Integrating the new CMake based build process

.gitignore

@@ -8,3 +8,10 @@
 *.rnapoly
 *.rnasubopt
 
+build/
+build/*
+
+include/pmfe_build_config.h
+wrapper-runner-script/PMFECommandRunner.sh
+wrapper-runner-script/PMFEDeveloperCommandRunner.sh
+

CMakeLists.txt

@@ -0,0 +1,307 @@
+#### CMakeLists.txt : CMake configuration and build script
+####                  for the gtDMMB/pmfe sources
+#### Author: Maxie D. Schmidt (github.com/maxieds)
+#### Created: 2020.11.02
+
+## CMake specific configuration and build environment settings:
+cmake_minimum_required(VERSION 3.10 FATAL_ERROR)
+
+set(CMAKE_DEBUG_POSTFIX d)
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED True)
+set(CMAKE_BUILD_TYPE Release)
+set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR}/bin)
+set(CMAKE_INCLUDE_CURRENT_DIR ON)
+set(CMAKE_C_COMPILER gcc)
+set(CMAKE_CXX_COMPILER g++)
+set(CMAKE_LINKER g++)
+set(SHELL /bin/bash)
+set(CMAKE_RULE_MESSAGES ON)
+set(CMAKE_VERBOSE_MAKEFILE ON)
+set(CMAKE_INTERPROCEDURAL_OPTIMIZATION TRUE)
+
+## Define the PMFE project and define the output binaries:
+project(gtDMMB_PMFE)
+
+set(PMFE_VERSION_MAJOR "1")
+set(PMFE_VERSION_MINOR "0")
+set(PMFE_VERSION_PATCH "0")
+set(VERSION "${PMFE_VERSION_MAJOR}.${PMFE_VERSION_MINOR}.${PMFE_VERSION_PATCH}")
+set(PMFE_PACKAGE_NAME "gtDMMB-PMFE")
+set(PMFE_PACKAGE_VERSION ${VERSION})
+set(PMFE_PACKAGE_STRING "${PMFE_PACKAGE_NAME} v${PMFE_PACKAGE_VERSION}")
+
+## Option to enable auto running of unit tests after recompiling:
+option(RUN_UNIT_TESTS "Enable running tests after build" OFF)
+
+## Configure pkg-config script for some dependency libraries (LIBGMP and LIBGMPXX):
+include(FindPkgConfig)
+if(NOT PKG_CONFIG_FOUND)
+     message(FATAL_ERROR "Unable to configure libGMP : pkg-config not found ..." )
+endif()
+
+if(APPLE)
+     execute_process(
+          COMMAND bash -c "echo -n $(greadlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'gmp-*' -type d -printf \"../%f\" | head -n1))"
+          OUTPUT_VARIABLE PkgConfigLocalPCFilesPath
+     )
+elseif(UNIX AND NOT APPLE)
+     execute_process(
+          COMMAND bash -c "echo -n $(readlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'gmp-*' -type d -printf \"../%f\" | head -n1))"
+          OUTPUT_VARIABLE PkgConfigLocalPCFilesPath
+     )
+endif()
+string(STRIP "${PkgConfigLocalPCFilesPath}" PkgConfigLocalPCFilesPath)
+
+set(ENV{PKG_CONFIG_PATH} "${PkgConfigLocalPCFilesPath}")
+execute_process(
+     COMMAND bash -c "pkg-config gmp --cflags"
+     OUTPUT_VARIABLE PC_GMP_INCLUDE_DIRS
+)
+string(STRIP "${PC_GMP_INCLUDE_DIRS}" PC_GMP_INCLUDE_DIRS)
+execute_process(
+     COMMAND bash -c "pkg-config gmp --libs --static"
+     OUTPUT_VARIABLE PC_GMP_LIBRARIES
+)
+string(STRIP "${PC_GMP_LIBRARIES}" PC_GMP_LIBRARIES)
+
+execute_process(
+     COMMAND bash -c "pkg-config gmpxx --cflags"
+     OUTPUT_VARIABLE PC_GMPXX_INCLUDE_DIRS
+)
+string(STRIP "${PC_GMPXX_INCLUDE_DIRS}" PC_GMPXX_INCLUDE_DIRS)
+execute_process(
+     COMMAND bash -c "pkg-config gmpxx --libs --static"
