Merge branch 'release/Version-4.46'

Author: shoops

.github/workflows/copasi_se.yml

@@ -81,7 +81,7 @@ jobs:
       shell: bash
       working-directory: ${{github.workspace}}
       run: |
-        curl -L http://bqfrank.spdns.org/Files/test-suite.zip  -o test-suite.zip
+        curl -L https://copasi.org/static/test-suite.zip -o test-suite.zip
         unzip -n -qq test-suite.zip
 
     - name: Configure COPASI (mac)

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2026 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -28,7 +28,7 @@
 ###############################################################################
 
 # we need at least cmake 2.8 for the FindLAPACK functions
-cmake_minimum_required (VERSION 2.8.12...3.19.1)
+cmake_minimum_required(VERSION 2.8...3.19)
 
 if(POLICY CMP0048)
   cmake_policy(SET CMP0048 NEW)
@@ -129,9 +129,10 @@ if (NOT WIN32 AND PREFER_STATIC)
 endif()
 
 if (CMAKE_MAJOR_VERSION LESS 3 OR CMAKE_MINOR_VERSION LESS 1)
-  set(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} "-std=c++11")
+  set(CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS} "-std=c++20")
 else()
-  set(CMAKE_CXX_STANDARD 11)
+  set(CMAKE_CXX_STANDARD 20)
+  set(CMAKE_CXX_EXTENSIONS OFF)
 endif()
 
 CHECK_FUNCTION_EXISTS(strptime HAVE_STRPTIME)
@@ -261,7 +262,7 @@ option(CLAPACK_NO_BLASWRAP "If defined the NO_BLASWRAP compile option will be ad
 set (ENABLE_JIT_DEFAULT OFF)
 
 if (APPLE)
-  if (CMAKE_OSX_ARCHITECTURES STREQUAL arm64)
+  if (CMAKE_OSX_ARCHITECTURES STREQUAL arm64 OR (NOT CMAKE_OSX_ARCHITECTURES AND CMAKE_SYSTEM_PROCESSOR MATCHES "arm64"))
     set (ENABLE_JIT_DEFAULT OFF)
   else()
     set (ENABLE_JIT_DEFAULT ON)
@@ -390,8 +391,20 @@ endif ()
 include_directories(BEFORE ${CLAPACK_INCLUDE_DIR})
 # set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${LAPACK_CFLAGS}")
 
+option(COPASI_USE_CROSSGUID "Use CrossGUID for UUID generation" OFF)
+if (COPASI_USE_CROSSGUID)
 find_package(CROSSGUID REQUIRED)
 include_directories(BEFORE ${CROSSGUID_INCLUDE_DIR})
+SET(UUID_MESSAGE "
+   UUID library         = CrossGUID
+   crossguid Libs       = ${CROSSGUID_LIBRARY}
+   cross include        = ${CROSSGUID_INCLUDE_DIR}
+")
+else()
+SET(UUID_MESSAGE "
+   UUID library         = stduuid
+")
+endif()
 
 if (ENABLE_JIT)
   find_package(NATIVEJIT REQUIRED)
@@ -492,10 +505,22 @@ if(BUILD_GUI)
     option(QT5_USE_WEBENGINE "Use QWebEngine instead of the deprecated QtWebKit for notes" OFF)
     option(QT5_USE_DATAVISUALIZATION "Use Qt5DataVisualization instead of the deprecated QwtPlot3D" ON)
     if (QT5_USE_DATAVISUALIZATION)
-    option(WITH_DATAVISUALIZATION_NAMESPACES "The DataVisualization modeule uses c++ namespaces" ON)
+    # compile a test program against the datavisualization
+    # to figure out whether the namespace flag is needed
+    if (NOT DEFINED WITH_DATAVISUALIZATION_NAMESPACES)
+    check_cxx_source_compiles("
+      #include <QtDataVisualization/Q3DSurface>
+      int main() {
+        QtDataVisualization::Q3DSurface surface;
+        return 0;
+      }"
+      DATAVISUALIZATION_USES_NAMESPACES)
+    
+    option(WITH_DATAVISUALIZATION_NAMESPACES "The DataVisualization modeule uses c++ namespaces" ${DATAVISUALIZATION_USES_NAMESPACES})
+    endif()
     endif()
     option(COPASI_USE_QTCHARTS "Use QtCharts instead of the Qwt" OFF)
-    option(COPASI_USE_QCUSTOMPLOT "Use QCustomPlot instead of the Qwt" OFF)
+    option(COPASI_USE_QCUSTOMPLOT "Use QCustomPlot instead of the Qwt" ON)
     if (COPASI_USE_QCUSTOMPLOT)
       find_package(QCP REQUIRED)
     endif()
@@ -509,7 +534,7 @@ if(BUILD_GUI)
     set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} Charts)
     endif()
 
