1. Added (copies) of lib and lib32 folders for OMP and pthreads

    libraries.  These are copies of what dev branch of iqtree2
    has (these are needed for Windows builds)
2. Decided, it's better if iqtree_config.h gets generated after all.
3. decenttree_update.sh copies lib and lib32 folder contents too.
4. A bunch of visual studio file extensions and "magic folders"
    are now excluded from source control.

Author: JamesBarbetti

.gitignore

@@ -1 +1,7 @@
 build/
+*.suo
+*.ipch
+/.vs
+/x64/Debug
+/x64/Release
+/decentTree.vcxproj.user

CMakeLists.txt

@@ -1,10 +1,10 @@
 #########################################################################
-# DecentTree cmake build definition
+# decenttree cmake build definition
 # Copyright (c) 2012-2020 Bui Quang Minh, Lam-Tung Nguyen, James Barbetti
 #########################################################################
 
-cmake_minimum_required(VERSION 2.8.10 FATAL_ERROR)
-project(decentTree)
+cmake_minimum_required(VERSION 3.18.0 FATAL_ERROR)
+project(decenttree)
 
 # Windows example usages:
 #------------------------
@@ -46,7 +46,6 @@ project(decentTree)
 # assuming you installed LLVM via Homebrew: brew install --with-toolchain llvm
 # cmake -G XCode -DCMAKE_XCODE_ATTRIBUTE_CC=/usr/local/opt/llvm/bin/clang -DCMAKE_XCODE_ATTRIBUTE_CXX=/usr/local/opt/llvm/bin/clang++ <source_dir>
 #
-#
 # Compile OpenMP version: cmake ....
 # Compile 32-bit version: cmake -DDECENTTREE_FLAGS=m32 ....
 # Compile static version: cmake -DDECENTTREE_FLAGS=static ....
@@ -60,12 +59,11 @@ project(decentTree)
 
 set(CMAKE_LEGACY_CYGWIN_WIN32 0)
 set(GCC_MIN_VERSION "4.8")
-add_definitions(-DDECENT_TREE)
 
 # The version number.
-set (decentTree_VERSION_MAJOR 1)
-set (decentTree_VERSION_MINOR 0)
-set (decentTree_VERSION_PATCH ".0")
+set (decenttree_VERSION_MAJOR 1)
+set (decenttree_VERSION_MINOR 0)
+set (decenttree_VERSION_PATCH ".0")
 
 if (CMAKE_C_COMPILER MATCHES "mpic")
     set(DECENTTREE_FLAGS "${DECENTTREE_FLAGS} mpi")
@@ -493,27 +491,6 @@ if (DECENTTREE_FLAGS MATCHES "libcxx")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
 endif()
 
-message("CMake build type: ${CMAKE_BUILD_TYPE}")
-
-if (CMAKE_BUILD_TYPE STREQUAL "Release")
-    message("C flags         : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_RELEASE}")
-    message("CXX flags       : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
-elseif (CMAKE_BUILD_TYPE STREQUAL "Debug")
-    message("C flags         : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_DEBUG}")
-    message("CXX flags       : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
-elseif (CMAKE_BUILD_TYPE STREQUAL "Profile")
-    message("C flags         : ${CMAKE_C_FLAGS_PROFILE} ")
-    message("CXX flags       : ${CMAKE_CXX_FLAGS_PROFILE} ")
-else()
-    message("C flags         : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_RELEASE}")
-    message("CXX flags       : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
-endif()
-
-message("LINKER flags    : ${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_RELEASE}")
-get_directory_property( COMPILER_DEFINITIONS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS )
-message("Compiler defns  : ${COMPILER_DEFINITIONS}")
-
-
 if (GCC)
     set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g -fno-inline-functions -fno-inline-functions-called-once -fno-default-inline -fno-inline")
     set(CMAKE_C_FLAGS_DEBUG "-O0 -g -fno-inline-functions -fno-inline-functions-called-once -fno-default-inline -fno-inline")
@@ -545,12 +522,15 @@ configure_file (
   "${PROJECT_BINARY_DIR}/decenttree_config.h"
   )
 
