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Update documentation examples #28

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60 changes: 35 additions & 25 deletions .bonsai/Bonsai.config
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
<?xml version="1.0" encoding="utf-8"?>
<PackageConfiguration xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
<Packages>
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<Package id="Bonsai.Core" version="2.8.1" />
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<Package id="Bonsai.Editor" version="2.8.1" />
<Package id="Bonsai" version="2.8.5" />
<Package id="Bonsai.Core" version="2.8.5" />
<Package id="Bonsai.Design" version="2.8.5" />
<Package id="Bonsai.Editor" version="2.8.5" />
<Package id="jacobslusser.ScintillaNET" version="3.6.3" />
<Package id="Markdig" version="0.18.1" />
<Package id="Microsoft.Web.WebView2" version="1.0.1823.32" />
Expand All @@ -13,6 +13,11 @@
<Package id="Rx-Linq" version="2.2.5" />
<Package id="Rx-PlatformServices" version="2.2.5" />
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<Package id="System.Resources.Extensions" version="8.0.0" />
<Package id="System.Runtime.CompilerServices.Unsafe" version="4.5.3" />
<Package id="YamlDotNet" version="13.1.1" />
</Packages>
<AssemblyReferences>
Expand All @@ -22,28 +27,33 @@
<AssemblyReference assemblyName="Bonsai.Editor" />
</AssemblyReferences>
<AssemblyLocations>
<AssemblyLocation assemblyName="Bonsai" processorArchitecture="MSIL" location="Packages\Bonsai.2.8.2\lib\net48\Bonsai.exe" />
<AssemblyLocation assemblyName="Bonsai.Core" processorArchitecture="MSIL" location="Packages\Bonsai.Core.2.8.1\lib\net462\Bonsai.Core.dll" />
<AssemblyLocation assemblyName="Bonsai.Design" processorArchitecture="MSIL" location="Packages\Bonsai.Design.2.8.0\lib\net462\Bonsai.Design.dll" />
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<AssemblyLocation assemblyName="Bonsai.Editor" processorArchitecture="MSIL" location="Packages/Bonsai.Editor.2.8.5/lib/net472/Bonsai.Editor.dll" />
<AssemblyLocation assemblyName="Markdig" processorArchitecture="MSIL" location="Packages/Markdig.0.18.1/lib/net40/Markdig.dll" />
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<AssemblyLocation assemblyName="Microsoft.Web.WebView2.WinForms" processorArchitecture="MSIL" location="Packages/Microsoft.Web.WebView2.1.0.1823.32/lib/net45/Microsoft.Web.WebView2.WinForms.dll" />
<AssemblyLocation assemblyName="Microsoft.Web.WebView2.Wpf" processorArchitecture="MSIL" location="Packages/Microsoft.Web.WebView2.1.0.1823.32/lib/net45/Microsoft.Web.WebView2.Wpf.dll" />
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<LibraryFolders>
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<LibraryFolder path="Packages\Microsoft.Web.WebView2.1.0.1823.32\runtimes\win-arm64\native_uap" platform="arm64" />
<LibraryFolder path="Packages\Microsoft.Web.WebView2.1.0.1823.32\runtimes\win-x64\native" platform="x64" />
<LibraryFolder path="Packages\Microsoft.Web.WebView2.1.0.1823.32\runtimes\win-x64\native_uap" platform="x64" />
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<LibraryFolder path="Packages\Microsoft.Web.WebView2.1.0.1823.32\runtimes\win-x86\native_uap" platform="x86" />
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<LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-x86/native" platform="x86" />
<LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-x86/native_uap" platform="x86" />
</LibraryFolders>
</PackageConfiguration>
5 changes: 3 additions & 2 deletions .config/dotnet-tools.json
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,11 @@
"isRoot": true,
"tools": {
"docfx": {
"version": "2.75.3",
"version": "2.77.0",
"commands": [
"docfx"
]
],
"rollForward": false
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}
}
}
2 changes: 1 addition & 1 deletion docs/bonsai
3 changes: 2 additions & 1 deletion docs/build.ps1
Original file line number Diff line number Diff line change
@@ -1,4 +1,5 @@
.\bonsai\modules\Export-Image.ps1 "..\src\Bonsai.ML.Visualizers\bin\Release\net472"
$projectFolders = Get-ChildItem "..\src\Bonsai.ML.*\bin\Release\net472" -Directory | Select-Object -Expand FullName
.\bonsai\modules\Export-Image.ps1 $projectFolders
$exampleEnvironments = Get-ChildItem -Directory -Recurse -Filter ".bonsai" -Path "examples"
foreach ($environment in $exampleEnvironments)
{
Expand Down
2 changes: 1 addition & 1 deletion docs/examples
Submodule examples updated 63 files
+8 −1 docs/toc.yml
+88 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Bonsai.config
