Revert "Merge branch 'release/Version-4.45' of https://github.com/cop…

…asi/COPASI into release/Version-4.45" This reverts commit 667039f, reversing changes made to cd582a7.
copasi · Dec 12, 2024 · f841edf · f841edf
1 parent 667039f
commit f841edf
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -938,7 +938,6 @@ message(STATUS "-----------------------------------------------------------
    Vendor               = ${BLA_VENDOR}
    LAPACK Libs          = ${CLAPACK_LIBRARIES}
    LAPACK LDFLAGS       = ${CLAPACK_LINKER_FLAGS}
-   LAPACK include       = ${CLAPACK_INCLUDE_DIR}
 
    crossguid Libs       = ${CROSSGUID_LIBRARY}
    cross include        = ${CROSSGUID_INCLUDE_DIR}

diff --git a/CMakeModules/FindCLAPACK.cmake b/CMakeModules/FindCLAPACK.cmake
@@ -1,4 +1,4 @@
-# Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2022 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -109,37 +109,24 @@ endif ()
 if (NOT LAPACK_FOUND)
   # cmake MKL Detection does only support MKL version 10 and older
   if (DEFINED ENV{MKLROOT})
-    message(STATUS "MKLROOT is: $ENV{MKLROOT}")
-    set(MKLROOT $ENV{MKLROOT} CACHE PATH "MKLROOT" FORCE)
-  endif()
-  if (DEFINED MKLROOT)
     set(BLA_VENDOR "Intel (MKL)")
 
     if (UNIX)
-      if ((COPASI_BUILD_TYPE EQUAL "32bit") AND EXISTS ${MKLROOT}/lib/ia32)
-        set(LAPACK_LIBRARIES "-Wl,--start-group ${MKLROOT}/lib/ia32/libmkl_intel.a ${MKLROOT}/lib/ia32/libmkl_core.a ${MKLROOT}/lib/ia32/libmkl_sequential.a -Wl,--end-group -lpthread -lm -ldl")
-      elseif (COPASI_BUILD_TYPE EQUAL "64bit" AND EXISTS ${MKLROOT}/lib/intel64)
-        set(LAPACK_LIBRARIES "-Wl,--start-group ${MKLROOT}/lib/intel64/libmkl_intel_lp64.a ${MKLROOT}/lib/intel64/libmkl_core.a ${MKLROOT}/lib/intel64/libmkl_sequential.a -Wl,--end-group -lpthread -lm -ldl")
-      elseif(EXISTS "${MKLROOT}/lib" AND EXISTS "${MKLROOT}/lib/libmkl_intel_lp64.a")
-        set(LAPACK_LIBRARIES "-Wl,--start-group ${MKLROOT}/lib/libmkl_intel_lp64.a ${MKLROOT}/lib/libmkl_core.a ${MKLROOT}/lib/libmkl_sequential.a -Wl,--end-group -lpthread -lm -ldl")
-      elseif(EXISTS ${MKLROOT}/lib AND EXISTS ${MKLROOT}/lib/libmkl_intel.a)
-        set(LAPACK_LIBRARIES "-Wl,--start-group ${MKLROOT}/lib/libmkl_intel.a ${MKLROOT}/lib/libmkl_core.a ${MKLROOT}/lib/libmkl_sequential.a -Wl,--end-group -lpthread -lm -ldl")
+      if (COPASI_BUILD_TYPE EQUAL "32bit")
+        set(LAPACK_LIBRARIES "-Wl,--start-group $ENV{MKLROOT}/lib/ia32/libmkl_intel.a $ENV{MKLROOT}/lib/ia32/libmkl_core.a $ENV{MKLROOT}/lib/ia32/libmkl_sequential.a -Wl,--end-group -lpthread -lm -ldl")
+      elseif (COPASI_BUILD_TYPE EQUAL "64bit")
+        set(LAPACK_LIBRARIES "-Wl,--start-group $ENV{MKLROOT}/lib/intel64/libmkl_intel_lp64.a $ENV{MKLROOT}/lib/intel64/libmkl_core.a $ENV{MKLROOT}/lib/intel64/libmkl_sequential.a -Wl,--end-group -lpthread -lm -ldl")
       endif ()
     else ()
-      if (COPASI_BUILD_TYPE EQUAL "32bit" AND EXISTS "${MKLROOT}/lib/ia32/")
-        set(LAPACK_LIBRARIES "${MKLROOT}/lib/ia32/mkl_intel_c.lib" "${MKLROOT}/lib/ia32/mkl_core.lib" "${MKLROOT}/lib/ia32/mkl_sequential.lib")
-      elseif (COPASI_BUILD_TYPE EQUAL "64bit" AND EXISTS "${MKLROOT}/lib/intel64/" )
-        set(LAPACK_LIBRARIES "${MKLROOT}/lib/intel64/mkl_intel_lp64.lib" "${MKLROOT}/lib/intel64/mkl_core.lib" "${MKLROOT}/lib/intel64/mkl_sequential.lib")
-      elseif (EXISTS "${MKLROOT}/lib/mkl_intel_lp64.lib")
-        set(LAPACK_LIBRARIES "${MKLROOT}/lib/mkl_intel_lp64.lib" "${MKLROOT}/lib/mkl_core.lib" "${MKLROOT}/lib/mkl_sequential.lib")        
+      if (COPASI_BUILD_TYPE EQUAL "32bit")
+        set(LAPACK_LIBRARIES "$ENV{MKLROOT}/lib/ia32/mkl_intel_c.lib" "$ENV{MKLROOT}/lib/ia32/mkl_core.lib" "$ENV{MKLROOT}/lib/ia32/mkl_sequential.lib")
+      elseif (COPASI_BUILD_TYPE EQUAL "64bit")
+        set(LAPACK_LIBRARIES "$ENV{MKLROOT}/lib/intel64/mkl_intel_lp64.lib" "$ENV{MKLROOT}/lib/intel64/mkl_core.lib" "$ENV{MKLROOT}/lib/intel64/mkl_sequential.lib")
       endif ()
     endif ()
 
