merge to master

2026-06-03 21:44:30 +08:00 · 2017-07-21 04:50:35 +02:00
parent b785d55569 d5094d9e8f
commit 12342c5643
11 changed files with 75 additions and 59 deletions
--- a/.gitignore
+++ b/.gitignore
@@ -6,6 +6,9 @@
 /.project
 /.pydevproject

+#- CLion files
+/cmake-build-*
+
 #- IDEA files
 /.idea

@@ -77,4 +80,4 @@ __pycache__/
 External/INCHI-API/*
 /rdkit/ML/Data/test_data/testgeneral.dat.pkl
 /rdkit/ML/Data/test_data/testquant.qdat.pkl
-.DS_Store
+.DS_Store
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 3.1)
 if(CMAKE_MAJOR_VERSION EQUAL 2 AND ((CMAKE_MINOR_VERSION EQUAL 8 AND CMAKE_PATCH_VERSION GREATER 1) OR CMAKE_MINOR_VERSION GREATER 8))
  cmake_policy(SET CMP0015 OLD)
 endif()
@@ -16,6 +16,8 @@ enable_testing()
 set(CMAKE_MODULE_PATH
    ${CMAKE_MODULE_PATH} "${CMAKE_CURRENT_SOURCE_DIR}/Code/cmake/Modules/")

+add_library(rdkit_base INTERFACE)
+
 option(RDK_BUILD_SWIG_WRAPPERS "build the SWIG wrappers" OFF )
 option(RDK_BUILD_PYTHON_WRAPPERS "build the standard python wrappers" ON )
 option(RDK_BUILD_COMPRESSED_SUPPLIERS "build in support for compressed MolSuppliers" OFF )
@@ -103,18 +105,20 @@ if(RDK_BUILD_SWIG_WRAPPERS)
 endif(RDK_BUILD_SWIG_WRAPPERS)

 if(CMAKE_SIZEOF_VOID_P MATCHES 4)
-  ADD_DEFINITIONS("-DRDK_32BIT_BUILD")
+  target_compile_definitions(rdkit_base INTERFACE "-DRDK_32BIT_BUILD")
 else()
-  ADD_DEFINITIONS("-DRDK_64BIT_BUILD")
+  target_compile_definitions(rdkit_base INTERFACE "-DRDK_64BIT_BUILD")
 endif()

 if(MINGW)
-  ADD_DEFINITIONS("-DBOOST_SYSTEM_NO_DEPRECATED")
+  target_compile_definitions(rdkit_base INTERFACE "-DBOOST_SYSTEM_NO_DEPRECATED")
 endif(MINGW)

 # defines macros: rdkit_python_extension, rdkit_test
 include(RDKitUtils)
 install(EXPORT ${RDKit_EXPORTED_TARGETS} DESTINATION ${RDKit_LibDir})
+install(TARGETS rdkit_base EXPORT ${RDKit_EXPORTED_TARGETS}
+        COMPONENT dev )

 # create and install package configuration and version files
 configure_file (
@@ -133,7 +137,7 @@ install(FILES
 # extra boost versions
 if(MSVC)
  SET(Boost_ADDITIONAL_VERSIONS "1.48" "1.48.0" "1.45" "1.45.0" "1.44" "1.44.0" "1.43" "1.43.0" "1.42" "1.42.0" "1.41" "1.41.0" "1.40" "1.40.0")
-  ADD_DEFINITIONS("-DBOOST_ALL_NO_LIB")
+  target_compile_definitions(rdkit_base INTERFACE "-DBOOST_ALL_NO_LIB")
 endif(MSVC)

 if(RDK_BUILD_INCHI_SUPPORT)
@@ -149,12 +153,12 @@ if(RDK_BUILD_PYTHON_WRAPPERS)
  endif (PYTHONINTERP_FOUND AND NOT Python_ADDITIONAL_VERSIONS)
  find_package(PythonLibs)
  if(CMAKE_MAJOR_VERSION EQUAL 2 AND CMAKE_MINOR_VERSION EQUAL 6)
-    include_directories(${PYTHON_INCLUDE_PATH})
+    target_include_directories(rdkit_base INTERFACE ${PYTHON_INCLUDE_PATH})
  else(CMAKE_MAJOR_VERSION EQUAL 2 AND CMAKE_MINOR_VERSION EQUAL 6)
-    include_directories(${PYTHON_INCLUDE_DIR})
+    target_include_directories(rdkit_base INTERFACE ${PYTHON_INCLUDE_DIR})
  endif(CMAKE_MAJOR_VERSION EQUAL 2 AND CMAKE_MINOR_VERSION EQUAL 6)
  find_package(NumPy REQUIRED)
-  include_directories(${PYTHON_NUMPY_INCLUDE_PATH})
+  target_include_directories(rdkit_base INTERFACE ${PYTHON_NUMPY_INCLUDE_PATH})

