.travis.yml

-# OpenMP projects should set the environment variable OMP_NUM_THREADS to a reasonably small value (say, 4). 
-dist: trusty
-sudo : false
-
 notifications:
     slack: veg-igem:rqQd95zjTuZoRNElekQx2CLf
     email:
         recipients:
-            - spond@temple.edu
             - steven@stevenweaver.org
+            - spond@temple.edu
+            - tuj86312@temple.edu
         on_success: change
         on_failure: always
 
 branches:
   only:
     - master
-    - beta
-
-env:
-  - METHOD_TEST=tests/hbltests/libv3/SLAC.wbf
-  - METHOD_TEST=tests/hbltests/libv3/SLAC-partitioned.wbf
-  - METHOD_TEST=tests/hbltests/libv3/FEL.wbf
-  - METHOD_TEST=tests/hbltests/libv3/MEME.wbf
-  - METHOD_TEST=tests/hbltests/libv3/MEME-partitioned.wbf
-  - METHOD_TEST=tests/hbltests/libv3/FUBAR.wbf
-  - METHOD_TEST=tests/hbltests/libv3/RELAX.wbf
-  - METHOD_TEST=tests/hbltests/libv3/aBSREL.wbf
-  - METHOD_TEST=tests/hbltests/libv3/BUSTED.wbf
-  - METHOD_TEST=tests/hbltests/libv3/LEISR.wbf
-  - METHOD_TEST=tests/hbltests/libv3/BGM.wbf
+    - develop
 
+dist: xenial
+sudo : false
 language: c++
-
 compiler: 
   - gcc
-  - clang
+script: 
+  - export OMP_NUM_THREADS=4
+  - travis_wait 60 eval $envSpecificTest
+
 
+matrix:
+  include:
+    # ---- Run all the tests with gcc-7 ----
+    - os: linux
+      env:
+        - envSpecificTest="bash ./test_kwargs.sh"
       addons:
         apt:
           sources:
@@ -44,18 +38,301 @@ addons:
           packages:
               - g++-7
               - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
     
+    - os: linux
+      env:
+        - envSpecificTest="bash ./run_unit_tests.sh"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
       install:
         - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
         - cmake . 
-  - make HYPHYMP
-  - make HYPHYGTEST
+        - make
 
-script: 
-  - export OMP_NUM_THREADS=8
-  - export LD_LIBRARY_PATH=/usr/local/clang/lib:$LD_LIBRARY_PATH
-  - ./HYPHYGTEST
-  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/math.bf
-  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/iofunctions.bf
-  - ./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/utilityfunctions.bf
-  - ./HYPHYMP LIBPATH=`pwd`/res/ $METHOD_TEST
+    - os: linux
+      env:
+        - envSpecificTest="export PATH=$PATH:$(pwd); cd; git clone https://gitlab.com/rdvelazquez/testiphy.git; cd testiphy; ./testiphy HYPHYMP"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+    
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/SLAC.wbf"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+    
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP SLAC --alignment ./tests/hbltests/libv3/data/partitioned.nex --branches Internal"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+    
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP FEL --alignment ./tests/hbltests/libv3/data/CD2.nex"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP MEME --alignment ./tests/hbltests/data/CD2.nex"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP MEME --alignment ./tests/hbltests/libv3/data/CD2.nex --branches GROUP1"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP FUBAR --alignment ./tests/hbltests/libv3/data/CD2.nex"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/RELAX.wbf"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP LIBPATH=`pwd`/res/ tests/hbltests/libv3/aBSREL.wbf"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP BUSTED --alignment ./tests/hbltests/data/CD2.nex --srv No --branches Internal"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./HYPHYMP BGM --alignment ./tests/hbltests/data/CD2.nex"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./hyphy fade --alignment ./tests/hbltests/data/CD2_AA.fna"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+    - os: linux
+      env:
+        - envSpecificTest="./hyphy gard --alignment ./tests/hbltests/data/CD2.nex"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-7
+              - gcc-7
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-7" CC="gcc-7"; fi
+        - cmake . 
+        - make
+
+
+    # ---- Just run the hbl unit tests with gcc-4, 5 and 6 ----
+    # gcc-4
+    - os: linux
+      env:
+        - envSpecificTest="bash ./run_unit_tests.sh"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-4.9
+              - gcc-4.9
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-4.9" CC="gcc-4.9"; fi
+        - cmake . 
+        - make
+
+    # gcc-5
+    - os: linux
+      env:
+        - envSpecificTest="bash ./run_unit_tests.sh"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-5
+              - gcc-5
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-5" CC="gcc-5"; fi
+        - cmake . 
+        - make
+
+    # gcc-6
+    - os: linux
+      env:
+        - envSpecificTest="bash ./run_unit_tests.sh"
+      addons:
+        apt:
+          sources:
+              - llvm-toolchain-precise
+              - ubuntu-toolchain-r-test
+              - george-edison55-precise-backports
+          packages:
+              - g++-6
+              - gcc-6
+      install:
+        - if [ "$CXX" = "g++" ]; then export CXX="g++-6" CC="gcc-6"; fi
+        - cmake . 
+        - make

CMakeLists.txt

-cmake_minimum_required(VERSION 3.0.0)
+cmake_minimum_required(VERSION 3.12)
 project(HyPhy)
 cmake_policy(VERSION 3.0.0)
-cmake_policy(SET CMP0026 NEW)
+#cmake_policy(SET CMP0026 OLD)
+#cmake_policy(SET CMP0004 OLD)
+
 
 set(CMAKE_CONFIGURATION_TYPES Release)
 
@@ -20,12 +22,14 @@ macro(PCL_CHECK_FOR_SSE3)
   include(CheckCXXSourceRuns)
   set(CMAKE_REQUIRED_FLAGS)
 
-  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+  #if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
       set(CMAKE_REQUIRED_FLAGS "-msse3")
-  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+  #endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
 
   check_cxx_source_runs("
       #include <pmmintrin.h>
+      #include <stdio.h>
+
       int main ()
       {
           __m128d a, b;
@@ -33,6 +37,7 @@ macro(PCL_CHECK_FOR_SSE3)
           a = _mm_loadu_pd (vals);
           b = _mm_hadd_pd (a,a);
           _mm_storeu_pd (vals, b);
+          printf (\"%g\", vals[0]);
           return (0);
       }"
       HAVE_SSE3_EXTENSIONS)
@@ -46,12 +51,14 @@ macro(PCL_CHECK_FOR_AVX)
   include(CheckCXXSourceRuns)
   set(CMAKE_REQUIRED_FLAGS)
 
