diff --git a/.github/workflows/dotnet.yml b/.github/workflows/dotnet.yml index 735b3557a..f89904dc3 100644 --- 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 index 559174294..b5b516a83 100644 --- 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 index e37dee889..4d0ba7ee2 100644 --- a/mzLib/BayesianEstimation/BayesianEstimation.csproj +++ b/mzLib/BayesianEstimation/BayesianEstimation.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -11,6 +11,7 @@ + diff --git a/mzLib/Chemistry/Chemistry.csproj b/mzLib/Chemistry/Chemistry.csproj index fc57948ce..816d4eefd 100644 --- a/mzLib/Chemistry/Chemistry.csproj +++ b/mzLib/Chemistry/Chemistry.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -9,6 +9,10 @@ full true + + + + diff --git a/mzLib/Development/Deconvolution/TestCases/TestDevelopmentTestCases.cs b/mzLib/Development/Deconvolution/TestCases/TestDevelopmentTestCases.cs index 9b62af60a..345d962c3 100644 --- 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 index 0dc946d45..0f0eaf199 100644 --- a/mzLib/Development/Development.csproj +++ b/mzLib/Development/Development.csproj @@ -1,16 +1,17 @@ - net6.0 + net8.0 x64 enable enable - - - + + + + diff --git a/mzLib/FlashLFQ/FlashLFQ.csproj b/mzLib/FlashLFQ/FlashLFQ.csproj index 52d33530e..097bf6131 100644 --- a/mzLib/FlashLFQ/FlashLFQ.csproj +++ b/mzLib/FlashLFQ/FlashLFQ.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -11,8 +11,9 @@ + - + diff --git a/mzLib/MassSpectrometry/MassSpectrometry.csproj b/mzLib/MassSpectrometry/MassSpectrometry.csproj index d803402ea..6af63b9e4 100644 --- a/mzLib/MassSpectrometry/MassSpectrometry.csproj +++ b/mzLib/MassSpectrometry/MassSpectrometry.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -11,6 +11,7 @@ + diff --git a/mzLib/MzIdentML/MzIdentML.csproj b/mzLib/MzIdentML/MzIdentML.csproj index 6adfa72d7..67eb6987f 100644 --- a/mzLib/MzIdentML/MzIdentML.csproj +++ b/mzLib/MzIdentML/MzIdentML.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -9,6 +9,10 @@ full true + + + + diff --git a/mzLib/MzLibUtil/MzLibUtil.csproj b/mzLib/MzLibUtil/MzLibUtil.csproj index 84d202daf..c6b5cf526 100644 --- a/mzLib/MzLibUtil/MzLibUtil.csproj +++ b/mzLib/MzLibUtil/MzLibUtil.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -11,7 +11,8 @@ - + + diff --git a/mzLib/Omics/Omics.csproj b/mzLib/Omics/Omics.csproj index 6493de1a6..8283d5d7b 100644 --- a/mzLib/Omics/Omics.csproj +++ b/mzLib/Omics/Omics.csproj @@ -1,12 +1,16 @@  - net6.0 + net8.0 x64 enable enable + + + + diff --git a/mzLib/Proteomics/Proteomics.csproj b/mzLib/Proteomics/Proteomics.csproj index a87d3a3a9..998b66e50 100644 --- a/mzLib/Proteomics/Proteomics.csproj +++ b/mzLib/Proteomics/Proteomics.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -28,4 +28,8 @@ + + + + diff --git a/mzLib/Readers/Readers.csproj b/mzLib/Readers/Readers.csproj index c2a7a1e4b..076ed9e40 100644 --- a/mzLib/Readers/Readers.csproj +++ b/mzLib/Readers/Readers.csproj @@ -1,17 +1,17 @@ - net6.0 + net8.0 x64 enable enable - - - - + + + + diff --git a/mzLib/SpectralAveraging/SpectralAveraging.csproj b/mzLib/SpectralAveraging/SpectralAveraging.csproj index 96bc3a953..a946e80d1 100644 --- a/mzLib/SpectralAveraging/SpectralAveraging.csproj +++ b/mzLib/SpectralAveraging/SpectralAveraging.csproj @@ -1,6 +1,6 @@  - net6.0 + net8.0 x64 @@ -15,6 +15,7 @@ + diff --git a/mzLib/Test/AveragingTests/TestSpectraFileAveraging.cs