+8 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/NuGet.config
+21 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Setup.ps1
+41 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/Setup.sh
+15 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/activate
+8 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/deactivate
+58 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/.bonsai/run
+183 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/LoadModelConfig.bonsai
+116 −0 examples/HiddenMarkovModels/ExtendedModelConfiguration/SaveModelConfig.bonsai
+131 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Bonsai.config
+8 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/NuGet.config
+21 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Setup.ps1
+41 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/Setup.sh
+15 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/activate
+8 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/deactivate
+58 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/.bonsai/run
+ examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/InferredBehavioralState.gif
+586 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/InferringBehavioralState.bonsai
+47 −0 examples/HiddenMarkovModels/InferringBehavioralStateFromKinematics/README.md
+129 −0 examples/HiddenMarkovModels/README.md
+134 −0 examples/HiddenMarkovModels/SimulatedData/.bonsai/Bonsai.config
+8 −0 examples/HiddenMarkovModels/SimulatedData/.bonsai/NuGet.config
+21 −0 examples/HiddenMarkovModels/SimulatedData/.bonsai/Setup.ps1
+41 −0 examples/HiddenMarkovModels/SimulatedData/.bonsai/Setup.sh
+14 −0 examples/HiddenMarkovModels/SimulatedData/.bonsai/activate
+8 −0 examples/HiddenMarkovModels/SimulatedData/.bonsai/deactivate
+42 −0 examples/HiddenMarkovModels/SimulatedData/.bonsai/run
+37 −0 examples/HiddenMarkovModels/SimulatedData/README.md
+395 −0 examples/HiddenMarkovModels/SimulatedData/SimulatedData.bonsai
+ examples/HiddenMarkovModels/SimulatedData/Simulation.gif
+84 −61 examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/Bonsai.config
+32 −16 examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/Setup.sh
+1 −0 examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/activate
+21 −10 examples/LinearDynamicalSystems/Kinematics/ForagingMouse/.bonsai/run
+18 −54 examples/LinearDynamicalSystems/Kinematics/ForagingMouse/ForagingMouse.bonsai
+87 −65 examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/Bonsai.config
+32 −16 examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/Setup.sh
+1 −0 examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/activate
+21 −10 examples/LinearDynamicalSystems/Kinematics/ForecastingForagingMouse/.bonsai/run
+87 −63 examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/Bonsai.config
+32 −16 examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/Setup.sh
+1 −0 examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/activate
+21 −10 examples/LinearDynamicalSystems/Kinematics/ModelOptimizationForagingMouse/.bonsai/run
+87 −65 examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/Bonsai.config
+32 −16 examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/Setup.sh
+1 −0 examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/activate
+21 −10 examples/LinearDynamicalSystems/Kinematics/SimulatedData/.bonsai/run
+24 −60 examples/LinearDynamicalSystems/Kinematics/SimulatedData/Simulation.bonsai
+86 −62 examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/Bonsai.config
+32 −16 examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/Setup.sh
+1 −0 examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/activate
+21 −10 examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/.bonsai/run
+14 −50 examples/LinearDynamicalSystems/Kinematics/ZebrafishCentroidTracking/ZebrafishTracking.bonsai
+72 −48 examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/Bonsai.config
+32 −16 examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/Setup.sh
+1 −0 examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/activate
+21 −10 examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/.bonsai/run
+3 −3 examples/LinearDynamicalSystems/LinearRegression/ReceptiveFieldSimpleCell/ReceptiveFieldSimpleCell.bonsai
+88 −66 examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/Bonsai.config
+32 −16 examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/Setup.sh
+1 −0 examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/activate
+21 −10 examples/LinearDynamicalSystems/LinearRegression/SimulatedData/.bonsai/run