Skip to content

Commit

Permalink
Merge pull request #28 from bonsai-rx/docs-update
Browse files Browse the repository at this point in the history 
Update documentation examples
  • Loading branch information
@glopesdev
glopesdev authored Oct 3, 2024
2 parents 1c1846c + 1f9cb89 commit 02c521b
Show file tree
Hide file tree
Showing 5 changed files with 42 additions and 30 deletions.
60 changes: 35 additions & 25 deletions .bonsai/Bonsai.config
View file
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>
<Package id="Bonsai" version="2.8.2" />
<Package id="Bonsai.Core" version="2.8.1" />
<Package id="Bonsai.Design" version="2.8.0" />
<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" />
<Package id="SvgNet" version="3.3.3" />
<Package id="System.Buffers" version="4.5.1" />
<Package id="System.Memory" version="4.5.5" />
<Package id="System.Numerics.Vectors" version="4.5.0" />
<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" />
<AssemblyLocation assemblyName="Bonsai.Editor" processorArchitecture="MSIL" location="Packages\Bonsai.Editor.2.8.1\lib\net472\Bonsai.Editor.dll" />
<AssemblyLocation assemblyName="Markdig" processorArchitecture="MSIL" location="Packages\Markdig.0.18.1\lib\net40\Markdig.dll" />
<AssemblyLocation assemblyName="Microsoft.Web.WebView2.Core" processorArchitecture="MSIL" location="Packages\Microsoft.Web.WebView2.1.0.1823.32\lib\net45\Microsoft.Web.WebView2.Core.dll" />
<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" />
<AssemblyLocation assemblyName="ScintillaNET" processorArchitecture="MSIL" location="Packages\jacobslusser.ScintillaNET.3.6.3\lib\net40\ScintillaNET.dll" />
<AssemblyLocation assemblyName="SVG" processorArchitecture="MSIL" location="Packages\SvgNet.3.3.3\lib\net462\SVG.dll" />
<AssemblyLocation assemblyName="System.Reactive.Core" processorArchitecture="MSIL" location="Packages\Rx-Core.2.2.5\lib\net45\System.Reactive.Core.dll" />
<AssemblyLocation assemblyName="System.Reactive.Interfaces" processorArchitecture="MSIL" location="Packages\Rx-Interfaces.2.2.5\lib\net45\System.Reactive.Interfaces.dll" />
<AssemblyLocation assemblyName="System.Reactive.Linq" processorArchitecture="MSIL" location="Packages\Rx-Linq.2.2.5\lib\net45\System.Reactive.Linq.dll" />
<AssemblyLocation assemblyName="System.Reactive.PlatformServices" processorArchitecture="MSIL" location="Packages\Rx-PlatformServices.2.2.5\lib\net45\System.Reactive.PlatformServices.dll" />
<AssemblyLocation assemblyName="YamlDotNet" processorArchitecture="MSIL" location="Packages\YamlDotNet.13.1.1\lib\net47\YamlDotNet.dll" />
<AssemblyLocation assemblyName="Bonsai" processorArchitecture="MSIL" location="Packages/Bonsai.2.8.5/lib/net48/Bonsai.exe" />
<AssemblyLocation assemblyName="Bonsai.Core" processorArchitecture="MSIL" location="Packages/Bonsai.Core.2.8.5/lib/net462/Bonsai.Core.dll" />
<AssemblyLocation assemblyName="Bonsai.Design" processorArchitecture="MSIL" location="Packages/Bonsai.Design.2.8.5/lib/net462/Bonsai.Design.dll" />
<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" />
<AssemblyLocation assemblyName="Microsoft.Web.WebView2.Core" processorArchitecture="MSIL" location="Packages/Microsoft.Web.WebView2.1.0.1823.32/lib/net45/Microsoft.Web.WebView2.Core.dll" />
<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" />
<AssemblyLocation assemblyName="ScintillaNET" processorArchitecture="MSIL" location="Packages/jacobslusser.ScintillaNET.3.6.3/lib/net40/ScintillaNET.dll" />
<AssemblyLocation assemblyName="SVG" processorArchitecture="MSIL" location="Packages/SvgNet.3.3.3/lib/net462/SVG.dll" />
<AssemblyLocation assemblyName="System.Buffers" processorArchitecture="MSIL" location="Packages/System.Buffers.4.5.1/lib/net461/System.Buffers.dll" />
<AssemblyLocation assemblyName="System.Memory" processorArchitecture="MSIL" location="Packages/System.Memory.4.5.5/lib/net461/System.Memory.dll" />
<AssemblyLocation assemblyName="System.Numerics.Vectors" processorArchitecture="MSIL" location="Packages/System.Numerics.Vectors.4.5.0/lib/net46/System.Numerics.Vectors.dll" />
<AssemblyLocation assemblyName="System.Reactive.Core" processorArchitecture="MSIL" location="Packages/Rx-Core.2.2.5/lib/net45/System.Reactive.Core.dll" />
<AssemblyLocation assemblyName="System.Reactive.Interfaces" processorArchitecture="MSIL" location="Packages/Rx-Interfaces.2.2.5/lib/net45/System.Reactive.Interfaces.dll" />
<AssemblyLocation assemblyName="System.Reactive.Linq" processorArchitecture="MSIL" location="Packages/Rx-Linq.2.2.5/lib/net45/System.Reactive.Linq.dll" />
<AssemblyLocation assemblyName="System.Reactive.PlatformServices" processorArchitecture="MSIL" location="Packages/Rx-PlatformServices.2.2.5/lib/net45/System.Reactive.PlatformServices.dll" />
<AssemblyLocation assemblyName="System.Resources.Extensions" processorArchitecture="MSIL" location="Packages/System.Resources.Extensions.8.0.0/lib/net462/System.Resources.Extensions.dll" />
<AssemblyLocation assemblyName="System.Runtime.CompilerServices.Unsafe" processorArchitecture="MSIL" location="Packages/System.Runtime.CompilerServices.Unsafe.4.5.3/lib/net461/System.Runtime.CompilerServices.Unsafe.dll" />
<AssemblyLocation assemblyName="YamlDotNet" processorArchitecture="MSIL" location="Packages/YamlDotNet.13.1.1/lib/net47/YamlDotNet.dll" />
</AssemblyLocations>
<LibraryFolders>
<LibraryFolder path="Packages\Microsoft.Web.WebView2.1.0.1823.32\runtimes\win-arm64\native" platform="arm64" />
<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" />
<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" />
<LibraryFolder path="Packages/Microsoft.Web.WebView2.1.0.1823.32/runtimes/win-arm64/native" platform="arm64" />
<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" />
<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
View file
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
}
}
}
2 changes: 1 addition & 1 deletion docs/bonsai
Submodule bonsai updated 3 files
+3 −2 modules/Export-Image.ps1
+11 −3 modules/Export-Tools.psm1
+5,950 −0 modules/svg11.dtd
3 changes: 2 additions & 1 deletion docs/build.ps1
View file
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

0 comments on commit 02c521b

Please sign in to comment.