b/mzLib/Test/AveragingTests/TestSpectraFileAveraging.cs index 3fb4c8428..f46db019d 100644 --- 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 index fe3e70c06..82d7ce715 100644 --- 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 index 7c5affb4e..76915eb9a 100644 --- 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 index c48034df4..d0212b6de 100644 --- 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 index a16232ab0..5d8f551ab 100644 --- 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 index 5c1d7568b..05251365c 100644 --- 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 index eed172009..5977d4b71 100644 --- 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 index c20e13255..826efca77 100644 --- 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 index c498c9759..2018158b1 100644 --- 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 index d0d2665d3..0b67c1508 100644 --- 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 index aa1642078..53528e166 100644 --- 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 index 3bcaa6d99..433b29020 100644 --- 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 index 7b5882009..728da9d1c 100644 --- a/mzLib/Test/Test.csproj +++ b/mzLib/Test/Test.csproj @@ -1,7 +1,7 @@  - net6.0-windows + net8.0-windows false x64 @@ -13,11 +13,12 @@ - - - + + + + - + diff --git a/mzLib/Test/TestAminoAcids.cs b/mzLib/Test/TestAminoAcids.cs index e16eb671a..acfcb473f 100644 --- 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 . -using Chemistry; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics.AminoAcidPolymer; using System; using System.Diagnostics.CodeAnalysis; diff --git a/mzLib/Test/TestChemicalFormula.cs b/mzLib/Test/TestChemicalFormula.cs index 124fb7548..483974a1f 100644 --- a/mzLib/Test/TestChemicalFormula.cs +++ b/mzLib/Test/TestChemicalFormula.cs @@ -19,11 +19,11 @@ using Chemistry; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Collections.Generic; using System.Diagnostics.CodeAnalysis; using System.Linq; -using SharpLearning.Containers.Matrices; using Stopwatch = System.Diagnostics.Stopwatch; namespace Test diff --git a/mzLib/Test/TestClassExtensions.cs b/mzLib/Test/TestClassExtensions.cs index 4de0e5ff5..326877386 100644 --- a/mzLib/Test/TestClassExtensions.cs +++ b/mzLib/Test/TestClassExtensions.cs @@ -1,8 +1,7 @@ using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.Diagnostics.CodeAnalysis; using MzLibUtil; -using System.IO; -using System.Linq; using System; using MassSpectrometry; using System.Collections.Generic; diff --git a/mzLib/Test/TestDeconvolution.cs b/mzLib/Test/TestDeconvolution.cs index 8af70f886..8f6cbb9ee 100644 --- a/mzLib/Test/TestDeconvolution.cs +++ b/mzLib/Test/TestDeconvolution.cs @@ -3,6 +3,7 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; @@ -11,8 +12,6 @@ using System.Globalization; using System.IO; using System.Linq; -using System.Reflection; -using MassSpectrometry; using Omics.Digestion; using Omics.Modifications; using Test.FileReadingTests; diff --git a/mzLib/Test/TestDigestionMotif.cs b/mzLib/Test/TestDigestionMotif.cs index 91f8cf059..39b7a1704 100644 --- a/mzLib/Test/TestDigestionMotif.cs +++ b/mzLib/Test/TestDigestionMotif.cs @@ -1,5 +1,7 @@ using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; +using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/mzLib/Test/TestElementsAndIsotopes.cs