C# Build Net6 library and tests using cmake (#7326)

* Dotnet core build and test for RDKit

* Cmake dot net build and ctest working on windows

* Remove old Linux mono build

* Update to net8 and create RDK_BUILD_DOTNET_CSHARP_TESTS flag

.gitignore

@@ -3,7 +3,12 @@
 /Code/JavaWrappers/gmwrapper/doc/*
 /Code/JavaWrappers/gmwrapper/build/*
 /Code/JavaWrappers/gmwrapper/build-test/*
-/Code/JavaWrappers/csharp_wrapper/swig_csharp
+/Code/JavaWrappers/csharp_wrapper/swig_csharp/*.cs
+/Code/JavaWrappers/csharp_wrapper/swig_csharp/*.cxx
+/Code/JavaWrappers/csharp_wrapper/swig_csharp/bin
+/Code/JavaWrappers/csharp_wrapper/swig_csharp/obj
+/Code/JavaWrappers/csharp_wrapper/RdkitTests/bin
+/Code/JavaWrappers/csharp_wrapper/RdkitTests/obj
 /Data/Fonts/ComicNeue-*
 /Data/Fonts/OFL.txt
 /vcpkg/*

CMakeLists.txt

@@ -40,6 +40,7 @@ option(RDK_BUILD_SLN_SUPPORT "include support for the SLN format" ON )
 option(RDK_TEST_MULTITHREADED "run some tests of multithreading" ON )
 option(RDK_BUILD_SWIG_JAVA_WRAPPER "build the SWIG JAVA wrappers (does nothing if RDK_BUILD_SWIG_WRAPPERS is not set)" ON )
 option(RDK_BUILD_SWIG_CSHARP_WRAPPER "build the experimental SWIG C# wrappers (does nothing if RDK_BUILD_SWIG_WRAPPERS is not set)" OFF )
+option(RDK_BUILD_DOTNET_CSHARP_TESTS "build the DotNet Core tests for C# wrappers (does nothing if RDK_BUILD_SWIG_CSHARP_WRAPPER is not set)" OFF )
 option(RDK_SWIG_STATIC "statically link rdkit libraries into the SWIG wrappers" ON )
 option(RDK_TEST_MMFF_COMPLIANCE "run MMFF compliance tests (requires tar/gzip)" ON )
 option(RDK_BUILD_CPP_TESTS "build the c++ tests (disabing can speed up builds" ON)

Code/JavaWrappers/csharp_wrapper/CMakeLists.txt

@@ -1,17 +1,6 @@
 project (GraphMolCSharp)
 
 include_directories( ${RDKit_ExternalDir} )
-
-# find the mcs executables on non-windows systems:
-if(NOT MSVC)
-  find_program(GMCS_EXE mcs)
-  if (NOT GMCS_EXE)
-	MESSAGE ("mcs (executable) is not found. Please add it to PATH and rerun cmake.")
-	MESSAGE(FATAL_ERROR "Cannot find required executable mcs")
-  endif (NOT GMCS_EXE)
-endif(NOT MSVC)
-
-
 SET_SOURCE_FILES_PROPERTIES(GraphMolCSharp.i PROPERTIES CPLUSPLUS ON )
 
 # Setup a few variables for environment-specific things
@@ -92,22 +81,32 @@ SWIG_LINK_LIBRARIES(RDKFuncs ${RDKit_Wrapper_Libs}
 INSTALL(TARGETS RDKFuncs
         DESTINATION ${CMAKE_CURRENT_SOURCE_DIR} )
 
+if (RDK_BUILD_DOTNET_CSHARP_TESTS)
 
-if(NOT MSVC)
-   # code adapted from the wrapper code for
-   # GDCM: http://gdcm.svn.sf.net/viewvc/gdcm/trunk/Wrapping/Java/CMakeLists.txt?view=markup
-   ADD_CUSTOM_COMMAND(
-     OUTPUT ${CMAKE_CURRENT_SOURCE_DIR}/RDKit2DotNet.dll
+  find_program(DOTNET_EXE dotnet)
+  if (NOT DOTNET_EXE)
+    MESSAGE("dotnet (executable) is not found.  Pleae add it to PATH and rerun cmake.")
+    MESSAGE(FATAL_ERROR "Cannot find required executable dotnet")
+  endif (NOT DOTNET_EXE)
 
