Merge branch 'release/Version-4.44'

Author: fbergmann

.github/workflows/copasi_se.yml

@@ -1,6 +1,7 @@
 name: Build and Test 
 
 on: 
+  workflow_dispatch:
   push:
     paths:
         - "**"
@@ -81,8 +82,15 @@ jobs:
         curl -L http://bqfrank.spdns.org/Files/test-suite.zip  -o test-suite.zip
         unzip -n -qq test-suite.zip
 
+    - name: Configure COPASI (mac)
+      shell: bash
+      if: matrix.platform == 'macos-latest'
+      run: |
+        cmake -G Ninja -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DSBML_TESTSUITE_RUN=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DENABLE_JIT=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/  -DBUILD_SBML_TESTSUITE:BOOL=ON -DSBML_TESTSUITE_CASES_DIR:PATH=$PWD/test-suite -S .  -B ./build_copasi
+
     - name: Configure COPASI
       shell: bash
+      if: matrix.platform != 'macos-latest'
       run: |
         cmake -G Ninja -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DSBML_TESTSUITE_RUN=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/  -DBUILD_SBML_TESTSUITE:BOOL=ON -DSBML_TESTSUITE_CASES_DIR:PATH=$PWD/test-suite -S .  -B ./build_copasi
 

.github/workflows/copasi_se_mp.yml

@@ -51,7 +51,7 @@ jobs:
     - name: Configure COPASI
       shell: bash
       run: |
-        cmake -B build_copasi -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/ -DENABLE_OMP=ON -S . 
+        cmake -B build_copasi -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/ -DENABLE_OMP=ON -DENABLE_JIT=OFF -S . 
         sed -i 's/libgomp.a/libgomp.so/g' build_copasi/CMakeCache.txt
         sed -i 's/libpthread.a/libpthread.so/g' build_copasi/CMakeCache.txt
 

.github/workflows/copasi_se_slackware.yml

@@ -50,7 +50,7 @@ jobs:
     - name: Configure COPASI
       shell: bash
       run: |
-        cmake -B build_copasi -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/ -DENABLE_OMP=ON -S . 
+        cmake -B build_copasi -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DCOPASI_INSTALL_C_API=ON -DBUILD_TESTS=ON -DBUILD_GUI=OFF -DCOPASI_DEPENDENCY_DIR=./dependencies/ -DCMAKE_INSTALL_PREFIX=./install/ -DENABLE_OMP=ON  -DENABLE_JIT=OFF  -S . 
         sed -i 's/libgomp.a/libgomp.so/g' build_copasi/CMakeCache.txt
         sed -i 's/libpthread.a/libpthread.so/g' build_copasi/CMakeCache.txt
 

.gitignore

@@ -83,3 +83,5 @@ python_copasi.egg-info
 /copasi-dependencies
 TestSuite/distribution/out.txt
 .~lock*
+
+tests/opt.cps

CMakeLists.txt

@@ -460,7 +460,10 @@ endif(ENABLE_OMP)
 
 # TODO raptor should be restricted to a version which is at least
 # 1.4.18, but lower then 2.0
+option(COPASI_USE_RAPTOR "Use Raptor (<2.0) for RDF support" ON)
+if (COPASI_USE_RAPTOR)
 find_package(RAPTOR REQUIRED)
+endif()
 
 # actually iconv is only needed on BSD like systems
 find_package(ICONV)

copasi/CMakeLists.txt

@@ -274,7 +274,6 @@ else()
 
   target_link_libraries(libCOPASISE-core
     ${CROSSGUID_LIBRARY} 
-    RAPTOR::RAPTOR
     ${LIBSBML_LIBRARY_NAME} 
     ${LIBSEDML_LIBRARY_NAME}
     ${LIBCOMBINE_LIBRARY_NAME}
@@ -283,6 +282,10 @@ else()
     ${NATIVEJIT_LIBRARY} 
     ${CPUFEATURES_LIBRARY}
   )
+  
+  if (COPASI_USE_RAPTOR)
+    target_link_libraries(libCOPASISE-core RAPTOR::RAPTOR)
+  endif()
 
   add_library (libCOPASISE-static STATIC $<TARGET_OBJECTS:libCOPASISE-core>)
 
@@ -308,13 +311,16 @@ endif (APPLE)
 
 target_link_libraries(libCOPASISE-static 
   ${CROSSGUID_LIBRARY} 
-  RAPTOR::RAPTOR
   ${LIBSBML_LIBRARY_NAME} 
   EXPAT::EXPAT
   ${CLAPACK_LIBRARIES} 
   ${NATIVEJIT_LIBRARY} 
   ${CPUFEATURES_LIBRARY})
 
+  if (COPASI_USE_RAPTOR)
+    target_link_libraries(libCOPASISE-static RAPTOR::RAPTOR)
+  endif()
+
  if (EXTRA_LIBS)
    target_link_libraries(libCOPASISE-static ${EXTRA_LIBS})   
  else ()
@@ -399,7 +405,11 @@ if(ENABLE_LIBCOPASISE_SHARED)
 
   target_link_libraries(libCOPASISE-shared ${LIBSEDML_LIBRARY_NAME})
 
