Fix typed clone methods and cleanup

k-ujihara · Feb 4, 2021 · 77761b5 · 77761b5
1 parent f1e9572
commit 77761b5
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Showing 152 changed files with 1,070 additions and 923 deletions.
diff --git a/.gitignore b/.gitignore
@@ -275,3 +275,5 @@ ModelManifest.xml
 !NCDK/x86/libinchi.dll
 !NCDK/x64/libinchi.dll
 !BuildAll.bat
+Test.sln
+Test/
diff --git a/BuildAll.bat b/BuildAll.bat
@@ -1,56 +1,75 @@
 pushd NCDK
+call :BuildProject NCDK
+if errorlevel 1 goto :ERROREND
+popd
+pushd NCDK.Math
 dotnet add package MathNet.Numerics.Signed
 dotnet restore
-call :BuildProject NCDK yes
+call :BuildProject NCDK.Math
+if errorlevel 1 goto :ERROREND
 popd
-pushd NCDK.Tests
+call :BuildNeGet NCDK
+if errorlevel 1 goto :ERROREND
+pushd NCDKTests
 call :BuildProject NCDKTests
+if errorlevel 1 goto :ERROREND
 popd
 
 pushd NCDK.RDF
 dotnet add package dotNetRDF
 dotnet restore
 call :BuildProject NCDK.RDF
+if errorlevel 1 goto :ERROREND
 popd
 pushd NCDK.RDFTests
 call :BuildProject NCDK.RDFTests
+if errorlevel 1 goto :ERROREND
 popd
 
 pushd NCDK.Legacy
 call :BuildProject NCDK.Legacy
+if errorlevel 1 goto :ERROREND
 popd
 pushd NCDK.LegacyTests
 call :BuildProject NCDK.LegacyTests
+if errorlevel 1 goto :ERROREND
 popd
 
 pushd NCDK.Display
-call :BuildProject NCDK.Display yes
+call :BuildProject NCDK.Display
+if errorlevel 1 goto :ERROREND
 popd
+call :BuildNeGet NCDK.Display
+if errorlevel 1 goto :ERROREND
 pushd NCDK.DisplayTests
 call :BuildProject NCDK.DisplayTests
+if errorlevel 1 goto :ERROREND
 popd
 
-goto END
+goto :END
 
 :BuildProject
-
 set ProjectName=%1
-set NuGetOption=%2
 if "%ProjectName%" == "" exit 1
-if "%NuGetOption%" == "yes" set NuGetOption=%1
 MSBuild "%ProjectName%.csproj" /t:Build /p:Configuration=Release
+if errorlevel 1 exit /b 1
+set ProjectName=
+exit /b
 
+:BuildNeGet
+set NuGetOption=%1
 if "%NuGetOption%" == "" goto SkipNuGet
 nuget pack "%NuGetOption%.nuspec" -Prop Configuration=Release -IncludeReferencedProjects
+if errorlevel 1 exit /b 1
 if "%MyNuGetDir%" neq "" (
 	xcopy /D /Y "*.nupkg" "%MyNuGetDir%"
 	del /Q "*.nupkg"
 )
-:SkipNuGet
-
 set ProjectName=
-set NuGetOption=
-
 exit /b
 
+:ERROREND
+
+exit /b 1
+
 :END
diff --git a/ExampleCodes/Formula/FullEnumerationFormulaGenerator_Example.cs b/ExampleCodes/Formula/FullEnumerationFormulaGenerator_Example.cs
@@ -26,7 +26,7 @@ public void Main()
 
             double minMass = 133.003;
             double maxMass = 133.005;
-            MolecularFormulaGenerator mfg = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
+            MolecularFormulaGenerator mfg = new MolecularFormulaGenerator(minMass, maxMass, mfRange);
             IMolecularFormulaSet mfSet = mfg.GetAllFormulas();
             #endregion
         }

diff --git a/ExampleCodes/Formula/MolecularFormulaGenerator_Example.cs b/ExampleCodes/Formula/MolecularFormulaGenerator_Example.cs
@@ -23,10 +23,9 @@ public void Main()
             mfRange.AddIsotope(p, 0, 10);
             mfRange.AddIsotope(s, 0, 10);
 
