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Update package names and namespaces in example workflows #39

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6 changes: 3 additions & 3 deletions examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Bonsai.config
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Expand Up @@ -7,7 +7,7 @@
<Package id="Bonsai.Editor" version="2.9.0" />
<Package id="Bonsai.ML" version="0.4.1" />
<Package id="Bonsai.ML.Data" version="0.4.1" />
<Package id="Bonsai.ML.HiddenMarkovModels" version="0.4.1" />
<Package id="Bonsai.ML.Hmm.Python" version="0.4.1" />
<Package id="Bonsai.ML.Python" version="0.4.1" />
<Package id="Bonsai.Scripting.Expressions" version="2.9.0" />
<Package id="Bonsai.Scripting.Python" version="0.3.0" />
Expand Down Expand Up @@ -41,7 +41,7 @@
<AssemblyReference assemblyName="Bonsai.Editor" />
<AssemblyReference assemblyName="Bonsai.ML" />
<AssemblyReference assemblyName="Bonsai.ML.Data" />
<AssemblyReference assemblyName="Bonsai.ML.HiddenMarkovModels" />
<AssemblyReference assemblyName="Bonsai.ML.Hmm.Python" />
<AssemblyReference assemblyName="Bonsai.ML.Python" />
<AssemblyReference assemblyName="Bonsai.Scripting.Expressions" />
<AssemblyReference assemblyName="Bonsai.Scripting.Python" />
Expand All @@ -54,7 +54,7 @@
<AssemblyLocation assemblyName="Bonsai.Editor" processorArchitecture="MSIL" location="Packages/Bonsai.Editor.2.9.0/lib/net472/Bonsai.Editor.dll" />
<AssemblyLocation assemblyName="Bonsai.ML" processorArchitecture="MSIL" location="Packages/Bonsai.ML.0.4.1/lib/net472/Bonsai.ML.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Data" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Data.0.4.1/lib/net472/Bonsai.ML.Data.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.HiddenMarkovModels" processorArchitecture="MSIL" location="Packages/Bonsai.ML.HiddenMarkovModels.0.4.1/lib/net472/Bonsai.ML.HiddenMarkovModels.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Hmm.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Hmm.Python.0.4.1/lib/net472/Bonsai.ML.Hmm.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Python.0.4.1/lib/net472/Bonsai.ML.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.Scripting.Expressions" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.2.9.0/lib/net472/Bonsai.Scripting.Expressions.dll" />
<AssemblyLocation assemblyName="Bonsai.Scripting.Python" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Python.0.3.0/lib/net472/Bonsai.Scripting.Python.dll" />
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6 changes: 3 additions & 3 deletions examples/HiddenMarkovModels/ExtendedModelConfiguration/LoadModelConfig.bonsai
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Expand Up @@ -4,7 +4,7 @@
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System"
xmlns:p1="clr-namespace:Bonsai.ML.HiddenMarkovModels;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns:p1="clr-namespace:Bonsai.ML.Hmm.Python;assembly=Bonsai.ML.Hmm.Python"
xmlns="https://bonsai-rx.org/2018/workflow">
<Workflow>
<Nodes>
Expand All @@ -14,7 +14,7 @@
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:GetRuntime" />
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:LoadHMMModule.bonsai" />
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:LoadHMMModule.bonsai" />
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:GetRuntime" />
</Expression>
Expand Down Expand Up @@ -49,7 +49,7 @@
<Property Name="Dimensions" Selector="Dimensions" />
</PropertyMappings>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:CreateHMM.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:CreateHMM.bonsai">
<Name>hmm</Name>
<NumStates>2</NumStates>
<Dimensions>2</Dimensions>
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10 changes: 5 additions & 5 deletions examples/HiddenMarkovModels/ExtendedModelConfiguration/SaveModelConfig.bonsai
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Expand Up @@ -2,9 +2,9 @@
<WorkflowBuilder Version="2.9.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xmlns:py="clr-namespace:Bonsai.Scripting.Python;assembly=Bonsai.Scripting.Python"
xmlns:p1="clr-namespace:Bonsai.ML.HiddenMarkovModels.Observations;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns:p2="clr-namespace:Bonsai.ML.HiddenMarkovModels.Transitions;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns:p3="clr-namespace:Bonsai.ML.HiddenMarkovModels;assembly=Bonsai.ML.HiddenMarkovModels"
xmlns:p1="clr-namespace:Bonsai.ML.Hmm.Python.Observations;assembly=Bonsai.ML.Hmm.Python"