b/mzLib/Test/TestElementsAndIsotopes.cs index c8a9342d0..a6f12b130 100644 --- a/mzLib/Test/TestElementsAndIsotopes.cs +++ b/mzLib/Test/TestElementsAndIsotopes.cs @@ -18,6 +18,7 @@ using Chemistry; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using Stopwatch = System.Diagnostics.Stopwatch; diff --git a/mzLib/Test/TestFragments.cs b/mzLib/Test/TestFragments.cs index c377f3551..ea4a307c3 100644 --- a/mzLib/Test/TestFragments.cs +++ b/mzLib/Test/TestFragments.cs @@ -17,10 +17,11 @@ // License along with Proteomics. If not, see . using Chemistry; -using Easy.Common.Extensions; using MassSpectrometry; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; +using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert; using Omics.Fragmentation; using Omics.Fragmentation.Peptide; using Proteomics; diff --git a/mzLib/Test/TestIsolation.cs b/mzLib/Test/TestIsolation.cs index 8026d1a64..d48772a02 100644 --- a/mzLib/Test/TestIsolation.cs +++ b/mzLib/Test/TestIsolation.cs @@ -19,6 +19,7 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics.AminoAcidPolymer; using System; using System.Linq; diff --git a/mzLib/Test/TestLibrarySpectrum.cs b/mzLib/Test/TestLibrarySpectrum.cs index 57d496b2c..ba0817f3c 100644 --- a/mzLib/Test/TestLibrarySpectrum.cs +++ b/mzLib/Test/TestLibrarySpectrum.cs @@ -1,10 +1,6 @@ using NUnit.Framework; -using Proteomics.PSM; -using System; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.Collections.Generic; -using System.Linq; -using System.Text; -using System.Threading.Tasks; using Omics.Fragmentation; using Omics.SpectrumMatch; diff --git a/mzLib/Test/TestMassMzCalculations.cs b/mzLib/Test/TestMassMzCalculations.cs index e4e739390..4f1e88f5a 100644 --- a/mzLib/Test/TestMassMzCalculations.cs +++ b/mzLib/Test/TestMassMzCalculations.cs @@ -17,6 +17,7 @@ using Chemistry; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using Stopwatch = System.Diagnostics.Stopwatch; diff --git a/mzLib/Test/TestModFits.cs b/mzLib/Test/TestModFits.cs index 3b0b2c225..48362d17f 100644 --- a/mzLib/Test/TestModFits.cs +++ b/mzLib/Test/TestModFits.cs @@ -1,4 +1,5 @@ using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using System; using Omics.Modifications; diff --git a/mzLib/Test/TestModifications.cs b/mzLib/Test/TestModifications.cs index 12f1566e3..021f08dc2 100644 --- a/mzLib/Test/TestModifications.cs +++ b/mzLib/Test/TestModifications.cs @@ -20,6 +20,8 @@ using MassSpectrometry; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; +using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert; using Proteomics; using Proteomics.AminoAcidPolymer; using Proteomics.ProteolyticDigestion; diff --git a/mzLib/Test/TestMzLibUtil.cs b/mzLib/Test/TestMzLibUtil.cs index d0ee538d6..364102afe 100644 --- a/mzLib/Test/TestMzLibUtil.cs +++ b/mzLib/Test/TestMzLibUtil.cs @@ -1,9 +1,5 @@ using NUnit.Framework; -using System; -using System.Collections.Generic; -using System.Linq; -using System.Text; -using System.Threading.Tasks; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using MzLibUtil; namespace Test diff --git a/mzLib/Test/TestPeptideWithSetMods.cs b/mzLib/Test/TestPeptideWithSetMods.cs index 549d504cf..4fe80b848 100644 --- a/mzLib/Test/TestPeptideWithSetMods.cs +++ b/mzLib/Test/TestPeptideWithSetMods.cs @@ -1,5 +1,7 @@ using Chemistry; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; +using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/mzLib/Test/TestPeptides.cs