fix package for linux

k-ujihara · Feb 28, 2021 · b4134ac · b4134ac
1 parent 77761b5
commit b4134ac
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Showing 18 changed files with 61,179 additions and 95 deletions.
diff --git a/MolViewer/Properties/AssemblyInfo.cs b/MolViewer/Properties/AssemblyInfo.cs
@@ -15,5 +15,5 @@
 [assembly: AssemblyCompany("Kazuya Ujihara")]
 [assembly: AssemblyCopyright("Copyright © 2016-2021 Kazuya Ujihara")]
 [assembly: AssemblyTrademark("")]
-[assembly: AssemblyVersion("1.6.0.0")]
-[assembly: AssemblyFileVersion("1.6.0.0")]
+[assembly: AssemblyVersion("1.6.1.0")]
+[assembly: AssemblyFileVersion("1.6.1.0")]
diff --git a/NCDK.Display.nuspec b/NCDK.Display.nuspec
@@ -1,30 +1,30 @@
 <?xml version="1.0" encoding="utf-8"?>
 <package xmlns="http://schemas.microsoft.com/packaging/2010/07/nuspec.xsd">
-  <metadata>
-    <id>NCDK.Display</id>
-    <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/a027f6689a34d9ede3bb9befad2d0f1c5b2bb711 snapshot.</releaseNotes>
-    <copyright>Copyright © 2016-2021 Kazuya Ujihara</copyright>
-    <tags>cdk cheminformatics chemistry toolkit</tags>
-	<frameworkAssemblies>
-      <frameworkAssembly assemblyName="PresentationCore" />
-      <frameworkAssembly assemblyName="PresentationFramework" />
-      <frameworkAssembly assemblyName="System.Windows.Presentation" />
-      <frameworkAssembly assemblyName="WindowsBase" />
-    </frameworkAssemblies>
-    <dependencies>
-      <dependency id="NCDK" version="1.6.0" />
-    </dependencies>
-  </metadata>
-  <files>
-    <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>
+    <metadata>
+        <id>NCDK.Display</id>
+        <version>1.6.1</version>
+        <title>NCDK.Display: Depiction module of NCDK</title>
+        <authors>Kazuya Ujihara</authors>
+        <owners>kazuya</owners>
+        <license type="expression">LGPL-2.1-only</license>
+        <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/a027f6689a34d9ede3bb9befad2d0f1c5b2bb711 snapshot.</releaseNotes>
+        <copyright>Copyright © 2016-2021 Kazuya Ujihara</copyright>
+        <tags>cdk cheminformatics chemistry toolkit</tags>
+        <frameworkAssemblies>
+            <frameworkAssembly assemblyName="PresentationCore" />
+            <frameworkAssembly assemblyName="PresentationFramework" />
+            <frameworkAssembly assemblyName="System.Windows.Presentation" />
+            <frameworkAssembly assemblyName="WindowsBase" />
+        </frameworkAssemblies>
+        <dependencies>
+            <dependency id="NCDK" version="1.6.1" />
+        </dependencies>
+    </metadata>
+    <files>
+        <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/NCDK.Display.csproj b/NCDK.Display/NCDK.Display.csproj
@@ -3,10 +3,8 @@
     <OutputType>Library</OutputType>
     <TargetFramework>net461</TargetFramework>
 
-    <AssemblyVersion>1.5.6.0</AssemblyVersion>
-    <FileVersion>1.5.6.0</FileVersion>
-    <Version>1.5.6</Version>
-    <Copyright>Copyright © 2016-2019 Kazuya Ujihara</Copyright>
+    <Version>1.6.1</Version>
+    <Copyright>Copyright © 2016-2021 Kazuya Ujihara</Copyright>
 