  if(PYTHON_VERSION_MAJOR EQUAL 3)
    # Find boost-python3 using name specified as command line option then fall back to commonly used names
@@ -231,10 +235,13 @@ if(APPLE)
  endif()
 endif(APPLE)

-include_directories(SYSTEM ${Boost_INCLUDE_DIRS})
+target_include_directories(rdkit_base SYSTEM INTERFACE ${Boost_INCLUDE_DIRS})
 link_directories(${Boost_LIBRARY_DIRS})

-include_directories(${RDKit_CodeDir})
+target_include_directories(rdkit_base INTERFACE
+                           $<BUILD_INTERFACE:${RDKit_CodeDir}>
+                           $<INSTALL_INTERFACE:${RDKit_HdrDir}>
+                           )


 # Detect clang, which masquerades as gcc.  CMake 2.6 doesn't know how to
@@ -244,8 +251,8 @@ string(REGEX MATCH "clang" CMAKE_COMPILER_IS_CLANG "${CMAKE_C_COMPILER}")
 if(RDK_BUILD_DESCRIPTORS3D)
  find_package(Eigen3)
  if(EIGEN3_FOUND)
-    ADD_DEFINITIONS("-DRDK_HAS_EIGEN3" "-DRDK_BUILD_DESCRIPTORS3D")
-    include_directories(${EIGEN3_INCLUDE_DIR})
+    target_compile_definitions(rdkit_base INTERFACE "-DRDK_HAS_EIGEN3" "-DRDK_BUILD_DESCRIPTORS3D")
+    target_include_directories(rdkit_base INTERFACE ${EIGEN3_INCLUDE_DIR})
  else(EIGEN3_FOUND)
    message("Eigen3 not found, disabling the Descriptors3D build.")
    set(RDK_BUILD_DESCRIPTORS3D OFF)
@@ -259,10 +266,10 @@ if(RDK_BUILD_THREADSAFE_SSS)
  find_package(Boost 1.39.0 COMPONENTS thread system)
  if(Boost_THREAD_FOUND AND Boost_SYSTEM_FOUND)
    set(Boost_LIBRARIES ${T_LIBS} ${Boost_LIBRARIES})
-    ADD_DEFINITIONS("-DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB")
+    target_compile_definitions(rdkit_base INTERFACE -DRDK_THREADSAFE_SSS -DBOOST_ALL_NO_LIB)
    set(RDKit_THREAD_LIBS ${Boost_THREAD_LIBRARY} ${Boost_SYSTEM_LIBRARY} ${CMAKE_THREAD_LIBS_INIT})
    if(RDK_TEST_MULTITHREADED)
-      ADD_DEFINITIONS("-DRDK_TEST_MULTITHREADED")
+      target_compile_definitions(rdkit_base INTERFACE "-DRDK_TEST_MULTITHREADED")
    endif()
  else()
    message("Boost thread or system not found. Disabling RDK_BUILD_THREADSAFE_SSS.")
@@ -360,13 +367,13 @@ endif(NOT RDK_INSTALL_INTREE)

 if (RDK_SQUASH_MVC_SECURE_WARNINGS)
  MESSAGE("== Squashing MSVC Security warnings (do not use during development)")
-  ADD_DEFINITIONS("-D_SCL_SECURE_NO_WARNINGS")
-  ADD_DEFINITIONS("/wd4996")
+  target_compile_definitions(rdkit_base INTERFACE "-D_SCL_SECURE_NO_WARNINGS")
+  target_compile_definitions(rdkit_base INTERFACE "/wd4996")
 endif(RDK_SQUASH_MVC_SECURE_WARNINGS)

 if(RDK_USE_STRICT_ROTOR_DEFINITION)
    MESSAGE("== Using strict rotor definition")
-    ADD_DEFINITIONS("-DRDK_USE_STRICT_ROTOR_DEFINITION")
+    target_compile_definitions(rdkit_base INTERFACE "-DRDK_USE_STRICT_ROTOR_DEFINITION")
 endif()

 add_subdirectory(External)
--- a/Code/GraphMol/CMakeLists.txt
+++ b/Code/GraphMol/CMakeLists.txt
@@ -11,7 +11,7 @@ rdkit_library(GraphMol
              LINK_LIBRARIES RDGeometryLib RDGeneral 
                 ${RDKit_THREAD_LIBS})

