Feature/159 Upgrade VTS to .NET 8.0

.github/workflows/deploy-pages-static.yml

@@ -29,24 +29,24 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Publish the docs to docs/_site
       - name: Dotnet Setup
-        uses: actions/setup-dotnet@v3
+        uses: actions/setup-dotnet@v4
         with:
-          dotnet-version: 7.x
+          dotnet-version: 8.x
       - run: dotnet tool update -g docfx
       - run: docfx documentation/docfx.json
 
       # Deploy the generated docs to GitHub Pages
       - name: Setup Pages
-        uses: actions/configure-pages@v3
+        uses: actions/configure-pages@v5
       - name: Upload artifact
-        uses: actions/upload-pages-artifact@v2
+        uses: actions/upload-pages-artifact@v3
         with:
           # Upload static files
           path: 'documentation/_site'
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v2
+        uses: actions/deploy-pages@v4

.github/workflows/dotnetbuildtest.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Setup .NET
       uses: actions/setup-dotnet@v4
       with:
-        dotnet-version: 6.0.x
+        dotnet-version: 8.0.x
     - name: Restore dependencies
       run: dotnet restore src\\VtsLibrary.sln
     - name: Build

BuildTestCore.ps1

@@ -11,6 +11,6 @@ dotnet test $PWD\src\Vts.Test\Vts.Test.csproj -c Release
 
 Write-Host "Publish the VTS dll to platform specific folders" -ForegroundColor Green
 Remove-Item $PWD\publish -Recurse -ErrorAction Ignore
-dotnet publish $PWD\src\Vts\Vts.csproj -f net6.0 -c Release -o $PWD\publish\win-x64 --self-contained false
-dotnet publish $PWD\src\Vts\Vts.csproj -f net6.0 -c Release -o $PWD\publish\linux-x64 --self-contained false
-dotnet publish $PWD\src\Vts\Vts.csproj -f net6.0 -c Release -o $PWD\publish\osx-x64 --self-contained false
+dotnet publish $PWD\src\Vts\Vts.csproj -c Release -o $PWD\publish\win-x64 --self-contained false
+dotnet publish $PWD\src\Vts\Vts.csproj -c Release -o $PWD\publish\linux-x64 --self-contained false
+dotnet publish $PWD\src\Vts\Vts.csproj -c Release -o $PWD\publish\osx-x64 --self-contained false

BuildTestReleaseMCCL.ps1

@@ -54,7 +54,7 @@ if (-not (Test-Path -LiteralPath $releasedir)) {
 # Create win-x64 zip
 $archive = $releasedir + "\MC_v" + $version + "_Win_x64.zip"
 $source = "publish\win-x64\*"
-Compress-Archive -Path $source -DestinationPath $archive 
+Compress-Archive -Force -Path $source -DestinationPath $archive 
 $matlabdir = "$PWD\matlab"
 $matlabfiles = "$matlabdir\post_processing\*"
 Compress-Archive -Path $matlabfiles -Update -DestinationPath $archive
@@ -66,7 +66,7 @@ Compress-Archive -Path $mcinversefiles -Update -DestinationPath $archive
 # Create linux-x64 zip
 $archive = $releasedir + "\MC_v" + $version + "_Linux_x64.zip"
 $source = "publish\linux-x64\*"
-Compress-Archive -Path $source -DestinationPath $archive 
+Compress-Archive -Force -Path $source -DestinationPath $archive 
 $matlabfiles = "$matlabdir\post_processing\*"
 Compress-Archive -Path $matlabfiles -Update -DestinationPath $archive
 $mcinversegeneralfiles = "$matlabdir\monte_carlo_inverse\general\*"
@@ -77,7 +77,7 @@ Compress-Archive -Path $mcinversefiles -Update -DestinationPath $archive
 # Create osx-x64 zip
 $archive = $releasedir + "\MC_v" + $version + "_Mac_x64.zip"
 $source = "publish\osx-x64\*"
-Compress-Archive -Path $source -DestinationPath $archive 
+Compress-Archive -Force -Path $source -DestinationPath $archive 
 $matlabfiles = "$matlabdir\post_processing\*"
 Compress-Archive -Path $matlabfiles -Update -DestinationPath $archive
 $mcinversegeneralfiles = "$matlabdir\monte_carlo_inverse\general\*"

src/Vts.Benchmark/Vts.Benchmark.csproj

@@ -2,11 +2,11 @@
 
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="BenchmarkDotNet" Version="0.13.12" />
+    <PackageReference Include="BenchmarkDotNet" Version="0.14.0" />
   </ItemGroup>
 
   <ItemGroup>

src/Vts.MonteCarlo.CommandLineApplication.Test/Vts.MonteCarlo.CommandLineApplication.Test.csproj

@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
 
     <IsPackable>false</IsPackable>
   </PropertyGroup>
@@ -23,7 +23,7 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.11.1" />
     <PackageReference Include="nunit" Version="3.14.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.5.0">
       <PrivateAssets>all</PrivateAssets>

src/Vts.MonteCarlo.CommandLineApplication/Vts.MonteCarlo.CommandLineApplication.csproj