     <PackageId>NCDK.Display</PackageId>
     <Product>NCDK.Display: Depiction module of NCDK</Product>

diff --git a/NCDK.DisplayTests/NCDK.DisplayTests.csproj b/NCDK.DisplayTests/NCDK.DisplayTests.csproj
@@ -7,7 +7,7 @@
     <AssemblyOriginatorKeyFile>ncdk.snk</AssemblyOriginatorKeyFile>
     <RootNamespace>NCDK</RootNamespace>
     <Authors>Kazuya Ujihara</Authors>
-    <Copyright>Copyright © 2016-2018 Kazuya Ujihara</Copyright>
+    <Copyright>Copyright © 2016-2021 Kazuya Ujihara</Copyright>
     <PackageLicenseUrl>https://github.com/kazuyaujihara/NCDK/blob/master/LICENSE</PackageLicenseUrl>
     <PackageProjectUrl>https://github.com/kazuyaujihara/NCDK</PackageProjectUrl>
     <RepositoryUrl>https://github.com/kazuyaujihara/NCDK</RepositoryUrl>
@@ -22,7 +22,7 @@
 
   <ItemGroup>
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.8.3" />
-    <PackageReference Include="Moq" Version="4.16.0" />
+    <PackageReference Include="Moq" Version="4.16.1" />
     <PackageReference Include="MSTest.TestAdapter" Version="2.1.2" />
     <PackageReference Include="MSTest.TestFramework" Version="2.1.2" />
   </ItemGroup>

diff --git a/NCDK.LegacyTests/NCDK.LegacyTests.csproj b/NCDK.LegacyTests/NCDK.LegacyTests.csproj
@@ -33,8 +33,8 @@
 
   <ItemGroup>
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.3.0" />
-    <PackageReference Include="MSTest.TestAdapter" Version="2.0.0" />
-    <PackageReference Include="MSTest.TestFramework" Version="2.0.0" />
+    <PackageReference Include="MSTest.TestAdapter" Version="2.1.2" />
+    <PackageReference Include="MSTest.TestFramework" Version="2.1.2" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/NCDK.Math/NCDK.Math.csproj b/NCDK.Math/NCDK.Math.csproj
@@ -5,7 +5,7 @@
     <RootNamespace>NCDK</RootNamespace>
     <SignAssembly>true</SignAssembly>
     <AssemblyOriginatorKeyFile>ncdk.snk</AssemblyOriginatorKeyFile>
-    <Version>1.6.0</Version>
+    <Version>1.6.1</Version>
     <Copyright>Copyright © 2016-2021 Kazuya Ujihara</Copyright>
     <PackageProjectUrl></PackageProjectUrl>
     <RepositoryType>git</RepositoryType>

diff --git a/NCDK.RDF/NCDK.RDF.csproj b/NCDK.RDF/NCDK.RDF.csproj
@@ -3,7 +3,7 @@
   <PropertyGroup>
     <TargetFrameworks>netstandard2.0</TargetFrameworks>
 
-    <Version>1.6.0</Version>
+    <Version>1.6.1</Version>
     <Copyright>Copyright © 2019-2021 Kazuya Ujihara</Copyright>
 
     <PackageId>NCDK.RDF</PackageId>
@@ -45,7 +45,7 @@
   </ItemGroup>
 
   <ItemGroup>
-    <PackageReference Include="dotNetRDF" Version="2.6.1" />
+    <PackageReference Include="dotNetRDF" Version="2.6.2" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/NCDK.RDFTests/NCDK.RDFTests.csproj b/NCDK.RDFTests/NCDK.RDFTests.csproj
@@ -7,7 +7,7 @@
     <RootNamespace>NCDK</RootNamespace>
     <SignAssembly>true</SignAssembly>
     <AssemblyOriginatorKeyFile>ncdk.snk</AssemblyOriginatorKeyFile>
-    <Copyright>Copyright © 2016-2019 Kazuya Ujihara</Copyright>
+    <Copyright>Copyright © 2016-2021 Kazuya Ujihara</Copyright>
     <PackageLicenseUrl>https://github.com/kazuyaujihara/NCDK/blob/master/LICENSE</PackageLicenseUrl>
     <PackageProjectUrl>https://github.com/kazuyaujihara/NCDK</PackageProjectUrl>
     <RepositoryUrl>https://github.com/kazuyaujihara/NCDK</RepositoryUrl>
@@ -27,8 +27,8 @@
 
