Add layout render

.github/workflows/main.yml

@@ -15,15 +15,15 @@ jobs:
       fail-fast: false
       matrix:
         platform:
-          - name: macos-12-release
+          - name: macos-13-release
             os_type: macos
-            os_name: macos-12
+            os_name: macos-13
             build_type: Release
             build_python: ON
             build_qt_antimony: ON
-          - name: macos-12-debug
+          - name: macos-13-debug
             os_type: macos
-            os_name: macos-12
+            os_name: macos-13
             build_type: Debug
             build_python: ON
             build_qt_antimony: ON
@@ -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: [ "v2.2.13" ]
         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
@@ -267,7 +267,7 @@ endif()
 if(WITH_LIBSBML_LIBXML)
     find_library(LIBXML_LIBRARY
         NAMES libxml2.lib libxml2.so libxml2.dylib libxml2 libxml2s libxml2sd
-	PATHS /usr/lib /usr/local/lib
+        PATHS /usr/lib /usr/local/lib
               ${CMAKE_SOURCE_DIR}
               ${CMAKE_SOURCE_DIR}/dependencies/lib
               ${LIBSBML_INCLUDE_DIR}/../lib
@@ -276,8 +276,8 @@ if(WITH_LIBSBML_LIBXML)
 
     #The libxml library requires the libz library, too.
     find_library(ZDLL_LIBRARY
-        NAMES zdll.lib zdll.so zdll.dylib zdll z zlibd.lib zlibstaticd.lib zlibmd.lib zlibstatic.lib
-	PATHS /usr/lib /usr/local/lib
+        NAMES zlibstatic.lib zlibstaticd.lib zlibstaticmd.lib zlibstatic zlibstaticd zlibstaticmd libz.a libz
+        PATHS /usr/lib /usr/local/lib
               ${CMAKE_SOURCE_DIR}
               ${CMAKE_SOURCE_DIR}/dependencies/lib
               ${LIBSBML_INCLUDE_DIR}/../lib
@@ -318,7 +318,7 @@ endif()
 
 if(WITH_LIBSBML_COMPRESSION)
     find_library(ZDLL_LIBRARY
-        NAMES zdll.lib zdll.so zdll.dylib zdll z zlibd.lib zlibstaticd.lib zlibmd.lib zlibstatic.lib
+    NAMES zlibstatic.lib zlibstaticd.lib zlibstaticmd.lib zlibstatic zlibstaticd zlibstaticmd zdll.lib zdll.so zdll.dylib zdll z libz.a 
 	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 sbmlnetwork/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