.NET 6.0 (smith-chem-wisc#615)

* net6.0 * merge upstream and update workflows * use nuget pack not dotnet pack * name * setup nuget separately * change release name back * readme * image before releases * replace webclient with httpclient * use multiline * use line concatenation for a couple places * no slash * use && * break up steps more * fix xml writer errors and such * more fixes * fix httpclient * code cleanup * add back comments Co-authored-by: MICHAEL SHORTREED <[email protected]>
trishorts · Apr 21, 2022 · b68aa96 · b68aa96
1 parent 3d0a4e4
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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: 5.0.x
+        dotnet-version: 6.0.x
     - name: Restore dependencies
       run: cd mzLib && dotnet restore
     - name: Build

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: 5.0.x
+          dotnet-version: 6.0.x
       - name: Set up NuGet
         uses: nuget/setup-nuget@v1
         with:

diff --git a/README.md b/README.md
@@ -2,7 +2,6 @@
 
 A library for mass spectrometry projects.
 
-
 [![GitHub Action Builds](https://github.com/smith-chem-wisc/mzLib/actions/workflows/dotnet.yml/badge.svg)](https://github.com/smith-chem-wisc/mzLib/actions/workflows/dotnet.yml)
 [![codecov](https://codecov.io/gh/smith-chem-wisc/mzLib/branch/master/graph/badge.svg)](https://codecov.io/gh/smith-chem-wisc/mzLib)
 [![Coverity Scan Build Status](https://scan.coverity.com/projects/10000/badge.svg)](https://scan.coverity.com/projects/mzlib)

diff --git a/mzLib/BayesianEstimation/BayesianEstimation.csproj b/mzLib/BayesianEstimation/BayesianEstimation.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/Chemistry/Chemistry.csproj b/mzLib/Chemistry/Chemistry.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/FlashLFQ/FlashLFQ.csproj b/mzLib/FlashLFQ/FlashLFQ.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/MassSpectrometry/MassSpectrometry.csproj b/mzLib/MassSpectrometry/MassSpectrometry.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/Mgf/Mgf.csproj b/mzLib/Mgf/Mgf.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/MzIdentML/MzIdentML.csproj b/mzLib/MzIdentML/MzIdentML.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/MzLibUtil/MzLibUtil.csproj b/mzLib/MzLibUtil/MzLibUtil.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/MzLibUtil/TextFileReading.cs b/mzLib/MzLibUtil/TextFileReading.cs
@@ -1,23 +1,20 @@
-using System;
-using System.Collections.Generic;
-using System.IO;
+using System.IO;
 using System.Reflection;
-using System.Text;
 
 namespace MzLibUtil
 {
     public static class TextFileReading
     {
-        readonly static FieldInfo charPosField = typeof(StreamReader).GetField("_charPos", BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.DeclaredOnly);
-        readonly static FieldInfo charLenField = typeof(StreamReader).GetField("_charLen", BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.DeclaredOnly);
-        readonly static FieldInfo charBufferField = typeof(StreamReader).GetField("_charBuffer", BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.DeclaredOnly);
+        private static readonly FieldInfo charPosField = typeof(StreamReader).GetField("_charPos", BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.DeclaredOnly);
+        private static readonly FieldInfo charLenField = typeof(StreamReader).GetField("_charLen", BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.DeclaredOnly);
+        private static readonly FieldInfo charBufferField = typeof(StreamReader).GetField("_charBuffer", BindingFlags.NonPublic | BindingFlags.Instance | BindingFlags.DeclaredOnly);
 
         /// <summary>
         /// The StreamReader object does not have a reliable method to get a byte position in
         /// a file. This method calculates it.
-        /// 
+        ///
         /// Code from: https://stackoverflow.com/questions/10189270/tracking-the-position-of-the-line-of-a-streamreader/34744440
-        /// 
+        ///
         /// See also alternative method:
         /// Code from: https://stackoverflow.com/questions/5404267/streamreader-and-seeking
         /// </summary>
@@ -35,4 +32,4 @@ public static long GetByteOffsetAtCurrentPosition(StreamReader reader)
             return reader.BaseStream.Position - reader.CurrentEncoding.GetByteCount(charBuffer, charPos, charLen - charPos);
         }
     }
-}
+}
diff --git a/mzLib/MzML/MzML.csproj b/mzLib/MzML/MzML.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/MzML/Mzml.cs b/mzLib/MzML/Mzml.cs
@@ -200,12 +200,10 @@ public static Mzml LoadAllStaticData(string filePath, FilteringParams filterPara
                 string sendCheckSum;
                 using (FileStream stream = File.OpenRead(filePath))
                 {
-                    using (SHA1Managed sha = new SHA1Managed())
-                    {
-                        byte[] checksum = sha.ComputeHash(stream);
-                        sendCheckSum = BitConverter.ToString(checksum)
-                            .Replace("-", string.Empty);
-                    }
+                    SHA1 sha = SHA1.Create();
+                    byte[] checksum = sha.ComputeHash(stream);
+                    sendCheckSum = BitConverter.ToString(checksum)
+                        .Replace("-", string.Empty);
                 }
                 sourceFile = new SourceFile(
                     @"no nativeID format",

