Merge branch 'main' into docs-dev

bonsai-rx · Jul 5, 2024 · c87231a · c87231a
2 parents 11afc29 + 1f027c3
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -0,0 +1,29 @@
+name: Build
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+  workflow_call:
+
+jobs:
+  build:
+    runs-on: windows-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4.1.1
+        with:
+          submodules: true
+
+      - name: Setup .NET Core SDK
+        uses: actions/setup-dotnet@v4.0.0
+        with:
+          dotnet-version: 8.x
+
+      - name: Restore NuGet Packages
+        run: dotnet restore Bonsai.ML.sln
+
+      - name: Build Solution
+        run: dotnet build Bonsai.ML.sln -c Release
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -5,27 +5,16 @@ on:
   workflow_dispatch:
 
 jobs:
-  build:
+  build_docs:
     runs-on: windows-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4.1.1
-        with:
-          submodules: true
+      - name: Build Solution
+        uses: ./.github/workflows/build.yml
 
       - name: Setup .NET Core SDK
         uses: actions/setup-dotnet@v4.0.0
         with:
           dotnet-version: 7.x
-
-      - name: Setup MSBuild
-        uses: microsoft/setup-msbuild@v2
-
-      - name: Restore NuGet Packages
-        run: msbuild -t:restore src/Bonsai.ML.sln
-
-      - name: Build Solution
-        run: msbuild src/Bonsai.ML.sln /p:Configuration=Release
 
       - name: Setup DocFX
         run: dotnet tool restore

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,20 @@
+# Builds and runs unit tests for the examples
+name: Test Examples
+
+on:
+  workflow_dispatch:
+
+jobs:
+  test:
+    runs-on: windows-latest
+    steps:
+      - name: Setup Python 3.10
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.10
+
+      - name: Build Solution
+        uses: ./.github/workflows/build.yml
+
+      - name: Run Tests
+        run: dotnet test Bonsai.ML.sln
diff --git a/Bonsai.ML.sln b/Bonsai.ML.sln
@@ -0,0 +1,58 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio Version 17
+VisualStudioVersion = 17.0.31903.59
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "src", "src", "{12312384-8828-4786-AE19-EFCEDF968290}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Bonsai.ML", "src\Bonsai.ML\Bonsai.ML.csproj", "{AA6BE73F-1E15-49A5-AC3C-CD069035C940}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Bonsai.ML.LinearDynamicalSystems", "src\Bonsai.ML.LinearDynamicalSystems\Bonsai.ML.LinearDynamicalSystems.csproj", "{17AABD18-E275-4409-9E33-3D755B809FF6}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Bonsai.ML.Visualizers", "src\Bonsai.ML.Visualizers\Bonsai.ML.Visualizers.csproj", "{196AA5C7-AE8A-477B-B01A-B94676EC60EE}"
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "tests", "tests", "{461FE3E2-21C4-47F9-8405-DF72326AAB2B}"
+EndProject
+Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "Bonsai.ML.LinearDynamicalSystems.Tests", "tests\Bonsai.ML.LinearDynamicalSystems.Tests\Bonsai.ML.LinearDynamicalSystems.Tests.csproj", "{81DB65B3-EA65-4947-8CF1-0E777324C082}"
+EndProject
+Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{FEFDDEAC-91FD-45DA-A67A-C76D538FD484}"
+	ProjectSection(SolutionItems) = preProject
+		Directory.Build.props = Directory.Build.props
+	EndProjectSection
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{AA6BE73F-1E15-49A5-AC3C-CD069035C940}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{AA6BE73F-1E15-49A5-AC3C-CD069035C940}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{AA6BE73F-1E15-49A5-AC3C-CD069035C940}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{AA6BE73F-1E15-49A5-AC3C-CD069035C940}.Release|Any CPU.Build.0 = Release|Any CPU
+		{17AABD18-E275-4409-9E33-3D755B809FF6}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{17AABD18-E275-4409-9E33-3D755B809FF6}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{17AABD18-E275-4409-9E33-3D755B809FF6}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{17AABD18-E275-4409-9E33-3D755B809FF6}.Release|Any CPU.Build.0 = Release|Any CPU
+		{196AA5C7-AE8A-477B-B01A-B94676EC60EE}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{196AA5C7-AE8A-477B-B01A-B94676EC60EE}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{196AA5C7-AE8A-477B-B01A-B94676EC60EE}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{196AA5C7-AE8A-477B-B01A-B94676EC60EE}.Release|Any CPU.Build.0 = Release|Any CPU
+		{81DB65B3-EA65-4947-8CF1-0E777324C082}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{81DB65B3-EA65-4947-8CF1-0E777324C082}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{81DB65B3-EA65-4947-8CF1-0E777324C082}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{81DB65B3-EA65-4947-8CF1-0E777324C082}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+	GlobalSection(NestedProjects) = preSolution
+		{AA6BE73F-1E15-49A5-AC3C-CD069035C940} = {12312384-8828-4786-AE19-EFCEDF968290}
+		{17AABD18-E275-4409-9E33-3D755B809FF6} = {12312384-8828-4786-AE19-EFCEDF968290}
+		{196AA5C7-AE8A-477B-B01A-B94676EC60EE} = {12312384-8828-4786-AE19-EFCEDF968290}
+		{81DB65B3-EA65-4947-8CF1-0E777324C082} = {461FE3E2-21C4-47F9-8405-DF72326AAB2B}
+	EndGlobalSection
+	GlobalSection(ExtensibilityGlobals) = postSolution
+		SolutionGuid = {B6468F13-97CD-45E0-9E1E-C122D7F1E09F}
+	EndGlobalSection
+EndGlobal
diff --git a/src/Directory.Build.props → Directory.Build.props b/src/Directory.Build.props → Directory.Build.props
@@ -14,6 +14,7 @@
     <PackageIcon>icon.png</PackageIcon>
     <IncludeSymbols>true</IncludeSymbols>
     <RepositoryType>git</RepositoryType>
+    <VersionPrefix>0.2.0</VersionPrefix>
     <VersionSuffix></VersionSuffix>
     <LangVersion>9.0</LangVersion>
   </PropertyGroup>

