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Change binary file to iqtree3
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‎CMakeLists.txt‎

Lines changed: 46 additions & 46 deletions
Original file line numberDiff line numberDiff line change
@@ -833,44 +833,44 @@ endif()
833833
option(BUILD_LIB "Build IQ-TREE2 library" OFF)
834834

835835
if (BUILD_LIB STREQUAL "ON")
836-
add_library(iqtree2
836+
add_library(iqtree3
837837
obsolete/parsmultistate.cpp
838838
obsolete/parsmultistate.h
839839
)
840840
else()
841-
add_executable(iqtree2
841+
add_executable(iqtree3
842842
obsolete/parsmultistate.cpp
843843
obsolete/parsmultistate.h
844844
)
845845
endif()
846846

847847
if (USE_CMAPLE_AA STREQUAL "ON")
848-
add_executable(iqtree2-aa
848+
add_executable(iqtree3-aa
849849
obsolete/parsmultistate.cpp
850850
obsolete/parsmultistate.h
851851
)
852852
endif()
853853

854854
if(Backtrace_FOUND)
855855
include_directories(${Backtrace_INCLUDE_DIR})
856-
target_link_libraries(iqtree2 ${Backtrace_LIBRARY})
856+
target_link_libraries(iqtree3 ${Backtrace_LIBRARY})
857857
if (USE_CMAPLE_AA STREQUAL "ON")
858-
target_link_libraries(iqtree2-aa ${Backtrace_LIBRARY})
858+
target_link_libraries(iqtree3-aa ${Backtrace_LIBRARY})
859859
endif()
860860
endif(Backtrace_FOUND)
861861

862862
if (USE_BOOSTER)
863-
target_link_libraries(iqtree2 booster)
863+
target_link_libraries(iqtree3 booster)
864864
if (USE_CMAPLE_AA STREQUAL "ON")
865-
target_link_libraries(iqtree2-aa booster)
865+
target_link_libraries(iqtree3-aa booster)
866866
endif()
867867
endif()
868868

869869
if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
870870
if (NOT IQTREE_FLAGS MATCHES "nosse")
871-
set_target_properties(iqtree2 ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator yaml-cpp phyloYAML main ${TARGET_CMAPLE} PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
871+
set_target_properties(iqtree3 ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator yaml-cpp phyloYAML main ${TARGET_CMAPLE} PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
872872
if (USE_CMAPLE_AA STREQUAL "ON")
873-
set_target_properties(iqtree2-aa ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator yaml-cpp phyloYAML main-aa maple-aa PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
873+
set_target_properties(iqtree3-aa ncl nclextra utils pda lbfgsb whtest sprng vectorclass model gsl alignment tree simulator yaml-cpp phyloYAML main-aa maple-aa PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
874874
endif()
875875
if (USE_TERRAPHAST)
876876
set_target_properties(terracetphast terraphast PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
@@ -893,7 +893,7 @@ if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
893893
endif()
894894

895895
if(USE_NN OR USE_OLD_NN)
896-
target_link_libraries(iqtree2 nn)
896+
target_link_libraries(iqtree3 nn)
897897
endif()
898898

899899
##################################################################
@@ -917,100 +917,100 @@ if (NOT IQTREE_FLAGS MATCHES "single")
917917
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /LIBPATH:${PROJECT_SOURCE_DIR}/lib")
918918
set(THREAD_LIB "pthreadVC2")
919919
elseif(CLANG AND WIN32)
920-
target_link_libraries(iqtree2 ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)
920+
target_link_libraries(iqtree3 ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)
921921
if (USE_CMAPLE_AA STREQUAL "ON")
922-
target_link_libraries(iqtree2-aa ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)
922+
target_link_libraries(iqtree3-aa ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)
923923
endif()
924924
endif()
925925
endif()
926926

927927
# basic linking librararies
928-
target_link_libraries(iqtree2 pll ncl nclextra utils pda lbfgsb whtest sprng vectorclass model
928+
target_link_libraries(iqtree3 pll ncl nclextra utils pda lbfgsb whtest sprng vectorclass model
929929
gsl alignment tree simulator terrace yaml-cpp phyloYAML main ${TARGET_CMAPLE} ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
930930

