Refactor CMakeLists on all systems

.github/workflows/conda-package-build.yml

@@ -21,3 +21,4 @@ jobs:
     uses: openalea/action-build-publish-anaconda/.github/workflows/openalea_ci.yml@main
     secrets:
       anaconda_token: ${{ secrets.ANACONDA_TOKEN }}
+

CMakeLists.txt

@@ -1,36 +1,87 @@
+# Initialize the CMake project
 cmake_minimum_required(VERSION 3.20)
 
-if(DEFINED SKBUILD_PROJECT_NAME AND DEFINED SKBUILD_PROJECT_VERSION)
-  project(
-    ${SKBUILD_PROJECT_NAME}
-    VERSION ${SKBUILD_PROJECT_VERSION}
-    DESCRIPTION "Statistical tools for OpenAlea"
-    LANGUAGES CXX)
-  message(STATUS "Building project version: ${SKBUILD_PROJECT_VERSION}")
+##################################################
+# If we are running in a Conda environment, we automatically
+# add the Conda env prefix to the CMAKE_PREFIX_PATH
+
+if(DEFINED ENV{CONDA_PREFIX})
+  list(APPEND CMAKE_PREFIX_PATH "$ENV{CONDA_PREFIX}")
+  #TODO: Windows Conda environments are structured differently,
+  #      how unfortunate is this?
+  list(APPEND CMAKE_PREFIX_PATH "$ENV{CONDA_PREFIX}/Library")
+endif()
+
+set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
+include("Anaconda")
+
+##################################################
+# Define the version
+
+if(SKBUILD)
+  set(STAT_TOOL_VERSION ${SKBUILD_PROJECT_VERSION})
 else()
-  project(stat_tool LANGUAGES CXX)
+  set(STAT_TOOL_VERSION "2.0.0")
 endif()
 
+project(openalea.stat_tool
+  VERSION ${STAT_TOOL_VERSION}
+  LANGUAGES CXX
+  DESCRIPTION "OpenAlea Stat Tool library for structure analysis")
+
+##################################################
+# Set CMake policies for this project
+
+# We allow <Package>_ROOT (env) variables for locating dependencies using find_paclage
+cmake_policy(SET CMP0074 NEW)
+# We allow target_sources to convert relative paths to absolute paths
+cmake_policy(SET CMP0076 NEW)
+ # for Python*_FIND_STRATEGY=LOCATION
+cmake_policy(SET CMP0094 NEW)
+cmake_policy(SET CMP0167 NEW)
+##################################################
+# Initialize some default paths
+# See https://cmake.org/cmake/help/latest/module/GNUInstallDirs.html
 include(GNUInstallDirs)
 
+##################################################
 # Set C++ standard and compile options
+
 set(CMAKE_CXX_STANDARD 14)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS ON)
-# set(CMAKE_CXX_FLAGS_RELEASE "-O2 -DNDEBUG")
+# set(CMAKE_CXX_EXTENSIONS ON)
+
+# This may be set in pyproject.toml
 set(CMAKE_VERBOSE_MAKEFILE ON)
+
+##################################################
+# For Python bindings, we need to enable position-independent code
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)  # For shared libs
 
-if(WIN32)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -enable-stdcall-fixup -enable-auto-import -enable-runtime-pseudo-reloc -s")
-endif()
+##################################################
+# TODO : REMOVE?
+# if(WIN32)
+#   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -enable-stdcall-fixup -enable-auto-import -enable-runtime-pseudo-reloc -s")
+# endif()
 
-if(DEFINED ENV{SKIP_BUILD})
-  message(STATUS "Skipping build of C/C++ extensions")
-  return()  # stops processing the CMakeLists here
-endif()
 