-  if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-      set(CMAKE_REQUIRED_FLAGS "-march=corei7-avx -mtune=corei7-avx")
-  endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+  #if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
+      set(CMAKE_REQUIRED_FLAGS "-mavx")
+  #endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
 
   check_cxx_source_runs("
       #include <immintrin.h>
+      #include <stdio.h>
+
       int main ()
       {
           __m256d a, b;
@@ -59,11 +66,43 @@ macro(PCL_CHECK_FOR_AVX)
           a = _mm256_loadu_pd (vals);
           b = _mm256_hadd_pd (a,a);
           _mm256_storeu_pd (vals, b);
+          printf (\"%g\", vals[0]);
           return (0);
       }"
       HAVE_AVX_EXTENSIONS)
 endmacro(PCL_CHECK_FOR_AVX)
 
+#-------------------------------------------------------------------------------
+# FMA3 MACROS
+#-------------------------------------------------------------------------------
+
+macro(PCL_CHECK_FOR_FMA3)
+    include(CheckCXXSourceRuns)
+    set(CMAKE_REQUIRED_FLAGS)
+
+    #if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
+        set(CMAKE_REQUIRED_FLAGS "-mavx -mfma ")
+    #endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
+
+    check_cxx_source_runs("
+    #include <immintrin.h>
+    #include <stdio.h>
+
+    int main ()
+    {
+        __m256d a, b, c;
+        double vals[4] = {2.};
+        a = _mm256_loadu_pd (vals);
+        b = _mm256_loadu_pd (vals);
+        c = _mm256_loadu_pd (vals);
+        a = _mm256_fmadd_pd      (a, b, c);
+        _mm256_storeu_pd (vals, a);
+        printf (\"%g\", vals[0]);
+        return 0;
+    }"
+    HAVE_FMA3)
+endmacro(PCL_CHECK_FOR_FMA3)
+
 
 #-------------------------------------------------------------------------------
 # set the CMAKE_MODULE_PATH so we can import OpenCL
@@ -71,21 +110,22 @@ endmacro(PCL_CHECK_FOR_AVX)
 set(CMAKE_MODULE_PATH cmake)
 set(HYPHY_VERSION 2.1)
 
-
 #-------------------------------------------------------------------------------
 # setup the files we'll be using
 #-------------------------------------------------------------------------------
 file(GLOB SRC_CORE src/core/*.cpp)
 file(GLOB SRC_GTESTS tests/gtests/*.cpp)
 file(GLOB SRC_NEW src/new/*.cpp)
+file(GLOB SRC_CONTRIB src/contrib/*.cpp)
 
 set(SRC_LINK src/lib/link/THyPhy.cpp)
 set(SRC_SQLITE3 contrib/SQLite-3.8.2/sqlite3.c)
 set(SRC_UNIXMAIN src/mains/unix.cpp)
 set(SRC_UTILS src/utils/hyphyunixutils.cpp)
 
-set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS})
 
+set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS} ${SRC_CONTRIB})
+set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")
 
 #-------------------------------------------------------------------------------
 # make it fast, scotty
@@ -95,6 +135,7 @@ set(DEFAULT_WARNING_FLAGS "-w")
 set(DEFAULT_DEBUG_WARNING_FLAGS "-Wall -Wno-int-to-pointer-cast -Wno-conversion-null -Wno-sign-compare -Wno-maybe-uninitialized")
 
 
+
 if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
     execute_process(
         COMMAND ${CMAKE_CXX_COMPILER} -dumpversion
@@ -108,7 +149,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
     if(${GCC_VERSION} VERSION_LESS 6.0)
       set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -std=gnu++14")
     else(${GCC_VERSION} VERSION_LESS 6.0)
-      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3")
+      set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -std=c++14")
     endif(${GCC_VERSION} VERSION_LESS 6.0)
 
     if(NOAVX)
@@ -125,8 +166,13 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
     else(NOAVX)
        PCL_CHECK_FOR_AVX()
        if(${HAVE_AVX_EXTENSIONS})
-            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=corei7-avx -mtune=corei7-avx")
+            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx")
             add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
+            PCL_CHECK_FOR_FMA3()
+            if (${HAVE_FMA3})
+                set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS}  -mfma")
+                add_definitions (-D_SLKP_USE_FMA3_INTRINSICS)
+            endif (${HAVE_FMA3})
         else(${HAVE_AVX_EXTENSIONS})
             PCL_CHECK_FOR_SSE3()
             if(${HAVE_SSE3_EXTENSIONS})
@@ -144,8 +190,13 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3")
     PCL_CHECK_FOR_AVX()
     if(${HAVE_AVX_EXTENSIONS})
-        set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=corei7-avx -mtune=corei7-avx ")
+        set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx")
         add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
+        PCL_CHECK_FOR_FMA3()
+        if (${HAVE_FMA3})
+            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mfma")
+            add_definitions (-D_SLKP_USE_FMA3_INTRINSICS)
+        endif (${HAVE_FMA3})
     else(${HAVE_AVX_EXTENSIONS})
         PCL_CHECK_FOR_SSE3()
         if(${HAVE_SSE3_EXTENSIONS})
@@ -155,7 +206,7 @@ if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
     endif (${HAVE_AVX_EXTENSIONS})
 
     set_property(
-     SOURCE ${SRC_CORE}
+     SOURCE ${SRC_CORE} ${SRC_NEW} ${SRC_UTILS} ${SRC_UNIXMAIN}
      APPEND_STRING PROPERTY  COMPILE_FLAGS " -std=c++14 "
     )
 endif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
@@ -171,28 +222,18 @@ if(NOT DEFINED DEFAULT_LINK_FLAGS)
     set(DEFAULT_LINK_FLAGS "")
 endif(NOT DEFINED DEFAULT_LINK_FLAGS)
 
+set(DEFAULT_LINK_FLAGS "${DEFAULT_LINK_FLAGS}  ")
+
 if(NOT DEFINED DEFAULT_WARNING_FLAGS)
     set(DEFAULT_WARNING_FLAGS "")
 endif(NOT DEFINED DEFAULT_WARNING_FLAGS)
 