-target_link_libraries(GraphMol ${RDKit_THREAD_LIBS})
+target_link_libraries(GraphMol PUBLIC ${RDKit_THREAD_LIBS})

 rdkit_headers(Atom.h
              atomic_data.h
--- a/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp
+++ b/Code/GraphMol/Descriptors/Wrap/rdMolDescriptors.cpp
@@ -1606,5 +1606,5 @@ BOOST_PYTHON_MODULE(rdMolDescriptors) {
  python::def("CalcAUTOCORR2D", calcAUTOCORR2Ds, (python::arg("mol")),
              docString.c_str());

-#endif  
+#endif
 }
--- a/Code/GraphMol/MolDraw2D/CMakeLists.txt
+++ b/Code/GraphMol/MolDraw2D/CMakeLists.txt
@@ -12,45 +12,41 @@ rdkit_headers(MolDraw2D.h
  DEST GraphMol/MolDraw2D
 )

-if(RDK_BUILD_QT_SUPPORT)
-  #find_package(Qt5 COMPONENTS Widgets OpenGL REQUIRED)
-  find_package(Qt5Widgets REQUIRED)
-  find_package(Qt5OpenGL REQUIRED)
-
-  include_directories(
-    ${Qt5Widgets_INCLUDE_DIRS}
-    ${Qt5OpenGL_INCLUDE_DIRS}
-    )
-
-  set(QTDRAW2D_SRC MolDraw2DQt.cpp)
-  set(EXTRA_LOCAL_LIBS ${EXTRA_LOCAL_LIBS} ${Qt5Widgets_LIBRARIES}  ${Qt5OpenGL_LIBRARIES} )
-  rdkit_headers(MolDraw2DQt.h DEST GraphMol/MolDraw2D)
-  SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
-endif(RDK_BUILD_QT_SUPPORT)
-
-if(RDK_BUILD_CAIRO_SUPPORT)
-  find_package(Cairo REQUIRED)
-  include_directories( ${CAIRO_INCLUDE_DIRS} )
-  set(EXTRA_LOCAL_LIBS ${EXTRA_LOCAL_LIBS} ${CAIRO_LIBRARIES} )
-  ADD_DEFINITIONS("-DRDK_CAIRO_BUILD")
-  set(CAIRODRAW2D_SRC MolDraw2DCairo.cpp)
-  rdkit_headers(MolDraw2DCairo.h DEST GraphMol/MolDraw2D)
-endif(RDK_BUILD_CAIRO_SUPPORT)
-
 rdkit_library(MolDraw2D MolDraw2D.cpp MolDraw2DSVG.cpp
-  ${CAIRODRAW2D_SRC} ${QTDRAW2D_SRC}
  MolDraw2DDetails.cpp MolDraw2DUtils.cpp
  LINK_LIBRARIES
  ChemReactions FileParsers SmilesParse Depictor MolTransforms RDGeometryLib
  RDGeneral SubstructMatch Subgraphs GraphMol EigenSolvers
 RDGeometryLib
-  ${RDKit_THREAD_LIBS} ${EXTRA_LOCAL_LIBS} )
+  ${RDKit_THREAD_LIBS} )
+
+if(RDK_BUILD_QT_SUPPORT)
+  #find_package(Qt5 COMPONENTS Widgets OpenGL REQUIRED)
+  find_package(Qt5Widgets REQUIRED)
+  find_package(Qt5OpenGL REQUIRED)
+
+  target_sources(MolDraw2D PRIVATE MolDraw2DQt.cpp)
+  target_include_directories(MolDraw2D PUBLIC ${Qt5Widgets_INCLUDE_DIRS} ${Qt5OpenGL_INCLUDE_DIRS})
+  target_compile_options(MolDraw2D PRIVATE "-std=c++11")
+  target_link_libraries(MolDraw2D PUBLIC ${Qt5Widgets_LIBRARIES} ${Qt5OpenGL_LIBRARIES})
+  rdkit_headers(MolDraw2DQt.h DEST GraphMol/MolDraw2D)
+endif(RDK_BUILD_QT_SUPPORT)
+
+if(RDK_BUILD_CAIRO_SUPPORT)
+  find_package(Cairo REQUIRED)
+  target_include_directories(MolDraw2D PUBLIC ${CAIRO_INCLUDE_DIRS})
+  target_compile_definitions(MolDraw2D PUBLIC "-DRDK_CAIRO_BUILD")
+  target_link_libraries(MolDraw2D PUBLIC ${CAIRO_LIBRARIES})
+  target_sources(MolDraw2D PRIVATE MolDraw2DCairo.cpp)
+  rdkit_headers(MolDraw2DCairo.h DEST GraphMol/MolDraw2D)
+endif(RDK_BUILD_CAIRO_SUPPORT)
+

