Add layout render

.github/workflows/main.yml

@@ -82,7 +82,7 @@ jobs:
         libroadrunner_deps_owner: [ "sys-bio" ]
         libroadrunner_deps_repo: [ "libroadrunner-deps" ]
         libroadrunner_deps_name: [ "libroadrunner-deps" ]
-        libroadrunner_deps_release_version: [ "v2.1.2" ]
+        libroadrunner_deps_release_version: [ "v2.2.7" ]
         python_version: [ "3.12" ]
 
     runs-on: ${{ matrix.platform.os_name }}

CMakeLists.txt

@@ -10,8 +10,8 @@ project(libantimony)
 #
 # Set up version information.
 #
-SET(LIBANTIMONY_VERSION_MAJOR 2)
-SET(LIBANTIMONY_VERSION_MINOR 15)
+SET(LIBANTIMONY_VERSION_MAJOR 3)
+SET(LIBANTIMONY_VERSION_MINOR 0)
 SET(LIBANTIMONY_VERSION_PATCH ".0")
 SET(LIBANTIMONY_VERSION_RELEASE "")
 
@@ -255,7 +255,7 @@ endif(WITH_CELLML)
 
 if(WITH_LIBSBML_EXPAT)
     find_library(EXPAT_LIBRARY
-        NAMES libexpat.lib libexpat.so libexpat.dylib libexpat expat.lib expat.so expat.dylib expat
+        NAMES libexpat.lib libexpat.so libexpat.dylib libexpat expat.lib expat.so expat.dylib expat libexpatdMD libexpatMD
 	PATHS /usr/lib /usr/local/lib
               ${CMAKE_SOURCE_DIR}
               ${CMAKE_SOURCE_DIR}/dependencies/lib
@@ -338,6 +338,30 @@ if(WITH_LIBSBML_COMPRESSION)
     set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${BZIP_LIBRARY} )
 endif()
 
+if(WITH_SBML)
+    find_library(SBMLNETWORK_LIBRARY
+        NAMES libsbmlnetwork-static.lib sbmlnetwork-static.lib libsbmlnetwork-static sbmlnetwork-static libsbmlnetwork-staticmdd libsbmlnetwork-staticmd libsbmlnetwork-staticd libsbmlnetwork-staticd.a
+	PATHS /usr/lib /usr/local/lib
+              ${CMAKE_SOURCE_DIR}
+              ${CMAKE_SOURCE_DIR}/dependencies/lib
+              ${LIBSBML_INCLUDE_DIR}/../lib
+        )
+    set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${SBMLNETWORK_LIBRARY} )
+
+    find_path(SBMLNETWORK_INCLUDE_DIR
+        NAMES libsbmlnetwork_common.h
+        PATHS /usr/include /usr/local/include  ${LIBSBML_INSTALL_DIR}/include
+        DOC "The directory containing the SBMLNetwork include files."
+              )
+
+    INCLUDE_DIRECTORIES(${INCLUDE_DIRECTORIES} ${SBMLNETWORK_INCLUDE_DIR} )
+    # SBMLNETWORK uses stuff from the 'dl' library on some platforms.  CMake defines CMAKE_DL_LIBS if so.
+    set(LIBANTIMONY_LIBS ${LIBANTIMONY_LIBS} ${CMAKE_DL_LIBS} )
+
+endif()
+
+message(STATUS "Antimony libs: ${LIBANTIMONY_LIBS}")
+
 ###############################################################################
 #
 # If WITH_SWIG is selected, we need to find swig
@@ -534,9 +558,9 @@ file(GLOB LIBANTIMONY_SOURCES
     ${ANTIMONY_SRC_DIR}cellmlx.cpp
     ${ANTIMONY_SRC_DIR}constraint.cpp
     ${ANTIMONY_SRC_DIR}dnastrand.cpp
-    ${ANTIMONY_SRC_DIR}uncertWrapper.cpp
     ${ANTIMONY_SRC_DIR}event.cpp
     ${ANTIMONY_SRC_DIR}formula.cpp
+    ${ANTIMONY_SRC_DIR}layoutWrapper.cpp
     ${ANTIMONY_SRC_DIR}module.cpp
     ${ANTIMONY_SRC_DIR}reactantlist.cpp
     ${ANTIMONY_SRC_DIR}reaction.cpp
@@ -548,6 +572,7 @@ file(GLOB LIBANTIMONY_SOURCES
     ${ANTIMONY_SRC_DIR}unitdef.cpp
     ${ANTIMONY_SRC_DIR}unitelement.cpp
     ${ANTIMONY_SRC_DIR}userfunction.cpp
+    ${ANTIMONY_SRC_DIR}uncertWrapper.cpp
     ${ANTIMONY_SRC_DIR}unitdef.cpp
     ${ANTIMONY_SRC_DIR}unitelement.cpp
     ${ANTIMONY_SRC_DIR}variable.cpp
@@ -570,10 +595,10 @@ file(GLOB LIBANTIMONY_HEADERS
         ${ANTIMONY_SRC_DIR}cellmlx.h
         ${ANTIMONY_SRC_DIR}constraint.h
         ${ANTIMONY_SRC_DIR}dnastrand.h
-        ${ANTIMONY_SRC_DIR}uncertWrapper.h
         ${ANTIMONY_SRC_DIR}enums.h
         ${ANTIMONY_SRC_DIR}event.h
         ${ANTIMONY_SRC_DIR}formula.h
+        ${ANTIMONY_SRC_DIR}layoutWrapper.h
         ${ANTIMONY_SRC_DIR}libutil.h
         ${ANTIMONY_SRC_DIR}module.h
         ${ANTIMONY_SRC_DIR}reactantlist.h
@@ -583,6 +608,7 @@ file(GLOB LIBANTIMONY_HEADERS
         ${ANTIMONY_SRC_DIR}sboTermWrapper.h
         ${ANTIMONY_SRC_DIR}stringx.h
         ${ANTIMONY_SRC_DIR}typex.h
+        ${ANTIMONY_SRC_DIR}uncertWrapper.h
         ${ANTIMONY_SRC_DIR}unitdef.h
         ${ANTIMONY_SRC_DIR}unitelement.h
         ${ANTIMONY_SRC_DIR}userfunction.h