@@ -2,7 +2,7 @@
 
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <AssemblyName>mc</AssemblyName>
     <RuntimeIdentifiers>win-x64;linux-x64;osx-x64</RuntimeIdentifiers>
     <RootNamespace>Vts.MonteCarlo.CommandLineApplication</RootNamespace>

src/Vts.MonteCarlo.PostProcessor.Test/Vts.MonteCarlo.PostProcessor.Test.csproj

@@ -1,13 +1,13 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
 
     <IsPackable>false</IsPackable>
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.11.1" />
     <PackageReference Include="nunit" Version="3.14.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.5.0">
       <PrivateAssets>all</PrivateAssets>

src/Vts.MonteCarlo.PostProcessor/Vts.MonteCarlo.PostProcessor.csproj

@@ -2,7 +2,7 @@
 
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <RootNamespace>Vts.MonteCarlo.PostProcessor</RootNamespace>
     <AssemblyName>mc_post</AssemblyName>
     <RuntimeIdentifiers>win-x64;linux-x64;osx-x64</RuntimeIdentifiers>

src/Vts.Scripting.Test/Vts.Scripting.Test.csproj

@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <ImplicitUsings>enable</ImplicitUsings>
     <Nullable>enable</Nullable>
 	<EnablePreviewFeatures>true</EnablePreviewFeatures>
@@ -11,7 +11,7 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.11.1" />
     <PackageReference Include="NUnit" Version="3.14.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.5.0" />
     <PackageReference Include="NUnit.Analyzers" Version="3.10.0">

src/Vts.Scripting/Vts.Scripting.csproj

@@ -2,7 +2,7 @@
 
   <PropertyGroup>
     <OutputType>Exe</OutputType>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <ImplicitUsings>enable</ImplicitUsings>
     <Nullable>enable</Nullable>
 	<EnablePreviewFeatures>true</EnablePreviewFeatures>

src/Vts.Test/Extensions/EnumerableExtensionsTests.cs

@@ -96,7 +96,7 @@ public void ToDictionary_returns_dictionary_from_key_value_pairs()
                 new KeyValuePair<string, string>("two", "second"),
                 new KeyValuePair<string, string>("three", "third")
             };
-            var dictionary = keyValuePairList.ToDictionary();
+            var dictionary = EnumerableExtensions.ToDictionary(keyValuePairList);
             Assert.IsInstanceOf<Dictionary<string, string>>(dictionary);
             Assert.AreEqual("first", dictionary["one"]);
             Assert.AreEqual("second", dictionary["two"]);

src/Vts.Test/Vts.Test.csproj

@@ -1,6 +1,6 @@
 <Project Sdk="Microsoft.NET.Sdk" ToolsVersion="Current">
   <PropertyGroup>
-	<TargetFramework>net6.0</TargetFramework>
+	<TargetFramework>net8.0</TargetFramework>
     <IsPackable>false</IsPackable>
   </PropertyGroup>
   <ItemGroup>
@@ -42,7 +42,7 @@
     <EmbeddedResource Include="Resources\sourcetest\inputAOfXAndYAndZ.txt" />
   </ItemGroup>
   <ItemGroup>
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.11.1" />
     <PackageReference Include="NSubstitute" Version="5.1.0" />
     <PackageReference Include="NUnit" Version="3.14.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.5.0">

src/Vts/MonteCarlo/Rng/DynamicCreatorMersenneTwister.cs

@@ -270,7 +270,7 @@ public struct mt_struct {
             /// </summary>
             public uint[] state; // if null then struct is mull
         } 
-        struct polynomial
+        struct Polynomial
         {
             public int[] x;
             public int deg;
@@ -279,7 +279,7 @@ struct prescr_t
         {
             public int sizeOfA;      // paramter size
             public uint[][] modlist; // size[_nirredpoly][pre.sizeOfA]
-            public polynomial[] preModPolys; // size[pre.sizeOfA+1]
+            public Polynomial[] preModPolys; // size[pre.sizeOfA+1]
         }
 