-include (CheckLibraryExists)
-
-CHECK_LIBRARY_EXISTS( "libamdlibm.so" "amd_log" "" HAS_AMD_LIBM)
-if(HAS_AMD_LIBM)
-    set(DEFAULT_LINK_FLAGS "${DEFAULT_LINK_FLAGS} -lamdlibm")
-    add_definitions(-D__USEAMDLOG__)
-endif(HAS_AMD_LIBM)
-
 
 #-------------------------------------------------------------------------------
 # OpenMP support
 #-------------------------------------------------------------------------------
 find_package(OpenMP)
 
-if(NOT ${OPENMP_FOUND})
-    set(OpenMP_CXX_FLAGS "")
-endif(NOT ${OPENMP_FOUND})
-
 #-------------------------------------------------------------------------------
 # default installation prefix
 #-------------------------------------------------------------------------------
@@ -202,10 +243,11 @@ endif()
 if(NOT DEFINED INSTALL_PREFIX)
     set(INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX} CACHE INTERNAL "Installation prefix" FORCE)
 endif()
+
 if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
-    set(DEFAULT_LIBRARIES pthread)
+	set(DEFAULT_LIBRARIES )
 else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
-    set(DEFAULT_LIBRARIES dl pthread)
+    set(DEFAULT_LIBRARIES dl)
 endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
 
 #-------------------------------------------------------------------------------
@@ -214,9 +256,9 @@ endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
 find_package(CURL)
 if(${CURL_FOUND} AND NOT APPLE)
     if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
-        set(DEFAULT_LIBRARIES pthread crypto curl ssl)
+        set(DEFAULT_LIBRARIES crypto curl ssl)
     else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
-        set(DEFAULT_LIBRARIES dl pthread crypto curl ssl)
+        set(DEFAULT_LIBRARIES dl crypto curl ssl)
     endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
     add_definitions (-D__HYPHYCURL__)
 endif(${CURL_FOUND} AND NOT APPLE)
@@ -243,7 +285,15 @@ add_custom_target(uninstall
     COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake
 )
 
-
+find_program(NODE npm)
+if(NOT NODE)
+    message("Node not installed; API documentation will not be generated")
+else(NOT NODE)
+    add_custom_target(
+        docs ALL
+        rm -rf ./docs && npm install -g documentation@4 && documentation build --polyglot -f md ./res/TemplateBatchFiles/libv3/**/*.bf -o ./docs.md
+    )
+endif(NOT NODE)
 
 
 #-------------------------------------------------------------------------------
@@ -274,12 +324,10 @@ set_property(
 #-------------------------------------------------------------------------------
 add_definitions(-D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__)
 
-if(CMAKE_SIZEOF_VOID_P EQUAL 8)
-    add_definitions(-D__HYPHY_64__)
-endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
 
 include_directories(
     src/core/include
+    src/contrib
     src/lib/Link src/new/include
     contrib/SQLite-3.8.2 # SQLite
     contrib/gtest-1.7.0/include
@@ -296,57 +344,24 @@ install(DIRECTORY res/ DESTINATION lib/hyphy)
 # HYPHYMP target
 #-------------------------------------------------------------------------------
 add_executable(
-    HYPHYMP
+    hyphy
     ${SRC_COMMON} ${SRC_UNIXMAIN}
 )
 
-target_link_libraries(HYPHYMP ${DEFAULT_LIBRARIES})
+if(${OPENMP_FOUND})
+    target_link_libraries(hyphy PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+else(${OPENMP_FOUND})
+    target_link_libraries(hyphy PRIVATE ${DEFAULT_LIBRARIES})
+endif(${OPENMP_FOUND})
 
-add_custom_target(MP DEPENDS HYPHYMP)
+add_custom_target(MP DEPENDS hyphy)
 
 install(
-    TARGETS HYPHYMP
+    TARGETS hyphy
     RUNTIME DESTINATION bin
     OPTIONAL
 )
 
-#-------------------------------------------------------------------------------
-# hyphy OpenCL target
-#-------------------------------------------------------------------------------
-find_package(OpenCL)
-if(${OPENCL_FOUND})
-
-    add_executable(
-        HYPHYOCL
-        EXCLUDE_FROM_ALL
-        ${SRC_COMMON} ${SRC_UNIXMAIN} ${CMAKE_CURRENT_BINARY_DIR}/src/ocl/opencl_kernels.h
-    )
-
-    include_directories(${OPENCL_INCLUDE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${CMAKE_CURRENT_BINARY_DIR}/src/ocl)
-    target_link_libraries(HYPHYOCL ${DEFAULT_LIBRARIES} ${OPENCL_LIBRARIES})
-
-    add_custom_target(OCL DEPENDS HYPHYOCL)
-    set_property(
-        TARGET HYPHYOCL
-        APPEND PROPERTY COMPILE_DEFINITIONS __MP__ __MP2__ __UNIX__ _HY_GPU_EXAMPLE_CALCULATOR MDSOCL
-    )
-    set_target_properties(
-        HYPHYOCL
-        PROPERTIES
-        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS}"
-        LINK_FLAGS "${DEFAULT_LINK_FLAGS}"
-    )
-    add_executable(
-        cl2hdr
-        EXCLUDE_FROM_ALL
-        contrib/cl2hdr.c
-    )
-    add_custom_command(
-        OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/src/ocl/opencl_kernels.h
-        COMMAND cl2hdr ${CMAKE_CURRENT_SOURCE_DIR}/src/ocl/opencl_kernels.cl ${CMAKE_CURRENT_BINARY_DIR}/src/ocl/opencl_kernels.h
-        DEPENDS cl2hdr ${CMAKE_CURRENT_SOURCE_DIR}/src/ocl/opencl_kernels.cl
-    )
-endif(${OPENCL_FOUND})
 
 
 #-------------------------------------------------------------------------------
@@ -358,12 +373,17 @@ if(${MPI_FOUND})
 
     add_executable(
         HYPHYMPI
+        EXCLUDE_FROM_ALL
         ${SRC_COMMON} ${SRC_UNIXMAIN}
     )
 
     include_directories(${MPI_INCLUDE_PATH})
 