-            var builder = Silent.ChemObjectBuilder.Instance;
             double minMass = 133.003;
             double maxMass = 133.005;
-            MolecularFormulaGenerator mfg = new MolecularFormulaGenerator(builder, minMass, maxMass, mfRange);
+            MolecularFormulaGenerator mfg = new MolecularFormulaGenerator(minMass, maxMass, mfRange);
             IMolecularFormulaSet mfSet = mfg.GetAllFormulas();
             #endregion
         }

diff --git a/MolViewer/MolViewer.csproj b/MolViewer/MolViewer.csproj
@@ -15,6 +15,7 @@
     <WarningLevel>4</WarningLevel>
     <AutoGenerateBindingRedirects>true</AutoGenerateBindingRedirects>
     <TargetFrameworkProfile />
+    <IsWebBootstrapper>false</IsWebBootstrapper>
     <PublishUrl>publish\</PublishUrl>
     <Install>true</Install>
     <InstallFrom>Disk</InstallFrom>
@@ -27,7 +28,6 @@
     <MapFileExtensions>true</MapFileExtensions>
     <ApplicationRevision>0</ApplicationRevision>
     <ApplicationVersion>1.0.0.%2a</ApplicationVersion>
-    <IsWebBootstrapper>false</IsWebBootstrapper>
     <UseApplicationTrust>false</UseApplicationTrust>
     <BootstrapperEnabled>true</BootstrapperEnabled>
   </PropertyGroup>
@@ -62,24 +62,24 @@
     <StartupObject>NCDK.MolViewer.App</StartupObject>
   </PropertyGroup>
   <ItemGroup>
-    <Reference Include="CommonServiceLocator, Version=2.0.5.0, Culture=neutral, PublicKeyToken=489b6accfaf20ef0, processorArchitecture=MSIL">
-      <HintPath>..\packages\CommonServiceLocator.2.0.5\lib\net46\CommonServiceLocator.dll</HintPath>
+    <Reference Include="CommonServiceLocator, Version=2.0.6.0, Culture=neutral, PublicKeyToken=489b6accfaf20ef0, processorArchitecture=MSIL">
+      <HintPath>..\packages\CommonServiceLocator.2.0.6\lib\net46\CommonServiceLocator.dll</HintPath>
     </Reference>
-    <Reference Include="Prism, Version=7.2.0.1422, Culture=neutral, PublicKeyToken=40ee6c3a2184dc59, processorArchitecture=MSIL">
-      <HintPath>..\packages\Prism.Core.7.2.0.1422\lib\net45\Prism.dll</HintPath>
+    <Reference Include="Microsoft.Xaml.Behaviors, Version=1.1.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a, processorArchitecture=MSIL">
+      <HintPath>..\packages\Microsoft.Xaml.Behaviors.Wpf.1.1.31\lib\net45\Microsoft.Xaml.Behaviors.dll</HintPath>
     </Reference>
-    <Reference Include="Prism.Wpf, Version=7.2.0.1422, Culture=neutral, PublicKeyToken=40ee6c3a2184dc59, processorArchitecture=MSIL">
-      <HintPath>..\packages\Prism.Wpf.7.2.0.1422\lib\net45\Prism.Wpf.dll</HintPath>
+    <Reference Include="Prism, Version=8.0.0.1909, Culture=neutral, PublicKeyToken=40ee6c3a2184dc59, processorArchitecture=MSIL">
+      <HintPath>..\packages\Prism.Core.8.0.0.1909\lib\net45\Prism.dll</HintPath>
+    </Reference>
+    <Reference Include="Prism.Wpf, Version=8.0.0.1909, Culture=neutral, PublicKeyToken=40ee6c3a2184dc59, processorArchitecture=MSIL">
+      <HintPath>..\packages\Prism.Wpf.8.0.0.1909\lib\net461\Prism.Wpf.dll</HintPath>
     </Reference>
     <Reference Include="System" />
     <Reference Include="System.Configuration" />
     <Reference Include="System.Data" />
     <Reference Include="System.ValueTuple, Version=4.0.3.0, Culture=neutral, PublicKeyToken=cc7b13ffcd2ddd51, processorArchitecture=MSIL">
       <HintPath>..\packages\System.ValueTuple.4.5.0\lib\net461\System.ValueTuple.dll</HintPath>
     </Reference>
-    <Reference Include="System.Windows.Interactivity, Version=4.5.0.0, Culture=neutral, PublicKeyToken=31bf3856ad364e35, processorArchitecture=MSIL">
-      <HintPath>..\packages\Prism.Wpf.7.2.0.1422\lib\net45\System.Windows.Interactivity.dll</HintPath>
-    </Reference>
     <Reference Include="System.Windows.Presentation" />
     <Reference Include="System.Xml" />
     <Reference Include="System.Core" />