b/mzLib/Test/TestPeptides.cs index c6a0193ce..bdd7778c8 100644 --- a/mzLib/Test/TestPeptides.cs +++ b/mzLib/Test/TestPeptides.cs @@ -19,6 +19,7 @@ using Chemistry; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics.AminoAcidPolymer; using Proteomics.ProteolyticDigestion; using System; diff --git a/mzLib/Test/TestProductMassesMightHaveDuplicates.cs b/mzLib/Test/TestProductMassesMightHaveDuplicates.cs index dd6702d16..af60acb98 100644 --- a/mzLib/Test/TestProductMassesMightHaveDuplicates.cs +++ b/mzLib/Test/TestProductMassesMightHaveDuplicates.cs @@ -1,6 +1,7 @@ using Chemistry; using MassSpectrometry; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using Proteomics.ProteolyticDigestion; using System; diff --git a/mzLib/Test/TestProteinDatabase.cs b/mzLib/Test/TestProteinDatabase.cs index b03fd98c7..fffa0ef55 100644 --- a/mzLib/Test/TestProteinDatabase.cs +++ b/mzLib/Test/TestProteinDatabase.cs @@ -1,4 +1,6 @@ using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; +using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert; using Proteomics; using System.Collections.Generic; using System.IO; diff --git a/mzLib/Test/TestProteinDigestion.cs b/mzLib/Test/TestProteinDigestion.cs index 2e430d67a..c0158593e 100644 --- a/mzLib/Test/TestProteinDigestion.cs +++ b/mzLib/Test/TestProteinDigestion.cs @@ -1,6 +1,8 @@ using Chemistry; using MassSpectrometry; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; +using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert; using Proteomics; using Proteomics.AminoAcidPolymer; using Proteomics.ProteolyticDigestion; diff --git a/mzLib/Test/TestProteinProperties.cs b/mzLib/Test/TestProteinProperties.cs index f22e71df9..6c8d866dd 100644 --- a/mzLib/Test/TestProteinProperties.cs +++ b/mzLib/Test/TestProteinProperties.cs @@ -1,4 +1,5 @@ using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics; using System; using System.Collections.Generic; diff --git a/mzLib/Test/TestPtmListLoader.cs b/mzLib/Test/TestPtmListLoader.cs index 3cdcf1412..dae556a02 100644 --- a/mzLib/Test/TestPtmListLoader.cs +++ b/mzLib/Test/TestPtmListLoader.cs @@ -1,6 +1,6 @@ using MzLibUtil; using NUnit.Framework; -using Proteomics; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.IO; using System.Linq; diff --git a/mzLib/Test/TestRangeAndTolerances.cs b/mzLib/Test/TestRangeAndTolerances.cs index dd248047c..8a08d94f0 100644 --- a/mzLib/Test/TestRangeAndTolerances.cs +++ b/mzLib/Test/TestRangeAndTolerances.cs @@ -18,6 +18,7 @@ using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Linq; using Stopwatch = System.Diagnostics.Stopwatch; diff --git a/mzLib/Test/TestRetentionTimePrediction.cs b/mzLib/Test/TestRetentionTimePrediction.cs index f312c92a0..7fc048375 100644 --- a/mzLib/Test/TestRetentionTimePrediction.cs +++ b/mzLib/Test/TestRetentionTimePrediction.cs @@ -1,5 +1,5 @@ using NUnit.Framework; -using Proteomics; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Proteomics.ProteolyticDigestion; using Proteomics.RetentionTimePrediction; using System; diff --git a/mzLib/Test/TestSpectra.cs b/mzLib/Test/TestSpectra.cs index 8a8b0eb15..e33d9adb1 100644 --- a/mzLib/Test/TestSpectra.cs +++ b/mzLib/Test/TestSpectra.cs @@ -22,6 +22,7 @@ using System; using System.Collections.Generic; using System.Linq; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using