+     OUTPUT_VARIABLE PC_GMPXX_LIBRARIES
+)
+string(STRIP "${PC_GMPXX_LIBRARIES}" PC_GMPXX_LIBRARIES)
+set(PC_GMPXX_LIBRARIES "-Wl,-rpath=${PkgConfigLocalPCFilesPath}/lib ${PC_GMPXX_LIBRARIES}")
+
+## Configure paths on requisite build time libraries (Boost):
+set(Boost_USE_STATIC_LIBS ON)
+set(Boost_USE_MULTITHREADED ON)
+set(Boost_USE_STATIC_RUNTIME ON)
+set(Boost_FIND_REQUIRED TRUE)
+set(Boost_FIND_QUIETLY TRUE)
+set(Boost_DEBUG FALSE)
+set(Boost_NO_BOOST_CMAKE TRUE)
+set(Boost_NO_SYSTEM_PATHS TRUE)
+if(NOT DEFINED BOOST_ROOT)
+     if(APPLE)
+          execute_process(
+               COMMAND bash "-c" "echo $(greadlink -f ${PROJECT_SOURCE_DIR}/../BoostLocalInstall)"
+               OUTPUT_VARIABLE BoostFileSystemRootPath
+          )
+     elseif(UNIX AND NOT APPLE)
+          execute_process(
+               COMMAND bash "-c" "echo $(readlink -f ${PROJECT_SOURCE_DIR}/../BoostLocalInstall)"
+               OUTPUT_VARIABLE BoostFileSystemRootPath
+          )
+     endif()
+     string(STRIP ${BoostFileSystemRootPath} BoostFileSystemRootPath)
+     set(BOOST_ROOT ${BoostFileSystemRootPath})
+     message(STATUS " >> Setting BOOST_ROOT: ${BOOST_ROOT}")
+endif()
+set(Boost_INCLUDE_DIR ${BOOST_ROOT}/include)
+set(Boost_LIBRARY_DIR ${BOOST_ROOT}/lib)
+
+#find_package(
+#     Boost ${BOOST_MIN_VERSION}
+#     COMPONENTS filesystem program_options system log log_setup thread atomic regex chrono
+#     REQUIRED
+#)
+#if(NOT Boost_FOUND)
+#    message(FATAL_ERROR "Boost Not Found ... Unable to complete the build")
+#endif()
+
+## Configure paths on requisite build time libraries (CGAL):
+if(APPLE)
+     execute_process(
+          COMMAND bash "-c" "echo $(greadlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'cgal*' -type d -printf \"${PROJECT_SOURCE_DIR}/../%f\n\" | head -n1))"
+          OUTPUT_VARIABLE CGALFileSystemRootPath
+          RESULT_VARIABLE CGALFileSystemRootPath_CmdResult
+     )
+     string(STRIP ${CGALFileSystemRootPath} CGALFileSystemRootPath)
+     set(CGAL_DIR ${CGALFileSystemRootPath})
+elseif(UNIX AND NOT APPLE)
+     execute_process(
+          COMMAND bash "-c" "echo $(readlink -f $(find .. -mindepth 1 -maxdepth 1 -iname 'cgal*' -type d -printf \"${PROJECT_SOURCE_DIR}/../%f\n\" | head -n1))"
+          OUTPUT_VARIABLE CGALFileSystemRootPath
+          RESULT_VARIABLE CGALFileSystemRootPath_CmdResult
+     )
+     string(STRIP ${CGALFileSystemRootPath} CGALFileSystemRootPath)
+     set(CGAL_DIR ${CGALFileSystemRootPath})
+endif()
+set(CGAL_DONT_OVERRIDE_CMAKE_FLAGS TRUE CACHE BOOL "Force CGAL to maintain CMAKE flags")
+file(GLOB CGALBaseFilesList "${CGAL_DIR}/*")
+set(CGALIncludeFilesList "")
+foreach(fsEntry ${CGALBaseFilesList})
+     if(NOT ${fsEntry} MATCHES ".*\\.svn\$" AND IS_DIRECTORY ${fsEntry}
+        AND IS_DIRECTORY ${fsEntry}/include)
+          list(APPEND CGALIncludeFilesList "${fsEntry}/include")
+     endif()
+endforeach()
+
+## Build the binaries for the PMFE project:
+
+add_custom_command(
