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Commiting the bulk of the CMake build transition config files -- It still fails with a GMP related linker error (to be fixed later)
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‎CMakeLists.txt‎

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#### CMakeLists.txt : CMake configuration and build script
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#### for the gtDMMB/pmfe sources
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#### Author: Maxie D. Schmidt (github.com/maxieds)
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#### Created: 2020.11.02
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## CMake specific configuration and build environment settings:
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cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
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set(CMAKE_DEBUG_POSTFIX d)
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set(CMAKE_CXX_STANDARD 14)
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set(CMAKE_CXX_STANDARD_REQUIRED True)
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set(CMAKE_BUILD_TYPE Release)
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set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR}/bin)
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set(CMAKE_INCLUDE_CURRENT_DIR ON)
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set(CMAKE_C_COMPILER gcc)
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set(CMAKE_CXX_COMPILER g++)
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set(CMAKE_LINKER g++)
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set(SHELL /bin/bash)
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set(CMAKE_RULE_MESSAGES ON)
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set(CMAKE_VERBOSE_MAKEFILE ON)
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set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
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## Define the PMFE project and define the output binaries:
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project(gtDMMB_PMFE)
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set(PMFE_VERSION_MAJOR "1")
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set(PMFE_VERSION_MINOR "0")
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set(PMFE_VERSION_PATCH "0")
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set(VERSION "${PMFE_VERSION_MAJOR}.${PMFE_VERSION_MINOR}.${PMFE_VERSION_PATCH}")
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set(PMFE_PACKAGE_NAME "gtDMMB-PMFE")
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set(PMFE_PACKAGE_VERSION ${VERSION})
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set(PMFE_PACKAGE_STRING "${PMFE_PACKAGE_NAME} v${PMFE_PACKAGE_VERSION}")
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## Option to enable auto running of unit tests after recompiling:
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option(RUN_UNIT_TESTS "Enable running tests after build" OFF)
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## Configure pkg-config script for some dependency libraries:
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include(FindPkgConfig)
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if(NOT PKG_CONFIG_FOUND)
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message(FATAL_ERROR "Unable to configure libGMP : pkg-config not found ..." )
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endif()
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if(APPLE)
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execute_process(
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COMMAND bash -c "echo -n $(greadlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'gmp-*' -type d -printf \"../%f\" | head -n1))"
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OUTPUT_VARIABLE PkgConfigLocalPCFilesPath
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)
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elseif(UNIX AND NOT APPLE)
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execute_process(
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COMMAND bash -c "echo -n $(readlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'gmp-*' -type d -printf \"../%f\" | head -n1))"
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OUTPUT_VARIABLE PkgConfigLocalPCFilesPath
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)
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endif()
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string(STRIP "${PkgConfigLocalPCFilesPath}" PkgConfigLocalPCFilesPath)
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set(ENV{PKG_CONFIG_PATH} "${PkgConfigLocalPCFilesPath}")
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execute_process(
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COMMAND bash -c "pkg-config gmp --libs --static"
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OUTPUT_VARIABLE PC_GMP_LIBRARIES
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)
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string(STRIP "${PC_GMP_LIBRARIES}" PC_GMP_LIBRARIES)
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execute_process(
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COMMAND bash -c "pkg-config gmp --cflags"
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OUTPUT_VARIABLE PC_GMP_INCLUDE_DIRS
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)
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string(STRIP "${PC_GMP_INCLUDE_DIRS}" PC_GMP_INCLUDE_DIRS)
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execute_process(
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COMMAND bash -c "pkg-config gmpxx --libs --static"
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OUTPUT_VARIABLE PC_GMPXX_LIBRARIES
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)
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string(STRIP "${PC_GMPXX_LIBRARIES}" PC_GMPXX_LIBRARIES)
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execute_process(
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COMMAND bash -c "pkg-config gmpxx --cflags"
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OUTPUT_VARIABLE PC_GMPXX_INCLUDE_DIRS
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)
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string(STRIP "${PC_GMPXX_INCLUDE_DIRS}" PC_GMPXX_INCLUDE_DIRS)
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## Configure paths on requisite build time libraries (Boost):
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set(Boost_USE_STATIC_LIBS ON)