diff --git a/mzLib/MzML/MzmlMethods.cs b/mzLib/MzML/MzmlMethods.cs
@@ -7,7 +7,7 @@
 using System.Linq;
 using System.Security.Cryptography;
 using System.Text;
-using System.Text.RegularExpressions;
+using System.Xml;
 using System.Xml.Serialization;
 
 namespace IO.MzML
@@ -974,12 +974,12 @@ public static void CreateAndWriteMyMzmlWithCalibratedSpectra(MsDataFile myMsData
 
             if (!writeIndexed)
             {
-                using (TextWriter writer = new StreamWriter(outputFile))
+                using (XmlWriter writer = XmlWriter.Create(outputFile, new() { NewLineChars = "\n", Indent = true }))
                 {
                     mzmlSerializer.Serialize(writer, mzML);
                 }
             }
-            else if (writeIndexed)
+            else
             {
                 Generated.indexedmzML indexedMzml = new Generated.indexedmzML();
                 indexedMzml.mzML = mzML;
@@ -992,9 +992,8 @@ public static void CreateAndWriteMyMzmlWithCalibratedSpectra(MsDataFile myMsData
                 };
 
                 // write the initial file to disk (just the mzML data in an indexedmzML wrapper, without the completed index)
-                using (TextWriter writer = new StreamWriter(outputFile))
+                using (XmlWriter writer = XmlWriter.Create(outputFile, new() { NewLineChars = "\n", Indent = true }))
                 {
-                    writer.NewLine = NewLine;
                     indexedSerializer.Serialize(writer, indexedMzml);
                 }
 
@@ -1095,9 +1094,8 @@ public static void CreateAndWriteMyMzmlWithCalibratedSpectra(MsDataFile myMsData
 
                 // write file w/ correct index and temporary checksum
                 indexedMzml.fileChecksum = "0";
-                using (TextWriter writer = new StreamWriter(outputFile))
+                using (XmlWriter writer = XmlWriter.Create(outputFile, new() { NewLineChars = "\n", Indent = true }))
                 {
-                    writer.NewLine = NewLine;
                     indexedSerializer.Serialize(writer, indexedMzml);
                 }
 
@@ -1106,9 +1104,8 @@ public static void CreateAndWriteMyMzmlWithCalibratedSpectra(MsDataFile myMsData
                 indexedMzml.fileChecksum = BitConverter.ToString(hash.Hash).Replace("-", string.Empty).ToLowerInvariant();
 
                 // write the final file w/ correct index and correct checksum
-                using (TextWriter writer = new StreamWriter(outputFile))
+                using (XmlWriter writer = XmlWriter.Create(outputFile, new() { NewLineChars = "\n", Indent = true }))
                 {
-                    writer.NewLine = NewLine;
                     indexedSerializer.Serialize(writer, indexedMzml);
                 }
             }

diff --git a/mzLib/Proteomics/Proteomics.csproj b/mzLib/Proteomics/Proteomics.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>
 

diff --git a/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs b/mzLib/Test/DatabaseTests/TestDatabaseLoaders.cs
@@ -588,7 +588,7 @@ public static void TestDownloadAvailableUniProtProteomes()
         {
             string filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests");
             string downloadedFilePath = ProteinDbRetriever.DownloadAvailableUniProtProteomes(filepath);
-            Assert.AreEqual(filepath + "\\availableUniProtProteomes.txt.gz", downloadedFilePath);
+            Assert.AreEqual(Path.Combine(filepath, "availableUniProtProteomes.txt.gz"), downloadedFilePath);
 
             Dictionary<string, string> uniprotProteoms = ProteinDbRetriever.UniprotProteomesList(downloadedFilePath);
 

diff --git a/mzLib/Test/Test.csproj b/mzLib/Test/Test.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0-windows</TargetFramework>
+    <TargetFramework>net6.0-windows</TargetFramework>
     <IsPackable>false</IsPackable>
     <Platforms>x64</Platforms>
   </PropertyGroup>
@@ -13,9 +13,9 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="NUnit" Version="3.12.0" />
-    <PackageReference Include="NUnit3TestAdapter" Version="3.16.1" />
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.5.0" />
+    <PackageReference Include="NUnit" Version="3.13.3" />
+    <PackageReference Include="NUnit3TestAdapter" Version="4.2.1" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.1.0" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/mzLib/Test/TestMsDataFile.cs b/mzLib/Test/TestMsDataFile.cs
@@ -188,9 +188,9 @@ public void TestAMoreRealFile()
 