diff --git a/README.md b/README.md
@@ -5,6 +5,7 @@ The Bonsai.ML project is a collection of packages with reactive infrastructure f
 * Bonsai.ML - provides core functionality across all Bonsai.ML packages.
 * Bonsai.ML.LinearDynamicalSystems - package for performing inference of linear dynamical systems. Interfaces with the [lds_python](https://github.com/joacorapela/lds_python) package.
   - *Bonsai.ML.LinearDynamicalSystems.Kinematics* - subpackage included in the LinearDynamicalSystems package which supports using the Kalman Filter to infer kinematic data.
+  - *Bonsai.ML.LinearDynamicalSystems.LinearRegression* - subpackage included in the LinearDynamicalSystems package which supports using the Kalman Filter to perform Bayesian linear regression.
 * Bonsai.ML.Visualizers - provides a set of visualizers for dynamic graphing/plotting.
 
 > [!NOTE]

diff --git a/docs/NuGet.config b/docs/NuGet.config
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="utf-8"?>
+<configuration>
+  <packageSources>
+    <add key="Build Packages" value="../src/bin/Release" />
+  </packageSources>
+</configuration>
diff --git a/docs/articles/LinearDynamicalSystems/lds-installation-guide-linux.md b/docs/articles/LinearDynamicalSystems/lds-installation-guide-linux.md
@@ -60,7 +60,7 @@ source .venv/bin/activate
 2. Install the lds_python package
 
 ```cmd
-pip install lds_python@git+https://github.com/joacorapela/lds_python@4233363320e021f77f9b3e124846ec2e49c0e741
+pip install lds_python@git+https://github.com/joacorapela/lds_python@f761c201f3df883503ecb67acef35ba846e3524c
 ```
 
 If you encounter errors during installation of the lds_python package, you will have to diagnose the issue and install the correct packge dependencies manually.

diff --git a/docs/articles/LinearDynamicalSystems/lds-installation-guide-windows.md b/docs/articles/LinearDynamicalSystems/lds-installation-guide-windows.md
@@ -65,7 +65,7 @@ Alternatively, you can use the `Setup.cmd` file to setup the bonsai environment
 2. Install the lds_python package
 
 ```cmd
-pip install lds_python@git+https://github.com/joacorapela/lds_python@4233363320e021f77f9b3e124846ec2e49c0e741
+pip install lds_python@git+https://github.com/joacorapela/lds_python@f761c201f3df883503ecb67acef35ba846e3524c
 ```
 
 If you encounter errors during installation of the lds_python package, you will have to diagnose the issue and install the correct packge dependencies manually.