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set(Boost_USE_MULTITHREADED ON)
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set(Boost_USE_STATIC_RUNTIME ON)
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set(Boost_FIND_REQUIRED TRUE)
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set(Boost_FIND_QUIETLY TRUE)
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set(Boost_DEBUG FALSE)
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set(Boost_NO_BOOST_CMAKE TRUE)
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set(Boost_NO_SYSTEM_PATHS TRUE)
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if(NOT DEFINED BOOST_ROOT)
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set(BoostFileSystemRootPath "../BoostLocalInstall")
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set(BOOST_ROOT ${PROJECT_SOURCE_DIR}/${BoostFileSystemRootPath})
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endif()
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set(Boost_INCLUDE_DIR ${BOOST_ROOT}/include)
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set(Boost_LIBRARY_DIR ${BOOST_ROOT}/lib)
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#find_package(
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# Boost ${BOOST_MIN_VERSION}
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# COMPONENTS filesystem program_options system log log_setup thread atomic regex chrono
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# REQUIRED
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#)
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#if(NOT Boost_FOUND)
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# message(FATAL_ERROR "Boost Not Found ... Unable to complete the build")
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#endif()
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## Configure paths on requisite build time libraries (CGAL):
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if(APPLE)
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execute_process(
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COMMAND bash "-c" "echo $(greadlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'cgal*' -type d -printf \"${PROJECT_SOURCE_DIR}/../%f\n\" | head -n1))"
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OUTPUT_VARIABLE CGALFileSystemRootPath
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RESULT_VARIABLE CGALFileSystemRootPath_CmdResult
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)
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string(STRIP ${CGALFileSystemRootPath} CGALFileSystemRootPath)
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set(CGAL_DIR ${CGALFileSystemRootPath})
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elseif(UNIX AND NOT APPLE)
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execute_process(
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COMMAND bash "-c" "echo $(readlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'cgal*' -type d -printf \"${PROJECT_SOURCE_DIR}/../%f\n\" | head -n1))"
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OUTPUT_VARIABLE CGALFileSystemRootPath
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RESULT_VARIABLE CGALFileSystemRootPath_CmdResult
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)
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string(STRIP ${CGALFileSystemRootPath} CGALFileSystemRootPath)
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set(CGAL_DIR ${CGALFileSystemRootPath})
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endif()
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set(CGAL_DONT_OVERRIDE_CMAKE_FLAGS TRUE CACHE BOOL "Force CGAL to maintain CMAKE flags")
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file(GLOB CGALBaseFilesList "${CGAL_DIR}/*")
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set(CGALIncludeFilesList "")
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foreach(fsEntry ${CGALBaseFilesList})
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if(NOT ${fsEntry} MATCHES ".*\\.svn\$" AND IS_DIRECTORY ${fsEntry}
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AND IS_DIRECTORY ${fsEntry}/include)
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list(APPEND CGALIncludeFilesList "${fsEntry}/include")
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endif()
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endforeach()
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# AND NOT EXISTS ${fsEntry}/include/CGAL/Regular_complex_d.h
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## Build the binaries for the PMFE project:
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add_custom_command(
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OUTPUT BuildConfigHeaderIsSetup
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COMMAND cmake "-P" "${PROJECT_SOURCE_DIR}/cmake/AutogenBuildConfigHeader.cmake"
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)
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add_custom_target(
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BuildConfigHeader ALL
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DEPENDS BuildConfigHeaderIsSetup
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)
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file(GLOB ALL_TARGET_SOURCES src/*.cc)
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include_directories(${CGALIncludeFilesList} "${Boost_INCLUDE_DIR}"
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"${PROJECT_SOURCE_DIR}/include" "${PROJECT_SOURCE_DIR}/iB4e"
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)
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link_libraries("${Boost_LIBRARY_DIR}/libboost_program_options.a" "${Boost_LIBRARY_DIR}/libboost_system.a"
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"${Boost_LIBRARY_DIR}/libboost_log.a"
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"${Boost_LIBRARY_DIR}/libboost_thread.a" "${Boost_LIBRARY_DIR}/libboost_atomic.a"
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"${Boost_LIBRARY_DIR}/libboost_regex.a" "${Boost_LIBRARY_DIR}/libboost_chrono.a")
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add_executable(
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pmfe_findmfe_bin ${ALL_TARGET_SOURCES} src/bin-findmfe.cc
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)
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add_dependencies(pmfe_findmfe_bin BuildConfigHeader)
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set_target_properties(
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pmfe_findmfe_bin PROPERTIES
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OUTPUT_NAME "pmfe-findmfe"
