Merge branch 'release/Version-4.43' into develop

.github/workflows/copasi_se.yml

@@ -23,7 +23,7 @@ jobs:
     runs-on: ${{ matrix.platform }}
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: seanmiddleditch/gha-setup-ninja@master
 
     - name: Add msbuild to PATH (Windows)
@@ -102,7 +102,7 @@ jobs:
       run: ctest -C $BUILD_TYPE -V
 
     - name: binary archive
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name:
           copasi-se-${{ matrix.platform }}

.github/workflows/copasi_se_mp.yml

@@ -22,7 +22,7 @@ jobs:
     container: quay.io/pypa/manylinux_2_28_x86_64
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Create Build Environment
       run: |
@@ -66,7 +66,7 @@ jobs:
       run: cmake --build . --config $BUILD_TYPE --target install
 
     - name: binary archive
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name:
           copasi-se-openmp-manylinux_2_28_x86_64

.github/workflows/copasi_se_slackware.yml

@@ -22,7 +22,7 @@ jobs:
     container: andy5995/slackware-build-essential:15.0
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
 
     - name: Create Build Environment
       run: |
@@ -65,7 +65,7 @@ jobs:
       run: cmake --build . --config $BUILD_TYPE --target install
 
     - name: binary archive
-      uses: actions/upload-artifact@v2
+      uses: actions/upload-artifact@v4
       with:
         name:
           copasi-se-openmp-slackware

.gitignore

@@ -4,6 +4,8 @@
 *.app
 *.bkp
 *.patch
+*.diff
+*.rej
 moc_*.cpp
 ui_*.h
 /build

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -376,7 +376,7 @@ find_package(LIBCOMBINE REQUIRED)
 
 if (ENABLE_FLEX_BISON)
   find_package(FLEX REQUIRED)
-  find_package(BISON REQUIRED) 
+  find_package(BISON REQUIRED)
   set(FLEX_BINARY ${FLEX_EXECUTABLE})
   set(FLEX_EXECUTABLE "${COPASI_SOURCE_DIR}/admin/flex.sh")
   set(BISON_BINARY ${BISON_EXECUTABLE})
@@ -406,31 +406,56 @@ endif (ENABLE_JIT)
 if (ENABLE_OMP)
   set(USE_OMP 1)
 
+  if (APPLE)
+    find_package (OpenMP)
+    if(NOT OpenMP_FOUND)
+      # libomp 15.0+ from brew is keg-only, so have to search in other locations.
+      # See https://github.com/Homebrew/homebrew-core/issues/112107#issuecomment-1278042927.
+      execute_process(COMMAND brew --prefix libomp
+                      OUTPUT_VARIABLE HOMEBREW_LIBOMP_PREFIX
+                      OUTPUT_STRIP_TRAILING_WHITESPACE)
+      set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
+      set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp -I${HOMEBREW_LIBOMP_PREFIX}/include")
+      set(OpenMP_C_LIB_NAMES omp)
+      set(OpenMP_CXX_LIB_NAMES omp)
+      set(OpenMP_omp_LIBRARY ${HOMEBREW_LIBOMP_PREFIX}/lib/libomp.dylib)
+    endif()
+  endif()
+
   find_package (OpenMP REQUIRED)
-  include_directories(BEFORE ${OpenMP_INCLUDE_PATH})
-
-  include(CheckCXXSourceCompiles)
-
-  function(detect_code_compiled code macro msg)
-    message(STATUS "Detecting ${msg}")
-    check_cxx_source_compiles("${code}" "${macro}" FAIL_REGEX "warning")
-
-    if(${macro})
-      message(STATUS "Detecting ${msg} - supported")
-    else(${macro})
-      message(STATUS "Detecting ${msg} - not supported")
-    endif(${macro})
-  endfunction(detect_code_compiled)
-
-  # Detect std::optional
-  detect_code_compiled("
-    #include <omp.h>
-    int main()
-    { 
-       omp_sched_t schedule = omp_sched_monotonic; 
-    }" 
-    OMP_HAVE_MONOTONIC 
-    "omp_sched_monotonic")
+
+  if (OpenMP_CXX_SPEC_DATE GREATER_EQUAL "201811")
+    # OpenMP 5.0 will always have monotonic scheduling
+    set(OMP_HAVE_MONOTONIC 1 CACHE INTERNAL "" FORCE)
+  else()
+    # otherwise we need to check
+    include_directories(BEFORE ${OpenMP_INCLUDE_PATH} ${OpenMP_CXX_INCLUDE_DIRS})
+
+    include(CheckCXXSourceCompiles)
+
+    function(detect_code_compiled code macro msg)
+      message(STATUS "Detecting ${msg}")
+      check_cxx_source_compiles("${code}" "${macro}" FAIL_REGEX "warning")
+
+      if(${macro})
+        message(STATUS "Detecting ${msg} - supported")
+      else(${macro})
+        message(STATUS "Detecting ${msg} - not supported")
+      endif(${macro})
+    endfunction(detect_code_compiled)
+
+    # Detect std::optional
+    detect_code_compiled("
+      #include <omp.h>
+      int main()
+      {
+        omp_sched_t schedule = omp_sched_monotonic;
+      }"
+      OMP_HAVE_MONOTONIC
+      "omp_sched_monotonic")
+  endif()
+
+
 endif(ENABLE_OMP)
 