diff --git a/MolViewer/Properties/AssemblyInfo.cs b/MolViewer/Properties/AssemblyInfo.cs
@@ -13,7 +13,7 @@
 [assembly: AssemblyMetadata("ProjectUrl", "https://github.com/kazuyaujihara/NCDK")]
 [assembly: AssemblyMetadata("LicenseUrl", "https://github.com/kazuyaujihara/NCDK/blob/master/LICENSE")]
 [assembly: AssemblyCompany("Kazuya Ujihara")]
-[assembly: AssemblyCopyright("Copyright © 2016-2019 Kazuya Ujihara")]
+[assembly: AssemblyCopyright("Copyright © 2016-2021 Kazuya Ujihara")]
 [assembly: AssemblyTrademark("")]
-[assembly: AssemblyVersion("1.5.6.0")]
-[assembly: AssemblyFileVersion("1.5.6.0")]
+[assembly: AssemblyVersion("1.6.0.0")]
+[assembly: AssemblyFileVersion("1.6.0.0")]
diff --git a/MolViewer/packages.config b/MolViewer/packages.config
@@ -1,7 +1,8 @@
 <?xml version="1.0" encoding="utf-8"?>
 <packages>
-  <package id="CommonServiceLocator" version="2.0.5" targetFramework="net461" />
-  <package id="Prism.Core" version="7.2.0.1422" targetFramework="net461" />
-  <package id="Prism.Wpf" version="7.2.0.1422" targetFramework="net461" />
+  <package id="CommonServiceLocator" version="2.0.6" targetFramework="net461" />
+  <package id="Microsoft.Xaml.Behaviors.Wpf" version="1.1.31" targetFramework="net461" />
+  <package id="Prism.Core" version="8.0.0.1909" targetFramework="net461" />
+  <package id="Prism.Wpf" version="8.0.0.1909" targetFramework="net461" />
   <package id="System.ValueTuple" version="4.5.0" targetFramework="net461" />
 </packages>
diff --git a/NCDK.Display/NCDK.Display.nuspec → NCDK.Display.nuspec b/NCDK.Display/NCDK.Display.nuspec → NCDK.Display.nuspec
@@ -2,16 +2,16 @@
 <package xmlns="http://schemas.microsoft.com/packaging/2010/07/nuspec.xsd">
   <metadata>
     <id>NCDK.Display</id>
-    <version>1.5.6</version>
+    <version>1.6.0</version>
     <title>NCDK.Display: Depiction module of NCDK</title>
     <authors>Kazuya Ujihara</authors>
     <owners>kazuya</owners>
     <licenseUrl>https://github.com/kazuyaujihara/NCDK/blob/master/LICENSE</licenseUrl>
     <projectUrl>https://github.com/kazuyaujihara/NCDK</projectUrl>
     <requireLicenseAcceptance>false</requireLicenseAcceptance>
     <description>Depiction module of NCDK</description>
-    <releaseNotes>This release is based on https://github.com/cdk/cdk/tree/c76443e0a69a4110c6a0fe65704abccce8a435ff snapshot.</releaseNotes>
-    <copyright>Copyright © 2016-2019 Kazuya Ujihara</copyright>
+    <releaseNotes>This release is based on https://github.com/cdk/cdk/tree/a027f6689a34d9ede3bb9befad2d0f1c5b2bb711 snapshot.</releaseNotes>
+    <copyright>Copyright © 2016-2021 Kazuya Ujihara</copyright>
     <tags>cdk cheminformatics chemistry toolkit</tags>
 	<frameworkAssemblies>
       <frameworkAssembly assemblyName="PresentationCore" />
@@ -20,11 +20,11 @@
       <frameworkAssembly assemblyName="WindowsBase" />
     </frameworkAssemblies>
     <dependencies>
-      <dependency id="NCDK" version="1.5.6" />
+      <dependency id="NCDK" version="1.6.0" />
     </dependencies>
   </metadata>
   <files>
-    <file src="bin/Release/net461/NCDK.Display.dll" target="lib/net461" />
-    <file src="bin/Release/net461/NCDK.Display.xml" target="lib/net461" />
+    <file src="NCDK.Display/bin/Release/net461/NCDK.Display.dll" target="lib/net461" />
+    <file src="NCDK.Display/bin/Release/net461/NCDK.Display.xml" target="lib/net461" />
   </files>
 </package>
diff --git a/NCDK.Display.sln b/NCDK.Display.sln
@@ -1,13 +1,17 @@
 