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COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
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)
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add_executable(
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pmfe_scorer_bin ${ALL_TARGET_SOURCES} src/bin-scorer.cc
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)
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add_dependencies(pmfe_findmfe_bin BuildConfigHeader)
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set_target_properties(
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pmfe_scorer_bin PROPERTIES
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OUTPUT_NAME "pmfe-scorer"
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COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
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)
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add_executable(
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pmfe_parametrizer_bin ${ALL_TARGET_SOURCES} src/bin-parametrizer.cc
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)
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add_dependencies(pmfe_findmfe_bin BuildConfigHeader)
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set_target_properties(
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pmfe_parametrizer_bin PROPERTIES
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OUTPUT_NAME "pmfe-parametrizer"
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COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
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)
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add_executable(
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pmfe_subopt_bin ${ALL_TARGET_SOURCES} src/bin-subopt.cc
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)
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add_dependencies(pmfe_findmfe_bin BuildConfigHeader)
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set_target_properties(
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pmfe_subopt_bin PROPERTIES
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OUTPUT_NAME "pmfe-subopt"
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COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
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)
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add_executable(
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pmfe_tests_bin ${ALL_TARGET_SOURCES} src/bin-tests.cc
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)
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add_dependencies(pmfe_findmfe_bin BuildConfigHeader)
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set_target_properties(
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pmfe_subopt_bin PROPERTIES
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OUTPUT_NAME "pmfe-tests"
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COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
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)
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## Install targets (both for binary sub-utilities and the
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## Python library to be used with SageMath):
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if(IS_DIRECTORY "/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9")
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set(RHEL_INCLUDE_APPENDS "-I/opt/rh/devtoolset-9/root/usr/include/c++/9")
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set(RHEL_LINKER_APPENDS "-L/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9")
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else()
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set(RHEL_INCLUDE_APPENDS "")
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set(RHEL_LINKER_APPENDS "")
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endif()
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if(APPLE)
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set(CMAKE_CXX_FLAGS
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"${CMAKE_CXX_FLAGS} -Wall -std=c++14 -stdlib=libc++ -fPIC -fopenmp -Wall -g -O3 \
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-DBOOST_LOG_DYN_LINK=0 -DCGAL_HEADER_ONLY -D_GLIBCXX_USE_CXX11_ABI=0 \
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-I/usr/local/include -Iinclude/ -IiB4e/ \
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${PC_GMP_INCLUDE_DIRS} ${PC_GMPXX_INCLUDE_DIRS} \
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-I${Boost_INCLUDE_DIR} ${CGAL_INCLUDE_DIRS}
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-DPMFE_PACKAGE_VERSION=\"${PMFE_PACKAGE_VERSION}\""
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)
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set(CMAKE_EXE_LINKER_FLAGS
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"${CMAKE_CXX_FLAGS} ${CMAKE_EXE_LINKER_FLAGS} \
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-L/usr/local/lib -lgmp -lgmpxx -lCGAL -lm -lboost_filesystem \
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-lboost_program_options -lboost_system -lboost_log -lboost_log_setup \
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-lc++ -lboost_log-mt \
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${PC_GMP_LIBRARIES} ${PC_GMPXX_LIBRARIES} ${Boost_LIBRARIES}"
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)
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elseif(UNIX AND NOT APPLE) # Primary target: Linux (typically RHEL)
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set(CMAKE_CXX_FLAGS
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"-fPIC -fopenmp -Wall -g -O3 -fvisibility=hidden -fvisibility-inlines-hidden \
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-DABI=0 -DBOOST_FILESYSTEM_NO_DEPRECATED -UBOOST_DISABLE_THREADS \
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-DBOOST_LOG_DYN_LINK=1 -BOOST_ALL_DYN_LINK=1 -D_GLIBCXX_USE_CXX11_ABI=1 \
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-DCGAL_HEADER_ONLY -DGAL_USE_LEDA=1 ${RHEL_INCLUDE_APPENDS} ${CMAKE_CXX_FLAGS}"
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)
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set(CMAKE_EXE_LINKER_FLAGS
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"${RHEL_LINKER_APPENDS} -L/usr/lib -L/usr/local/lib \
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${PC_GMP_LIBRARIES} ${PC_GMPXX_LIBRARIES} ${CMAKE_EXE_LINKER_FLAGS} -L${Boost_LIBRARY_DIR} \
