smith-chem-wisc · trishorts · Jun 19, 2024 · Nov 18, 2021 · Nov 18, 2021 · Feb 4, 2022
diff --git a/.github/workflows/dotnet.yml b/.github/workflows/dotnet.yml
@@ -15,7 +15,7 @@ jobs:
     - name: Set up .NET
       uses: actions/setup-dotnet@v1
       with:
-        dotnet-version: 6.0.x
+        dotnet-version: 8.0.x
     - name: Restore dependencies
       run: cd mzLib && dotnet restore
     - name: Build
@@ -25,9 +25,9 @@ jobs:
     - name: Build (TestFlashLFQ)
       run: cd mzLib && dotnet build --no-restore ./TestFlashLFQ/TestFlashLFQ.csproj
     - name: Add coverlet collector (Test)
-      run: cd mzLib && dotnet add Test/Test.csproj package coverlet.collector -v 6.0.0
+      run: cd mzLib && dotnet add Test/Test.csproj package coverlet.collector -v 6.0.2
     - name: Add coverlet collector (TestFlashLFQ)
-      run: cd mzLib && dotnet add TestFlashLFQ/TestFlashLFQ.csproj package coverlet.collector -v 6.0.0
+      run: cd mzLib && dotnet add TestFlashLFQ/TestFlashLFQ.csproj package coverlet.collector -v 6.0.2
     - name: Test
       run: cd mzLib && dotnet test --no-build --verbosity normal --collect:"XPlat Code Coverage" /p:CoverletOutputFormat=cobertura ./Test/Test.csproj
     - name: TestFlashLFQ

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -14,7 +14,7 @@ jobs:
       - name: Setup .NET
         uses: actions/setup-dotnet@v1
         with:
-          dotnet-version: 6.0.x
+          dotnet-version: 8.0.x
       - name: Set up NuGet
         uses: nuget/setup-nuget@v1
         with:

diff --git a/mzLib/BayesianEstimation/BayesianEstimation.csproj b/mzLib/BayesianEstimation/BayesianEstimation.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 
@@ -11,6 +11,7 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
   </ItemGroup>
 

diff --git a/mzLib/Chemistry/Chemistry.csproj b/mzLib/Chemistry/Chemistry.csproj
@@ -1,14 +1,18 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)'=='Release'">
     <DebugType>full</DebugType>
     <DebugSymbols>true</DebugSymbols>
   </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
+  </ItemGroup>
 
   <ItemGroup>
     <ProjectReference Include="..\MzLibUtil\MzLibUtil.csproj" />

diff --git a/mzLib/Development/Deconvolution/TestCases/TestDevelopmentTestCases.cs b/mzLib/Development/Deconvolution/TestCases/TestDevelopmentTestCases.cs
@@ -1,5 +1,6 @@
 using MzLibUtil;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using MassSpectrometry;
 using System.Diagnostics.CodeAnalysis;
 using Readers;

diff --git a/mzLib/Development/Development.csproj b/mzLib/Development/Development.csproj
@@ -1,16 +1,17 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
 	  <Platforms>x64</Platforms>
     <ImplicitUsings>enable</ImplicitUsings>
     <Nullable>enable</Nullable>
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.1.0" />
-    <PackageReference Include="NUnit" Version="3.13.3" />
-    <PackageReference Include="NUnit3TestAdapter" Version="4.2.1" />
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
+    <PackageReference Include="NUnit" Version="4.1.0" />
+    <PackageReference Include="NUnit3TestAdapter" Version="4.5.0" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/mzLib/FlashLFQ/FlashLFQ.csproj b/mzLib/FlashLFQ/FlashLFQ.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 
@@ -11,8 +11,9 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
-    <PackageReference Include="NetSerializer" Version="4.1.1" />
+    <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="SharpLearning.Optimization" Version="[0.28.0]" />
   </ItemGroup>
 

diff --git a/mzLib/MassSpectrometry/MassSpectrometry.csproj b/mzLib/MassSpectrometry/MassSpectrometry.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 
@@ -11,6 +11,7 @@
   </PropertyGroup>
 
   <ItemGroup>
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
   </ItemGroup>
 

diff --git a/mzLib/MzIdentML/MzIdentML.csproj b/mzLib/MzIdentML/MzIdentML.csproj
@@ -1,14 +1,18 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)'=='Release'">
     <DebugType>full</DebugType>
     <DebugSymbols>true</DebugSymbols>
   </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
+  </ItemGroup>
 