-    if(${SELECT_QT} MATCHES "Qt6")
+    if(${SELECT_QT} MATCHES "Qt6" OR SELECT_QT STREQUAL "Any")
     # for xml sax parser and qregex
     set (ADDITIONAL_QT5_MODULES ${ADDITIONAL_QT5_MODULES} Core5Compat)
     endif()
@@ -947,8 +972,7 @@ message(STATUS "-----------------------------------------------------------
    LAPACK LDFLAGS       = ${CLAPACK_LINKER_FLAGS}
    LAPACK include       = ${CLAPACK_INCLUDE_DIR}
 
-   crossguid Libs       = ${CROSSGUID_LIBRARY}
-   cross include        = ${CROSSGUID_INCLUDE_DIR}
+   ${UUID_MESSAGE}
 
    Expat version        = ${EXPAT_VERSION}
    Expat Libs           = ${EXPAT_LIBRARY}

CMakeModules/FindCPUFEATURES.cmake

@@ -1,4 +1,4 @@
-# Copyright (C) 2020 - 2022 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2020 - 2026 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -16,16 +16,28 @@
 string(TOUPPER ${PROJECT_NAME} _UPPER_PROJECT_NAME)
 set(_PROJECT_DEPENDENCY_DIR ${_UPPER_PROJECT_NAME}_DEPENDENCY_DIR)
 
-find_package(CPUFEATURES CONFIG REQUIRED
+find_package(CPUFEATURES CONFIG QUIET
   CONFIGS CpuFeaturesConfig.cmake
   PATHS $ENV{CPUFEATURES_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake
         ${${_PROJECT_DEPENDENCY_DIR}}/${CMAKE_INSTALL_LIBDIR}/cmake
         ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
         /usr/${CMAKE_INSTALL_LIBDIR}/cmake
         ${CONAN_LIB_DIRS_CPUFEATURES}/cmake
-  PATH_SUFFIXES CpuFeatures
+    PATH_SUFFIXES CpuFeatures
+    NO_DEFAULT_PATH
 )
 
+find_package(CPUFEATURES CONFIG QUIET
+  CONFIGS CpuFeaturesConfig.cmake
+  PATHS $ENV{CPUFEATURES_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake
+        ${${_PROJECT_DEPENDENCY_DIR}}/${CMAKE_INSTALL_LIBDIR}/cmake
+        ${${_PROJECT_DEPENDENCY_DIR}}/lib/cmake
+        /usr/${CMAKE_INSTALL_LIBDIR}/cmake
+        ${CONAN_LIB_DIRS_CPUFEATURES}/cmake
+    PATH_SUFFIXES CpuFeatures
+)
+
+
 if (NOT CPUFEATURES_FOUND)
   message(VERBOSE "cpu_features Fallback $ENV{CPUFEATURES_DIR}/${CMAKE_INSTALL_LIBDIR}/cmake")
   # Fallback if no CONFIG is found
@@ -49,7 +61,7 @@ if (NOT CPUFEATURES_FOUND)
   endif (NOT CPUFEATURES_INCLUDE_DIR)
 