931931
if (USE_CMAPLE_AA STREQUAL "ON")
932-
target_link_libraries(iqtree2-aa pll ncl nclextra utils pda lbfgsb whtest sprng vectorclass model
932+
target_link_libraries(iqtree3-aa pll ncl nclextra utils pda lbfgsb whtest sprng vectorclass model
933933
gsl alignment tree simulator terrace yaml-cpp phyloYAML main-aa maple-aa ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
934934
endif()
935935

936936
# onnxruntime library
937937
if (USE_NN OR USE_OLD_NN)
938938
if (onnxruntime_LIBRARIES)
939-
target_link_libraries(iqtree2 ${onnxruntime_LIBRARIES})
939+
target_link_libraries(iqtree3 ${onnxruntime_LIBRARIES})
940940
else()
941941
if (APPLE)
942-
target_link_libraries(iqtree2 /usr/local/lib/libonnxruntime.dylib)
942+
target_link_libraries(iqtree3 /usr/local/lib/libonnxruntime.dylib)
943943
elseif(UNIX)
944-
target_link_libraries(iqtree2 /usr/local/lib/libonnxruntime.so)
944+
target_link_libraries(iqtree3 /usr/local/lib/libonnxruntime.so)
945945
else()
946-
target_link_libraries(iqtree2 onnxruntime)
946+
target_link_libraries(iqtree3 onnxruntime)
947947
endif()
948948
endif()
949949
endif()
950950

951951
if (USE_TERRAPHAST)
952-
target_link_libraries(iqtree2 terracetphast)
952+
target_link_libraries(iqtree3 terracetphast)
953953
if (USE_CMAPLE_AA STREQUAL "ON")
954-
target_link_libraries(iqtree2-aa terracetphast)
954+
target_link_libraries(iqtree3-aa terracetphast)
955955
endif()
956956
endif()
957957

958958
if (USE_LSD2)
959-
target_link_libraries(iqtree2 lsd2)
959+
target_link_libraries(iqtree3 lsd2)
960960
if (USE_CMAPLE_AA STREQUAL "ON")
961-
target_link_libraries(iqtree2-aa lsd2)
961+
target_link_libraries(iqtree3-aa lsd2)
962962
endif()
963963
endif()
964964

965965
if (NOT IQTREE_FLAGS MATCHES "nosse")
966-
target_link_libraries(iqtree2 kernelsse)
966+
target_link_libraries(iqtree3 kernelsse)
967967
if (USE_CMAPLE_AA STREQUAL "ON")
968-
target_link_libraries(iqtree2-aa kernelsse)
968+
target_link_libraries(iqtree3-aa kernelsse)
969969
endif()
970970
endif()
971971

972972
# MPI libraries
973973
if (IQTREE_FLAGS MATCHES "mpi")
974974
if (NOT CMAKE_CXX_COMPILER MATCHES "mpi")
975-
target_link_libraries(iqtree2 ${MPI_CXX_LIBRARIES})
975+
target_link_libraries(iqtree3 ${MPI_CXX_LIBRARIES})
976976
if (USE_CMAPLE_AA STREQUAL "ON")
977-
target_link_libraries(iqtree2-aa ${MPI_CXX_LIBRARIES})
977+
target_link_libraries(iqtree3-aa ${MPI_CXX_LIBRARIES})
978978
endif()
979979
endif()
980980
endif()
981981

982982
# SSE, AVX etc. libraries
983983
if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
984-
target_link_libraries(iqtree2 pllavx kernelavx kernelfma)
984+
target_link_libraries(iqtree3 pllavx kernelavx kernelfma)
985985
if (USE_CMAPLE_AA STREQUAL "ON")
986-
target_link_libraries(iqtree2-aa pllavx kernelavx kernelfma)
986+
target_link_libraries(iqtree3-aa pllavx kernelavx kernelfma)
987987
endif()
988988
if (IQTREE_FLAGS MATCHES "KNL")
989-
target_link_libraries(iqtree2 kernelavx512)
989+
target_link_libraries(iqtree3 kernelavx512)
990990
if (USE_CMAPLE_AA STREQUAL "ON")
991-
target_link_libraries(iqtree2-aa kernelavx512)
991+
target_link_libraries(iqtree3-aa kernelavx512)
992992
endif()
993993
endif()
994994
endif()
995995