 rdkit_test(moldraw2DTest1 test1.cpp LINK_LIBRARIES
  ChemReactions FileParsers SmilesParse Depictor RDGeometryLib
  RDGeneral SubstructMatch Subgraphs GraphMol MolTransforms EigenSolvers
 RDGeometryLib
-  MolDraw2D ${RDKit_THREAD_LIBS} ${EXTRA_LOCAL_LIBS} )
+  MolDraw2D ${RDKit_THREAD_LIBS} )

 rdkit_test(moldraw2DRxnTest1 rxn_test1.cpp LINK_LIBRARIES
    ChemReactions FileParsers SmilesParse Depictor RDGeometryLib
--- a/Code/GraphMol/Subgraphs/CMakeLists.txt
+++ b/Code/GraphMol/Subgraphs/CMakeLists.txt
@@ -1,10 +1,10 @@
-include_directories(${CMAKE_SOURCE_DIR}/External/boost-numeric-bindings)
-
 rdkit_library(Subgraphs Subgraphs.cpp SubgraphUtils.cpp
              LINK_LIBRARIES GraphMol )

 rdkit_headers(Subgraphs.h
              SubgraphUtils.h DEST GraphMol/Subgraphs)

+target_include_directories(Subgraphs PUBLIC $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/External/boost-numeric-bindings>)
+
 rdkit_test(testSubgraphs1 test1.cpp LINK_LIBRARIES Subgraphs SmilesParse GraphMol RDGeometryLib RDGeneral  )
 rdkit_test(testSubgraphs2 test2.cpp LINK_LIBRARIES SmilesParse Subgraphs GraphMol RDGeometryLib RDGeneral  )
--- a/Code/JavaWrappers/CMakeLists.txt
+++ b/Code/JavaWrappers/CMakeLists.txt
@@ -2,6 +2,8 @@ find_package(SWIG REQUIRED)
 include(${SWIG_USE_FILE})

 INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR})
+include_directories(${RDKit_CodeDir})
+include_directories(${Boost_INCLUDE_DIRS})

 SET(CMAKE_SWIG_FLAGS "")

--- a/Code/Numerics/EigenSolvers/CMakeLists.txt
+++ b/Code/Numerics/EigenSolvers/CMakeLists.txt
@@ -3,7 +3,7 @@ rdkit_library(EigenSolvers PowerEigenSolver.cpp LINK_LIBRARIES RDGeneral)
 rdkit_headers(PowerEigenSolver.h DEST Numerics/EigenSolvers)

 IF (LAPACK_FOUND)
-include_directories(${CMAKE_SOURCE_DIR}/External/boost-numeric-bindings)
 rdkit_test(tesEigensolvers testEigenSolvers.cpp
           LINK_LIBRARIES EigenSolvers  RDGeneral )
+target_include_directories(tesEigenSolvers PUBLIC ${CMAKE_SOURCE_DIR}/External/boost-numeric-bindings)
 ENDIF (LAPACK_FOUND)
--- a/Code/RDGeneral/CMakeLists.txt
+++ b/Code/RDGeneral/CMakeLists.txt
@@ -28,7 +28,7 @@ if(MINGW)
  endif()
 endif(MINGW)