xmlns:p2="clr-namespace:Bonsai.ML.Hmm.Python.Transitions;assembly=Bonsai.ML.Hmm.Python"
xmlns:p3="clr-namespace:Bonsai.ML.Hmm.Python;assembly=Bonsai.ML.Hmm.Python"
xmlns:io="clr-namespace:Bonsai.IO;assembly=Bonsai.System"
xmlns:rx="clr-namespace:Bonsai.Reactive;assembly=Bonsai.Core"
xmlns="https://bonsai-rx.org/2018/workflow">
Expand All @@ -16,7 +16,7 @@
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:GetRuntime" />
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:LoadHMMModule.bonsai" />
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:LoadHMMModule.bonsai" />
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:GetRuntime" />
</Expression>
Expand Down Expand Up @@ -64,7 +64,7 @@
<Property Name="NumStates" />
<Property Name="Dimensions" />
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:CreateHMM.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:CreateHMM.bonsai">
<Name>hmm</Name>
<NumStates>2</NumStates>
<Dimensions>2</Dimensions>
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24 changes: 12 additions & 12 deletions examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Bonsai.config
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Expand Up @@ -11,10 +11,10 @@
<Package id="Bonsai.ML" version="0.4.1" />
<Package id="Bonsai.ML.Data" version="0.4.1" />
<Package id="Bonsai.ML.Design" version="0.4.1" />
<Package id="Bonsai.ML.HiddenMarkovModels" version="0.4.1" />
<Package id="Bonsai.ML.HiddenMarkovModels.Design" version="0.4.1" />
<Package id="Bonsai.ML.LinearDynamicalSystems" version="0.4.1" />
<Package id="Bonsai.ML.LinearDynamicalSystems.Design" version="0.4.1" />
<Package id="Bonsai.ML.Hmm.Python" version="0.4.1" />
<Package id="Bonsai.ML.Hmm.Python.Design" version="0.4.1" />
<Package id="Bonsai.ML.Lds.Python" version="0.4.1" />
<Package id="Bonsai.ML.Lds.Python.Design" version="0.4.1" />
<Package id="Bonsai.ML.Python" version="0.4.1" />
<Package id="Bonsai.Scripting.Expressions" version="2.9.0" />
<Package id="Bonsai.Scripting.Python" version="0.3.0" />
Expand Down Expand Up @@ -61,10 +61,10 @@
<AssemblyReference assemblyName="Bonsai.ML" />
<AssemblyReference assemblyName="Bonsai.ML.Data" />
<AssemblyReference assemblyName="Bonsai.ML.Design" />
<AssemblyReference assemblyName="Bonsai.ML.HiddenMarkovModels" />
<AssemblyReference assemblyName="Bonsai.ML.HiddenMarkovModels.Design" />
<AssemblyReference assemblyName="Bonsai.ML.LinearDynamicalSystems" />
<AssemblyReference assemblyName="Bonsai.ML.LinearDynamicalSystems.Design" />
<AssemblyReference assemblyName="Bonsai.ML.Hmm.Python" />
<AssemblyReference assemblyName="Bonsai.ML.Hmm.Python.Design" />
<AssemblyReference assemblyName="Bonsai.ML.Lds.Python" />
<AssemblyReference assemblyName="Bonsai.ML.Lds.Python.Design" />
<AssemblyReference assemblyName="Bonsai.ML.Python" />
<AssemblyReference assemblyName="Bonsai.Scripting.Expressions" />
<AssemblyReference assemblyName="Bonsai.Scripting.Python" />
Expand All @@ -83,10 +83,10 @@
<AssemblyLocation assemblyName="Bonsai.ML" processorArchitecture="MSIL" location="Packages/Bonsai.ML.0.4.1/lib/net472/Bonsai.ML.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Data" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Data.0.4.1/lib/net472/Bonsai.ML.Data.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Design.0.4.1/lib/net472/Bonsai.ML.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.HiddenMarkovModels" processorArchitecture="MSIL" location="Packages/Bonsai.ML.HiddenMarkovModels.0.4.1/lib/net472/Bonsai.ML.HiddenMarkovModels.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.HiddenMarkovModels.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.HiddenMarkovModels.Design.0.4.1/lib/net472/Bonsai.ML.HiddenMarkovModels.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.LinearDynamicalSystems" processorArchitecture="MSIL" location="Packages/Bonsai.ML.LinearDynamicalSystems.0.4.1/lib/net472/Bonsai.ML.LinearDynamicalSystems.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.LinearDynamicalSystems.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.LinearDynamicalSystems.Design.0.4.1/lib/net472/Bonsai.ML.LinearDynamicalSystems.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Hmm.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Hmm.Python.0.4.1/lib/net472/Bonsai.ML.Hmm.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Hmm.Python.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Hmm.Python.Design.0.4.1/lib/net472/Bonsai.ML.Hmm.Python.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Lds.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Lds.Python.0.4.1/lib/net472/Bonsai.ML.Lds.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Lds.Python.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Lds.Python.Design.0.4.1/lib/net472/Bonsai.ML.Lds.Python.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Python.0.4.1/lib/net472/Bonsai.ML.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.Scripting.Expressions" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Expressions.2.9.0/lib/net472/Bonsai.Scripting.Expressions.dll" />