Stopwatch = System.Diagnostics.Stopwatch; namespace Test diff --git a/mzLib/Test/TestSpectralSimilarity.cs b/mzLib/Test/TestSpectralSimilarity.cs index 1b0a78296..1d4b53819 100644 --- a/mzLib/Test/TestSpectralSimilarity.cs +++ b/mzLib/Test/TestSpectralSimilarity.cs @@ -2,6 +2,7 @@ using MassSpectrometry.MzSpectra; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System; using System.Collections.Generic; diff --git a/mzLib/Test/Transcriptomics/TestRnase.cs b/mzLib/Test/Transcriptomics/TestRnase.cs index 2657cb08e..db7d3e3dc 100644 --- a/mzLib/Test/Transcriptomics/TestRnase.cs +++ b/mzLib/Test/Transcriptomics/TestRnase.cs @@ -1,9 +1,7 @@ using NUnit.Framework; -using System; -using System.Collections.Generic; +using Assert = NUnit.Framework.Legacy.ClassicAssert; using System.Diagnostics.CodeAnalysis; using System.IO; -using System.Linq; using Proteomics.ProteolyticDigestion; using Transcriptomics.Digestion; diff --git a/mzLib/TestFlashLFQ/TestFlashLFQ.cs b/mzLib/TestFlashLFQ/TestFlashLFQ.cs index b94e32cf0..748941195 100644 --- a/mzLib/TestFlashLFQ/TestFlashLFQ.cs +++ b/mzLib/TestFlashLFQ/TestFlashLFQ.cs @@ -5,12 +5,13 @@ using MathNet.Numerics.Statistics; using MzLibUtil; using NUnit.Framework; +using Assert = NUnit.Framework.Legacy.ClassicAssert; +using CollectionAssert = NUnit.Framework.Legacy.CollectionAssert; using Proteomics.AminoAcidPolymer; using System; using System.Collections.Generic; using System.IO; using System.Linq; -using Easy.Common.Extensions; using Test.FileReadingTests; using UsefulProteomicsDatabases; using ChromatographicPeak = FlashLFQ.ChromatographicPeak; diff --git a/mzLib/TestFlashLFQ/TestFlashLFQ.csproj b/mzLib/TestFlashLFQ/TestFlashLFQ.csproj index 06d014d2c..aa4f19039 100644 --- a/mzLib/TestFlashLFQ/TestFlashLFQ.csproj +++ b/mzLib/TestFlashLFQ/TestFlashLFQ.csproj @@ -1,7 +1,7 @@  - net6.0-windows + net8.0-windows false x64 @@ -13,9 +13,10 @@ - - - + + + + diff --git a/mzLib/Transcriptomics/Transcriptomics.csproj b/mzLib/Transcriptomics/Transcriptomics.csproj index a670300ca..f9962577c 100644 --- a/mzLib/Transcriptomics/Transcriptomics.csproj +++ b/mzLib/Transcriptomics/Transcriptomics.csproj @@ -1,7 +1,7 @@ - net6.0 + net8.0 x64 enable enable @@ -12,6 +12,10 @@ true + + + + diff --git a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj b/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj index 590324de2..d4e73fa42 100644 --- a/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj +++ b/mzLib/UsefulProteomicsDatabases/UsefulProteomicsDatabases.csproj @@ -1,7 +1,7 @@  - net6.0 + net8.0 x64 @@ -11,7 +11,8 @@ - + + diff --git a/mzLib/mzLib.nuspec b/mzLib/mzLib.nuspec index 5d5400e95..f66fdbe95 100644 --- a/mzLib/mzLib.nuspec +++ b/mzLib/mzLib.nuspec @@ -12,8 +12,8 @@ Library for mass spectrometry projects. Chemistry Spectrometry - - + + @@ -22,8 +22,8 @@ - - + + @@ -37,48 +37,48 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/mzLib/mzPlot/mzPlot.csproj b/mzLib/mzPlot/mzPlot.csproj index b8de36731..ec7550390 100644 --- a/mzLib/mzPlot/mzPlot.csproj +++ b/mzLib/mzPlot/mzPlot.csproj @@ -1,11 +1,12 @@  - net6.0-windows + net8.0-windows x64 + diff --git a/mzLib/pepXML/pepXML.csproj b/mzLib/pepXML/pepXML.csproj index e77e73219..aff6dfbfa 100644 --- a/mzLib/pepXML/pepXML.csproj +++ b/mzLib/pepXML/pepXML.csproj @@ -1,7 +1,7 @@ - net6.0 + net8.0 x64 @@ -9,5 +9,9 @@ full true + + + +