 # TODO raptor should be restricted to a version which is at least
@@ -457,7 +482,7 @@ if(BUILD_GUI)
   if (QT_USE_TEXTBROSWSER)
     set(QT_USE_TEXTBROWSER ON)
   endif()
-  
+
   if (${SELECT_QT} MATCHES "Qt5" OR
       ${SELECT_QT} MATCHES "Qt6" OR
       ${SELECT_QT} MATCHES "Any")
@@ -473,20 +498,20 @@ if(BUILD_GUI)
       find_package(QCP REQUIRED)
     endif()
     option(WITH_LEGACY_OPENGL "Use Legacy OpenGL visualization" OFF)
-    
+
     set (ADDITIONAL_QT5_MODULES)
     if (QT5_USE_DATAVISUALIZATION)
     set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} DataVisualization)
     endif()
     if (COPASI_USE_QTCHARTS)
     set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} Charts)
     endif()
-    
+
     if(${SELECT_QT} MATCHES "Qt6")
     # for xml sax parser and qregex
     set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} Core5Compat)
     endif()
-    
+
 
     if (QT_USE_TEXTBROWSER)
       QT_FIND_MODULES( Concurrent
@@ -496,7 +521,7 @@ if(BUILD_GUI)
                        Network
                        OpenGL
                        PrintSupport
-                       Svg 
+                       Svg
                        Xml
                        ${ADDITIONAL_QT5_MODULES}
       )
@@ -547,7 +572,7 @@ if(BUILD_GUI)
     set(COPASI_USE_QWT ON)
   endif()
   # check for qwtplot3d
-  
+
   if (NOT QT5_USE_DATAVISUALIZATION)
   find_package(QWTPLOT3D REQUIRED)
   endif()
@@ -564,7 +589,7 @@ if(BUILD_GUI)
   option(ENABLE_SBW_INTEGRATION "Enable SBW Integration" ON)
   if (ENABLE_SBW_INTEGRATION)
   find_package(SBW REQUIRED)
-  
+
   # set up definitions for SBW
   if(UNIX)
   if(APPLE)
@@ -610,7 +635,7 @@ if (ENABLE_CSHARP OR ENABLE_JAVA OR ENABLE_PYTHON OR ENABLE_PERL OR ENABLE_OCTAV
   endif ()
 
   find_package(SWIG REQUIRED)
-  
+
 endif ()
 
 option (ENABLE_TIME_SENS "Enables Time Sensitivities task in UI." ON)
@@ -637,7 +662,7 @@ option (BUILD_SBML_TESTSUITE "Build the program to run the new SBML testsuite."
 option (BUILD_STOCHASTIC_TESTSUITE "Build the program to run the SBML stochastic testsuite." OFF)
 option (BUILD_FRANKS_TESTSUITE "Build the program to run the Frank Bergmann's SBML tests." OFF)
 
-option (BUILD_TESTS "Compiles CPPUNIT Testrunners." OFF)
+option (BUILD_TESTS "Compiles CPPUNIT/Catch2 Testrunners." OFF)
 mark_as_advanced(BUILD_TESTS)
 
 if (BUILD_TESTS)
@@ -758,18 +783,21 @@ if(MSVC OR USING_INTEL)
                 endif(${flag_var} MATCHES "/Zi")
 
             endforeach(flag_var)
-            
+
             if (MSVC AND WIN32 AND NOT MSVC_VERSION VERSION_LESS 142 AND CMAKE_VERSION VERSION_GREATER 3.13)
-              # enable edit & continue for debug builds of msvc 
+              # enable edit & continue for debug builds of msvc
               add_link_options($<$<CONFIG:Debug>:/INCREMENTAL>)
               add_compile_options($<$<CONFIG:Debug>:/ZI>)
-
+              add_compile_options("$<$<CXX_COMPILER_ID:MSVC>:/EHsc>")
             endif()
     endif()
 
 endif(MSVC OR USING_INTEL)
 
-
+if (EMSCRIPTEN)
+add_compile_options(-fexceptions)
+add_link_options(-fexceptions -sINITIAL_MEMORY=65536000 -sALLOW_MEMORY_GROWTH=1)
+endif(EMSCRIPTEN)
 
 set(APPS "" CACHE INTERNAL "")
 set(DIRS "${COPASI_DEPENDENCY_DIR}/bin;${COPASI_DEPENDENCY_DIR}/lib" CACHE INTERNAL "")
@@ -926,7 +954,7 @@ message(STATUS "-----------------------------------------------------------
    Qt version           = ${QT_VERSION}
    Qt lib               = ${QT_LIBRARIES}
    Qt include           = ${QT_INCLUDE_DIRS}
-      
+
    QWT version          = ${QWT_VERSION_STRING} (0x${QWT_VERSION_NUMERIC})
    QWT lib              = ${QWT_LIBRARY}
    QWT include          = ${QWT_INCLUDE_DIR}
@@ -952,7 +980,7 @@ message(STATUS "-----------------------------------------------------------
    NativeJIT lib        = ${NATIVEJIT_LIBRARY}
    NativeJIT include    = ${NATIVEJIT_INCLUDE_DIR}
    NativeJIT CXX Flags  = ${NATIVEJIT_COMPILE_OPTIONS}
-   
+
    cpu_features lib     = ${CPUFEATURES_LIBRARY}
    cpu_features include = ${CPUFEATURES_INCLUDE_DIR}
 