   find_library(CPUFEATURES_LIBRARY 
-    NAMES cpu_features
+    NAMES cpu_features cpu_features.lib
     PATHS $ENV{CPUFEATURES_DIR}/lib
           $ENV{CPUFEATURES_DIR}
           ${${_PROJECT_DEPENDENCY_DIR}}/${CMAKE_INSTALL_LIBDIR}
@@ -67,7 +79,18 @@ if (NOT CPUFEATURES_FOUND)
 
   if (NOT CPUFEATURES_LIBRARY)
     find_library(CPUFEATURES_LIBRARY 
-        NAMES cpu_features)
+        NAMES cpu_features  cpu_features.lib
+        PATHS $ENV{CPUFEATURES_DIR}/lib
+        $ENV{CPUFEATURES_DIR}
+        ${${_PROJECT_DEPENDENCY_DIR}}/${CMAKE_INSTALL_LIBDIR}
+        ${${_PROJECT_DEPENDENCY_DIR}}/lib
+        ${${_PROJECT_DEPENDENCY_DIR}})
+  endif (NOT CPUFEATURES_LIBRARY)
+
+
+  if (NOT CPUFEATURES_LIBRARY)
+    find_library(CPUFEATURES_LIBRARY 
+        NAMES cpu_features  cpu_features.lib)
   endif (NOT CPUFEATURES_LIBRARY)
 
   set(CPUFEATURES_FOUND ${CPUFEATURES_LIBRARY})
@@ -87,6 +110,10 @@ else ()
     get_target_property(CPUFEATURES_LIBRARY CpuFeatures::cpu_features IMPORTED_LOCATION_NOCONFIG)
   endif()
 
+  if (NOT CPUFEATURES_LIBRARY)
+    get_target_property(CPUFEATURES_LIBRARY CpuFeatures::cpu_features IMPORTED_LOCATION_RELWITHDEBINFO)
+  endif()
+
   get_target_property(CPUFEATURES_INTERFACE_LINK_LIBRARIES CpuFeatures::cpu_features INTERFACE_LINK_LIBRARIES)
 
   if (CPUFEATURES_INTERFACE_LINK_LIBRARIES)

CMakeModules/FindNATIVEJIT.cmake

@@ -1,4 +1,4 @@
-# Copyright (C) 2020 - 2022 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2020 - 2026 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -113,6 +113,10 @@ else ()
     get_target_property(NATIVEJIT_LIBRARY NativeJIT IMPORTED_LOCATION_DEBUG)
   endif()
 
+  if (NOT NATIVEJIT_LIBRARY)
+    get_target_property(NATIVEJIT_LIBRARY NativeJIT IMPORTED_LOCATION_RELWITHDEBINFO)
+  endif()
+
   if (NOT NATIVEJIT_LIBRARY)
     get_target_property(NATIVEJIT_LIBRARY NativeJIT IMPORTED_LOCATION_NOCONFIG)
   endif()
@@ -129,6 +133,10 @@ else ()
     get_target_property(CODEGEN_LIBRARY CodeGen IMPORTED_LOCATION_DEBUG)
   endif()
 
+  if (NOT CODEGEN_LIBRARY)
+    get_target_property(CODEGEN_LIBRARY CodeGen IMPORTED_LOCATION_RELWITHDEBINFO)
+  endif()
+
   if (NOT CODEGEN_LIBRARY)
     get_target_property(CODEGEN_LIBRARY CodeGen IMPORTED_LOCATION_NOCONFIG)
   endif()  