-    set(CLAPACK_INCLUDE_DIR ${MKLROOT}/include)
     add_definitions(-DHAVE_MKL)
     set(LAPACK_FOUND "Yes")
-    set(USE_MKL 1)
-
   endif ()
 endif ()
 
@@ -301,9 +288,9 @@ find_path(CLAPACK_INCLUDE_DIR clapack.h
 endif(NOT CLAPACK_INCLUDE_DIR)
 
 
-if (CLAPACK_INCLUDE_DIR AND NOT DEFINED MKLROOT)
+if (CLAPACK_INCLUDE_DIR)
   add_definitions(-DHAVE_CLAPACK_H)
-endif (CLAPACK_INCLUDE_DIR AND NOT DEFINED MKLROOT)
+endif (CLAPACK_INCLUDE_DIR)
 
 if (NOT CLAPACK_INCLUDE_DIR)
   find_path(CLAPACK_INCLUDE_DIR lapack.h
@@ -326,7 +313,7 @@ if (NOT CLAPACK_INCLUDE_DIR)
 endif (NOT CLAPACK_INCLUDE_DIR)
 
 if (NOT CLAPACK_INCLUDE_DIR)
-  set(CLAPACK_INCLUDE_DIR "${COPASI_SOURCE_DIR}/copasi/lapack")
+  set(CLAPACK_INCLUDE_DIR "${COPASI_SOURCE_DIR}")
 endif (NOT CLAPACK_INCLUDE_DIR)
 
 

diff --git a/InnoSetup/COPASI.sh b/InnoSetup/COPASI.sh
@@ -1,5 +1,5 @@
 #!/bin/bash
-# Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2022 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -14,15 +14,6 @@
 # of Manchester. 
 # All rights reserved. 
 
-
-
-
-
-
-
-
-
-
 # Echo all bash commands to ease debugging
 set -x
 
@@ -41,98 +32,72 @@ EOF
 GUID=$(echo $GUID | sed 'y/abcdef/ABCDEF/')
 productcode=${GUID:0:8}-${GUID:8:4}-${GUID:12:4}-${GUID:16:4}-${GUID:20:12}
 