-if (MSVC)
+# RPath settings
+set(CMAKE_SKIP_BUILD_RPATH FALSE)
+set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
+set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
+list(
+  FIND
+  CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES
+  ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}
+  isSystemDir
+)
+if("${isSystemDir}" STREQUAL "-1")
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR})
+endif("${isSystemDir}" STREQUAL "-1")
+
+
+if (WIN32)
     string(REGEX REPLACE "/W3" "/W0" ${CMAKE_CXX_FLAGS} "${${CMAKE_CXX_FLAGS}}") 
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /MD")
 
@@ -42,21 +93,91 @@ endif()
 option(WITH_EFENCE "Build with efence library" OFF)
 option(WITH_TEST "Build tests" OFF)
 
-find_package(Python3 COMPONENTS Interpreter Development REQUIRED)
-message(STATUS "Python_INCLUDE_DIRS: ${Python_INCLUDE_DIRS}")
-message(STATUS "Python_EXECUTABLE: ${Python_EXECUTABLE}")
-message(STATUS "Python LIB : " ${Python_LIBRARIES})
-#include_directories(${Python_INCLUDE_DIRS})
+##################################################
+# Add a library for stat_tool and its Python wrappers
+add_library(oastat_tool SHARED)
 
-include(cmake/wrapper.cmake)
+##################################################
+# Find external dependencies
+find_package(Python COMPONENTS Interpreter Development.Module REQUIRED)
+find_package(Boost REQUIRED COMPONENTS python)
 
-set(boost_python python${Python3_VERSION_MAJOR}${Python3_VERSION_MINOR})
-find_package(Boost REQUIRED COMPONENTS ${boost_python})
+##################################################
+# Setup lib, inc, defines for C++ oastat_tool lib
+
+target_include_directories(oastat_tool
+  PUBLIC
+    ${Boost_INCLUDE_DIRS}
+)
+
+# Export symbols on Windows
+if (WIN32 OR MSVC)
+  target_compile_definitions(oastat_tool PUBLIC STAT_TOOL_MAKEDLL)
+endif()
+
+# Optionally add efence
+if(WITH_EFENCE)
+  target_compile_definitions(oastat_tool PUBLIC DEBUG)
+  target_link_libraries(oastat_tool PUBLIC efence)
+endif()
+
+# Add files to build
+add_subdirectory(src/cpp/stat_tool)
+
+
+##################################################
+# Add a Python binding library 
+python_add_library(_stat_tool MODULE)
+
+target_include_directories(oastat_tool
+  PUBLIC
+    "src/cpp"
+)
+
+target_link_libraries(_stat_tool
+  PRIVATE
+    oastat_tool
+    Boost::python
+    Python::Module
+  )
+
+  target_compile_definitions(_stat_tool PRIVATE BOOST_ALL_NO_LIB)
+
+  # Control the output name of the produced shared library
+  set_target_properties(_stat_tool PROPERTIES PREFIX "")
+  set_target_properties(_stat_tool PROPERTIES OUTPUT_NAME "_stat_tool")
+  if(WIN32)
+    set_target_properties(_stat_tool PROPERTIES SUFFIX ".pyd")
+  elseif(APPLE)
+    set_target_properties(_stat_tool PROPERTIES SUFFIX ".so")
+  endif()
 
-add_subdirectory("src/cpp/stat_tool")
 add_subdirectory("src/wrapper/")
 
+
+if(APPLE)
+    set_target_properties(_stat_tool PROPERTIES INSTALL_RPATH "@loader_path/.")
+elseif(UNIX)
+    set_target_properties(_stat_tool PROPERTIES INSTALL_RPATH "$ORIGIN/.")
+endif()
+
+##################################################
+# Install targets and headers for stat_tool lib
+install(TARGETS oastat_tool
+            RUNTIME DESTINATION "${CONDA_ENV}bin/"
+            LIBRARY DESTINATION "${CONDA_ENV}lib/"
+            ARCHIVE DESTINATION "${CONDA_ENV}lib/"
+            PUBLIC_HEADER DESTINATION "${CONDA_ENV}include/stat_tool"
+)
+
+install(
+  TARGETS
+    _stat_tool
+  DESTINATION "${SKBUILD_PLATLIB_DIR}/openalea/stat_tool"
+)
+
 # Optionally handle tests
+# TODO TO TEST
 if(WITH_TEST)
   enable_testing()
   add_subdirectory(test/cpp)

