Merge pull request #15 from bonsai-rx/automated-tests

Add support for unit testing

.github/workflows/build.yml

@@ -17,11 +17,13 @@ jobs:
         with:
           submodules: true
 
-      - name: Setup MSBuild
-        uses: microsoft/setup-msbuild@v2
+      - name: Setup .NET Core SDK
+        uses: actions/setup-dotnet@v4.0.0
+        with:
+          dotnet-version: 8.x
 
       - name: Restore NuGet Packages
-        run: msbuild -t:restore src/Bonsai.ML.sln
+        run: dotnet restore Bonsai.ML.sln
 
       - name: Build Solution
-        run: msbuild src/Bonsai.ML.sln /p:Configuration=Release
+        run: dotnet build Bonsai.ML.sln -c Release

.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

Bonsai.ML.sln

@@ -0,0 +1,50 @@
+
+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("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Bonsai.ML", "src\Bonsai.ML\Bonsai.ML.csproj", "{AA6BE73F-1E15-49A5-AC3C-CD069035C940}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Bonsai.ML.LinearDynamicalSystems", "src\Bonsai.ML.LinearDynamicalSystems\Bonsai.ML.LinearDynamicalSystems.csproj", "{17AABD18-E275-4409-9E33-3D755B809FF6}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "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("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "Bonsai.ML.LinearDynamicalSystems.Tests", "tests\Bonsai.ML.LinearDynamicalSystems.Tests\Bonsai.ML.LinearDynamicalSystems.Tests.csproj", "{81DB65B3-EA65-4947-8CF1-0E777324C082}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	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(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
+EndGlobal

tests/Bonsai.ML.LinearDynamicalSystems.Tests/Bonsai.ML.LinearDynamicalSystems.Tests.csproj

@@ -0,0 +1,29 @@
+<Project Sdk="Microsoft.NET.Sdk">
+  <PropertyGroup>
+    <EnableUnsafeBinaryFormatterSerialization>true</EnableUnsafeBinaryFormatterSerialization>
+    <TargetFramework>net8.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+    <IsPackable>false</IsPackable>
+    <IsTestProject>true</IsTestProject>
+    <LangVersion>preview</LangVersion>
+  </PropertyGroup>
+  <ItemGroup>
+    <PackageReference Include="Bonsai.System" Version="2.8.1" />
+    <PackageReference Include="coverlet.collector" Version="6.0.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.8.0" />
+    <PackageReference Include="MSTest.TestAdapter" Version="3.1.1" />
+    <PackageReference Include="MSTest.TestFramework" Version="3.1.1" />
+  </ItemGroup>
+  <ItemGroup>
+    <Using Include="Microsoft.VisualStudio.TestTools.UnitTesting" />
+  </ItemGroup>
+  <ItemGroup>
+    <Content Include="ReceptiveFieldSimpleCell/*" Exclude="ReceptiveFieldSimpleCell/*.cs">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </Content>
+</ItemGroup>
+  <ItemGroup>
+    <ProjectReference Include="..\..\src\Bonsai.ML.LinearDynamicalSystems\Bonsai.ML.LinearDynamicalSystems.csproj" />
+  </ItemGroup>
+</Project>

tests/Bonsai.ML.LinearDynamicalSystems.Tests/ReceptiveFieldSimpleCell/ReceptiveFieldSimpleCellTest.cs