+    if(${OPENMP_FOUND})
+        target_link_libraries(HYPHYMPI ${DEFAULT_LIBRARIES} ${MPI_LIBRARIES} OpenMP::OpenMP_CXX)
+    else(${OPENMP_FOUND})
         target_link_libraries(HYPHYMPI ${DEFAULT_LIBRARIES} ${MPI_LIBRARIES})
+    endif(${OPENMP_FOUND})
 
     install(
         TARGETS HYPHYMPI
@@ -379,14 +399,73 @@ if(${MPI_FOUND})
         APPEND PROPERTY COMPILE_DEFINITIONS __HYPHYMPI__ __UNIX__ _HYPHY_LIBDIRECTORY_="${CMAKE_INSTALL_PREFIX}/lib/hyphy"
     )
 
+    message ("${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS}")
+
     set_target_properties(
         HYPHYMPI
         PROPERTIES
+        if(${OPENMP_FOUND})
             COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
             LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
+        else(${OPENMP_FOUND})
+            COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS}"
+            LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS}"
+        endif(${OPENMP_FOUND})
     )
 endif(${MPI_FOUND})
 
+#-------------------------------------------------------------------------------
+# hyphy profile target
+#-------------------------------------------------------------------------------
+add_executable(
+    HYPHY-PROFILE
+    EXCLUDE_FROM_ALL
+    ${SRC_COMMON} ${SRC_UNIXMAIN}
+)
+
+if(${OPENMP_FOUND})
+    target_link_libraries(HYPHY-PROFILE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+else(${OPENMP_FOUND})
+    target_link_libraries(HYPHY-PROFILE ${DEFAULT_LIBRARIES})
+endif(${OPENMP_FOUND})
+
+add_custom_target(PROFILE DEPENDS HYPHY-PROFILE)
+
+
+set_target_properties(
+    HYPHY-PROFILE
+    PROPERTIES
+    if(${OPENMP_FOUND})
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-instr-generate -fcoverage-mapping "
+        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-instr-generate "
+    else(${OPENMP_FOUND})
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS}-g -fprofile-instr-generate -fcoverage-mapping "
+        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} -g  -fprofile-instr-generate "
+    endif(${OPENMP_FOUND})
+)
+
+#-------------------------------------------------------------------------------
+ # hyphy profile target
+ #-------------------------------------------------------------------------------
+ add_executable(
+     HYPHY-GPERF
+     EXCLUDE_FROM_ALL
+     ${SRC_COMMON} ${SRC_UNIXMAIN}
+ )
+
+  target_link_libraries(HYPHY-PROFILE ${DEFAULT_LIBRARIES})
+
+  add_custom_target(GPERF DEPENDS HYPHY-GPERF)
+
+
+  set_target_properties(
+     HYPHY-GPERF
+     PROPERTIES
+          COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -g  "
+         LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} -g  -L/usr/local/Cellar/gperftools/2.7/lib/ -lprofiler -ltcmalloc  "
+     endif(${OPENMP_FOUND})
+ )
+
 
 #-------------------------------------------------------------------------------
 # hyphy debug target
@@ -397,7 +476,12 @@ add_executable(
     ${SRC_COMMON} ${SRC_UNIXMAIN}
 )
 
+if(${OPENMP_FOUND})
+    target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
+else(${OPENMP_FOUND})
     target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES})
+endif(${OPENMP_FOUND})
+
 add_custom_target(DEBUG DEPENDS HYPHYDEBUG)
 
 
@@ -405,8 +489,13 @@ add_custom_target(DEBUG DEPENDS HYPHYDEBUG)
 set_target_properties(
     HYPHYDEBUG
     PROPERTIES
-    COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-arcs -ftest-coverage -pg -O0 "
-    LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-arcs -ftest-coverage -pg -O0 "
+    if(${OPENMP_FOUND})
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -g -fsanitize=address -fsanitize=leak -O0 "
+        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g -fsanitize=address -O0 "
+    else(${OPENMP_FOUND})
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -g -fsanitize=address -fsanitize=leak -O0 "
+        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} -g -fsanitize=address -O0 "
+    endif(${OPENMP_FOUND})
 )
 
 
@@ -430,8 +519,13 @@ set_property(
 set_target_properties(
     HYPHYGTEST
     PROPERTIES
+    if(${OPENMP_FOUND})
         COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
         LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
+    else(${OPENMP_FOUND})
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
+        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
+    endif(${OPENMP_FOUND})
 )
 
 
@@ -441,30 +535,47 @@ set_target_properties(
 
 if(UNIX)
     set_property(
-        TARGET HYPHYMP HYPHYGTEST HYPHYDEBUG
+        TARGET hyphy HYPHYGTEST HYPHYDEBUG HYPHY-PROFILE HYPHY-GPERF
         APPEND PROPERTY COMPILE_DEFINITIONS __UNIX__
     )
 endif(UNIX)
 
 set_property(
-    TARGET HYPHYMP
+    TARGET hyphy
     APPEND PROPERTY COMPILE_DEFINITIONS __MP__ __MP2__
 )
 
 set_property(
-    TARGET HYPHYMP HYPHYGTEST HYPHYDEBUG
+    TARGET hyphy HYPHYGTEST HYPHYDEBUG
+    APPEND PROPERTY COMPILE_DEFINITIONS _HYPHY_LIBDIRECTORY_="${CMAKE_INSTALL_PREFIX}/lib/hyphy"
+)
+
+set_property(
+    TARGET hyphy HYPHYGTEST HYPHYDEBUG HYPHY-PROFILE
     APPEND PROPERTY COMPILE_DEFINITIONS _HYPHY_LIBDIRECTORY_="${CMAKE_INSTALL_PREFIX}/lib/hyphy"
 )
 
+
 set_property(
     TARGET HYPHYDEBUG HYPHYGTEST
     APPEND PROPERTY COMPILE_DEFINITIONS __HYPHYDEBUG__
 )
 
 set_target_properties(
-    HYPHYMP
+    hyphy
     PROPERTIES
-    COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${OpenMP_CXX_FLAGS}"
-    LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
+    if(${OPENMP_FOUND})
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -g "
+        LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS} -g "
+    else(${OPENMP_FOUND})
+        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} -g "
+        LINK_FLAGS "${DEFAULT_LINK_FLAGS} -g "
+    endif(${OPENMP_FOUND})
 )
 
+macro(makeLink src dest target)
+  add_custom_command(TARGET ${target} POST_BUILD
+    COMMAND ln -sf ${dest} ${src} DEPENDS ${dest} COMMENT "mklink ${src} -> ${dest}")
+endmacro()
+makeLink(HYPHYMP hyphy hyphy)
+