996996
# setup the executable name
997997
##################################################################
998-
set_target_properties(iqtree2 PROPERTIES OUTPUT_NAME "iqtree2${EXE_SUFFIX}")
998+
set_target_properties(iqtree3 PROPERTIES OUTPUT_NAME "iqtree3${EXE_SUFFIX}")
999999
if (USE_CMAPLE_AA STREQUAL "ON")
1000-
set_target_properties(iqtree2-aa PROPERTIES OUTPUT_NAME "iqtree2-aa${EXE_SUFFIX}")
1000+
set_target_properties(iqtree3-aa PROPERTIES OUTPUT_NAME "iqtree3-aa${EXE_SUFFIX}")
10011001
endif()
10021002

10031003
# strip the release build
10041004
if (NOT IQTREE_FLAGS MATCHES "nostrip" AND CMAKE_BUILD_TYPE STREQUAL "Release" AND (GCC OR CLANG) AND NOT APPLE) # strip is not necessary for MSVC
10051005
if (WIN32)
1006-
ADD_CUSTOM_COMMAND(TARGET iqtree2 POST_BUILD COMMAND strip $<TARGET_FILE:iqtree2>)
1006+
ADD_CUSTOM_COMMAND(TARGET iqtree3 POST_BUILD COMMAND strip $<TARGET_FILE:iqtree3>)
10071007
if (USE_CMAPLE_AA STREQUAL "ON")
1008-
ADD_CUSTOM_COMMAND(TARGET iqtree2-aa POST_BUILD COMMAND strip $<TARGET_FILE:iqtree2-aa>)
1008+
ADD_CUSTOM_COMMAND(TARGET iqtree3-aa POST_BUILD COMMAND strip $<TARGET_FILE:iqtree3-aa>)
10091009
endif()
10101010
elseif (NOT APPLE)
1011-
ADD_CUSTOM_COMMAND(TARGET iqtree2 POST_BUILD COMMAND strip $<TARGET_FILE:iqtree2>)
1011+
ADD_CUSTOM_COMMAND(TARGET iqtree3 POST_BUILD COMMAND strip $<TARGET_FILE:iqtree3>)
10121012
if (USE_CMAPLE_AA STREQUAL "ON")
1013-
ADD_CUSTOM_COMMAND(TARGET iqtree2-aa POST_BUILD COMMAND strip $<TARGET_FILE:iqtree2-aa>)
1013+
ADD_CUSTOM_COMMAND(TARGET iqtree3-aa POST_BUILD COMMAND strip $<TARGET_FILE:iqtree3-aa>)
10141014
endif()
10151015
endif()
10161016
endif()
@@ -1024,40 +1024,40 @@ endif()
10241024
if (WIN32)
10251025
if (MSVC)
10261026
if (CLANG_UNDER_VS)
1027-
ADD_CUSTOM_COMMAND(TARGET iqtree2 POST_BUILD COMMAND copy "iqtree2${EXE_SUFFIX}.exe" "iqtree2${EXE_SUFFIX}-click.exe")
1027+
ADD_CUSTOM_COMMAND(TARGET iqtree3 POST_BUILD COMMAND copy "iqtree3${EXE_SUFFIX}.exe" "iqtree3${EXE_SUFFIX}-click.exe")
10281028
if (USE_CMAPLE_AA STREQUAL "ON")
1029-
ADD_CUSTOM_COMMAND(TARGET iqtree2-aa POST_BUILD COMMAND copy "iqtree2-aa${EXE_SUFFIX}.exe" "iqtree2-aa${EXE_SUFFIX}-click.exe")
1029+
ADD_CUSTOM_COMMAND(TARGET iqtree3-aa POST_BUILD COMMAND copy "iqtree3-aa${EXE_SUFFIX}.exe" "iqtree3-aa${EXE_SUFFIX}-click.exe")
10301030
endif()
10311031
else()
1032-
ADD_CUSTOM_COMMAND(TARGET iqtree2 POST_BUILD COMMAND copy "Release\\iqtree2${EXE_SUFFIX}.exe" "Release\\iqtree2${EXE_SUFFIX}-click.exe")
1032+
ADD_CUSTOM_COMMAND(TARGET iqtree3 POST_BUILD COMMAND copy "Release\\iqtree3${EXE_SUFFIX}.exe" "Release\\iqtree3${EXE_SUFFIX}-click.exe")
10331033
if (USE_CMAPLE_AA STREQUAL "ON")
1034-
ADD_CUSTOM_COMMAND(TARGET iqtree2-aa POST_BUILD COMMAND copy "Release\\iqtree2-aa${EXE_SUFFIX}.exe" "Release\\iqtree2-aa${EXE_SUFFIX}-click.exe")
1034+
ADD_CUSTOM_COMMAND(TARGET iqtree3-aa POST_BUILD COMMAND copy "Release\\iqtree3-aa${EXE_SUFFIX}.exe" "Release\\iqtree3-aa${EXE_SUFFIX}-click.exe")
10351035
endif()
10361036
endif()
10371037
else()
1038-
ADD_CUSTOM_COMMAND(TARGET iqtree2 POST_BUILD COMMAND copy "iqtree2${EXE_SUFFIX}.exe" "iqtree2${EXE_SUFFIX}-click.exe")
1038+
ADD_CUSTOM_COMMAND(TARGET iqtree3 POST_BUILD COMMAND copy "iqtree3${EXE_SUFFIX}.exe" "iqtree3${EXE_SUFFIX}-click.exe")
10391039
if (USE_CMAPLE_AA STREQUAL "ON")
1040-
ADD_CUSTOM_COMMAND(TARGET iqtree2-aa POST_BUILD COMMAND copy "iqtree2-aa${EXE_SUFFIX}.exe" "iqtree2-aa${EXE_SUFFIX}-click.exe")
1040+
ADD_CUSTOM_COMMAND(TARGET iqtree3-aa POST_BUILD COMMAND copy "iqtree3-aa${EXE_SUFFIX}.exe" "iqtree3-aa${EXE_SUFFIX}-click.exe")
10411041
endif()
10421042
endif()
10431043
endif()
10441044