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-static -lboost_filesystem -lboost_program_options -lboost_system \
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-lboost_log -lboost_log_setup -lpthread -lm"
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)
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endif()
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set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_EXE_LINKER_FLAGS}")
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set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_EXE_LINKER_FLAGS}")
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install(
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TARGETS pmfe_findmfe_bin pmfe_scorer_bin pmfe_parametrizer_bin pmfe_subopt_bin pmfe_tests_bin
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DESTINATION ${EXECUTABLE_OUTPUT_PATH}
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)
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## Backup the old wrapper scripts and copy the new ones in their place:
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install(
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SCRIPT cmake/PostBuildAutogenWrapperScript.cmake
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)
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set(UserRunnerScriptPath "../../PMFECommandRunner.sh")
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set(DevRunnerScriptPath "../../PMFEDeveloperCommandRunner.sh")
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set(SageInitScriptPath "../../init.sage")
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set(SageInitScriptNestedPath "../SageInit/init.sage")
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execute_process (
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COMMAND bash -c
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"cp ${UserRunnerScriptPath} ${UserRunnerScriptPath}.bak &&
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cp ${DevRunnerScriptPath} ${DevRunnerScriptPath}.bak &&
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cp ${SageInitScriptPath} ${SageInitScriptPath}.bak &&
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cp ${SageInitScriptNestedPath} ${SageInitScriptNestedPath}.bak"
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)
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execute_process (
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COMMAND bash -c
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"touch wrapper-runner-script/PMFECommandRunner.sh &&
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cp wrapper-runner-script/PMFECommandRunner.sh ${UserRunnerScriptPath} &&
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touch wrapper-runner-script/PMFEDeveloperCommandRunner.sh &&
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cp wrapper-runner-script/PMFEDeveloperCommandRunner.sh ${DevRunnerScriptPath} &&
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cp wrapper-runner-script/init.sage ${SageInitScriptPath} &&
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cp wrapper-runner-script/init.sage ${SageInitScriptNestedPath}"
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)
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## Running of unit tests configuration:
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function(Func_runUnitTest UnitTestName)
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add_test(NAME "PMFEUnitTestCheck-${UnitTestName}" COMMAND pmfe-tests -n ${UnitTestName} -a -s)
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set_tests_properties(
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"PMFEUnitTestCheck-${UnitTestName}" PROPERTIES
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PASS_REGULAR_EXPRESSION "All tests passed .*"
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)
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endfunction(Func_runUnitTest)
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if(RUN_UNIT_TESTS)
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enable_testing()
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message("Running *ALL* unit tests -- NOTE: This can take a long time -- ...")
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Func_runUnitTest("16S")
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Func_runUnitTest("5S")
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Func_runUnitTest("asuum")
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Func_runUnitTest("atabira")
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Func_runUnitTest("bbigemina")
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Func_runUnitTest("biological")
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Func_runUnitTest("cdiphtheriae")
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Func_runUnitTest("celegans")
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Func_runUnitTest("combinatorial")
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Func_runUnitTest("dmobilis")
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Func_runUnitTest("ecoli")
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Func_runUnitTest("ecuniculi")
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Func_runUnitTest("ehexamita")
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Func_runUnitTest("garboreum")
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Func_runUnitTest("gardaea")
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Func_runUnitTest("gintestinalis")
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Func_runUnitTest("gmuris")
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Func_runUnitTest("hsapiens")
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Func_runUnitTest("hvolcanii")
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Func_runUnitTest("ldelbrueckii")
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Func_runUnitTest("mfe")
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Func_runUnitTest("onivara")
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Func_runUnitTest("random")
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Func_runUnitTest("rnorvegicus")
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Func_runUnitTest("stokodaii")
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Func_runUnitTest("synthetic")
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Func_runUnitTest("tRNA")
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Func_runUnitTest("vnecatrix")
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Func_runUnitTest("zmays")
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endif()

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