<AssemblyLocation assemblyName="Bonsai.Scripting.Python" processorArchitecture="MSIL" location="Packages/Bonsai.Scripting.Python.0.3.0/lib/net472/Bonsai.Scripting.Python.dll" />
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18 changes: 9 additions & 9 deletions ...HiddenMarkovModels/InferringBehavioralStateFromKinematics/InferringBehavioralState.bonsai
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Expand Up @@ -19,8 +19,8 @@
<Expression xsi:type="Combinator">
<Combinator xsi:type="py:GetRuntime" />
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:LoadHMMModule.bonsai" />
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.LinearDynamicalSystems:LoadLDSModule.bonsai" />
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:LoadHMMModule.bonsai" />
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Lds.Python:LoadLDSModule.bonsai" />
<Expression xsi:type="GroupWorkflow">
<Name>MouseTracking</Name>
<Workflow>
Expand Down Expand Up @@ -307,7 +307,7 @@
</Edges>
</Workflow>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.LinearDynamicalSystems:Kinematics.CreateObservation2D.bonsai" />
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Lds.Python:Kinematics.CreateObservation2D.bonsai" />
<Expression xsi:type="rx:BehaviorSubject">
<Name>Centroid</Name>
</Expression>
Expand All @@ -325,7 +325,7 @@
<Property Name="Pos_y0" Selector="Y" />
</PropertyMappings>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.LinearDynamicalSystems:Kinematics.CreateKFModel.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Lds.Python:Kinematics.CreateKFModel.bonsai">
<Name>KFmodel</Name>
<Fps>60</Fps>
<Pos_x0>668.08917236328125</Pos_x0>
Expand All @@ -342,7 +342,7 @@
<Expression xsi:type="rx:BehaviorSubject">
<Name>KFParameters</Name>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:CreateHMM.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:CreateHMM.bonsai">
<Name>hmm</Name>
<NumStates>6</NumStates>
<Dimensions>2</Dimensions>
Expand All @@ -359,7 +359,7 @@
<Expression xsi:type="SubscribeSubject">
<Name>Centroid</Name>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.LinearDynamicalSystems:Kinematics.PerformInference.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Lds.Python:Kinematics.PerformInference.bonsai">
<Name>KFmodel</Name>
</Expression>
<Expression xsi:type="WorkflowOutput" />
Expand Down Expand Up @@ -434,7 +434,7 @@
<rx:Count>1</rx:Count>
</Combinator>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:InferState.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:InferState.bonsai">
<Name>hmm</Name>
</Expression>
<Expression xsi:type="WorkflowOutput" />
Expand Down Expand Up @@ -464,7 +464,7 @@
<Expression xsi:type="SubscribeSubject">
<Name>HMMObservation</Name>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:RunFitAsync.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:RunFitAsync.bonsai">
<BatchSize>1000</BatchSize>
<Name>hmm</Name>
<NumIterations>50</NumIterations>
Expand All @@ -473,7 +473,7 @@
<TransitionParams>true</TransitionParams>
<ObservationParams>true</ObservationParams>
</Expression>
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.HiddenMarkovModels:CheckFitFinished.bonsai">
<Expression xsi:type="IncludeWorkflow" Path="Bonsai.ML.Hmm.Python:CheckFitFinished.bonsai">
<Name>hmm</Name>
<TimerFrequency>PT1S</TimerFrequency>
</Expression>
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2 changes: 1 addition & 1 deletion examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md
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Expand Up @@ -27,7 +27,7 @@ If you used the bootstrapping method, you don't have to worry about the package
* Bonsai - Numerics v0.9.0

> [!WARNING]
> This example builds on the [LDS Kinematics Foraging Mouse example](../../LinearDynamicalSystems/Kinematics/ForagingMouse/README.md) and requires both the *Bonsai.ML.LinearDynamicalSystems* package and the *Bonsai.ML.HiddenMarkovModels* package. See the installation guide to ensure both packages are installed and working correctly.