-     COMMAND ${CMAKE_COMMAND} -E make_directory swig_csharp
+  ADD_CUSTOM_COMMAND(
+    OUTPUT RDKitDotNetLib SYMBOLIC
+  
+    COMMAND ${CMAKE_COMMAND} -E copy $<TARGET_FILE:RDKFuncs> ${CMAKE_CURRENT_SOURCE_DIR}
+    COMMAND ${DOTNET_EXE} build RDKitDotNetCore.sln
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+    DEPENDS RDKFuncs
+  )
+  
+  ADD_CUSTOM_TARGET(RDKitDotNet ALL
+     DEPENDS RDKFuncs RDKitDotNetLib
+     COMMENT "Building RDKit DotNet project"
+  )
+  
+  ADD_TEST(
+    NAME CSharpTests
+    COMMAND ${DOTNET_EXE} test RDKitDotNetCore.sln "-l:console$<SEMICOLON>verbosity=normal" 
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+  )
 
-     ## 1. run this custom command only after swig has been run.
-     COMMAND ${GMCS_EXE} -platform:${PLATFORM} -out:RDKit2DotNet.dll -t:library "swig_csharp/*.cs"
-       WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-     DEPENDS "${swig_generated_file_fullname}"
-   )
-   ADD_CUSTOM_TARGET(RDKFuncsDLL ALL
-     DEPENDS RDKFuncs ${CMAKE_CURRENT_SOURCE_DIR}/RDKit2DotNet.dll
-     COMMENT "building mono dll"
-   )
-endif(NOT MSVC)
+endif()

Code/JavaWrappers/csharp_wrapper/RDKitCSharpTest/MolToFromByteArray.cs

@@ -1,30 +0,0 @@
-// Linux:
-// compile with
-// mcs -platform:x64 -r:../RDKit2DotNet.dll -out:MolToFromByteArray.exe  MolToFromByteArray.cs
-// and run with
-// LD_LIBRARY_PATH=..:$RDBASE/lib:$LD_LIBRARY_PATH MONO_PATH=.. mono MolToFromByteArray.exe
-
-using System.IO;
-using System.Diagnostics;
-using GraphMolWrap;
-
-public class MolToFromByteArrayTest
-{
-    static void Main(string[] args)
-    { 
-		string smi = "CN(C)c1ccc2c(=O)cc[nH]c2c1";
-		string pklFileName = "quinolone.pkl";
-		{
-			ROMol mol = RWMol.MolFromSmiles(smi);
-			byte[] pkl = mol.ToByteArray();
-            File.WriteAllBytes(pklFileName, pkl);
-			mol.Dispose();
-		}
-		{
-			byte[] pkl = File.ReadAllBytes(pklFileName);
-			ROMol mol = ROMol.FromByteArray(pkl);
-			Debug.Assert(mol.MolToSmiles() == smi);
-			mol.Dispose();
-		}
-   }
-}

Code/JavaWrappers/csharp_wrapper/RDKitDotNetCore.sln

@@ -0,0 +1,28 @@
+
+Microsoft Visual Studio Solution File, Format Version 12.00
+# Visual Studio Version 17
+VisualStudioVersion = 17.0.31903.59
+MinimumVisualStudioVersion = 10.0.40219.1
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "RDKitDotNetCoreWrapper", "swig_csharp\RDKitDotNetCoreWrapper.csproj", "{B97DDA0A-D8BF-4653-926B-F13DFC27FA7C}"
+EndProject
+Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "RDKitCSharpTest", "RdkitTests\RDKitCSharpTest.csproj", "{65A680C7-921C-47CF-9737-BF8726396B92}"
+EndProject
+Global
+	GlobalSection(SolutionConfigurationPlatforms) = preSolution
+		Debug|Any CPU = Debug|Any CPU
+		Release|Any CPU = Release|Any CPU
+	EndGlobalSection
+	GlobalSection(SolutionProperties) = preSolution
+		HideSolutionNode = FALSE
+	EndGlobalSection
+	GlobalSection(ProjectConfigurationPlatforms) = postSolution
+		{B97DDA0A-D8BF-4653-926B-F13DFC27FA7C}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{B97DDA0A-D8BF-4653-926B-F13DFC27FA7C}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{B97DDA0A-D8BF-4653-926B-F13DFC27FA7C}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{B97DDA0A-D8BF-4653-926B-F13DFC27FA7C}.Release|Any CPU.Build.0 = Release|Any CPU
+		{65A680C7-921C-47CF-9737-BF8726396B92}.Debug|Any CPU.ActiveCfg = Debug|Any CPU
+		{65A680C7-921C-47CF-9737-BF8726396B92}.Debug|Any CPU.Build.0 = Debug|Any CPU
+		{65A680C7-921C-47CF-9737-BF8726396B92}.Release|Any CPU.ActiveCfg = Release|Any CPU
+		{65A680C7-921C-47CF-9737-BF8726396B92}.Release|Any CPU.Build.0 = Release|Any CPU
+	EndGlobalSection
+EndGlobal