             var precursorScan = myMsDataFile.GetOneBasedScan(theScan.OneBasedPrecursorScanNumber.Value);
             theScan.RefineSelectedMzAndIntensity(precursorScan.MassSpectrum);
-            Assert.AreEqual(.32872, theScan.SelectedIonIntensity, 0.01);
-            Assert.AreEqual(693.9892, theScan.SelectedIonMZ, 0.01);
-            Assert.AreEqual(693.655, theScan.SelectedIonMonoisotopicGuessMz, 0.001);
+            Assert.AreEqual(.32872, (double)theScan.SelectedIonIntensity, 0.01);
+            Assert.AreEqual(693.9892, (double)theScan.SelectedIonMZ, 0.01);
+            Assert.AreEqual(693.655, (double)theScan.SelectedIonMonoisotopicGuessMz, 0.001);
 
             Assert.AreNotEqual(0, myMsDataFile.GetOneBasedScan(2).MassSpectrum.FirstX);
 

diff --git a/mzLib/Test/TestRawFileReader.cs b/mzLib/Test/TestRawFileReader.cs
@@ -38,6 +38,7 @@ public static void TestLoadAllStaticDataRawFileReader(string infile, string outf
             Mzml.LoadAllStaticData(outfile2);
             Console.WriteLine($"Analysis time for TestLoadAllStaticDataRawFileReader({infile}): {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
         }
+
         /// <summary>
         /// Tests the dynamic connection for thermorawfilereader
         /// </summary>
@@ -72,8 +73,9 @@ public static void TestDynamicConnectionRawFileReader()
 
             Console.WriteLine($"Analysis time for TestDynamicConnectionRawFileReader: {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
         }
+
         /// <summary>
-        /// Test Peak Filtering for ThermoRawFileReader
+        /// Tests peak filtering for ThermoRawFileReader
         /// </summary>
         /// <param name="infile"></param>
         [Test]
@@ -122,6 +124,7 @@ public static void TestPeakFilteringRawFileReader(string infile)
             Console.WriteLine($"Analysis time for TestPeakFilteringRawFileReader: {stopwatch.Elapsed.Hours}h " +
                 $"{stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
         }
+
         /// <summary>
         /// Test Thermo License for ThermoRawFileReader
         /// </summary>
@@ -136,6 +139,7 @@ public static void TestThermoLicence()
 
             Console.WriteLine($"Analysis time for TestThermoLicence: {stopwatch.Elapsed.Hours}h {stopwatch.Elapsed.Minutes}m {stopwatch.Elapsed.Seconds}s");
         }
+
         /// <summary>
         /// Test that raw files can be opened dynamically in ThermoRawFileReader
         /// </summary>
@@ -202,6 +206,7 @@ public static void TestDynamicRaw(string fileName)
                 }
             }
         }
+
         /// <summary>
         /// Tests that you can read EtHCD files in ThermoRawFileReader
         /// </summary>

diff --git a/mzLib/TestFlashLFQ/TestFlashLFQ.csproj b/mzLib/TestFlashLFQ/TestFlashLFQ.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0-windows</TargetFramework>
+    <TargetFramework>net6.0-windows</TargetFramework>
     <IsPackable>false</IsPackable>
     <Platforms>x64</Platforms>
   </PropertyGroup>
@@ -13,9 +13,9 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="NUnit" Version="3.12.0" />
-    <PackageReference Include="NUnit3TestAdapter" Version="3.16.1" />
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.5.0" />
+    <PackageReference Include="NUnit" Version="3.13.3" />
+    <PackageReference Include="NUnit3TestAdapter" Version="4.2.1" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.1.0" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/mzLib/ThermoRawFileReader/ThermoRawFileReader.cs b/mzLib/ThermoRawFileReader/ThermoRawFileReader.cs
@@ -85,12 +85,10 @@ public static ThermoRawFileReader LoadAllStaticData(string filePath, IFilteringP
             string sendCheckSum;
             using (FileStream stream = File.OpenRead(filePath))
             {
-                using (SHA1Managed sha = new SHA1Managed())
-                {
-                    byte[] checksum = sha.ComputeHash(stream);
-                    sendCheckSum = BitConverter.ToString(checksum)
-                        .Replace("-", string.Empty);
-                }
+                SHA1 sha = SHA1.Create();
+                byte[] checksum = sha.ComputeHash(stream);
+                sendCheckSum = BitConverter.ToString(checksum)
+                    .Replace("-", string.Empty);
             }
 
             SourceFile sourceFile = new SourceFile(

diff --git a/mzLib/ThermoRawFileReader/ThermoRawFileReader.csproj b/mzLib/ThermoRawFileReader/ThermoRawFileReader.csproj
@@ -1,7 +1,7 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFramework>net5.0</TargetFramework>
+    <TargetFramework>net6.0</TargetFramework>
     <Platforms>x64</Platforms>
   </PropertyGroup>