 Microsoft Visual Studio Solution File, Format Version 12.00
-# Visual Studio 15
-VisualStudioVersion = 15.0.27130.2024
+# Visual Studio Version 16
+VisualStudioVersion = 16.0.30907.101
 MinimumVisualStudioVersion = 10.0.40219.1
 Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "Solution Items", "Solution Items", "{3ED0556C-42B8-4FEF-9606-B0474A2E69D2}"
 	ProjectSection(SolutionItems) = preProject
+		BuildAll.bat = BuildAll.bat
 		ChemObjectConfig.ttinclude = ChemObjectConfig.ttinclude
 		Config.ttinclude = Config.ttinclude
 		IncludeExamples.ttinclude = IncludeExamples.ttinclude
+		NCDK.Display.nuspec = NCDK.Display.nuspec
+		NCDK.nuspec = NCDK.nuspec
+		NCDK.targets = NCDK.targets
 	EndProjectSection
 EndProject
 Project("{9A19103F-16F7-4668-BE54-9A1E7A4F7556}") = "NCDK", "NCDK\NCDK.csproj", "{B0B5EACF-5F39-42D0-BACD-1FF559CCC8B2}"

diff --git a/NCDK.DisplayTests/NCDK.DisplayTests.csproj b/NCDK.DisplayTests/NCDK.DisplayTests.csproj
@@ -21,10 +21,10 @@
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.3.0" />
-    <PackageReference Include="Moq" Version="4.13.0" />
-    <PackageReference Include="MSTest.TestAdapter" Version="2.0.0" />
-    <PackageReference Include="MSTest.TestFramework" Version="2.0.0" />
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.8.3" />
+    <PackageReference Include="Moq" Version="4.16.0" />
+    <PackageReference Include="MSTest.TestAdapter" Version="2.1.2" />
+    <PackageReference Include="MSTest.TestFramework" Version="2.1.2" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/NCDK.Legacy/NCDK.Legacy.csproj b/NCDK.Legacy/NCDK.Legacy.csproj
@@ -1,27 +1,26 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFrameworks>net461;netstandard2.0</TargetFrameworks>
-    <Version>1.5.7</Version>
+    <TargetFrameworks>netcoreapp3.1;netstandard2.0</TargetFrameworks>
+    <Version>1.6.0</Version>
     <Authors>Kazuya Ujihara</Authors>
     <Product>NCDK</Product>
     <Description>The legacy classes of NCDK.</Description>
-    <Copyright>Copyright © 2019 Kazuya Ujihara</Copyright>
-    <PackageLicenseUrl>https://github.com/kazuyaujihara/NCDK/blob/master/LICENSE</PackageLicenseUrl>
+    <Copyright>Copyright © 2019-2021 Kazuya Ujihara</Copyright>
+    <PackageLicenseUrl></PackageLicenseUrl>
     <PackageProjectUrl>https://github.com/kazuyaujihara/NCDK</PackageProjectUrl>
     <RepositoryUrl>https://github.com/kazuyaujihara/NCDK</RepositoryUrl>
     <RepositoryType>git</RepositoryType>
     <SignAssembly>true</SignAssembly>
