.0.0 (Newtonsoft.Json v13.0.0.0)")]
     [System.AttributeUsage(System.AttributeTargets.Class | System.AttributeTargets.Interface, AllowMultiple = true)]
     internal class JsonInheritanceAttribute : System.Attribute