CONTRIBUTING.md

@@ -29,7 +29,11 @@ Prefix variables that are meant to be private or auxiliary with an underscore, a
 
 ### Functions, classes  
 
-Capital case, as in `ComputeExpression()` or `VariableContainer` (class). 
+Capital case, as in `ComputeExpression()` or `VariableContainer` (class). Prefix the names of *auxiliary* classes and types with an `_`.
+
+### Simple types
+
+Types such as enums, structs, and typedefs should prefixed with `hy` and followed by capital case identifiers, e.g. `hyFloat`
 
 #### Cheap functions
 
@@ -39,6 +43,10 @@ If a function is *cheap* to call (i.e. don't worry about caching the result), na
 
 Capital case prefixed with a lower case `k`, as in `kHarvestFrequenciesResolveAmbiguities`
 
+### Bit-flags 
+
+Capital case prefixed with `f`, as in `fSearchCaseSensitive`
+
 ### Environment variables (HBL only)
 
 All capitals with underscore-separated words, as in `LIKELIHOOD_FUNCTION_EXPORT_FORMAT`

README.md

-HyPhy - Hypothesis testing using Phylogenies
-============================================
+# HyPhy - Hypothesis testing using Phylogenies
 
-Introduction
-------------
-HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. 
+HyPhy is an open-source software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. It features a complete graphical user interface (GUI) and a rich scripting language for limitless customization of analyses. Additionally, HyPhy features support for parallel computing environments (via message passing interface (MPI)) and it can be compiled as a shared library and called from other programming environments such as Python and R. HyPhy is the computational backbone powering datamonkey.org. Additional information is available at hyphy.org.
 
-Requirements
-------------
-* cmake >= 3.0
-* gcc >= 4.9
-* libcurl
+## Quick Start
+
+#### Install  
+`conda install hyphy`
+
+#### Run with Command Line Arguments
+`hyphy <method_name> --alignment <path_to_alignment_file> <additional_method_specific_arguments>`  
++ _`<method_name>` is the name of the analysis you wish to run (can be: absrel, bgm, busted, fade, fel, fubar, gard, meme, relax or slac)_
++ _`<path_to_alignment_file>` is the relative or absolute path to a fasta, nexus or phylib file containing an alignment and tree_
++ _A list of the available `<additional_method_specific_arguments>` can be seen by running `hyphy <method_name> --help`_
 
-Installation
-------------
+or  
 
-Hyphy depends on CMake for its build system.
+#### Run in Interactive Mode
+`hyphy -i`  
 
-To install, make sure you have CMake >3.0 installed. Hyphy is dependent on other development libraries like
-libcurl and libpthread. Libcurl requires development libraries such as crypto++ and openssl ( or gnutls depending on your configuration)
-On Ubuntu these are libcurl-dev, libcrypto++-dev and libssl-dev.
+## Building from Source
 
-You can download a specific release from this repository or if you prefer the master branch simply 
-clone the repo with
+#### Requirements
+* cmake >= 3.12
+* gcc >= 4.9
+* libcurl
+* libpthread
+* openmp (can be installed on mac via `brew install libomp`)
+
+#### Download
+You can download a specific release [here](https://github.com/veg/hyphy/releases) or clone this repo with
 
 `git clone https://github.com/veg/hyphy.git`
 
-Change your directory to the newly cloned directory
+Change your directory to the downloaded/cloned directory
 
 `cd hyphy`
 
-Configure the project from the source directory using CMake.
-
+#### Build
 `cmake .`
 
-If you prefer to use other build systems, such as Xcode,
-configure using the -G switch
+`make install`
 
-`cmake -G Xcode .`
+## Additional Options for Building from Source
 
-CMake supports a number of build system generators,
-feel free to peruse these and use them if you wish.
+#### Build Systems
+If you prefer to use other build systems, such as Xcode, configure using the -G switch
 
-By default, HyPhy installs into `/usr/local`
-but it can be installed on any location of your system 
-by providing an installation prefix
+`cmake -G Xcode .`
 
-`cmake -DINSTALL_PREFIX=/location/of/choice`
+CMake supports a number of build system generators, feel free to peruse these and use them if you wish.
 
-For example, this configuration will install hyphy at /opt/hyphy
+If you are on an OS X platform, you can specify which OS X SDK to use
 
-`mkdir -p /opt/hyphy`
+`cmake -DCMAKE_OSX_SYSROOT=/Developer/SDKs/MacOSX10.9.sdk/ .`
 
-`cmake -DINSTALL_PREFIX=/opt/hyphy .`
+If building on a heterogeneous cluster with some nodes that do not support auto-vectorization  
 
-If building on a hetereogenous cluster with some nodes that do not support auto-vectorization
 `cmake -DNOAVX=ON .`.
 
-If you're on a UNIX-compatible system,
-and you're comfortable with GNU make,
-then run `make` with one of the following build targets:
+If you're on a UNIX-compatible system, and you're comfortable with GNU make, then run `make` with one of the following build targets:
 
-+   MAC - build a Mac Carbon application
-+   HYPHYGTK - HYPHY with GTK
-+   SP - build a HyPhy executable (HYPHYSP) without multiprocessing
-+   MP - build a HyPhy executable (HYPHYMP) using pthreads to do multiprocessing
++   MP or hyphy - build a HyPhy executable (This used to be "HYPHYMP" but is now just "hyphy") using pthreads to do multiprocessing
 +   MPI - build a HyPhy executable (HYPHYMPI) using MPI to do multiprocessing
 +   HYPHYMPI - build a HyPhy executable (HYPHYMPI) using openMPI 
 +   LIB - build a HyPhy library (libhyphy_mp) using pthreads to do multiprocessing
 -   GTEST - build HyPhy's gtest testing executable (HYPHYGTEST)
 
-For example to create a MPI build of HYPHY using openMPI ensure that you 
-have openmpi installed and available on your  path. You can check if this
-is the case after running 
-`cmake .` you should see something similar to this in your output
+#### Example (MPI build of hyphy using openMPI)
+Ensure that you have openmpi installed and available on your  path. You can check if this is the case after running `cmake .` you should see something similar to this in your output
 
 `-- Found MPI_C: /opt/scyld/openmpi/1.6.3/gnu/lib/libmpi.so;/usr/lib64/libibverbs.so;/usr/lib64/libdat.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so;/usr/lib64/libtorque.so;/usr/lib64/libm.so;/usr/lib64/libnuma.so;/usr/lib64/librt.so;/usr/lib64/libnsl.so;/usr/lib64/libutil.so;/usr/lib64/libm.so `
 
@@ -86,13 +81,35 @@ And then run make install to install the software
 
 `make install`
 
-+   HYPHYMP(I) will be installed at  `/location/of/choice/bin`
++   hyphy will be installed at  `/location/of/choice/bin`
 +   libhyphy_mp.(so/dylib/dll) will be installed at `/location/of/choice/lib`
 +   HyPhy's standard library of batchfiles will go into `/location/of/choice/lib/hyphy`
 
-HYPHYGTEST isn't installed normally,
-because it serves no utility outside of testing.
+
+#### Building for Testing
+HYPHYGTEST isn't installed normally, because it serves no utility outside of testing.
 
