Remove function definitions

CMakeLists.txt

@@ -11,7 +11,7 @@ project(libantimony)
 # Set up version information.
 #
 SET(LIBANTIMONY_VERSION_MAJOR 2)
-SET(LIBANTIMONY_VERSION_MINOR 14)
+SET(LIBANTIMONY_VERSION_MINOR 15)
 SET(LIBANTIMONY_VERSION_PATCH ".0")
 SET(LIBANTIMONY_VERSION_RELEASE "")
 

src/antimony_api.cpp

@@ -11,6 +11,7 @@
 #include <sbml/SBMLTypes.h>
 #include <sbml/xml/XMLOutputStream.h>
 #include <sbml/Model.h>
+#include <sbml/conversion/SBMLFunctionDefinitionConverter.h>
 #endif
 
 #ifndef NCELLML
@@ -306,6 +307,12 @@ LIB_EXTERN long loadAntimonyFile(const char* filename)
 #ifndef NSBML
 void LoadSBML(SBMLDocument* doc)
 {
+    if (g_registry.GetRemoveFunctionDefinitions()) {
+        SBMLConverter* converter = new SBMLFunctionDefinitionConverter();
+        converter->setDocument(doc);
+        int cret = converter->convert();
+
+    }
 #ifdef USE_COMP
   string mainsbmlname = getNameFromSBMLObject(doc->getModel(), "doc");
   CompSBMLDocumentPlugin* compdoc = static_cast<CompSBMLDocumentPlugin*>(doc->getPlugin("comp"));
@@ -556,16 +563,21 @@ LIB_EXTERN void clearPreviousLoads()
   g_registry.ClearAll();
 }
 
-LIB_EXTERN void   addDirectory(const char* directory)
+LIB_EXTERN void addDirectory(const char* directory)
 {
   g_registry.AddDirectory(directory);
 }
 
-LIB_EXTERN void   clearDirectories()
+LIB_EXTERN void clearDirectories()
 {
   g_registry.ClearDirectories();
 }
 
+LIB_EXTERN void setRemoveFunctionDefinitions(bool removeFunctionDefinitions)
+{
+    g_registry.SetRemoveFunctionDefinitions(removeFunctionDefinitions);
+}
+
 LIB_EXTERN char* getLastError()
 {
   return getCharStar((g_registry.GetError()).c_str());

src/antimony_api.h

@@ -127,10 +127,12 @@ LIB_EXTERN long   loadAntimonyString(const char* model);
  * Loads a file and parses it (using libSBML) as an SBML file.  On an error, the error is saved, -1 is returned, and no information is stored.
  * @return a long integer indicating the index of the file read and stored.  On an error, returns -1 and no information is stored.
  * NOTE:  This function is unavailable when libAntimony is compiled with the '-NSBML' flag.
+ * Also note that by default, function definitions are removed.
  *
  * @param filename The filename as a character string.  May be either absolute or relative to the directory the executable is being run from.
  *
  * @see getLastError()
+ * @see setRemoveFunctionDefinitions()
  */
 LIB_EXTERN long   loadSBMLFile(const char* filename);
 
@@ -140,10 +142,12 @@ LIB_EXTERN long   loadSBMLFile(const char* filename);
  * Loads a string and parses it (using libSBML) as an SBML file.  On an error, the error is saved, -1 is returned, and no information is stored.
  * @return a long integer indicating the index of the string read and stored.  On an error, returns -1 and no information is stored.
  * NOTE:  This function is unavailable when libAntimony is compiled with the '-NSBML' flag.
+ * Also note that by default, function definitions are removed.
  *
  * @param model The model, in SBML format.
  *
  * @see getLastError()
+ * @see setRemoveFunctionDefinitions()
  */
 LIB_EXTERN long   loadSBMLString(const char* model);
 
@@ -153,11 +157,13 @@ LIB_EXTERN long   loadSBMLString(const char* model);
  * Loads a string and parses it (using libSBML) as an SBML file.  On an error, the error is saved, -1 is returned, and no information is stored.  This function additionally allows you to set the location of the string, in case there are relative file references in the file (as there can be in some hierarchical models).
  * @return a long integer indicating the index of the string read and stored.  On an error, returns -1 and no information is stored.
  * NOTE:  This function is unavailable when libAntimony is compiled with the '-NSBML' flag.
+ * Also note that by default, function definitions are removed.
  *
  * @param model The model, in SBML format.
  * @param location The location of the file (i.e. "file1.xml" or "/home/user/sbml/models/file.xml")
  *
  * @see getLastError()
+ * @see setRemoveFunctionDefinitions()
  */
 LIB_EXTERN long   loadSBMLStringWithLocation(const char* model, const char* location);
 #endif
@@ -221,6 +227,12 @@ LIB_EXTERN void   addDirectory(const char* directory);
  */
 LIB_EXTERN void   clearDirectories();
 
+/**
+ * Sets whether to remove function definitions on import from SBML.
+ * By default, is set to 'true'.
+ */
+LIB_EXTERN void   setRemoveFunctionDefinitions(bool removeFunctionDefinitions);
+
 