-# if NO_COPY environment variable is set, skip the copy step
-if [ -n "${NO_COPY}" ]; then
-    echo "Skipping copy step"
-    cd ${SOURCE}/InnoSetup
-
-    workdir=${SOURCE}/InnoSetup
-    workdir=$(echo "$workdir" | sed 's/\//\\/g')
-    workdir=$(echo "$workdir" | sed 's/^\\c\\/C:\\/')
-    workdir=$(echo "$workdir" | sed 's/^\\d\\/D:\\/')
-    workdir=$(echo "$workdir" | sed 's/^\\e\\/E:\\/')
-    workdir=${workdir//\\/\\\\}
-
-    stagedir=${SETUP_DIR}/package
-    stagedir=$(echo "$stagedir" | sed 's/\//\\/g')
-    stagedir=$(echo "$stagedir" | sed 's/^\\c\\/C:\\/')
-    stagedir=$(echo "$stagedir" | sed 's/^\\d\\/D:\\/')
-    stagedir=$(echo "$stagedir" | sed 's/^\\e\\/E:\\/')
-
-    stagedir=${stagedir//\\/\\\\}
-
-else
-
-    [ -e ${SETUP_DIR}/package ] && rm -rf ${SETUP_DIR}/package
-    mkdir ${SETUP_DIR}/package
-    pushd ${SETUP_DIR}/package
-
-    # Create directory structure
-    tar -xvf ${BUILD_ROOT}/src/windows.tgz
-
-    # Copy README
-    cp ${SOURCE}/README.Win32 README.txt
-    chmod 644 README.txt
-
-    # Copy license
-    cp ${SOURCE}/copasi/ArtisticLicense.txt LICENSE.txt
-    chmod 644 LICENSE.txt
-
-    # Copy configuration resources
-    mkdir -p share/copasi/config
-    cp ${SOURCE}/copasi/MIRIAM/MIRIAMResources.xml share/copasi/config
-    chmod 444 share/copasi/config/*
-
-    # Copy examples
-    mkdir -p share/copasi/examples
-    cp ${SOURCE}/TestSuite/distribution/* share/copasi/examples
-    chmod 444 share/copasi/examples/*
-    chmod 777 share/copasi/examples
-
-    # Copy icons
-    mkdir -p share/copasi/icons
-    cp ${SOURCE}/copasi/UI/icons/Copasi.ico share/copasi/icons
-    cp ${SOURCE}/copasi/UI/icons/CopasiDoc.ico share/copasi/icons
-    chmod 644 share/copasi/icons/*
-
-    # Copy wizard resource
-    mkdir -p share/copasi/doc/html
-    cp ${SOURCE}/copasi/wizard/help_html/*.html share/copasi/doc/html
-    chmod 644 share/copasi/doc/html/*.html
-
-    mkdir -p share/copasi/doc/html/figures
-    cp ${SOURCE}/copasi/wizard/help_html/figures/*.png \
-        share/copasi/doc/html/figures
-    chmod 644 share/copasi/doc/html/figures/*.png
-
-    # 32 bit files
-    cp "${BUILD_32_MD}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiUI/CopasiUI.exe"  bin/32
-    chmod 755 bin/32/CopasiUI.exe
-    cp "${BUILD_32_MT}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiSE/CopasiSE.exe"  bin/32
-    chmod 755 bin/32/CopasiSE.exe
-    cp ${SOURCE}/InnoSetup/qt.conf bin/32
-    chmod 644 bin/32/qt.conf
-
-    # 64 bit files
-    cp "${BUILD_64_MD}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiUI/CopasiUI.exe"  bin/64
-    chmod 755 bin/64/CopasiUI.exe
-    cp "${BUILD_64_MT}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiSE/CopasiSE.exe"  bin/64
-    chmod 755 bin/64/CopasiSE.exe
-    cp ${SOURCE}/InnoSetup/qt.conf bin/64
-    chmod 644 bin/64/qt.conf
-
-    # Execute InnoSetup to create Installation package
-    cd ${SOURCE}/InnoSetup
-
-    workdir=$(cygpath -wa .)
-    workdir=${workdir//\\/\\\\}
-
-    stagedir=$(cygpath -wa "${SETUP_DIR}/package")
-    stagedir=${stagedir//\\/\\\\}
-
-fi
-
-
+[ -e ${SETUP_DIR}/package ] && rm -rf ${SETUP_DIR}/package
+mkdir ${SETUP_DIR}/package
+pushd ${SETUP_DIR}/package
+
+# Create directory structure
+tar -xvf ${BUILD_ROOT}/src/windows.tgz
+
+# Copy README
+cp ${SOURCE}/README.Win32 README.txt
+chmod 644 README.txt
+
+# Copy license
+cp ${SOURCE}/copasi/ArtisticLicense.txt LICENSE.txt
+chmod 644 LICENSE.txt
+
+# Copy configuration resources
+mkdir -p share/copasi/config
+cp ${SOURCE}/copasi/MIRIAM/MIRIAMResources.xml share/copasi/config
+chmod 444 share/copasi/config/*
+
+# Copy examples
+mkdir -p share/copasi/examples
+cp ${SOURCE}/TestSuite/distribution/* share/copasi/examples
+chmod 444 share/copasi/examples/*
+chmod 777 share/copasi/examples
+
+# Copy icons
+mkdir -p share/copasi/icons
+cp ${SOURCE}/copasi/UI/icons/Copasi.ico share/copasi/icons
+cp ${SOURCE}/copasi/UI/icons/CopasiDoc.ico share/copasi/icons
+chmod 644 share/copasi/icons/*
+
+# Copy wizard resource
+mkdir -p share/copasi/doc/html
+cp ${SOURCE}/copasi/wizard/help_html/*.html share/copasi/doc/html
+chmod 644 share/copasi/doc/html/*.html
+
+mkdir -p share/copasi/doc/html/figures
+cp ${SOURCE}/copasi/wizard/help_html/figures/*.png \
+    share/copasi/doc/html/figures
+chmod 644 share/copasi/doc/html/figures/*.png
+
+# 32 bit files
+cp "${BUILD_32_MD}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiUI/CopasiUI.exe"  bin/32
+chmod 755 bin/32/CopasiUI.exe
+cp "${BUILD_32_MT}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiSE/CopasiSE.exe"  bin/32
+chmod 755 bin/32/CopasiSE.exe
+cp ${SOURCE}/InnoSetup/qt.conf bin/32
+chmod 644 bin/32/qt.conf
+
+# 64 bit files
+cp "${BUILD_64_MD}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiUI/CopasiUI.exe"  bin/64
+chmod 755 bin/64/CopasiUI.exe
+cp "${BUILD_64_MT}/build/COPASI.${DIR_SUFFIX}/copasi/CopasiSE/CopasiSE.exe"  bin/64
+chmod 755 bin/64/CopasiSE.exe
+cp ${SOURCE}/InnoSetup/qt.conf bin/64
+chmod 644 bin/64/qt.conf
+
+# Execute InnoSetup to create Installation package
+cd ${SOURCE}/InnoSetup
+
+workdir=$(cygpath -wa .)
+workdir=${workdir//\\/\\\\}
+
+stagedir=$(cygpath -wa "${SETUP_DIR}/package")
+stagedir=${stagedir//\\/\\\\}
 