 To test HyPhy, build with the  GTEST target and run ./HYPHYGTEST from the source directory.  
 `make GTEST`  
 `./HYPHYGTEST`
+
+#### Executable Location
+
+By default, HyPhy installs into `/usr/local` but it can be installed on any location of your system by providing an installation prefix
+
+`cmake -DINSTALL_PREFIX=/location/of/choice`
+
+For example, this configuration will install hyphy at /opt/hyphy
+
+`mkdir -p /opt/hyphy`
+
+`cmake -DINSTALL_PREFIX=/opt/hyphy .`
+
+#### Building Documentation
+
+```
+make docs
+cd docs
+python3 -m http.server
+```
+

conf/travis-install-mpi.sh

-#!/bin/sh
-# This configuration file was taken originally from the mpi4py project
-# <http://mpi4py.scipy.org/>, and then modified for Julia
-
-set -e
-set -x
-
-MPI_IMPL="$1"
-os=`uname`
-
-case "$os" in
-    Darwin)
-        brew update
-        brew upgrade cmake
-      brew upgrade gcc
-        case "$MPI_IMPL" in
-            mpich|mpich3)
-                brew install mpich
-                ;;
-            openmpi)
-                brew install openmpi
-                ;;
-            *)
-                echo "Unknown MPI implementation: $MPI_IMPL"
-                exit 1
-                ;;
-        esac
-    ;;
-
-    Linux)
-        sudo apt-get update -q
-        case "$MPI_IMPL" in
-            mpich1)
-                sudo apt-get install -y gfortran mpich-shmem-bin libmpich-shmem1.0-dev
-                ;;
-            mpich2)
-                sudo apt-get install -y gfortran mpich2 libmpich2-3 libmpich2-dev
-                ;;
-            mpich|mpich3)
-                sudo apt-get install -y gfortran libcr0 default-jdk hwloc libmpich10 libmpich-dev
-                wget -q http://de.archive.ubuntu.com/ubuntu/pool/universe/m/mpich/mpich_3.0.4-6ubuntu1_amd64.deb
-                sudo dpkg -i ./mpich_3.0.4-6ubuntu1_amd64.deb
-                # rm -f ./mpich_3.1-1ubuntu_amd64.deb
-                ;;
-            openmpi)
-                sudo apt-get install -y gfortran
-                wget --no-check-certificate https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz
-                tar -zxf openmpi-1.10.2.tar.gz
-                cd openmpi-1.10.2
-                sh ./configure --prefix=$HOME/OpenMPI > /dev/null
-                make -j > /dev/null
-                sudo make install > /dev/null
-                ;;
-            *)
-                echo "Unknown MPI implementation: $MPI_IMPL"
-                exit 1
-                ;;
-        esac
-        ;;
-
-    *)
-        echo "Unknown operating system: $os"
-        exit 1
-        ;;
-esac

debian/changelog

+hyphy (2.5.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Secure URI in copyright format
+  * Remove trailing whitespace in debian/changelog
+  TODO: Fix build failure
+
+ -- Andreas Tille <tille@debian.org>  Sun, 28 Jul 2019 01:08:15 +0200
+
 hyphy (2.3.14+dfsg-2) unstable; urgency=medium
 
   [ Saira Hussain ]

debian/compat

-11

debian/control

@@ -3,13 +3,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
-               cmake (>= 3.0),
+Build-Depends: debhelper-compat (= 12),
+               cmake,
                mpi-default-dev,
                libcurl4-gnutls-dev | libcurl4-dev,
                libssl-dev,
                libsqlite3-dev
-Standards-Version: 4.3.1
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/hyphy
 Vcs-Git: https://salsa.debian.org/med-team/hyphy.git
 Homepage: http://hyphy.org/

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Contact: Steven Weaver <sweaver@ucsd.edu>
 Upstream-Name: HyPhy
 Source: https://github.com/veg/hyphy/releases

debian/patches/drop_profiling_option.patch

@@ -5,25 +5,19 @@ Bug-Debian: http://bugs.debian.org/793345
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -416,8 +416,8 @@ add_custom_target(DEBUG DEPENDS HYPHYDEB
- set_target_properties(
-     HYPHYDEBUG
-     PROPERTIES
--    COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-arcs -ftest-coverage -pg -O0 "
--    LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-arcs -ftest-coverage -pg -O0 "
-+    COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS}"
-+    LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
- )
- 
- 
-@@ -441,8 +441,8 @@ set_property(
- set_target_properties(
+@@ -543,11 +543,11 @@ set_target_properties(
      HYPHYGTEST
      PROPERTIES
+     if(${OPENMP_FOUND})
 -        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
 -        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
 +        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3"
 +        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} -msse3"
+     else(${OPENMP_FOUND})
+-        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
+-        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -msse3 -g -fprofile-arcs -ftest-coverage -pg"
++        COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -msse3"
++        LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -msse3"
+     endif(${OPENMP_FOUND})
  )
  