 /** \} */
 

src/bindings/python/createAntimonyLib.py

@@ -106,6 +106,7 @@ def parse_function(line, comment, functions):
    args = []
    for onearg in argvec:
       onearg = onearg.strip()
+      onearg = onearg.replace(" = false", "")
       if len(onearg)==0:
          continue
       lastspace = onearg.rfind(" ")

src/registry.cpp

@@ -52,6 +52,7 @@ Registry::Registry()
     m_writeTimestampToSBML(false),
     m_bareNumbersAreDimensionless(false),
     m_eof(false),
+    m_removeFunctionDefinitions(true),
     input(NULL)
 {
   string main = MAINMODULE;
@@ -1450,6 +1451,16 @@ void Registry::FixTimeInFunctions()
   }
 }
 
+void Registry::SetRemoveFunctionDefinitions(bool removeFunctionDefinitions)
+{
+    m_removeFunctionDefinitions = removeFunctionDefinitions;
+}
+
+bool Registry::GetRemoveFunctionDefinitions()
+{
+    return m_removeFunctionDefinitions;
+}
+
 bool Registry::ProcessGlobalCVTerm(const string* name, const string* qual, vector<string>* resources)
 {
   if (name && qual && resources) {

src/registry.h

@@ -70,6 +70,8 @@ class Registry
   bool m_bareNumbersAreDimensionless;
   bool m_eof;
 
+  bool m_removeFunctionDefinitions;
+
 public:
   Registry();
   ~Registry();
@@ -199,6 +201,9 @@ class Registry
   UserFunction* GetUserFunction(std::string name);
   void FixTimeInFunctions();
 
+  void SetRemoveFunctionDefinitions(bool removeFunctionDefinitions);
+  bool GetRemoveFunctionDefinitions();
+
   // CV terms
   bool ProcessGlobalCVTerm(const std::string* name, const std::string* qual, std::vector<std::string>* resources);
 

src/test/TestRunner.cpp

@@ -120,6 +120,7 @@ main (int argc, char* argv[])
 { 
   int num_failed;
   g_registry.SetWriteNameToSBML(false);
+  g_registry.SetRemoveFunctionDefinitions(false);
 
   setTestDataDirectory();
 

src/test/test-data/BIOMD0000000118.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 function GAMMA(VV, theta, sigma)
   1/(1 + exp(-(VV - theta)/sigma));
 end

src/test/test-data/BIOMD0000000696.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *Boada2016___Incoherent_type_1_feed_forward_loop__I1_FFL()
 
   // Compartments and Species:

src/test/test-data/SBO_compartment_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Compartments and Species:
 compartment a;
 

src/test/test-data/SBO_event_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Events:
 E0: at time > 3: b = 4;
 

src/test/test-data/SBO_function_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 function foo()
   3;
 end

src/test/test-data/SBO_localvar_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *foo()
 
   // Variable initializations:

src/test/test-data/SBO_module_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *foo()
 end
 

src/test/test-data/SBO_param2_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = 3;
 

src/test/test-data/SBO_param_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 

src/test/test-data/SBO_reaction_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Compartments and Species:
 species A;
 

src/test/test-data/SBO_species_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Compartments and Species:
 species a;
 

src/test/test-data/SBO_submodel_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model foo()
 end
 

src/test/test-data/SBO_submodel_shadowed_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model foo()
 
   // Variable initializations:

src/test/test-data/algrule_id_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Algebraic Rules:
 alg1: 0 = x - 2;
 

src/test/test-data/algrule_idname_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Algebraic Rules:
 alg1: 0 = x - 2;
 

src/test/test-data/algrule_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Algebraic Rules:
 _alg0: 0 = x - 2;
 

src/test/test-data/autopromoted_units_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model foo(p)
 
   // Variable initializations:

src/test/test-data/coefficientOfVariation_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 

src/test/test-data/confidenceInterval_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 

src/test/test-data/created_element_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = 3;
 

src/test/test-data/created_model_parts_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *foo()
 
   // Variable initializations:

src/test/test-data/created_model_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *foo()
 
   // Variable initializations:

src/test/test-data/creator_blank_model_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *foo()
 
   // Variable initializations:

src/test/test-data/creator_one_element_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = 3;
 

src/test/test-data/creator_one_model_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *foo()
 
   // Variable initializations:

src/test/test-data/creator_two_model_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *foo()
 
   // Variable initializations:

src/test/test-data/credibleInterval_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/default_compartment.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *def_comp()
 
   // Compartments and Species:

src/test/test-data/distribution_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/encodes_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = 3;
 

src/test/test-data/externalParameter1_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 

src/test/test-data/externalParameter2_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/externalParameter3_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/from-libsbml/CompTest.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 
 // Warnings from automatic translation:
 //    Unable to create port constraint__constraint0 in model CompModel because Constraint elements do not have IDs in SBML, and therefore cannot be made into ports in Antimony.

src/test/test-data/from-libsbml/QTPop.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 function get2DArrayElement(a, b, c)
   a;
 end

src/test/test-data/from-libsbml/comp.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/exchangetest.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 model *testmod()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/replace_rules_and_constraints.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.14.0
+// Created by libAntimony v2.15.0
 
 // Warnings from automatic translation:
 //    Unable to create port rule__iBioSim7 in model CompModel because RateRule elements only exist as part of other Antimony elements, and do not function as their own separate entities which may be flagged as a port.