+configure_file (
+"${PROJECT_SOURCE_DIR}/iqtree_config.h.in"
+"${PROJECT_BINARY_DIR}/iqtree_config.h"
+)
+
 # add the binary tree to the search path for include files
 # so that we will find decenttree_config.h
 include_directories("${PROJECT_BINARY_DIR}")
 
-#zlib will be detected for appearance
-#include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7")
 
 if (NOT DECENTTREE_FLAGS MATCHES "nozlib")
     find_package(ZLIB)
@@ -572,11 +552,36 @@ endif(ZLIB_FOUND)
 add_subdirectory(vectorclass)
 LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}")
 
+add_compile_definitions(USE_PROGRESS_DISPLAY=1)
+add_compile_definitions(USE_VECTORCLASS_LIBRARY=1)
+add_compile_definitions(USE_GZSTREAM=1)
+add_compile_definitions(DECENT_TREE=1)
+
+message("CMake build type: ${CMAKE_BUILD_TYPE}")
+message("CMake source dir: ${CMAKE_SOURCE_DIR}")
+if (CMAKE_BUILD_TYPE STREQUAL "Release")
+    message("C flags         : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_RELEASE}")
+    message("CXX flags       : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+elseif (CMAKE_BUILD_TYPE STREQUAL "Debug")
+    message("C flags         : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_DEBUG}")
+    message("CXX flags       : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
+elseif (CMAKE_BUILD_TYPE STREQUAL "Profile")
+    message("C flags         : ${CMAKE_C_FLAGS_PROFILE} ")
+    message("CXX flags       : ${CMAKE_CXX_FLAGS_PROFILE} ")
+else()
+    message("C flags         : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_RELEASE}")
+    message("CXX flags       : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
+endif()
+message("LINKER flags    : ${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_RELEASE}")
+get_directory_property( COMPILER_DEFINITIONS DIRECTORY ${CMAKE_SOURCE_DIR} COMPILE_DEFINITIONS )
+message("Compiler defns  : ${COMPILER_DEFINITIONS}")
+message("Binary directory: ${PROJECT_BINARY_DIR}")
+
 ##################################################################
 # the main executable
 ##################################################################
 
-add_executable(decentTree
+add_executable(decenttree
     decenttree.cpp
     flatmatrix.cpp flatmatrix.h
     starttree.cpp starttree.h
@@ -592,9 +597,9 @@ add_executable(decentTree
     operatingsystem.cpp operatingsystem.h safe_io.h)
 
 if(ZLIB_FOUND)
-  target_link_libraries(decentTree ${ZLIB_LIBRARIES})
+  target_link_libraries(decenttree ${ZLIB_LIBRARIES})
 else(ZLIB_FOUND)
-  target_link_libraries(decentTree zlibstatic)
+  target_link_libraries(decenttree zlibstatic)
 endif(ZLIB_FOUND)
 
 add_executable(hod_tree
@@ -611,15 +616,10 @@ endif(Backtrace_FOUND)
 
 if (NOT DECENTTREE_FLAGS MATCHES "avx" AND NOT DECENTTREE_FLAGS MATCHES "fma")
     if (NOT DECENTTREE_FLAGS MATCHES "nosse")
-        set_target_properties(decentTree vectorclass PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
+        set_target_properties(decenttree vectorclass PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
     endif()
 endif()
 