- 

debian/patches/msse_option_only_if_available.patch

 Description: Make sure that also in tests the existence of SSE3 extension is done
+ --> deactivated
 Bug-Debian: http://bugs.debian.org/793344
 Author: Andreas Tille <tille@debian.org>
 Last-Update: Thu, 23 Jul 2015 13:12:54 +0200

debian/patches/remove_arch_specific_flags.patch

-Author: Andreas Tille
-Last-Update: Mon, 26 Oct 2015 11:19:57 +0100
-Bug-Debian: http://bugs.debian.org/802994
-Description: remove optimizations for the local machine
-
---- a/CMakeLists.txt
-+++ b/CMakeLists.txt
-@@ -47,7 +47,7 @@ macro(PCL_CHECK_FOR_AVX)
-   set(CMAKE_REQUIRED_FLAGS)
- 
-   if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
--      set(CMAKE_REQUIRED_FLAGS "-march=corei7-avx -mtune=corei7-avx")
-+      set(CMAKE_REQUIRED_FLAGS "")
-   endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
- 
-   check_cxx_source_runs("
-@@ -124,7 +124,7 @@ if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMP
-     else(NOAVX)
-        PCL_CHECK_FOR_AVX()
-        if(${HAVE_AVX_EXTENSIONS})
--            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=corei7-avx -mtune=corei7-avx")
-+            set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ")
-             add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
-         else(${HAVE_AVX_EXTENSIONS})
-             PCL_CHECK_FOR_SSE3()

debian/patches/remove_unneeded_test.patch

@@ -13,11 +13,11 @@ Bug-Debian: http://bugs.debian.org/793346
  
 -TEST_F(SimpleListTest,_LengthConstructorTest){
 -    _SimpleList sl((long)7);
--    EXPECT_EQ(8,sizeof(sl.lData));
+-    EXPECT_EQ(8,sizeof(sl.list_data));
 -}
 +//TEST_F(SimpleListTest,_LengthConstructorTest){
 +//    _SimpleList sl((long)7);
-+//    EXPECT_EQ(8,sizeof(sl.lData));
++//    EXPECT_EQ(8,sizeof(sl.list_data));
 +//}
  
  TEST_F(SimpleListTest, _PopulateTest){

debian/patches/series

 use_debian_sqlite.patch
-spelling.patch
 drop_profiling_option.patch
 remove_unneeded_test.patch
-msse_option_only_if_available.patch
-remove_arch_specific_flags.patch
+# msse_option_only_if_available.patch

debian/patches/spelling.patch

-Author: Andreas Tille <tille@debian.org>
-Last-Update: Mon, 29 Jun 2015 11:13:57 +0200
-Description: Fix two spelling issues
-
---- a/src/core/batchlan.cpp
-+++ b/src/core/batchlan.cpp
-@@ -7383,7 +7383,7 @@ bool    _ElementaryCommand::ConstructMPI
- 
- //____________________________________________________________________________________
- bool    _ElementaryCommand::ConstructCategoryMatrix (_String&source, _ExecutionList&target)
--// syntax: ConstructCategoryMatrix (receptacle, likelihood function, [COMPLETE/SHORT, which partitions to include -- a matrix agrument] )
-+// syntax: ConstructCategoryMatrix (receptacle, likelihood function, [COMPLETE/SHORT, which partitions to include -- a matrix argument] )
- {
-     _List pieces;
-     ExtractConditions (source,blConstructCM.sLength,pieces,',');
---- a/src/core/include/calcnode.h
-+++ b/src/core/include/calcnode.h
-@@ -471,7 +471,7 @@ public:
-     _AssociativeList*
-     SplitsIdentity                      (_PMathObj);
-     /* 20090609: SLKP
--        given a tree agrument (p), the function returns an AVL with a 2x1 matrix (key "CLUSTERS")
-+        given a tree argument (p), the function returns an AVL with a 2x1 matrix (key "CLUSTERS")
-         and a string (key "CONSENSUS");
-         The first cell contains the number of splits in *this
-         The second cell contains the number of splits in the argument that are present in *this

debian/patches/use_debian_sqlite.patch

@@ -6,20 +6,21 @@ Description: Use Debian packaged sqlite3
 
 --- a/CMakeLists.txt
 +++ b/CMakeLists.txt
-@@ -79,11 +79,10 @@ file(GLOB SRC_GTESTS tests/gtests/*.cpp)
- file(GLOB SRC_NEW src/new/*.cpp)
+@@ -119,12 +119,11 @@ file(GLOB SRC_NEW src/new/*.cpp)
+ file(GLOB SRC_CONTRIB src/contrib/*.cpp)
  
  set(SRC_LINK src/lib/link/THyPhy.cpp)
 -set(SRC_SQLITE3 contrib/SQLite-3.8.2/sqlite3.c)
  set(SRC_UNIXMAIN src/mains/unix.cpp)
  set(SRC_UTILS src/utils/hyphyunixutils.cpp)
  
--set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS})
-+set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_UTILS})
  
+-set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS} ${SRC_CONTRIB})
++set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_UTILS} ${SRC_CONTRIB})
+ set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")
  
  #-------------------------------------------------------------------------------
-@@ -210,6 +209,36 @@ if(${CURL_FOUND} AND NOT APPLE)
+@@ -264,6 +263,36 @@ if(${CURL_FOUND} AND NOT APPLE)
  endif(${CURL_FOUND} AND NOT APPLE)
  
  #-------------------------------------------------------------------------------
@@ -56,7 +57,7 @@ Description: Use Debian packaged sqlite3
  # gtest dependency
  #-------------------------------------------------------------------------------
  add_subdirectory(contrib/gtest-1.7.0)
-@@ -243,11 +272,6 @@ set_property(
+@@ -305,11 +334,6 @@ set_property(
  )
  
  set_property(
@@ -68,9 +69,9 @@ Description: Use Debian packaged sqlite3
      SOURCE src/core/calcnode2.cpp
      APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"
  )
-@@ -269,7 +293,6 @@ endif(CMAKE_SIZEOF_VOID_P EQUAL 8)
- include_directories(
+@@ -329,7 +353,6 @@ include_directories(
      src/core/include
+     src/contrib
      src/lib/Link src/new/include
 -    contrib/SQLite-3.8.2 # SQLite
      contrib/gtest-1.7.0/include