cmake/Anaconda.cmake

@@ -0,0 +1,133 @@
+# Anaconda Check
+if (DEFINED ENV{CONDA_PREFIX})
+    # Anaconda Environment
+    message(STATUS "Anaconda environment detected: " $ENV{CONDA_PREFIX})
+
+    set(CMAKE_INCLUDE_PATH "$ENV{CONDA_PREFIX}/include" ${CMAKE_INCLUDE_PATH})
+    set(CMAKE_LIBRARY_PATH "$ENV{CONDA_PREFIX}/lib" ${CMAKE_LIBRARY_PATH})
+
+    if (DEFINED ENV{PREFIX})
+        file(TO_CMAKE_PATH $ENV{PREFIX} TMP_CONDA_ENV)
+    else()
+        file(TO_CMAKE_PATH $ENV{CONDA_PREFIX} TMP_CONDA_ENV)
+    endif()
+
+    if (WIN32)
+        set(CONDA_ENV "${TMP_CONDA_ENV}/Library/")
+    else()
+        set(CONDA_ENV "${TMP_CONDA_ENV}/")
+    endif()
+
+    set(CONDA_PYTHON_ENV "${TMP_CONDA_ENV}/")
+
+    set(USE_CONDA ON)
+
+else()
+    message(STATUS "Compilation outside an anaconda environment.")
+    set(USE_CONDA OFF)
+endif()
+
+
+if (DEFINED ENV{CONDA_BUILD})
+    message(STATUS "Conda build detected. " $ENV{CONDA_BUILD})
+
+    if (WIN32)
+        set(Python_ROOT_DIR "${PREFIX}")
+    endif()
+
+    # specify the cross compiler
+    #set(CMAKE_C_COMPILER $ENV{CC})
+    #set(CMAKE_LINKER $ENV{LD})
+    #set(CMAKE_AR $ENV{AR})
+    #set(CMAKE_NM $ENV{NM})
+    #set(CMAKE_RANLIB $ENV{RANLIB})
+    #set(CMAKE_STRIP $ENV{STRIP})
+    #set(CMAKE_INSTALL_NAME_TOOL $ENV{INSTALL_NAME_TOOL})
+
+    #if (APPLE)
+    #    set(CMAKE_OSX_ARCHITECTURES $ENV{OSX_ARCH})
+    #endif()
+
+    #set(CMAKE_CXX_COMPILER $ENV{CXX})
+    #set(CMAKE_CXX_COMPILER_RANLIB $ENV{RANLIB})
+    #set(CMAKE_CXX_COMPILER_AR $ENV{AR})
+
+    # where is the target environment
+    set(CMAKE_FIND_ROOT_PATH $ENV{PREFIX} $ENV{BUILD_PREFIX})
+    if (APPLE)
+        list(APPEND CMAKE_FIND_ROOT_PATH $ENV{CONDA_BUILD_SYSROOT} )
+    endif()
+    if (WIN32)
+        list(APPEND CMAKE_FIND_ROOT_PATH $ENV{BUILD_PREFIX}/Library/usr $ENV{PREFIX}/Library/usr)
+        set(CMAKE_INCLUDE_PATH "$ENV{BUILD_PREFIX}/Library/usr/include" ${CMAKE_INCLUDE_PATH})
+        set(CMAKE_LIBRARY_PATH "$ENV{BUILD_PREFIX}/Library/usr/lib" ${CMAKE_LIBRARY_PATH})
+    endif()
+    if (UNIX)
+        # I add both old stype and new style cdts : https://github.com/conda-forge/cdt-builds#old-stylelegacy-vs-new-style-cdts
+        list(APPEND CMAKE_FIND_ROOT_PATH $ENV{BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot $ENV{BUILD_PREFIX}/$ENV{HOST}/sysroot )
+        list(APPEND CMAKE_FIND_ROOT_PATH $ENV{PREFIX}/x86_64-conda-linux-gnu/sysroot $ENV{PREFIX}/$ENV{HOST}/sysroot )
+
+        link_directories($ENV{BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/lib64 $ENV{BUILD_PREFIX}/$ENV{HOST}/sysroot/lib64)