10451045
##############################################################
10461046
# add the install targets
10471047
##############################################################
1048-
install (TARGETS iqtree2 DESTINATION bin)
1048+
install (TARGETS iqtree3 DESTINATION bin)
10491049
if (USE_CMAPLE_AA STREQUAL "ON")
1050-
install (TARGETS iqtree2-aa DESTINATION bin)
1050+
install (TARGETS iqtree3-aa DESTINATION bin)
10511051
endif()
10521052
install (FILES "${PROJECT_SOURCE_DIR}/example/models.nex" DESTINATION .)
10531053
install (FILES "${PROJECT_SOURCE_DIR}/example/example.phy" DESTINATION .)
10541054
install (FILES "${PROJECT_SOURCE_DIR}/example/example.nex" DESTINATION .)
10551055
install (FILES "${PROJECT_SOURCE_DIR}/example/example.cf" DESTINATION .)
10561056

10571057
if (WIN32)
1058-
install (FILES "${BINARY_DIR}/iqtree2${EXE_SUFFIX}-click.exe" DESTINATION bin)
1058+
install (FILES "${BINARY_DIR}/iqtree3${EXE_SUFFIX}-click.exe" DESTINATION bin)
10591059
if (USE_CMAPLE_AA STREQUAL "ON")
1060-
install (FILES "${BINARY_DIR}/iqtree2-aa${EXE_SUFFIX}-click.exe" DESTINATION bin)
1060+
install (FILES "${BINARY_DIR}/iqtree3-aa${EXE_SUFFIX}-click.exe" DESTINATION bin)
10611061
endif()
10621062
if (NOT IQTREE_FLAGS MATCHES "single" AND MSVC)
10631063
install(FILES "${PROJECT_SOURCE_DIR}/lib/pthreadVC2.dll" DESTINATION bin)

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