   <ItemGroup>
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="16.3.0" />
-    <PackageReference Include="MSTest.TestAdapter" Version="2.0.0" />
-    <PackageReference Include="MSTest.TestFramework" Version="2.0.0" />
+    <PackageReference Include="MSTest.TestAdapter" Version="2.1.2" />
+    <PackageReference Include="MSTest.TestFramework" Version="2.1.2" />
   </ItemGroup>
 
   <ItemGroup>

diff --git a/NCDK.nuspec b/NCDK.nuspec
@@ -1,35 +1,50 @@
 <?xml version="1.0" encoding="utf-8"?>
 <package xmlns="http://schemas.microsoft.com/packaging/2010/07/nuspec.xsd">
-  <metadata>
-    <id>NCDK</id>
-    <version>1.6.0</version>
-    <title>NCDK: library of algorithms for structural cheminformatics</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>NCDK is C# implementation of the Chemistry Development Kit (CDK), which is an open-source library of algorithms for structural cheminformatics and bioinformatics.</description>
-    <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>
-    <dependencies>
-      <dependency id="MathNet.Numerics.Signed" version="4.15.0" />
-    </dependencies>
-  </metadata>
-  <files>
-    <file src="NCDK.targets" target="build/" />
-    <file src="NCDK/bin/Release/netcoreapp3.1/NCDK.dll" target="lib/netcoreapp3.1" />
-    <file src="NCDK/bin/Release/netcoreapp3.1/NCDK.xml" target="lib/netcoreapp3.1" />
-    <file src="NCDK.Math/bin/Release/netcoreapp3.1/NCDK.Math.dll" target="lib/netcoreapp3.1" />
-    <file src="NCDK.Math/bin/Release/netcoreapp3.1/NCDK.Math.xml" target="lib/netcoreapp3.1" />
-    <file src="NCDK/bin/Release/netstandard2.0/NCDK.dll" target="lib/netstandard2.0" />
-    <file src="NCDK/bin/Release/netstandard2.0/NCDK.xml" target="lib/netstandard2.0" />
-    <file src="NCDK.Math/bin/Release/netstandard2.0/NCDK.Math.dll" target="lib/netstandard2.0" />
-    <file src="NCDK.Math/bin/Release/netstandard2.0/NCDK.Math.xml" target="lib/netstandard2.0" />
-    <file src="NCDK/runtimes/win-x64/native/libinchi.dll" target="runtimes/win-x64/native" />
-    <file src="NCDK/runtimes/win-x86/native/libinchi.dll" target="runtimes/win-x86/native" />
-    <file src="NCDK/runtimes/linux-x64/native/libinchi.so.1.05.00" target="runtimes/linux-x64/native" />
-    <file src="NCDK/runtimes/linux-x86/native/libinchi.so.1.05.00" target="runtimes/linux-x86/native" />
-  </files>
+    <metadata>
+        <id>NCDK</id>
+        <version>1.6.1</version>
+        <title>NCDK: library of algorithms for structural cheminformatics</title>
+        <authors>Kazuya Ujihara</authors>
+        <owners>kazuya</owners>
+        <license type="expression">LGPL-2.1-only</license>
+        <projectUrl>https://github.com/kazuyaujihara/NCDK</projectUrl>
+        <requireLicenseAcceptance>false</requireLicenseAcceptance>
+        <description>NCDK is C# implementation of the Chemistry Development Kit (CDK), which is an open-source library of algorithms for structural cheminformatics and bioinformatics.</description>
+        <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>
+        <dependencies>