@@ -976,7 +1004,7 @@ message(STATUS "-----------------------------------------------------------
    JIT Compilation          = ${ENABLE_JIT}
    OpenMP                   = ${ENABLE_OMP}
 
-   CXX Flags                = ${CMAKE_CXX_FLAGS} 
+   CXX Flags                = ${CMAKE_CXX_FLAGS}
    Additional Defines       = ${DirDefs}
 
   Language Bindings:

CMakeModules/FindEXPAT.cmake

@@ -34,6 +34,7 @@ find_path(EXPAT_INCLUDE_DIR expat.h
     PATHS $ENV{EXPAT_DIR}/include
             $ENV{EXPAT_DIR}
             ${${_PROJECT_DEPENDENCY_DIR}}/include
+            CMAKE_FIND_ROOT_PATH_BOTH
             NO_DEFAULT_PATH)
 
 if (NOT EXPAT_INCLUDE_DIR)
@@ -48,6 +49,7 @@ find_path(EXPAT_INCLUDE_DIR expat.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
+          CMAKE_FIND_ROOT_PATH_BOTH
           NO_DEFAULT_PATH)
 endif ()
 
@@ -64,6 +66,7 @@ find_library(EXPAT_LIBRARY
           ${${_PROJECT_DEPENDENCY_DIR}}/lib64
           ${${_PROJECT_DEPENDENCY_DIR}}/lib
           ${${_PROJECT_DEPENDENCY_DIR}}
+          CMAKE_FIND_ROOT_PATH_BOTH
           NO_DEFAULT_PATH)
 
 if (NOT EXPAT_LIBRARY)
@@ -81,6 +84,7 @@ find_library(EXPAT_LIBRARY
           /opt/csw/lib   # Blastwave
           /opt/lib
           /usr/freeware/lib64
+          CMAKE_FIND_ROOT_PATH_BOTH
           NO_DEFAULT_PATH)
 endif()
 

CMakeModules/FindICONV.cmake

@@ -40,6 +40,7 @@ FIND_PATH(ICONV_INCLUDE_DIR iconv.h
          /usr/local/include
          /opt/local/include
          ${${_PROJECT_DEPENDENCY_DIR}}/include
+         CMAKE_FIND_ROOT_PATH_BOTH
 )
 
 FIND_LIBRARY(ICONV_LIBRARIES NAMES iconv libiconv
@@ -49,6 +50,7 @@ FIND_LIBRARY(ICONV_LIBRARIES NAMES iconv libiconv
          /opt/local/lib
          ${${_PROJECT_DEPENDENCY_DIR}}/${CMAKE_INSTALL_LIBDIR}
          ${${_PROJECT_DEPENDENCY_DIR}}/lib
+         CMAKE_FIND_ROOT_PATH_BOTH
 )
 
 IF(ICONV_INCLUDE_DIR AND ICONV_LIBRARIES) 

CMakeModules/FindLIBSBML.cmake

@@ -33,11 +33,21 @@ endif()
 
 message (VERBOSE "Looking for ${LIBSBML_LIBRARY_NAME}")
 
-find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET)
 
 string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
 set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)
 
+find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET
+  PATHS ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
+        ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
+        ${CONAN_LIB_DIRS_LIBSBML}/cmake
+        CMAKE_FIND_ROOT_PATH_BOTH
+        NO_DEFAULT_PATH)
+
+if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)        
+  find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET)
+endif()
+
 if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)
   find_package(${LIBSBML_LIBRARY_NAME} CONFIG QUIET
     PATHS /usr/lib/cmake
@@ -48,6 +58,7 @@ if (NOT ${LIBSBML_LIBRARY_NAME}_FOUND)
           ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
           ${${_PROJECT_DEPENDENCY_DIR}}/lib64/cmake
           ${CONAN_LIB_DIRS_LIBSBML}/cmake
+          CMAKE_FIND_ROOT_PATH_BOTH
   )
 endif()
 
@@ -111,6 +122,7 @@ find_path(LIBSBML_INCLUDE_DIR sbml/SBase.h
           /opt/csw/include   # Blastwave
           /opt/include
           /usr/freeware/include
+          CMAKE_FIND_ROOT_PATH_BOTH
     NO_DEFAULT_PATH)
 
 if (NOT LIBSBML_INCLUDE_DIR)