     <AssemblyOriginatorKeyFile>ncdk.snk</AssemblyOriginatorKeyFile>
     <RootNamespace>NCDK</RootNamespace>
-    <AssemblyVersion>1.5.6.0</AssemblyVersion>
-    <FileVersion>1.5.6.0</FileVersion>
-    <PackageReleaseNotes>This release is based on [cdk 2019-11-27](https://github.com/cdk/cdk/tree/c76443e0a69a4110c6a0fe65704abccce8a435ff) snapshot.</PackageReleaseNotes>
+    <PackageReleaseNotes>This release is based on [cdk 2021-01-31](https://github.com/cdk/cdk/tree/a027f6689a34d9ede3bb9befad2d0f1c5b2bb711f) snapshot.</PackageReleaseNotes>
+    <PackageLicenseExpression>LGPL 2.1</PackageLicenseExpression>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
     <NoWarn>1701;1702;0612;1573;1591</NoWarn>
-    <DocumentationFile>bin\Release\net461\NCDK.Legacy.xml</DocumentationFile>
+    <DocumentationFile>bin\Release\$(TargetFramework)\NCDK.Legacy.xml</DocumentationFile>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|AnyCPU'">

diff --git a/NCDK.Math/NCDK.Math.csproj b/NCDK.Math/NCDK.Math.csproj
@@ -1,10 +1,20 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFrameworks>netstandard2.0</TargetFrameworks>
+    <TargetFrameworks>netcoreapp3.1;netstandard2.0</TargetFrameworks>
     <RootNamespace>NCDK</RootNamespace>
     <SignAssembly>true</SignAssembly>
     <AssemblyOriginatorKeyFile>ncdk.snk</AssemblyOriginatorKeyFile>
+    <Version>1.6.0</Version>
+    <Copyright>Copyright © 2016-2021 Kazuya Ujihara</Copyright>
+    <PackageProjectUrl></PackageProjectUrl>
+    <RepositoryType>git</RepositoryType>
+    <PackageTags>cdk cheminformatics chemistry toolkit</PackageTags>
+    <RepositoryUrl>https://github.com/kazuyaujihara/NCDK</RepositoryUrl>
+    <Product>NCDK.Math: Math functions of NCDK</Product>
+    <PackageLicenseExpression>LPGL 2.1</PackageLicenseExpression>
+    <Description>Math package for NCDK.</Description>
+    <PackageReleaseNotes>This release is based on [cdk 2021-01-31](https://github.com/cdk/cdk/tree/a027f6689a34d9ede3bb9befad2d0f1c5b2bb711f) snapshot.</PackageReleaseNotes>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
@@ -15,12 +25,12 @@
     <NoWarn>1701;1702;0162,0164,0219,0612,0618,0672,0809,1591,3021,1573</NoWarn>
   </PropertyGroup>
 
-  <PropertyGroup Condition="'$(Configuration)|$(TargetFramework)|$(Platform)'=='Release|net461|AnyCPU'">
-    <DocumentationFile>bin\Release\net461\NCDK.Math.xml</DocumentationFile>
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
+    <DocumentationFile>bin\Release\$(TargetFramework)\NCDK.Math.xml</DocumentationFile>
   </PropertyGroup>
 