   <ItemGroup>
     <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />

diff --git a/mzLib/MzLibUtil/MzLibUtil.csproj b/mzLib/MzLibUtil/MzLibUtil.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 
@@ -11,7 +11,8 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Easy.Common" Version="4.3.0" />
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
+    <PackageReference Include="Easy.Common" Version="6.7.0" />
     <PackageReference Include="MathNet.Numerics" Version="5.0.0" />
     <PackageReference Include="Microsoft.Win32.Registry" Version="5.0.0" />
   </ItemGroup>

diff --git a/mzLib/Omics/Omics.csproj b/mzLib/Omics/Omics.csproj
@@ -1,12 +1,16 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
 	<Platforms>x64</Platforms>
     <ImplicitUsings>enable</ImplicitUsings>
     <Nullable>enable</Nullable>
   </PropertyGroup>
 
+  <ItemGroup>
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
+  </ItemGroup>
+
   <ItemGroup>
     <ProjectReference Include="..\Chemistry\Chemistry.csproj" />
     <ProjectReference Include="..\MassSpectrometry\MassSpectrometry.csproj" />

diff --git a/mzLib/Proteomics/Proteomics.csproj b/mzLib/Proteomics/Proteomics.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0</TargetFramework>
+    <TargetFramework>net8.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 
@@ -28,4 +28,8 @@
     <Folder Include="Fragmentation\" />
   </ItemGroup>
 
+  <ItemGroup>
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
+  </ItemGroup>
+
 </Project>
diff --git a/mzLib/Readers/Readers.csproj b/mzLib/Readers/Readers.csproj
@@ -1,17 +1,17 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
 	<PropertyGroup>
-		<TargetFramework>net6.0</TargetFramework>
+		<TargetFramework>net8.0</TargetFramework>
 		<Platforms>x64</Platforms>
 		<ImplicitUsings>enable</ImplicitUsings>
 		<Nullable>enable</Nullable>
 	</PropertyGroup>
 
 	<ItemGroup>
-		<PackageReference Include="CsvHelper" Version="30.0.1" />
-		<PackageReference Include="OpenMcdf" Version="2.2.1.12" />
-		<PackageReference Include="OpenMcdf.Extensions" Version="2.2.1.4" />
-		<PackageReference Include="System.Data.SQLite" Version="1.0.117" />
+		<PackageReference Include="CsvHelper" Version="32.0.3" />
+		<PackageReference Include="OpenMcdf" Version="2.3.1" />
+		<PackageReference Include="OpenMcdf.Extensions" Version="2.3.1" />
+		<PackageReference Include="System.Data.SQLite" Version="1.0.118" />
 	</ItemGroup>
 
 	<ItemGroup>

diff --git a/mzLib/SpectralAveraging/SpectralAveraging.csproj b/mzLib/SpectralAveraging/SpectralAveraging.csproj
@@ -1,6 +1,6 @@
 <Project Sdk="Microsoft.NET.Sdk">
 	<PropertyGroup>
-		<TargetFramework>net6.0</TargetFramework>
+		<TargetFramework>net8.0</TargetFramework>
 		<Platforms>x64</Platforms>
 	</PropertyGroup>
 
@@ -15,6 +15,7 @@
 	</ItemGroup>
 
 	<ItemGroup>
+		<PackageReference Include="CsvHelper" Version="32.0.3" />
 		<PackageReference Include="MathNet.Numerics" Version="5.0.0" />
 		<PackageReference Include="Nett" Version="0.15.0" />
 	</ItemGroup>

diff --git a/mzLib/Test/AveragingTests/TestSpectraFileAveraging.cs b/mzLib/Test/AveragingTests/TestSpectraFileAveraging.cs
@@ -1,15 +1,10 @@
-using System;
-using System.Collections.Generic;
-using System.Diagnostics;
+using System.Collections.Generic;
 using System.Diagnostics.CodeAnalysis;
 using System.IO;
 using System.Linq;
-using System.Reflection;
-using System.Text;
 using MassSpectrometry;
-using MzLibUtil;
 using NUnit.Framework;
-using Proteomics.ProteolyticDigestion;
+using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert;
 using Readers;
 using SpectralAveraging;
 

diff --git a/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs b/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs
@@ -19,6 +19,7 @@
 using MassSpectrometry;
 using MzLibUtil;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Proteomics;
 using System;
 using System.Collections.Generic;

diff --git a/mzLib/Test/DatabaseTests/TestProteinReader.cs b/mzLib/Test/DatabaseTests/TestProteinReader.cs
@@ -21,6 +21,7 @@
 using System.IO;
 using System.Linq;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Omics.Modifications;
 using Proteomics;
 using UsefulProteomicsDatabases;