Code/JavaWrappers/csharp_wrapper/RdkitTests/MolToFromByteArray.cs

@@ -0,0 +1,36 @@
+// Linux:
+// compile with
+// mcs -platform:x64 -r:../RDKit2DotNet.dll -out:MolToFromByteArray.exe  MolToFromByteArray.cs
+// and run with
+// LD_LIBRARY_PATH=..:$RDBASE/lib:$LD_LIBRARY_PATH MONO_PATH=.. mono MolToFromByteArray.exe
+
+using System.IO;
+using System.Diagnostics;
+using GraphMolWrap;
+using Xunit;
+
+namespace RdkitTests
+{
+    public class MolToFromByteArrayTest
+    {
+        [Fact]
+        public void TestMolToFromByteArray()
+        {
+            string smi = "CN(C)c1ccc2c(=O)cc[nH]c2c1";
+            string pklFileName = "quinolone.pkl";
+            {
+                ROMol mol = RWMol.MolFromSmiles(smi);
+                byte[] pkl = mol.ToByteArray();
+                File.WriteAllBytes(pklFileName, pkl);
+                mol.Dispose();
+            }
+            {
+                byte[] pkl = File.ReadAllBytes(pklFileName);
+                ROMol mol = ROMol.FromByteArray(pkl);
+                Assert.Equal(smi, mol.MolToSmiles());
+                mol.Dispose();
+                File.Delete(pklFileName);
+            }
+        }
+    }
+}

Code/JavaWrappers/csharp_wrapper/RdkitTests/RDKitCSharpTest.csproj

@@ -0,0 +1,41 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>net8.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+
+    <IsPackable>false</IsPackable>
+  </PropertyGroup>
+
+  <ItemGroup>
+    <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.1.0" />
+    <PackageReference Include="xunit" Version="2.4.1" />
+    <PackageReference Include="xunit.runner.visualstudio" Version="2.4.3">
+      <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
+      <PrivateAssets>all</PrivateAssets>
+    </PackageReference>
+    <PackageReference Include="coverlet.collector" Version="3.1.2">
+      <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
+      <PrivateAssets>all</PrivateAssets>
+    </PackageReference>
+  </ItemGroup>
+
+  <ItemGroup>
+    <ProjectReference Include="..\swig_csharp\RDKitDotNetCoreWrapper.csproj" />
+  </ItemGroup>
+
+  <Target Name="CopyCustomContent1" AfterTargets="AfterBuild" Condition=" '$(OS)' == 'Windows_NT' ">
+          <Copy SourceFiles="../RDKFuncs.dll" DestinationFolder="$(OutDir)" />
+  </Target>
+  <Target Name="CopyCustomContent2" AfterTargets="CopyCustomContent1" Condition=" '$(OS)' != 'Windows_NT' ">
+          <Copy SourceFiles="../RDKFuncs.so" DestinationFolder="$(OutDir)" />
+  </Target>	  
+
+  <ItemGroup>
+    <None Update="xunit.runner.json">
+      <CopyToOutputDirectory>Always</CopyToOutputDirectory>
+    </None>
+  </ItemGroup>
+
+</Project>