src/annotated.cpp

@@ -94,7 +94,7 @@ string Annotated::GetCreatorStringFor(const string& id) const
 {
     string ret = "";
     ModelHistory* mh = const_cast<ModelHistory*>(&m_history);
-    for (size_t v = 0; v < mh->getNumCreators(); v++) {
+    for (unsigned int v = 0; v < mh->getNumCreators(); v++) {
         string left = id + " creator" + to_string(v+1) + ".";
         ModelCreator* mc = mh->getCreator(v);
         if (mc->isSetName()) {
@@ -318,7 +318,7 @@ void Annotated::AppendNotes(const std::vector<std::string>& resources)
     }
 }
 
-bool Annotated::addCreatorInfo(int creator_number, const string& creator_substr, const vector<string>& resources)
+bool Annotated::addCreatorInfo(unsigned int creator_number, const string& creator_substr, const vector<string>& resources)
 {
     ModelCreator* creator = NULL;
     if (creator_number <= m_history.getNumCreators()) {
@@ -518,7 +518,7 @@ void Annotated::PopulateCVTerms(SBase* sbmlobj)
   if (sbmlobj->isSetCreatedDate()) {
       SetCreated(sbmlobj->getCreatedDate());
   }
-  for (size_t i = 0; i < sbmlobj->getNumModifiedDates(); i++) {
+  for (unsigned int i = 0; i < sbmlobj->getNumModifiedDates(); i++) {
       AppendModified(sbmlobj->getModifiedDate(i));
   }
   if (sbmlobj->isSetModelHistory()) {

src/annotated.h

@@ -62,7 +62,7 @@ std::vector<std::string> ResourcesToVector(const libsbml::CVTerm* t) const;
   void AppendBiolQualifiers(const libsbml::BiolQualifierType_t qual, const std::vector<std::string>& resources);
   // appends notes (just strings)
   void AppendNotes(const std::vector<std::string>& resources);
-  bool addCreatorInfo(int creator_number, const std::string& creator_substr, const std::vector<std::string>& resources);
+  bool addCreatorInfo(unsigned int creator_number, const std::string& creator_substr, const std::vector<std::string>& resources);
   void SetCreated(libsbml::Date* date);
   bool SetCreated(const std::string& date);
   bool SetCreated(const std::string& qual, const std::string& date);