-  target_link_libraries(libCOPASISE-shared RAPTOR::RAPTOR ${LIBSBML_LIBRARY_NAME} EXPAT::EXPAT ${CLAPACK_LIBRARIES})
+  if (COPASI_USE_RAPTOR)
+    target_link_libraries(libCOPASISE-shared RAPTOR::RAPTOR)
+  endif()
+
+  target_link_libraries(libCOPASISE-shared ${LIBSBML_LIBRARY_NAME} EXPAT::EXPAT ${CLAPACK_LIBRARIES})
 
   if (ENABLE_OMP)
     target_link_libraries(libCOPASISE-shared OpenMP::OpenMP_CXX)

copasi/CopasiDataModel/CDataModel.cpp

@@ -1082,9 +1082,14 @@ bool CDataModel::newModel(CProcessReport * pProcessReport,
   // set content type to COPASI
   mData.mContentType = ContentType::COPASI;
 
-  CRegisteredCommonName::setEnabled(false);
-  commonAfterLoad(pProcessReport, deleteOldData);
-  CRegisteredCommonName::setEnabled(true);
+  if (CRegisteredCommonName::isEnabled())
+    {
+      CRegisteredCommonName::setEnabled(false);
+      commonAfterLoad(pProcessReport, deleteOldData);
+      CRegisteredCommonName::setEnabled(true);
+    }
+  else
+    commonAfterLoad(pProcessReport, deleteOldData);
 
   return true;
 }

copasi/CopasiSE/CopasiSE.cpp

@@ -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.
@@ -784,8 +784,10 @@ int validate()
 
         try
           {
+            std::ostream * pOstream = &std::cout;
+
             success =
-              TaskList[i].initialize(CCopasiTask::OUTPUT_SE, pDataModel, NULL);
+              TaskList[i].initialize(CCopasiTask::OUTPUT_SE, pDataModel, pOstream);
 
             // We need to check whether the result is saved in any form.
             // If not we need to stop right here to avoid wasting time.
@@ -810,8 +812,6 @@ int validate()
 
             retcode = 1;
           }
-
-        pDataModel->finish();
       }
 
   return retcode;

copasi/MIRIAM/CModelMIRIAMInfo.cpp

@@ -1,26 +1,26 @@
-// 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.
-
-// Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual
-// Properties, Inc., University of Heidelberg, and University of
-// of Connecticut School of Medicine.
-// All rights reserved.
-
-// Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual
-// Properties, Inc., University of Heidelberg, and The University
-// of Manchester.
-// All rights reserved.
-
-// Copyright (C) 2008 - 2009 by Pedro Mendes, Virginia Tech Intellectual
-// Properties, Inc., EML Research, gGmbH, University of Heidelberg,
-// and The University of Manchester.
-// All rights reserved.
-
-// Copyright (C) 2007 by Pedro Mendes, Virginia Tech Intellectual
-// Properties, Inc. and EML Research, gGmbH.
-// All rights reserved.
+// 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. 
+
+// Copyright (C) 2017 - 2018 by Pedro Mendes, Virginia Tech Intellectual 
+// Properties, Inc., University of Heidelberg, and University of 
+// of Connecticut School of Medicine. 
+// All rights reserved. 
+
+// Copyright (C) 2010 - 2016 by Pedro Mendes, Virginia Tech Intellectual 
+// Properties, Inc., University of Heidelberg, and The University 
+// of Manchester. 
+// All rights reserved. 
+
+// Copyright (C) 2008 - 2009 by Pedro Mendes, Virginia Tech Intellectual 
+// Properties, Inc., EML Research, gGmbH, University of Heidelberg, 
+// and The University of Manchester. 
+// All rights reserved. 
+
+// Copyright (C) 2007 by Pedro Mendes, Virginia Tech Intellectual 
+// Properties, Inc. and EML Research, gGmbH. 
+// All rights reserved. 
 
 #include <iostream>
 #include <fstream>
@@ -29,8 +29,8 @@
 #include "copasi/copasi.h"
 
 #include "copasi/MIRIAM/CModelMIRIAMInfo.h"
-#include "copasi/MIRIAM/CRDFWriter.h"
 #include "copasi/MIRIAM/CRDFLiteral.h"
+#include "copasi/MIRIAM/CRDFWriter.h"
 #include "copasi/MIRIAM/CRDFParser.h"
 #include "copasi/MIRIAM/CConstants.h"
 #include "copasi/MIRIAM/CRDFObject.h"
@@ -527,7 +527,11 @@ void CMIRIAMInfo::load(CDataContainer * pObject)
   if (mpAnnotation != NULL &&
       !mpAnnotation->getMiriamAnnotation().empty())
     {
+    #ifdef COPASI_USE_RAPTOR
       mpRDFGraph = CRDFParser::graphFromXml(mpAnnotation->getMiriamAnnotation());
+    #else
+      mpRDFGraph = CRDFGraph::fromString(mpAnnotation->getMiriamAnnotation());
+    #endif
     }
 
   if (mpRDFGraph == NULL)
@@ -564,8 +568,11 @@ bool CMIRIAMInfo::save()
     {
       mpRDFGraph->clean();
       mpRDFGraph->updateNamespaces();
-
+#ifdef COPASI_USE_RAPTOR
       mpAnnotation->setMiriamAnnotation(CRDFWriter::xmlFromGraph(mpRDFGraph), mpAnnotation->getKey(), mpAnnotation->getKey());
+#else
+      mpAnnotation->setMiriamAnnotation(mpRDFGraph->toXmlString(), mpAnnotation->getKey(), mpAnnotation->getKey());
+#endif
 
       return true;
     }