+    OUTPUT "${PROJECT_SOURCE_DIR}/include/pmfe_build_config.h"
+    COMMAND cmake "-P" "${PROJECT_SOURCE_DIR}/cmake/AutogenBuildConfigHeader.cmake"
+    COMMAND touch "${PROJECT_SOURCE_DIR}/include/pmfe_build_config.h"
+)
+add_custom_target(
+     BuildConfigHeader ALL
+     DEPENDS "${PROJECT_SOURCE_DIR}/include/pmfe_build_config.h"
+)
+
+file(GLOB ALL_TARGET_SOURCES src/*.cc)
+include_directories(${CGALIncludeFilesList} "${Boost_INCLUDE_DIR}"
+                    "${PROJECT_SOURCE_DIR}/include" "${PROJECT_SOURCE_DIR}/iB4e"
+)
+
+add_executable(
+    pmfe-findmfe ${ALL_TARGET_SOURCES} src/bin-utils/bin-findmfe.cc
+)
+add_dependencies(pmfe-findmfe BuildConfigHeader)
+set_target_properties(
+     pmfe-findmfe PROPERTIES
+     OUTPUT_NAME "pmfe-findmfe"
+     COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
+)
+
+add_executable(
+    pmfe-scorer ${ALL_TARGET_SOURCES} src/bin-utils/bin-scorer.cc
+)
+add_dependencies(pmfe-scorer BuildConfigHeader)
+set_target_properties(
+     pmfe-scorer PROPERTIES
+     OUTPUT_NAME "pmfe-scorer"
+     COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
+)
+
+add_executable(
+    pmfe-parametrizer ${ALL_TARGET_SOURCES} src/bin-utils/bin-parametrizer.cc
+)
+add_dependencies(pmfe-parametrizer BuildConfigHeader)
+set_target_properties(
+     pmfe-parametrizer PROPERTIES
+     OUTPUT_NAME "pmfe-parametrizer"
+     COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
+)
+
+add_executable(
+    pmfe-subopt ${ALL_TARGET_SOURCES} src/bin-utils/bin-subopt.cc
+)
+add_dependencies(pmfe-subopt BuildConfigHeader)
+set_target_properties(
+     pmfe-subopt PROPERTIES
+     OUTPUT_NAME "pmfe-subopt"
+     COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
+)
+
+add_executable(
+    pmfe-tests ${ALL_TARGET_SOURCES} src/test-utils/test-pmfe.cc src/bin-utils/bin-tests.cc
+)
+add_dependencies(pmfe-tests BuildConfigHeader)
+set_target_properties(
+     pmfe-tests PROPERTIES
+     OUTPUT_NAME "pmfe-tests"
+     COMPILE_FLAGS "${CMAKE_CXX_FLAGS}"
+)
+
+## Install targets (both for binary sub-utilities and the
+## Python library to be used with SageMath):
+if(IS_DIRECTORY "/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9")
+     set(RHEL_INCLUDE_APPENDS "-I/opt/rh/devtoolset-9/root/usr/include/c++/9")
+     set(RHEL_LINKER_APPENDS "-L/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9")
+else()
+     set(RHEL_INCLUDE_APPENDS "")
+     set(RHEL_LINKER_APPENDS "")
+endif()
+if(APPLE)
+    set(CMAKE_CXX_FLAGS
+        "${CMAKE_CXX_FLAGS} -Wall -std=c++14 -stdlib=libc++ -fPIC -fopenmp -Wall -g -O3 \
+        -DBOOST_LOG_DYN_LINK=0 -DCGAL_HEADER_ONLY -D_GLIBCXX_USE_CXX11_ABI=0 \
+        -I/usr/local/include -Iinclude/ -IiB4e/ \
+        ${PC_GMP_INCLUDE_DIRS} ${PC_GMPXX_INCLUDE_DIRS} \
+        -I${Boost_INCLUDE_DIR} ${CGAL_INCLUDE_DIRS}
+        -DPMFE_PACKAGE_VERSION=\"${PMFE_PACKAGE_VERSION}\""
+    )
+    set(CMAKE_EXE_LINKER_FLAGS
+        "${CMAKE_CXX_FLAGS} ${CMAKE_EXE_LINKER_FLAGS} \
+        -L/usr/local/lib -lgmp -lgmpxx -lCGAL -lm -lboost_filesystem \