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Bonsai.ML.LinearDynamicalSystems.csproj b/src/Bonsai.ML.LinearDynamicalSystems/Bonsai.ML.LinearDynamicalSystems.csproj
@@ -4,7 +4,6 @@
     <Description>A Bonsai package for implementing the Kalman Filter using python.</Description>
     <PackageTags>Bonsai Rx ML KalmanFilter LinearDynamicalSystems</PackageTags>
     <TargetFrameworks>net472;netstandard2.0</TargetFrameworks>
-    <Version>0.1.0</Version>
   </PropertyGroup>
   <ItemGroup>
     <PackageReference Include="Bonsai.Core" Version="2.8.1" />

diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/Forecast.cs b/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/Forecast.cs
@@ -0,0 +1,64 @@
+using System;
+using System.Reactive;
+using System.Reactive.Linq;
+using System.Collections.ObjectModel;
+using System.Xml.Serialization;
+using System.ComponentModel;
+using Newtonsoft.Json;
+using Python.Runtime;
+using System.Collections.Generic;
+
+namespace Bonsai.ML.LinearDynamicalSystems.Kinematics
+{
+    /// <summary>
+    /// Represents an operator for converting forecasts from a Kalman Filter Kinematics python class into a list of forecasted results.
+    /// </summary>
+    [Combinator]
+    [Description("Forecasts for a Kalman Filter Kinematics (KFK) model.")]
+    [WorkflowElementCategory(ElementCategory.Transform)]
+    public class Forecast
+    {
+        /// <summary>
+        /// Gets or sets the list of forecast results.
+        /// </summary>
+        [XmlIgnore()]
+        [JsonProperty("forecasts")]
+        [Description("The list of forecast results.")]
+        public List<ForecastResult> ForecastResults { get; private set; }
+
+        /// <summary>
+        /// Converts a PyObject representing a Kalman Filter forecast into a Forecast class representing a list of forecasted results.
+        /// </summary>
+        public IObservable<Forecast> Process(IObservable<PyObject> source)
+        {
+            return Observable.Select(source, pyObject => {
+
+                dynamic pyObj = pyObject;
+
+                var xs = (PyObject[])pyObj[0];
+                var Ps = (PyObject[])pyObj[1];
+                var dts = (double[])pyObj[2];
+
+                var results = new List<ForecastResult>();
+
+                for (int i = 0; i < xs.Length; i++)
+                {
+                    double[,] x = (double[,])PythonHelper.ConvertPythonObjectToCSharp(xs[i]);
+                    double[,] P = (double[,])PythonHelper.ConvertPythonObjectToCSharp(Ps[i]);
+                    var state = new State {X=x, P=P};
+                    var kinematicState = new KinematicState(state);
+
+                    var dt = dts[i];
+                    var timestep = TimeSpan.FromSeconds(dt);
+
+                    results.Add(new ForecastResult(kinematicState, timestep));
+                }
+
+                return new Forecast {
+                    ForecastResults = results
+                };
+            });
+        }
+    }
+}
+
diff --git a/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/ForecastResult.cs b/src/Bonsai.ML.LinearDynamicalSystems/Kinematics/ForecastResult.cs
@@ -0,0 +1,36 @@
+using System;
+using Newtonsoft.Json;
+using Python.Runtime;
+using System.Collections.Generic;
+using System.Xml.Serialization;
+using System.ComponentModel;
+
+namespace Bonsai.ML.LinearDynamicalSystems.Kinematics
+{
+    /// <summary>
+    /// Forecast result representing a collection of forecasted states at future timesteps
+    /// </summary>
+    public class ForecastResult
+    {
+        /// <summary>
+        /// Gets or privately sets the kinematic state of the forecasted result.
+        /// </summary>
+        public KinematicState KinematicState { get; private set; }
+
+        /// <summary>
+        /// Gets or privately sets the future time step of the forecasted result.
+        /// </summary>
+        public TimeSpan Timestep { get; private set; }
+
+        /// <summary>
+        /// Initializes a new instance of the <see cref="ForecastResult"/> class.
+        /// </summary>
+        /// <param name="kinematicState">The kinematic state of the forecasted result.</param>
+        /// <param name="timestep">The future timestep of the forecasted result.</param>
+        public ForecastResult(KinematicState kinematicState, TimeSpan timestep)
+        {
+            KinematicState = kinematicState;
+            Timestep = timestep;
+        }
+    }
+}