+        link_directories($ENV{BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/lib $ENV{BUILD_PREFIX}/$ENV{HOST}/sysroot/lib)
+        link_directories($ENV{BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib64 $ENV{BUILD_PREFIX}/$ENV{HOST}/sysroot/usr/lib64)
+        link_directories($ENV{BUILD_PREFIX}/x86_64-conda-linux-gnu/sysroot/usr/lib $ENV{BUILD_PREFIX}/$ENV{HOST}/sysroot/usr/lib)
+    endif()
+
+    message(STATUS "CMAKE_FIND_ROOT_PATH :")
+    foreach(dir ${CMAKE_FIND_ROOT_PATH})
+        message(STATUS " - " ${dir})
+    endforeach()
+
+    # search for programs in the build host directories
+    set(CMAKE_FIND_ROOT_PATH_MODE_PROGRAM BOTH)
+    # for libraries and headers in the target directories
+    set(CMAKE_FIND_ROOT_PATH_MODE_LIBRARY ONLY)
+    set(CMAKE_FIND_ROOT_PATH_MODE_INCLUDE ONLY)
+
+    set(USE_CONDA_BUILD ON)
+else()
+    set(USE_CONDA_BUILD OFF)
+endif()
+
+function(oa_default_install)
+    if(USE_CONDA_BUILD)
+        set(CMAKE_INSTALL_PREFIX $ENV{PREFIX} CACHE PATH "..." FORCE)
+    elseif()
+        set(CMAKE_INSTALL_PREFIX ${CONDA_ENV} CACHE PATH "..." FORCE)
+    else()
+        set(CMAKE_INSTALL_PREFIX ${CMAKE_CURRENT_SOURCE_DIR}/build CACHE PATH "..." FORCE)
+    endif()
+    message(STATUS "Default install prefix to " ${CMAKE_INSTALL_PREFIX})
+endfunction()
+
+if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+    oa_default_install()
+elseif (NOT DEFINED CMAKE_INSTALL_PREFIX)
+    oa_default_install()
+else()
+    message(STATUS "Install Prefix: " ${CMAKE_INSTALL_PREFIX})
+endif()
+
+function(install_share sharedirectory project)
+    install(DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/${sharedirectory}/ DESTINATION "${CONDA_ENV}/share/${project}")
+endfunction()
+
+
+function(install_oalib libname)
+    message("Installing ${libname} in ${CONDA_ENV}lib/")
+    install(TARGETS ${libname}
+            RUNTIME DESTINATION "${CONDA_ENV}bin/"
+            LIBRARY DESTINATION "${CONDA_ENV}lib/"
+            ARCHIVE DESTINATION "${CONDA_ENV}lib/"
+     )
+endfunction()
+
+function(install_oabin libname)
+    message("Installing ${libname} in ${CONDA_ENV}bin/")
+    install(TARGETS ${libname} RUNTIME DESTINATION "${CONDA_ENV}bin/")
+endfunction()
+
+function(install_oaheaders directory exclude)
+    message("Installing header from ${directory} in ${CONDA_ENV}include/")
+    install(DIRECTORY ${directory} DESTINATION "${CONDA_ENV}include/" FILES_MATCHING PATTERN "*.h" PATTERN "*.hpp" PATTERN ${exclude} EXCLUDE)
+endfunction()