CMakeModules/FindZLIB.cmake

@@ -1,4 +1,4 @@
-# Copyright (C) 2022 - 2024 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2022 - 2026 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -43,11 +43,12 @@ if (NOT (ZLIB_INCLUDE_DIR AND ZLIB_LIBRARY) OR NOT ZLIB_FOUND)
               NO_DEFAULT_PATH)
 
     if (NOT ZLIB_INCLUDE_DIR)
-        find_path(ZLIB_INCLUDE_DIR zlib.h zlib/zlib.h)
+        find_path(ZLIB_INCLUDE_DIR zlib.h zlib/zlib.h
+        CMAKE_FIND_ROOT_PATH_BOTH )
     endif ()
 
     find_library(ZLIB_LIBRARY 
-	    NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a 
+	    NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a libzdll.a
 	    PATHS $ENV{ZLIB_DIR}/lib
 	          $ENV{ZLIB_DIR}/lib-dbg
 	          $ENV{ZLIB_DIR}
@@ -65,7 +66,8 @@ if (NOT (ZLIB_INCLUDE_DIR AND ZLIB_LIBRARY) OR NOT ZLIB_FOUND)
              NO_DEFAULT_PATH)
 
     if (NOT ZLIB_LIBRARY)
-        find_library(ZLIB_LIBRARY NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a)
+        find_library(ZLIB_LIBRARY NAMES zdll.lib z zlib.lib libzlib zlib libzlib.a libzdll.a
+        CMAKE_FIND_ROOT_PATH_BOTH )
     endif ()
 
     if (NOT WIN32)
@@ -80,6 +82,24 @@ if (NOT (ZLIB_INCLUDE_DIR AND ZLIB_LIBRARY) OR NOT ZLIB_FOUND)
         endif (PC_ZLIB_FOUND)
     endif (NOT WIN32)
 
+    
+    # make sure that we have a valid zip library
+    file(TO_CMAKE_PATH "${ZLIB_LIBRARY}" LIBZ_CMAKE_PATH)
+    include (CheckLibraryExists)
+    check_library_exists("${LIBZ_CMAKE_PATH}" "gzopen" "" LIBZ_FOUND_SYMBOL)
+    if(NOT LIBZ_FOUND_SYMBOL)
+        # this is odd, but on windows this check always fails! must be a
+        # bug in the current cmake version so for now only issue this
+        # warning on linux
+        if(UNIX)
+            message(WARNING
+"The chosen zlib library does not appear to be valid because it is
+missing certain required symbols. Please check that ${LIBZ_LIBRARY} is
+the correct zlib library. For details about the error, please see
+CMakeError.log or CMakeConfigureLog.yaml in the build directory.")
+        endif()
+    endif()
+
     mark_as_advanced(ZLIB_INCLUDE_DIR ZLIB_LIBRARY)
 
 endif () # Check for cached values

ChooseQtVersion.cmake

@@ -1,4 +1,4 @@
-# Copyright (C) 2019 - 2023 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2026 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -8,7 +8,7 @@
 # of Connecticut School of Medicine. 
 # All rights reserved. 
 
-cmake_minimum_required (VERSION 2.8.12...3.19.1)
+cmake_minimum_required(VERSION 2.8...3.19)
 
 set(SELECT_QT "Any" CACHE STRING "The prefered Qt version one of: Qt6, Qt5, Qt4 or Any" )
 if (DEFINED SELECT_QT)

LinuxTGZ/COPASI.sh

@@ -1,5 +1,5 @@
 #!/bin/bash
-# Copyright (C) 2019 - 2025 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2026 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -123,6 +123,10 @@ if [ -n "${COPASI_LINUXDEPLOYQT}" ]; then
   echo "running linuxdeployqt"
   echo ${COPASI_LINUXDEPLOYQT} ./CopasiUI  -always-overwrite -bundle-non-qt-libs -qmake=`which qmake` -extra-plugins=platforms/libqxcb.so
   ${COPASI_LINUXDEPLOYQT} ./CopasiUI  -always-overwrite -bundle-non-qt-libs -qmake=`which qmake` -extra-plugins=platforms/libqxcb.so
+  if [ -n "${EXTRA_LIBS}" ]; then
+    # copy all files from extra_libs to lib
+    cp -r ${EXTRA_LIBS}/* lib/    
+  fi;
   popd
 fi