> This example builds on the [LDS Kinematics Foraging Mouse example](../../LinearDynamicalSystems/Kinematics/ForagingMouse/README.md) and requires both the *Bonsai.ML.Lds.Python* package and the *Bonsai.ML.Hmm.Python* package. See the installation guide to ensure both packages are installed and working correctly.

### Workflow

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18 changes: 9 additions & 9 deletions examples/HiddenMarkovModels/SimulatedData/.bonsai/Bonsai.config
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Expand Up @@ -12,9 +12,9 @@
<Package id="Bonsai.ML" version="0.4.1" />
<Package id="Bonsai.ML.Data" version="0.4.1" />
<Package id="Bonsai.ML.Design" version="0.4.1" />
<Package id="Bonsai.ML.HiddenMarkovModels" version="0.4.1" />
<Package id="Bonsai.ML.HiddenMarkovModels.Design" version="0.4.1" />
<Package id="Bonsai.ML.LinearDynamicalSystems" version="0.4.1" />
<Package id="Bonsai.ML.Hmm.Python" version="0.4.1" />
<Package id="Bonsai.ML.Hmm.Python.Design" version="0.4.1" />
<Package id="Bonsai.ML.Lds.Python" version="0.4.1" />
<Package id="Bonsai.ML.Python" version="0.4.1" />
<Package id="Bonsai.Numerics" version="0.10.0" />
<Package id="Bonsai.Scripting.Expressions" version="2.9.0" />
Expand Down Expand Up @@ -63,9 +63,9 @@
<AssemblyReference assemblyName="Bonsai.ML" />
<AssemblyReference assemblyName="Bonsai.ML.Data" />
<AssemblyReference assemblyName="Bonsai.ML.Design" />
<AssemblyReference assemblyName="Bonsai.ML.HiddenMarkovModels" />
<AssemblyReference assemblyName="Bonsai.ML.HiddenMarkovModels.Design" />
<AssemblyReference assemblyName="Bonsai.ML.LinearDynamicalSystems" />
<AssemblyReference assemblyName="Bonsai.ML.Hmm.Python" />
<AssemblyReference assemblyName="Bonsai.ML.Hmm.Python.Design" />
<AssemblyReference assemblyName="Bonsai.ML.Lds.Python" />
<AssemblyReference assemblyName="Bonsai.ML.Python" />
<AssemblyReference assemblyName="Bonsai.Numerics" />
<AssemblyReference assemblyName="Bonsai.Scripting.Expressions" />
Expand All @@ -86,9 +86,9 @@
<AssemblyLocation assemblyName="Bonsai.ML" processorArchitecture="MSIL" location="Packages/Bonsai.ML.0.4.1/lib/net472/Bonsai.ML.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Data" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Data.0.4.1/lib/net472/Bonsai.ML.Data.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Design.0.4.1/lib/net472/Bonsai.ML.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.HiddenMarkovModels" processorArchitecture="MSIL" location="Packages/Bonsai.ML.HiddenMarkovModels.0.4.1/lib/net472/Bonsai.ML.HiddenMarkovModels.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.HiddenMarkovModels.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.HiddenMarkovModels.Design.0.4.1/lib/net472/Bonsai.ML.HiddenMarkovModels.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.LinearDynamicalSystems" processorArchitecture="MSIL" location="Packages/Bonsai.ML.LinearDynamicalSystems.0.4.1/lib/net472/Bonsai.ML.LinearDynamicalSystems.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Hmm.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Hmm.Python.0.4.1/lib/net472/Bonsai.ML.Hmm.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Hmm.Python.Design" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Hmm.Python.Design.0.4.1/lib/net472/Bonsai.ML.Hmm.Python.Design.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Lds.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Lds.Python.0.4.1/lib/net472/Bonsai.ML.Lds.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.ML.Python" processorArchitecture="MSIL" location="Packages/Bonsai.ML.Python.0.4.1/lib/net472/Bonsai.ML.Python.dll" />
<AssemblyLocation assemblyName="Bonsai.Numerics" processorArchitecture="MSIL" location="Packages/Bonsai.Numerics.0.10.0/lib/net462/Bonsai.Numerics.dll" />
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