+        -lboost_program_options -lboost_system -lboost_log -lboost_log_setup \
+        -lc++ -lboost_log-mt \
+        ${PC_GMP_LIBRARIES} ${PC_GMPXX_LIBRARIES} ${Boost_LIBRARIES}"
+    )
+elseif(UNIX AND NOT APPLE) # Primary target: Linux (typically RHEL)
+    set(CMAKE_CXX_FLAGS
+        "-fPIC -fopenmp -Wall -g -O3 -fvisibility=hidden -fvisibility-inlines-hidden \
+        -DABI=0 -DBOOST_FILESYSTEM_NO_DEPRECATED -UBOOST_DISABLE_THREADS \
+        -DBOOST_LOG_DYN_LINK=1 -BOOST_ALL_DYN_LINK=1 -D_GLIBCXX_USE_CXX11_ABI=1 \
+        -DCGAL_HEADER_ONLY -DGAL_USE_LEDA=1 ${RHEL_INCLUDE_APPENDS} ${CMAKE_CXX_FLAGS}"
+    )
+    set(CMAKE_EXE_LINKER_FLAGS
+        "${RHEL_LINKER_APPENDS} -L/usr/lib -L/usr/local/lib \
+        ${CMAKE_EXE_LINKER_FLAGS} -L${Boost_LIBRARY_DIR} -Wl,-rpath=${Boost_LIBRARY_DIR} \
+        -lboost_filesystem -lboost_program_options -lboost_system \
+        -lboost_log -lboost_log_setup -lpthread -lm \
+        ${PC_GMPXX_LIBRARIES} ${PC_GMP_LIBRARIES}"
+    )
+endif()
+
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_EXE_LINKER_FLAGS}")
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_EXE_LINKER_FLAGS}")
+
+install(
+     TARGETS pmfe-findmfe pmfe-scorer pmfe-parametrizer pmfe-subopt pmfe-tests
+     DESTINATION ${EXECUTABLE_OUTPUT_PATH}
+)
+
+## Backup the old wrapper scripts and copy the new ones in their place:
+execute_process(
+     COMMAND cmake "-P" "${PROJECT_SOURCE_DIR}/cmake/PostBuildAutogenWrapperScript.cmake"
+)
+
+## Running of unit tests configuration:
+function(Func_runUnitTest UnitTestName)
+     add_test(NAME "PMFEUnitTestCheck-${UnitTestName}" COMMAND pmfe-tests -n ${UnitTestName} -a -s)
+     set_tests_properties(
+         "PMFEUnitTestCheck-${UnitTestName}" PROPERTIES
+         PASS_REGULAR_EXPRESSION "All tests passed .*"
+     )
+endfunction(Func_runUnitTest)
+
+if(RUN_UNIT_TESTS)
+     enable_testing()
+     message("Running *ALL* unit tests -- NOTE: This can take a long time -- ...")
+     Func_runUnitTest("16S")
+     Func_runUnitTest("5S")
+     Func_runUnitTest("asuum")
+     Func_runUnitTest("atabira")
+     Func_runUnitTest("bbigemina")
+     Func_runUnitTest("biological")
+     Func_runUnitTest("cdiphtheriae")
+     Func_runUnitTest("celegans")
+     Func_runUnitTest("combinatorial")
+     Func_runUnitTest("dmobilis")
+     Func_runUnitTest("ecoli")
+     Func_runUnitTest("ecuniculi")
+     Func_runUnitTest("ehexamita")
+     Func_runUnitTest("garboreum")
+     Func_runUnitTest("gardaea")
+     Func_runUnitTest("gintestinalis")
+     Func_runUnitTest("gmuris")
+     Func_runUnitTest("hsapiens")
+     Func_runUnitTest("hvolcanii")
+     Func_runUnitTest("ldelbrueckii")
+     Func_runUnitTest("mfe")
+     Func_runUnitTest("onivara")
+     Func_runUnitTest("random")
+     Func_runUnitTest("rnorvegicus")
+     Func_runUnitTest("stokodaii")
+     Func_runUnitTest("synthetic")
+     Func_runUnitTest("tRNA")
+     Func_runUnitTest("vnecatrix")
+     Func_runUnitTest("zmays")
+endif()