diff --git a/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs b/mzLib/Test/DatabaseTests/TestProteomicsReadWrite.cs
@@ -4,6 +4,7 @@
 using System.Linq;
 using MassSpectrometry;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Omics.Fragmentation;
 using Omics.Modifications;
 using Proteomics;

diff --git a/mzLib/Test/DatabaseTests/TestVariantProtein.cs b/mzLib/Test/DatabaseTests/TestVariantProtein.cs
@@ -3,6 +3,7 @@
 using System.IO;
 using System.Linq;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Omics.Modifications;
 using Proteomics;
 using Proteomics.ProteolyticDigestion;

diff --git a/mzLib/Test/FileReadingTests/TestMgf.cs b/mzLib/Test/FileReadingTests/TestMgf.cs
@@ -3,6 +3,7 @@
 using System.Linq;
 using MassSpectrometry;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Readers;
 using MzLibUtil;
 using Stopwatch = System.Diagnostics.Stopwatch;

diff --git a/mzLib/Test/FileReadingTests/TestMsDataFile.cs b/mzLib/Test/FileReadingTests/TestMsDataFile.cs
@@ -21,7 +21,8 @@
 using MassSpectrometry;
 using MzLibUtil;
 using NUnit.Framework;
-using Proteomics;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
+using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert;
 using Proteomics.AminoAcidPolymer;
 using Proteomics.ProteolyticDigestion;
 using System;

diff --git a/mzLib/Test/FileReadingTests/TestMzML.cs b/mzLib/Test/FileReadingTests/TestMzML.cs
@@ -9,6 +9,7 @@
 using MzIdentML;
 using MzLibUtil;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Proteomics.AminoAcidPolymer;
 using Readers;
 using Stopwatch = System.Diagnostics.Stopwatch;

diff --git a/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs b/mzLib/Test/FileReadingTests/TestPsmFromTsv.cs
@@ -1,5 +1,5 @@
 using NUnit.Framework;
-using Proteomics.ProteolyticDigestion;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Proteomics.PSM;
 using System;
 using System.Collections.Generic;

diff --git a/mzLib/Test/FileReadingTests/TestRawFileReader.cs b/mzLib/Test/FileReadingTests/TestRawFileReader.cs
@@ -1,12 +1,10 @@
 using System;
-using System.Collections.Generic;
-using System.Collections.Specialized;
 using System.Diagnostics;
 using System.IO;
 using System.Linq;
 using MassSpectrometry;
-using MzLibUtil;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Readers;
 
 namespace Test.FileReadingTests

diff --git a/mzLib/Test/FileReadingTests/TestToppicResultFiles.cs b/mzLib/Test/FileReadingTests/TestToppicResultFiles.cs
@@ -6,6 +6,7 @@
 using MassSpectrometry;
 using Newtonsoft.Json;
 using NUnit.Framework;
+using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert;
 using Readers;
 
 namespace Test.FileReadingTests

diff --git a/mzLib/Test/SpectrumProcessingAndFiltering.cs b/mzLib/Test/SpectrumProcessingAndFiltering.cs
@@ -2,6 +2,7 @@
 using Readers;
 using MassSpectrometry;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using System;
 using System.Collections.Generic;
 using System.Diagnostics.CodeAnalysis;

diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net6.0-windows</TargetFramework>
+    <TargetFramework>net8.0-windows</TargetFramework>
     <IsPackable>false</IsPackable>
     <Platforms>x64</Platforms>
   </PropertyGroup>
@@ -13,11 +13,12 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="NUnit" Version="3.13.3" />
-    <PackageReference Include="NUnit3TestAdapter" Version="4.2.1" />
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.1.0" />
+    <PackageReference Include="CsvHelper" Version="32.0.3" />
+    <PackageReference Include="NUnit" Version="4.1.0" />
+    <PackageReference Include="NUnit3TestAdapter" Version="4.5.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />
     <PackageReference Include="SharpLearning.Optimization" Version="0.28.0" />
-    <PackageReference Include="TopDownProteomics" Version="0.0.287" />
+    <PackageReference Include="TopDownProteomics" Version="0.0.297" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/mzLib/Test/TestAminoAcids.cs b/mzLib/Test/TestAminoAcids.cs
@@ -16,8 +16,8 @@
 // You should have received a copy of the GNU Lesser General Public
 // License along with Proteomics. If not, see <http://www.gnu.org/licenses/>.
 
-using Chemistry;
 using NUnit.Framework;
+using Assert = NUnit.Framework.Legacy.ClassicAssert;
 using Proteomics.AminoAcidPolymer;
 using System;
 using System.Diagnostics.CodeAnalysis;