+            <dependency id="MathNet.Numerics.Signed" version="4.15.0" />
+            <!--
+            <dependency id="dotNetRDF" version="2.6.2" />
+            -->
+        </dependencies>
+    </metadata>
+    <files>
+        <file src="NCDK.targets" target="build/" />
+        <file src="NCDK/bin/Release/netcoreapp3.1/NCDK.dll" target="lib/netcoreapp3.1" />
+        <file src="NCDK/bin/Release/netcoreapp3.1/NCDK.xml" target="lib/netcoreapp3.1" />
+        <file src="NCDK.Math/bin/Release/netcoreapp3.1/NCDK.Math.dll" target="lib/netcoreapp3.1" />
+        <file src="NCDK.Math/bin/Release/netcoreapp3.1/NCDK.Math.xml" target="lib/netcoreapp3.1" />
+        <!--
+        <file src="NCDK.RDF/bin/Release/netcoreapp3.1/NCDK.RDF.dll" target="lib/netcoreapp3.1" />
+        <file src="NCDK.RDF/bin/Release/netcoreapp3.1/NCDK.RDF.xml" target="lib/netcoreapp3.1" />
+        <file src="NCDK.Legacy/bin/Release/netcoreapp3.1/NCDK.Legacy.dll" target="lib/netcoreapp3.1" />
+        <file src="NCDK.Legacy/bin/Release/netcoreapp3.1/NCDK.Legacy.xml" target="lib/netcoreapp3.1" />
+        -->
+        <file src="NCDK/bin/Release/netstandard2.0/NCDK.dll" target="lib/netstandard2.0" />
+        <file src="NCDK/bin/Release/netstandard2.0/NCDK.xml" target="lib/netstandard2.0" />
+        <file src="NCDK.Math/bin/Release/netstandard2.0/NCDK.Math.dll" target="lib/netstandard2.0" />
+        <file src="NCDK.Math/bin/Release/netstandard2.0/NCDK.Math.xml" target="lib/netstandard2.0" />
+        <!--
+        <file src="NCDK.RDF/bin/Release/netstandard2.0/NCDK.RDF.dll" target="lib/netstandard2.0" />
+        <file src="NCDK.RDF/bin/Release/netstandard2.0/NCDK.RDF.xml" target="lib/netstandard2.0" />
+        <file src="NCDK.Legacy/bin/Release/netstandard2.0/NCDK.Legacy.dll" target="lib/netstandard2.0" />
+        <file src="NCDK.Legacy/bin/Release/netstandard2.0/NCDK.Legacy.xml" target="lib/netstandard2.0" />
+        -->
+        <file src="NCDK/runtimes/win-x64/native/libinchi.dll" target="runtimes/win-x64/native" />
+        <file src="NCDK/runtimes/win-x86/native/libinchi.dll" target="runtimes/win-x86/native" />
+        <file src="NCDK/runtimes/linux-x64/native/libinchi.so" target="runtimes/linux-x64/native" />
+        <file src="NCDK/runtimes/linux-x86/native/libinchi.so" target="runtimes/linux-x86/native" />
+    </files>
 </package>
diff --git a/NCDK/Graphs/Invariant/CanonOpts.cs b/NCDK/Graphs/Invariant/CanonOpts.cs
@@ -25,7 +25,7 @@ namespace NCDK.Graphs.Invariant
 {
     /// <summary>
     /// Basic flavor options to tweak canonical invariants, note these deliberately mirror some fields
-    /// from the <see cref="NCDK.Smiles.SmiFlavor"/> .
+    /// from the <see cref="NCDK.Smiles.SmiFlavors"/> .
     /// </summary>
     public static class CanonOpts
     {

diff --git a/NCDK/IO/MDLV2000Reader.cs b/NCDK/IO/MDLV2000Reader.cs
@@ -694,11 +694,7 @@ internal IAtom ReadAtomFast(string line, IChemObjectBuilder builder, Dictionary<
             // xxxxx.xxxxyyyyy.yyyyzzzzz.zzzz aaaddcccssshhhbbbvvvHHHrrriiimmmnnneee
 