Code/JavaWrappers/csharp_wrapper/RdkitTests/ToMolMemoryTest.cs

@@ -7,7 +7,8 @@ namespace RdkitTests
 {
     public class ToMolMemoryTest
     {
-        private static readonly long hundredMB = 1024 * 1024 * 100;
+        private static readonly long OneHundredMB = 1024 * 1024 * 100;
+        private static readonly long TwoHundredMB = OneHundredMB * 2;
 
         private static void gc()
         {
@@ -24,22 +25,28 @@ namespace RdkitTests
                 "CC(C)C[C@H](NC(=O)[C@H](CC(=O)O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CO)NC(=O)[C@@H]1CCCN1C(=O)[C@H](CCC(N)=O)NC(=O)[C@@H](N)CS)C(=O)N[C@@H](CCC(N)=O)C(=O)N[C@@H](CS)C(=O)O";
 
             var before = Process.GetCurrentProcess().VirtualMemorySize64;
+            var privateBefore = Process.GetCurrentProcess().PrivateMemorySize64;
             long after;
-            for (int i = 0; i < 10000; ++i)
+            long privateAfter;
+            for (int i = 0; i < 500; ++i)
             {
-                using RWMol mol = RDKFuncs.SmilesToMol(smi);
-                mol?.Dispose();
-                if (i % 1000 == 0)
+                RWMol mol = RDKFuncs.SmilesToMol(smi);
+                RWMol mol2 = RWMol.MolFromSmiles(smi);
+                if (i % 50 == 0)
                 {
                     gc();
                     after = Process.GetCurrentProcess().VirtualMemorySize64;
-                    Assert.True(after - before < hundredMB);
+                    Assert.True(after - before < TwoHundredMB);
+                    privateAfter = Process.GetCurrentProcess().PrivateMemorySize64;
+                    Assert.True(privateAfter - privateBefore < OneHundredMB);
                 }
             }
 
             gc();
             after = Process.GetCurrentProcess().VirtualMemorySize64;
-            Assert.True(after - before < hundredMB);
+            Assert.True(after - before < TwoHundredMB);
+            privateAfter = Process.GetCurrentProcess().PrivateMemorySize64;
+            Assert.True(privateAfter - privateBefore < OneHundredMB);
         }
 
         [Fact]
@@ -65,21 +72,20 @@ M  END
 ";
             var before = Process.GetCurrentProcess().VirtualMemorySize64;
             long after;
-            for (int i = 0; i < 10000; ++i)
+            for (int i = 0; i < 500; ++i)
             {
-                using RWMol mol = RDKFuncs.MolBlockToMol(block);
-                mol?.Dispose();
-                if (i % 1000 == 0)
+                RWMol mol = RDKFuncs.MolBlockToMol(block);
+                if (i % 50 == 0)
                 {
                     gc();
                     after = Process.GetCurrentProcess().VirtualMemorySize64;
-                    Assert.True(after - before < hundredMB);
+                    Assert.True(after - before < TwoHundredMB);
                 }
             }
 
             gc();
             after = System.Diagnostics.Process.GetCurrentProcess().PeakVirtualMemorySize64;
-            Assert.True(after - before < hundredMB);
+            Assert.True(after - before < TwoHundredMB);
         }
     }
 }

Code/JavaWrappers/csharp_wrapper/RdkitTests/Usings.cs

@@ -0,0 +1 @@
+global using Xunit;

Code/JavaWrappers/csharp_wrapper/RdkitTests/xunit.runner.json

@@ -0,0 +1,4 @@
+{
+  "parallelizeTestCollections": false,
+  "maxParallelThreads": -1
+}

Code/JavaWrappers/csharp_wrapper/swig_csharp/RDKitDotNetCoreWrapper.csproj

@@ -0,0 +1,15 @@
+<Project Sdk="Microsoft.NET.Sdk">
+
+  <PropertyGroup>
+    <TargetFramework>net8.0</TargetFramework>
+    <ImplicitUsings>enable</ImplicitUsings>
+    <Nullable>enable</Nullable>
+  </PropertyGroup>
+
+  <Target Name="CopyCustomContent1" AfterTargets="AfterBuild" Condition=" '$(OS)' == 'Windows_NT' ">
+	  <Copy SourceFiles="../RDKFuncs.dll" DestinationFolder="$(OutDir)" />
+  </Target>
+  <Target Name="CopyCustomContent2" AfterTargets="CopyCustomContent1" Condition=" '$(OS)' != 'Windows_NT' ">
+	  <Copy SourceFiles="../RDKFuncs.so" DestinationFolder="$(OutDir)" />
+  </Target>
+</Project>