-target_link_libraries(RDGeneral ${RDKit_THREAD_LIBS} ${MSVC_RUNTIME_DLL})
+target_link_libraries(RDGeneral PUBLIC ${RDKit_THREAD_LIBS} ${MSVC_RUNTIME_DLL})

 rdkit_headers(Exceptions.h
              BadFileException.h
--- a/Code/cmake/Modules/RDKitUtils.cmake
+++ b/Code/cmake/Modules/RDKitUtils.cmake
@@ -38,7 +38,8 @@ macro(rdkit_library)
  CDR(RDKLIB_SOURCES ${RDKLIB_DEFAULT_ARGS})
  if(MSVC)
    add_library(${RDKLIB_NAME} ${RDKLIB_SOURCES})
-    target_link_libraries(${RDKLIB_NAME} ${Boost_SYSTEM_LIBRARY} )
+    target_link_libraries(${RDKLIB_NAME} PUBLIC rdkit_base)
+    target_link_libraries(${RDKLIB_NAME} PUBLIC ${Boost_SYSTEM_LIBRARY} )
    INSTALL(TARGETS ${RDKLIB_NAME} EXPORT ${RDKit_EXPORTED_TARGETS}
            DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
            COMPONENT dev )
@@ -48,11 +49,22 @@ macro(rdkit_library)
    # boundaries. As of now (June 2010), this doesn't work
    # with g++ unless libraries are shared.
      add_library(${RDKLIB_NAME} SHARED ${RDKLIB_SOURCES})
+      target_link_libraries(${RDKLIB_NAME} PUBLIC rdkit_base)
      INSTALL(TARGETS ${RDKLIB_NAME} EXPORT ${RDKit_EXPORTED_TARGETS}
              DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
              COMPONENT runtime )
      if(RDK_INSTALL_STATIC_LIBS)
        add_library(${RDKLIB_NAME}_static ${RDKLIB_SOURCES})
+        target_link_libraries(${RDKLIB_NAME}_static PUBLIC rdkit_base)
+        foreach(RDKLIB_LINK_LIBRARY ${RDKLIB_LINK_LIBRARIES})
+          set(STATIC_LIB ${RDKLIB_LINK_LIBRARY}_static)
+          # if the static variant exist, link against it, otherwise link against the unmodified name (-> boost, etc)
+          if (TARGET ${STATIC_LIB})
+            target_link_libraries(${RDKLIB_NAME}_static PUBLIC ${STATIC_LIB})
+          else()
+            target_link_libraries(${RDKLIB_NAME}_static PUBLIC ${RDKLIB_LINK_LIBRARY})
+          endif()
+        endforeach()
        INSTALL(TARGETS ${RDKLIB_NAME}_static EXPORT ${RDKit_EXPORTED_TARGETS}
                DESTINATION ${RDKit_LibDir}/${RDKLIB_DEST}
                COMPONENT dev )
@@ -61,7 +73,7 @@ macro(rdkit_library)

      endif(RDK_INSTALL_STATIC_LIBS)
    IF(RDKLIB_LINK_LIBRARIES)
-      target_link_libraries(${RDKLIB_NAME} ${RDKLIB_LINK_LIBRARIES})
+      target_link_libraries(${RDKLIB_NAME} PUBLIC ${RDKLIB_LINK_LIBRARIES})
    ENDIF(RDKLIB_LINK_LIBRARIES)
  endif(MSVC)
  if(WIN32)
--- a/Docs/Book/Install.md
+++ b/Docs/Book/Install.md
@@ -154,11 +154,7 @@ Here things are more difficult. Check this wiki page for information: https://co
 ##### Installing prerequisites from source

 -   Required packages:
-  -   cmake. You need version 2.6 (or more recent). http://www.cmake.org if your linux distribution doesn't have an appropriate package.
-
-         > **note**
-         >
-         > It seems that v2.8 is a better bet than v2.6. It might be worth compiling your own copy of v2.8 even if v2.6 is already installed.
+  -   cmake. You need version 3.1 (or more recent). http://www.cmake.org if your linux distribution doesn't have an appropriate package.

  - The following are required if you are planning on using the Python wrappers
      -   The python headers. This probably means that you need to install the python-dev package (or whatever it's called) for your linux distribution.