             string symbol;
-<<<<<<< HEAD
-            double x = 0, y = 0, z = 0;
-=======
             double x, y, z;
->>>>>>> Fix typed Clone methods and cleanup
             int massDiff = 0;
             int charge = 0;
             int parity = 0;
@@ -899,19 +895,14 @@ internal IBond ReadBondFast(string line, IChemObjectBuilder builder, IAtom[] ato
 
             if (isQuery && !(bond is QueryBond))
             {
-<<<<<<< HEAD
-                var order = bond.Order;
-=======
->>>>>>> Fix typed Clone methods and cleanup
                 Expr expr;
                 if (bond.IsAromatic)
                 {
                     expr = new Expr(ExprType.IsAromatic);
                 }
                 else
                 {
-                    expr = new Expr(ExprType.Order,
-                                    bond.Order.Numeric());
+                    expr = new Expr(ExprType.Order, bond.Order.Numeric());
                 }
                 bond = new QueryBond(atoms[u], atoms[v], expr);
             }

diff --git a/NCDK/Isomorphisms/Matchers/QueryAtomContainer.cs b/NCDK/Isomorphisms/Matchers/QueryAtomContainer.cs
@@ -303,7 +303,7 @@ public static void Create(IAtomContainer dst, IAtomContainer src, params ExprTyp
         /// Please note not all <see cref="ExprType"/>s are currently supported, if you
         /// require a specific type that you think is useful please open an issue.
         /// </remarks>
-        /// <param name="mol">the molecule</param>
+        /// <param name="src">the molecule</param>
         /// <param name="opts">set of the expr types to match</param>
         /// <returns>the query molecule</returns>
         public static QueryAtomContainer Create(IAtomContainer src, params ExprType[] opts)

diff --git a/NCDK/NCDK.csproj b/NCDK/NCDK.csproj
@@ -3,9 +3,7 @@
   <PropertyGroup>
     <TargetFrameworks>netcoreapp3.1;netstandard2.0</TargetFrameworks>
 
-    <AssemblyVersion>1.6.0.0</AssemblyVersion>
-    <FileVersion>1.6.0.0</FileVersion>
-    <Version>1.6.0</Version>
+    <Version>1.6.1</Version>
     <Copyright>Copyright © 2016-2021 Kazuya Ujihara</Copyright>
 
     <PackageId>NCDK</PackageId>
@@ -56,6 +54,10 @@
     <DocumentationFile>bin\Release\netstandard2.0\NCDK.xml</DocumentationFile>
   </PropertyGroup>
 
+  <PropertyGroup Condition="'$(Configuration)|$(TargetFramework)|$(Platform)'=='Release|netcoreapp3.1|AnyCPU'">
+    <DocumentationFile>C:\Users\ujiha\Documents\NCDK\NCDK\NCDK.xml</DocumentationFile>
+  </PropertyGroup>
+
   <ItemGroup>
     <Compile Remove="QSAR\Descriptors\Atomic\%24AtomicDescriptor.tt.cs" />
     <Compile Remove="QSAR\Descriptors\Atomic\%24ProtonDescriptor.tt.cs" />
@@ -297,10 +299,10 @@
       <Generator>TextTemplatingFileGenerator</Generator>
       <LastGenOutput>$ExampleCodes.cs</LastGenOutput>
     </None>
-    <None Update="runtimes\linux-x64\native\libinchi.so.1.05.00">
+    <None Update="runtimes\linux-x64\native\libinchi.so">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
-    <None Update="runtimes\linux-x86\native\libinchi.so.1.05.00">
+    <None Update="runtimes\linux-x86\native\libinchi.so">
       <CopyToOutputDirectory>PreserveNewest</CopyToOutputDirectory>
     </None>
     <None Update="TT\AdductFormula.tt">