help/Commands/query.bf

-classStyle = "\n\\section*{_INSERT_DATA_FOR_Command_HERE_}\\begin{tabular}{lr}\\parbox[t]{2in}{\\textit{_INSERT_DATA_FOR_Class_HERE_\\newline _INSERT_DATA_FOR_Revised_HERE_}}&\\parbox{4in}{\\textsf{_INSERT_DATA_FOR_Description_HERE_}}\\end{tabular}"+
-"\n\n\\texttt{_INSERT_DATA_FOR_Syntax_HERE_}\\scriptsize{\\begin{flushleft}_INSERT_DATA_FOR_Notes_HERE_\\end{flushleft}}Example\\linebreak\\linespread{0.3}\\fbox{\\parbox{6in}{\\tiny\\begin{alltt}_INSERT_DATA_FOR_Example_HERE_\\end{alltt}}}\\linespread{1}\n";
-
-latexTop    = "\\documentclass[11pt]{article}\\usepackage{amssymb}\\usepackage{alltt}\\textwidth    = 6.25 in\\textheight  = 9 in\\oddsidemargin = 0.0 in\\evensidemargin = 0.0 in\\topmargin = 0.0 in\\headheight = 0.0 in\\headsep = 0.0 in\\parskip = 0.2in\\parindent = 0.0in\\begin{document}";
-latexBottom = "\end{document}";
-/*--------------------------------------------------*/
-
-function countHits (dummy)
-{
-	hitNames[hitCount] = SQL_ROW_DATA[0];
-	hitDescs[hitCount] = SQL_ROW_DATA[1];
-	hitCount = hitCount + 1;
-	return 0;
-}
-
-/*--------------------------------------------------*/
-
-function echoQuery (dummy)
-{
-	colCount = Columns (SQL_ROW_DATA);
-	if (doExport)
-	{
-		cText = classStyle;
-		for (cc=0; cc<colCount; cc=cc+1)
-		{
-			cName  = SQL_COLUMN_NAMES[cc];
-			
-			inLines = {{""}};
-			cr = SQL_ROW_DATA[cc]&&2;
-			if (Abs(cr))
-			{
-				sscanf (cr,"Lines",inLines);
-				c = "";
-				for (k=0; k<Columns(inLines)-1;k=k+1)
-				{
-					if (Abs(inLines[k]))
-					{
-						c = c+inLines[k]+"\\linebreak\n";
-					}
-					else
-					{
-						c = c+"\n\n";
-					}
-				}
-				c = c+inLines[k];
-				
-				cr = "#&$%~_^{}";
-				
-				for (rcc = 0; rcc < Abs(cr); rcc=rcc+1)
-				{
-					crp = "\\"+cr[rcc];
-					c=c^{{crp,crp}};
-				}
-
-				c=c^{{"\\|","$|$"}};
-				c=c^{{"\\[","$[$"}};
-				c=c^{{"\\]","$]$"}};
-
-				/*cr=cr^{{"\\\\\\\\","$\\backslash$"}};*/
-				
-				cText  = cText^{{"_INSERT_DATA_FOR_"+cName+"_HERE_",c}};
-				sscanf (cName,"Raw",rcc);
-			}
-			else
-			{
-				cText  = cText^{{"_INSERT_DATA_FOR_"+cName+"_HERE_","N/A"}};			
-			}
-		}	
-		fprintf (latexFile,"\n", cText);
-	}
-	else
-	{
-		for (cc=0; cc<colCount; cc=cc+1)
-		{
-			cName  = SQL_COLUMN_NAMES[cc];
-			cChars = Abs(cName);
-			
-			underLine = "";
-			
-			for (ck=0; ck<cChars;ck=ck+1)
-			{
-				underLine = underLine+"-";
-			}	
-			
-			fprintf (stdout, "\n", SQL_COLUMN_NAMES[cc],"\n",underLine,"\n", SQL_ROW_DATA[cc]&&2,"\n");
-		}
-	}
-	return 0;
-}
-
-/*--------------------------------------------------*/
-
-if (QUERY_FIELD == "Window")
-{
-	filePath = HYPHY_BASE_DIRECTORY + "Help" + DIRECTORY_SEPARATOR + "Commands"+DIRECTORY_SEPARATOR+"reference.sql";
-	OpenWindow (DATABASEWINDOW,{{filePath}},"SCREEN_WIDTH-100;SCREEN_HEIGHT-100;50;50");
-	return 0;
-}
-
-DoSQL (SQL_OPEN,"reference.sql",dbID);
-hitCount        = 0;
-hitNames        = {};
-hitDescs		= {}; 
-
-if (QUERY_FIELD == "Export")
-{
-	QUERY_FIELD = "Command";
-	doExport = 1;
-}
-else
-{
-	doExport = 0;
-}
-
-sqlQuery = "select Command, Description from HYPHY_REFERENCE where "+QUERY_FIELD+" glob '*" + QUERY_TERM+"*' order by Command";
-
-DoSQL (dbID,sqlQuery,"return countHits(0);");
-
-if (hitCount == 0)
-{
-	fprintf (stdout, "\nNo records matched your query\n");
-}
-else
-{
-	if (doExport)
-	{
-		DEFAULT_FILE_SAVE_NAME = "Commands.tex";
-		SetDialogPrompt ("Export a LaTex document to:");
-		fprintf (PROMPT_FOR_FILE, CLEAR_FILE,latexTop);
-		latexFile = LAST_FILE_PATH;
-		
-	}
-	if (hitCount > 1)
-	{
-		hitRecords = {hitCount,2};
-		for (cc=0; cc<hitCount; cc=cc+1)
-		{
-			hitRecords[cc][0] = hitNames[cc];
-			hitRecords[cc][1] = hitDescs[cc];
-		}
-		
-		ChoiceList (hitCount,"Choose a command",0,SKIP_NONE,hitRecords);
-
-		if (hitCount[0]<0)
-		{
-			DoSQL (SQL_CLOSE,"",dbID);
-			return 0;
-		}		
-		
-		for (h=0; h<Columns(hitCount); h=h+1)
-		{
-			hc = hitCount [h];
-			hitNames[0] = hitNames[hc];
-			DoSQL (dbID,"select Command, Class, Syntax, Description, Notes, Example, Revised from HYPHY_REFERENCE where Command = '" + hitNames[0]+"' order by Command","return echoQuery(0);");	
-		}
-		hitDescs    = 0;
-		hitRecords  = 0;
-	}
-	else
-	{
-		DoSQL (dbID,"select Command, Class, Syntax, Description, Notes, Example, Revised from HYPHY_REFERENCE where Command = '" + hitNames[0]+"' order by Command","return echoQuery(0);");
-	}
-	hitNames = 0;
-	if (doExport)
-	{
-		fprintf (latexFile,latexBottom);
-	}
-}
-
-DoSQL (SQL_CLOSE,"",dbID);