   <ItemGroup>
-    <PackageReference Include="MathNet.Numerics.Signed" Version="4.9.0" />
+    <PackageReference Include="MathNet.Numerics.Signed" Version="4.15.0" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/NCDK.RDF/NCDK.RDF.csproj b/NCDK.RDF/NCDK.RDF.csproj
@@ -1,19 +1,17 @@
 <Project Sdk="Microsoft.NET.Sdk">
 
   <PropertyGroup>
-    <TargetFrameworks>net461;netstandard2.0</TargetFrameworks>
+    <TargetFrameworks>netstandard2.0</TargetFrameworks>
 
-    <AssemblyVersion>1.5.6.0</AssemblyVersion>
-    <FileVersion>1.5.6.0</FileVersion>
-    <Version>1.5.7</Version>
-    <Copyright>Copyright © 2019 Kazuya Ujihara</Copyright>
+    <Version>1.6.0</Version>
+    <Copyright>Copyright © 2019-2021 Kazuya Ujihara</Copyright>
 
     <PackageId>NCDK.RDF</PackageId>
     <Product>NCDK.RDF: RDF package for NCDK</Product>
     <Description>RDF package for NCDK.</Description>
 
     <PackageTags>cdk cheminformatics chemistry toolkit</PackageTags>
-    <PackageReleaseNotes>This release is based on [cdk 2019-11-27](https://github.com/cdk/cdk/tree/c76443e0a69a4110c6a0fe65704abccce8a435ff) snapshot.</PackageReleaseNotes>
+    <PackageReleaseNotes>This release is based on [cdk 2021-01-31](https://github.com/cdk/cdk/tree/a027f6689a34d9ede3bb9befad2d0f1c5b2bb711f) snapshot.</PackageReleaseNotes>
     <GeneratePackageOnBuild>false</GeneratePackageOnBuild>
 
     <Authors>Kazuya Ujihara</Authors>
@@ -24,7 +22,8 @@
     <AssemblyOriginatorKeyFile>ncdk.snk</AssemblyOriginatorKeyFile>
     <RootNamespace>NCDK</RootNamespace>
     <PackageProjectUrl>https://github.com/kazuyaujihara/NCDK</PackageProjectUrl>
-    <PackageLicenseUrl>https://github.com/kazuyaujihara/NCDK/blob/master/LICENSE</PackageLicenseUrl>
+    <PackageLicenseUrl></PackageLicenseUrl>
+    <PackageLicenseExpression>LPGL 2.1</PackageLicenseExpression>
   </PropertyGroup>
 
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
@@ -37,20 +36,16 @@
     <NoWarn>1701;1702;0162,0164,0219,0612,0618,0672,0809,1591,3021,1573</NoWarn>
   </PropertyGroup>
 
-  <PropertyGroup Condition="'$(Configuration)|$(TargetFramework)|$(Platform)'=='Release|net461|AnyCPU'">
-    <DocumentationFile>bin\Release\net461\NCDK.RDF.xml</DocumentationFile>
-  </PropertyGroup>
-
-  <PropertyGroup Condition="'$(Configuration)|$(TargetFramework)|$(Platform)'=='Release|netstandard2.0|AnyCPU'">
-    <DocumentationFile>bin\Release\netstandard2.0\NCDK.RDF.xml</DocumentationFile>
+  <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|AnyCPU'">
+    <DocumentationFile>bin\Release\$(TargetFramework)\NCDK.RDF.xml</DocumentationFile>
   </PropertyGroup>
-  
+
   <ItemGroup>
     <Compile Include="..\NCDK\Properties\InternalVisibles..cs" Link="Properties\InternalVisibles..cs" />
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="dotNetRDF" Version="2.2.0" />
+    <PackageReference Include="dotNetRDF" Version="2.6.1" />
   </ItemGroup>
 
   <ItemGroup>