 #   modify product code, product version, and package name
 sed -e '/#define MyAppVersion/s/".*"/"'${MyAppVersion}'"/' \

diff --git a/cmake-set-dependencies.cmake b/cmake-set-dependencies.cmake
@@ -1,4 +1,4 @@
-# Copyright (C) 2019 - 2024 by Pedro Mendes, Rector and Visitors of the 
+# Copyright (C) 2019 - 2022 by Pedro Mendes, Rector and Visitors of the 
 # University of Virginia, University of Heidelberg, and University 
 # of Connecticut School of Medicine. 
 # All rights reserved. 
@@ -68,7 +68,7 @@ if (NOT EXISTS ${RAPTOR_LIBRARY})
 set (RAPTOR_LIBRARY ${COPASI_DEPENDENCY_DIR}/lib/raptor.lib CACHE FILEPATH "raptor library" FORCE)
 endif()
 
-if (NOT DEFINED MKLROOT AND (NOT BLA_VENDOR OR "${BLA_VENDOR}" STREQUAL "COPASI Dependencies"))
+if (NOT BLA_VENDOR OR "${BLA_VENDOR}" STREQUAL "COPASI Dependencies")
   # clapack
   set (CLAPACK_INCLUDE_DIR ${COPASI_DEPENDENCY_DIR}/include CACHE PATH "clapack include directory" FORCE)
 

diff --git a/copasi/CMakeLists.txt b/copasi/CMakeLists.txt
@@ -225,7 +225,7 @@ endif(EXTRA_MOC_OPTIONS)
   set(QWT_VERSION 0x0${QWT_VERSION_NUMERIC})
   set(COPASI_UI_MOC_OPTIONS ${COPASI_UI_MOC_OPTIONS} -DQWT_VERSION=0x0${QWT_VERSION_NUMERIC})
 
-  if (CLAPACK_FOUND AND NOT USE_MKL)
+  if (CLAPACK_FOUND)
     set(USE_CLAPACK 1)
   elseif (USE_MKL)
     set(USE_MKL 1)
@@ -509,14 +509,12 @@ if(BUILD_GUI)
            DOC "Path to the uic executable"
            PATHS ${Qt6Widgets_DIR}/../../../bin/
                  ${Qt6Widgets_DIR}/../../../share/qt/libexec/
-                 ${Qt6Widgets_DIR}/../../../libexec/qt6/
            )
 
     if (NOT EXISTS "${Qt6Widgets_UIC_EXECUTABLE}")
       message(FATAL_ERROR "Need UIC executable to compile GUI, it should be in: 
           ${Qt6Widgets_DIR}/../../../bin
           ${Qt6Widgets_DIR}/../../../share/qt/libexec
-          ${Qt6Widgets_DIR}/../../../libexec/qt6/
           ")
     endif()
   endif()