@@ -0,0 +1,195 @@
+using System;
+using System.IO.Compression;
+using System.Runtime.InteropServices;
+using System.Diagnostics;
+using System.Reflection;
+using Newtonsoft.Json;
+
+namespace Bonsai.ML.LinearDynamicalSystems.Tests.ReceptiveFieldSimpleCell;
+
+[TestClass]
+public class ReceptiveFieldSimpleCellTest
+{
+    private string basePath = Path.Combine(AppDomain.CurrentDomain.BaseDirectory, "ReceptiveFieldSimpleCell");
+    private int nSamples = 10000;
+
+    private void RunProcess(string fileName, string fmtArg)
+    {
+        var start = new ProcessStartInfo
+        {
+            FileName = fileName,
+            Arguments = fmtArg,
+            RedirectStandardOutput = true,
+            RedirectStandardInput = true,
+            RedirectStandardError = true,
+            UseShellExecute = false,
+            CreateNoWindow = true,
+        };
+
+        using (var process = new Process {StartInfo = start})
+        {
+            process.Start();
+            var output = process.StandardOutput.ReadToEnd();
+            var error = process.StandardError.ReadToEnd();
+            process.WaitForExit();
+
+            if (!string.IsNullOrEmpty(output))
+            {
+                Console.WriteLine("Standard Output: ");
+                Console.WriteLine(output);
+            }
+
+            if (!string.IsNullOrEmpty(error))
+            {
+                Console.WriteLine("Standard Error: ");
+                Console.WriteLine(error);
+            }
+        }
+    }
+
+    private void DownloadData(string basePath)
+    {
+        string zipFileUrl = "https://zenodo.org/records/10879253/files/ReceptiveFieldSimpleCell.zip";
+        string outputPath = Path.Combine(basePath, "data");
+        string tempFilePath = Path.Combine(Path.GetTempPath(), "tempfile.zip");
+
+        try
+        {
+            using (var httpClient = new HttpClient())
+            {
+                var responseBytes = httpClient.GetByteArrayAsync(zipFileUrl).Result;
+                File.WriteAllBytes(tempFilePath, responseBytes);
+                Console.WriteLine("File downloaded successfully.");
+            }
+
+            ZipFile.ExtractToDirectory(tempFilePath, outputPath, true);
+            Console.WriteLine("File extracted successfully.");
+        }
+
+        catch (Exception ex)
+        {
+            Console.WriteLine($"An error occurred: {ex.Message}");
+        }
+
+        finally
+        {
+            if (File.Exists(tempFilePath))
+            {
+                File.Delete(tempFilePath);
+                Console.WriteLine("Temporary file deleted.");
+            }
+        }
+    }
+
+    private void RunPythonScript(string basePath)
+    {
+        var pythonExec = RuntimeInformation.IsOSPlatform(OSPlatform.Windows)
+            ? "python"
+            : "python3";
+        var scriptPath = Path.Combine(basePath, "run_python_test.py");
+        RunProcess(pythonExec, $"\"{scriptPath}\" {basePath} {nSamples}");
+
+        Console.WriteLine("Run python script finished.");
+    }
+
+    private async Task RunBonsaiWorkflow(string basePath)
+    {
+        var currentDirectory = Environment.CurrentDirectory;
+        Environment.CurrentDirectory = basePath;
+        try
+        {
+            var workflowPath = Path.Combine(basePath, "receptive_field.bonsai");
+            await WorkflowHelper.RunWorkflow(
+                workflowPath,
+                properties: [("NSamples", nSamples)]);
+            Console.WriteLine("Run bonsai workflow finished.");
+        }
+        finally { Environment.CurrentDirectory = currentDirectory; }
+    }
+
+    private string GetJsonData(string jsonFileName)
+    {
+        string jsonString = File.ReadAllText(jsonFileName);
+        State state = JsonConvert.DeserializeObject<State>(jsonString);
+        string jsonState = JsonConvert.SerializeObject(state);
+        return jsonState;
+    }
+
+    private State GetStateFromJson(string jsonFileName)
+    {
+        string jsonString = File.ReadAllText(jsonFileName);
+        State state = JsonConvert.DeserializeObject<State>(jsonString);
+        return state;
+    }
+
+    private bool CompareJSONData(string basePath, double tolerance = 1e-9)
+    {
+        var originalFileName = Path.Combine(basePath, "original-receptivefield.json");
+        var bonsaiFileName = Path.Combine(basePath, "bonsai-receptivefield.json");
+        var pythonFileName = Path.Combine(basePath, "python-receptivefield.json");
+
+        var originalOutput = GetStateFromJson(originalFileName);
+        var bonsaiOutput = GetStateFromJson(bonsaiFileName);
+        var pythonOutput = GetStateFromJson(pythonFileName);
+
+        try
+        {
+            for (int i = 0; i < bonsaiOutput.X.GetLength(0); i++)
+            {
+                for (int j = 0; j < bonsaiOutput.X.GetLength(1); j++)
+                {
+                    if (Math.Abs(bonsaiOutput.X[i,j] - pythonOutput.X[i,j]) > tolerance || Math.Abs(originalOutput.X[i,j] - pythonOutput.X[i,j]) > tolerance)
+                    {
+                        Console.WriteLine($"Discrepency found comparing X at index ({i},{j}) with tolerance {tolerance}: bonsaiOutput = {bonsaiOutput.X[i,j]}, pythonOutput = {pythonOutput.X[i,j]}, originalOutput = {originalOutput.X[i,j]}.");
+                        return false;
+                    }
+                }
+            }
+            for (int i = 0; i < bonsaiOutput.P.GetLength(0); i++)
+            {
+                for (int j = 0; j < bonsaiOutput.P.GetLength(1); j++)
+                {
+                    if (Math.Abs(bonsaiOutput.P[i,j] - pythonOutput.P[i,j]) > tolerance || Math.Abs(originalOutput.P[i,j] - pythonOutput.P[i,j]) > tolerance)
+                    {
+                        Console.WriteLine($"Discrepency found comparing P at index ({i},{j}) with tolerance {tolerance}: bonsaiOutput = {bonsaiOutput.P[i,j]}, pythonOutput = {pythonOutput.P[i,j]}, originalOutput = {originalOutput.P[i,j]}.");
+                        return false;
+                    }
+                }
+            }
+        }
+        catch
+        {
+            return false;
+        }
+        return true;
+    }
+
+    [TestInitialize]
+    [DeploymentItem("run_python_test.py")]
+    [DeploymentItem("receptive_field.py")]
+    [DeploymentItem("receptive_field.bonsai")]
+    [DeploymentItem("original-receptivefield.json")]
+    public async Task TestSetup()
+    {
+        Directory.CreateDirectory(basePath);
+        DownloadData(basePath);
+        RunPythonScript(basePath);
+        await RunBonsaiWorkflow(basePath);
+    }
+
+    [TestMethod]
+    public void CompareResults()
+    {
+        var result = CompareJSONData(basePath);
+        Assert.IsTrue(result);
+    }
+
+    [TestCleanup]
+    public void Cleanup()
+    {
+        if (Directory.Exists(basePath))
+        {
+            Directory.Delete(basePath, true);
+        }
+    }
+}