-add_compile_definitions(USE_PROGRESS_DISPLAY=1)
-add_compile_definitions(USE_VECTORCLASS_LIBRARY=1)
-add_compile_definitions(USE_GZSTREAM=1)
-
-
 ##################################################################
 # setup linking flags
 ##################################################################
@@ -647,9 +647,9 @@ if (NOT DECENTTREE_FLAGS MATCHES "single")
         endif()
     elseif(CLANG AND WIN32)
         if (BINARY32)
-            target_link_libraries(decentTree ${PROJECT_SOURCE_DIR}/lib32/libiomp5md.dll)
+            target_link_libraries(decenttree ${PROJECT_SOURCE_DIR}/lib32/libiomp5md.dll)
         else()
-            target_link_libraries(decentTree ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)
+            target_link_libraries(decenttree ${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll)
         endif()
 #        set(THREAD_LIB "ompstatic")
     endif()
@@ -661,7 +661,7 @@ if (NOT DECENTTREE_FLAGS MATCHES "single")
 endif()
 
 # basic linking librararies
-target_link_libraries(decentTree vectorclass
+target_link_libraries(decenttree vectorclass
     ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB} ${ATOMIC_LIB})
 
 # MPI libraries
@@ -673,7 +673,7 @@ endif()
 
 # setup the executable name
 ##################################################################
-set_target_properties(decentTree PROPERTIES OUTPUT_NAME "decentTree${EXE_SUFFIX}")
+set_target_properties(decenttree PROPERTIES OUTPUT_NAME "decenttree${EXE_SUFFIX}")
 
 # strip the release build
 if (NOT DECENTTREE_FLAGS MATCHES "no-strip" AND CMAKE_BUILD_TYPE STREQUAL "Release" AND (GCC OR CLANG) AND NOT APPLE) # strip is not necessary for MSVC
@@ -692,19 +692,19 @@ endif()
 
 if (WIN32)
     if (MSVC)
-        #ADD_CUSTOM_COMMAND(TARGET decentTree POST_BUILD COMMAND copy "${BINARY_DIR}/decentTree${EXE_SUFFIX}.exe" "${BINARY_DIR}/decentTree${EXE_SUFFIX}-click.exe")
+        #ADD_CUSTOM_COMMAND(TARGET decenttree POST_BUILD COMMAND copy "${BINARY_DIR}/decenttree${EXE_SUFFIX}.exe" "${BINARY_DIR}/decentTree${EXE_SUFFIX}-click.exe")
     else()
-        ADD_CUSTOM_COMMAND(TARGET decentTree POST_BUILD COMMAND copy "decentTree${EXE_SUFFIX}.exe" "decentTree${EXE_SUFFIX}-click.exe")
+        ADD_CUSTOM_COMMAND(TARGET decenttree POST_BUILD COMMAND copy "decenttree${EXE_SUFFIX}.exe" "decentTree${EXE_SUFFIX}-click.exe")
     endif()
 endif()
 
 ##############################################################
 # add the install targets
 ##############################################################
-install (TARGETS decentTree DESTINATION bin)
+install (TARGETS decenttree DESTINATION bin)
 
 if (WIN32 OR WIN64)
-    install (FILES "${BINARY_DIR}/decentTree${EXE_SUFFIX}-click.exe" DESTINATION bin)
+    install (FILES "${BINARY_DIR}/decenttree${EXE_SUFFIX}-click.exe" DESTINATION bin)
     if (NOT DECENTTREE_FLAGS MATCHES "single" AND MSVC)
         if (BINARY32)
             install(FILES  "${PROJECT_SOURCE_DIR}/lib32/pthreadVC2.dll" DESTINATION bin)

decenttree_update.sh

@@ -18,6 +18,8 @@ cp heapsort.h gzstream.cpp gzstream.h progress.cpp progress.h safe_io.h ../../de
 cp operatingsystem.cpp operatingsystem.h timeutil.h my_assert.h         ../../decenttree
 cd ..
 cp -R zlib-1.2.7      ../decenttree
+cp -R lib             ../decenttree
+cp -R lib32           ../decenttree
 cp -R libmac          ../decenttree
 cp -R vectorclass     ../decenttree
 cp iqtree_config.h.in ../decenttree