         struct eqdeg_t
@@ -601,9 +601,9 @@ private int prescreening_dc(prescr_t pre, uint aaa)
         }
         private void init_prescreening_dc(ref prescr_t pre, int m, int n, int r, int w)
         {
-            polynomial pl;
+            Polynomial pl;
             pre.sizeOfA = w;
-            pre.preModPolys = new polynomial[pre.sizeOfA + 1]; 
+            pre.preModPolys = new Polynomial[pre.sizeOfA + 1]; 
             make_pre_mod_polys(ref pre, m, n, r, w);
             pre.modlist = new uint[_nirredpoly][];
             for (int i = 0; i < _nirredpoly; i++)
@@ -619,7 +619,7 @@ private void init_prescreening_dc(ref prescr_t pre, int m, int n, int r, int w)
             }
             //was in original code: for loop (i eq 0 until i lt pre.sizeOfA) then free poly -> don't need this
         }
-        private void next_irred_poly(ref polynomial pl, int nth)
+        private void next_irred_poly(ref Polynomial pl, int nth)
         {
             int i, max_deg;
             for (max_deg = 0, i = 0; i <= _max_irred_deg; i++)
@@ -632,9 +632,9 @@ private void next_irred_poly(ref polynomial pl, int nth)
             }
             pl.deg = max_deg;
         }
-        private void make_modlist(ref prescr_t pre, polynomial pl, int nPoly)
+        private void make_modlist(ref prescr_t pre, Polynomial pl, int nPoly)
         {
-            polynomial tmpPl;
+            Polynomial tmpPl;
             int i;
             for (i = 0; i <= pre.sizeOfA; i++)
             {
@@ -648,7 +648,7 @@ private void make_modlist(ref prescr_t pre, polynomial pl, int nPoly)
         /// </summary>
         /// <param name="wara">first polynomial</param>
         /// <param name="waru">second polynomial</param>
-        private void polynomial_mod(ref polynomial wara, polynomial waru) // waru is "const" in C code
+        private void polynomial_mod(ref Polynomial wara, Polynomial waru) // waru is "const" in C code
         {
             int deg_diff, i; 
             while (wara.deg >= waru.deg)
@@ -668,7 +668,7 @@ private void polynomial_mod(ref polynomial wara, polynomial waru) // waru is "co
                 wara.deg = i;
             }
         }
-        private uint word2bit(polynomial pl)
+        private uint word2bit(Polynomial pl)
         {
             uint bx = 0;
             for (int i = pl.deg; i > 0; i--)
@@ -719,7 +719,7 @@ private int is_reducible(prescr_t pre, uint aaa, uint[] polylist)
         /// <param name="ww"></param>
         private void make_pre_mod_polys(ref prescr_t pre, int mm, int nn, int rr, int ww)
         {
-            polynomial t, t0, s, s0;  // orig code had t1 and s1 in this list
+            Polynomial t, t0, s, s0;  // orig code had t1 and s1 in this list
             int i;
             int j = 0;
             t = new_poly(0);
@@ -758,18 +758,18 @@ private void make_pre_mod_polys(ref prescr_t pre, int mm, int nn, int rr, int ww
         /// </summary>
         /// <param name="pl">polynomial to be duplicated</param>
         /// <returns>polynomial class</returns>
-        private polynomial polynomial_dup(polynomial pl)
+        private Polynomial polynomial_dup(Polynomial pl)
         {
-            polynomial pt = new_poly(pl.deg);
+            Polynomial pt = new_poly(pl.deg);
             for (int i = pl.deg; i >= 0; i--)
             {
                 pt.x[i] = pl.x[i];
             }
             return pt;
         }
-        private polynomial polynomial_mult(polynomial p0, polynomial p1)
+        private Polynomial polynomial_mult(Polynomial p0, Polynomial p1)
         {
-            polynomial p;
+            Polynomial p;
             if ((p0.deg < 0) || (p1.deg < 0))
             {
                 p = new_poly(-1);
@@ -788,9 +788,9 @@ private polynomial polynomial_mult(polynomial p0, polynomial p1)
             }
             return p;
         }
-        private polynomial make_tntm(int n, int m)
+        private Polynomial make_tntm(int n, int m)
         {
-            polynomial p = new_poly(n);
+            Polynomial p = new_poly(n);
             p.x[m] = 1;
             p.x[n] = p.x[m];
             return p;
@@ -802,9 +802,9 @@ private polynomial make_tntm(int n, int m)
         /// </summary>
         /// <param name="degree">degree of polynomial created</param>
         /// <returns>polynomial class</returns>
-        private polynomial new_poly(int degree)
+        private Polynomial new_poly(int degree)
         {
-            polynomial p = new polynomial();
+            Polynomial p = new Polynomial();
             p.deg = degree;
             if (degree < 0)
             {

src/Vts/Vts.csproj

@@ -1,6 +1,6 @@
 <Project Sdk="Microsoft.NET.Sdk" ToolsVersion="Current">
   <PropertyGroup>
-	<TargetFramework>net6.0</TargetFramework>
+	<TargetFramework>net8.0</TargetFramework>
     <Description>The VTS (Virtual Tissue Simulator) is an open source library for .NET that was designed as a modular and scalable platform to provide an integrated suite of computational tools to define, solve, visualize, and analyze relevant forward and inverse radiative transport problems in Biomedical Optics.</Description>
     <Company>Virtual Photonics Technology Initiative</Company>
     <Copyright>Copyright © 2024 Laser Microbeam and Medical Program</Copyright>
@@ -134,7 +134,7 @@
     <PackageReference Include="Microsoft.CSharp" Version="4.7.0" />
     <PackageReference Include="Microsoft.Extensions.DependencyInjection" Version="8.0.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
-    <PackageReference Include="NLog" Version="5.3.2" />
+    <PackageReference Include="NLog" Version="5.3.3" />
     <PackageReference Include="System.Reactive" Version="6.0.1" />
     <PackageReference Include="System.Reflection" Version="4.3.0" />
   </ItemGroup>