diff --git a/CMakeLists.txt b/CMakeLists.txt index bf7fc49d..9349c976 100644 --- a/CMakeLists.txt +++ b/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 "") diff --git a/src/antimony_api.cpp b/src/antimony_api.cpp index 21313d55..d23bb068 100644 --- a/src/antimony_api.cpp +++ b/src/antimony_api.cpp @@ -11,6 +11,7 @@ #include #include #include +#include #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(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()); diff --git a/src/antimony_api.h b/src/antimony_api.h index 182a5f6d..ffd6c7af 100644 --- a/src/antimony_api.h +++ b/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); + /** \} */ diff --git a/src/bindings/python/createAntimonyLib.py b/src/bindings/python/createAntimonyLib.py index 68ccd23d..17fadbca 100644 --- a/src/bindings/python/createAntimonyLib.py +++ b/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(" ") diff --git a/src/registry.cpp b/src/registry.cpp index 425a5082..82754f62 100644 --- a/src/registry.cpp +++ b/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* resources) { if (name && qual && resources) { diff --git a/src/registry.h b/src/registry.h index 035624f8..b727f0ac 100644 --- a/src/registry.h +++ b/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* resources); diff --git a/src/test/TestRunner.cpp b/src/test/TestRunner.cpp index f0129d1f..9f4e1542 100644 --- a/src/test/TestRunner.cpp +++ b/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(); diff --git a/src/test/test-data/BIOMD0000000118.txt b/src/test/test-data/BIOMD0000000118.txt index 3b0dc7d4..8b19950a 100644 --- a/src/test/test-data/BIOMD0000000118.txt +++ b/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 diff --git a/src/test/test-data/BIOMD0000000696.txt b/src/test/test-data/BIOMD0000000696.txt index 230bec0e..ba00a07b 100644 --- a/src/test/test-data/BIOMD0000000696.txt +++ b/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: diff --git a/src/test/test-data/SBO_compartment_rt.txt b/src/test/test-data/SBO_compartment_rt.txt index 893bc833..bfcf1567 100644 --- a/src/test/test-data/SBO_compartment_rt.txt +++ b/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; diff --git a/src/test/test-data/SBO_event_rt.txt b/src/test/test-data/SBO_event_rt.txt index c8fc6464..8910d8b7 100644 --- a/src/test/test-data/SBO_event_rt.txt +++ b/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; diff --git a/src/test/test-data/SBO_function_rt.txt b/src/test/test-data/SBO_function_rt.txt index ce0cf781..9cef8757 100644 --- a/src/test/test-data/SBO_function_rt.txt +++ b/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 diff --git a/src/test/test-data/SBO_localvar_rt.txt b/src/test/test-data/SBO_localvar_rt.txt index 2f6bb658..965624b0 100644 --- a/src/test/test-data/SBO_localvar_rt.txt +++ b/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: diff --git a/src/test/test-data/SBO_module_rt.txt b/src/test/test-data/SBO_module_rt.txt index 49a5acec..d22b3946 100644 --- a/src/test/test-data/SBO_module_rt.txt +++ b/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 diff --git a/src/test/test-data/SBO_param2_rt.txt b/src/test/test-data/SBO_param2_rt.txt index 83bc0ffb..8467aa81 100644 --- a/src/test/test-data/SBO_param2_rt.txt +++ b/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; diff --git a/src/test/test-data/SBO_param_rt.txt b/src/test/test-data/SBO_param_rt.txt index b7b7a282..8b642efa 100644 --- a/src/test/test-data/SBO_param_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/SBO_reaction_rt.txt b/src/test/test-data/SBO_reaction_rt.txt index b17519b9..3ebf09a5 100644 --- a/src/test/test-data/SBO_reaction_rt.txt +++ b/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; diff --git a/src/test/test-data/SBO_species_rt.txt b/src/test/test-data/SBO_species_rt.txt index 7b176627..b05e266f 100644 --- a/src/test/test-data/SBO_species_rt.txt +++ b/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; diff --git a/src/test/test-data/SBO_submodel_rt.txt b/src/test/test-data/SBO_submodel_rt.txt index 5c64de9d..8f089c16 100644 --- a/src/test/test-data/SBO_submodel_rt.txt +++ b/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 diff --git a/src/test/test-data/SBO_submodel_shadowed_rt.txt b/src/test/test-data/SBO_submodel_shadowed_rt.txt index a45de965..370ee915 100644 --- a/src/test/test-data/SBO_submodel_shadowed_rt.txt +++ b/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: diff --git a/src/test/test-data/algrule_id_rt.txt b/src/test/test-data/algrule_id_rt.txt index cd4a3d0e..8040f1a4 100644 --- a/src/test/test-data/algrule_id_rt.txt +++ b/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; diff --git a/src/test/test-data/algrule_idname_rt.txt b/src/test/test-data/algrule_idname_rt.txt index 31b50196..0b7f48e2 100644 --- a/src/test/test-data/algrule_idname_rt.txt +++ b/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; diff --git a/src/test/test-data/algrule_rt.txt b/src/test/test-data/algrule_rt.txt index 2b6806b0..d888c70b 100644 --- a/src/test/test-data/algrule_rt.txt +++ b/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; diff --git a/src/test/test-data/autopromoted_units_rt.txt b/src/test/test-data/autopromoted_units_rt.txt index 4691fdd1..fe276d28 100644 --- a/src/test/test-data/autopromoted_units_rt.txt +++ b/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: diff --git a/src/test/test-data/coefficientOfVariation_rt.txt b/src/test/test-data/coefficientOfVariation_rt.txt index 4d398f67..ece5305a 100644 --- a/src/test/test-data/coefficientOfVariation_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/confidenceInterval_rt.txt b/src/test/test-data/confidenceInterval_rt.txt index 08cbd46b..4c262e96 100644 --- a/src/test/test-data/confidenceInterval_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/created_element_rt.txt b/src/test/test-data/created_element_rt.txt index 57170add..0a646001 100644 --- a/src/test/test-data/created_element_rt.txt +++ b/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; diff --git a/src/test/test-data/created_model_parts_rt.txt b/src/test/test-data/created_model_parts_rt.txt index 22eb6f9f..dc17d771 100644 --- a/src/test/test-data/created_model_parts_rt.txt +++ b/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: diff --git a/src/test/test-data/created_model_rt.txt b/src/test/test-data/created_model_rt.txt index 22eb6f9f..dc17d771 100644 --- a/src/test/test-data/created_model_rt.txt +++ b/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: diff --git a/src/test/test-data/creator_blank_model_rt.txt b/src/test/test-data/creator_blank_model_rt.txt index 80637806..06eab890 100644 --- a/src/test/test-data/creator_blank_model_rt.txt +++ b/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: diff --git a/src/test/test-data/creator_one_element_rt.txt b/src/test/test-data/creator_one_element_rt.txt index 6f2f4917..c82f8368 100644 --- a/src/test/test-data/creator_one_element_rt.txt +++ b/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; diff --git a/src/test/test-data/creator_one_model_rt.txt b/src/test/test-data/creator_one_model_rt.txt index f4b3a359..8015083b 100644 --- a/src/test/test-data/creator_one_model_rt.txt +++ b/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: diff --git a/src/test/test-data/creator_two_model_rt.txt b/src/test/test-data/creator_two_model_rt.txt index 5d607937..ed8b01a2 100644 --- a/src/test/test-data/creator_two_model_rt.txt +++ b/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: diff --git a/src/test/test-data/credibleInterval_rt.txt b/src/test/test-data/credibleInterval_rt.txt index 6a9ef3ee..b0e84bc1 100644 --- a/src/test/test-data/credibleInterval_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/default_compartment.txt b/src/test/test-data/default_compartment.txt index d16c276c..3980c57d 100644 --- a/src/test/test-data/default_compartment.txt +++ b/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: diff --git a/src/test/test-data/distribution_rt.txt b/src/test/test-data/distribution_rt.txt index ac063b7f..8a9caaaa 100644 --- a/src/test/test-data/distribution_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/encodes_rt.txt b/src/test/test-data/encodes_rt.txt index 88eeaf38..8c4c3466 100644 --- a/src/test/test-data/encodes_rt.txt +++ b/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; diff --git a/src/test/test-data/externalParameter1_rt.txt b/src/test/test-data/externalParameter1_rt.txt index e4ba8866..6014db5f 100644 --- a/src/test/test-data/externalParameter1_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/externalParameter2_rt.txt b/src/test/test-data/externalParameter2_rt.txt index 2f21ad3e..920c605d 100644 --- a/src/test/test-data/externalParameter2_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/externalParameter3_rt.txt b/src/test/test-data/externalParameter3_rt.txt index 442e1732..96a77a41 100644 --- a/src/test/test-data/externalParameter3_rt.txt +++ b/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 = ; diff --git a/src/test/test-data/from-libsbml/CompTest.txt b/src/test/test-data/from-libsbml/CompTest.txt index 14617903..026247dd 100644 --- a/src/test/test-data/from-libsbml/CompTest.txt +++ b/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. diff --git a/src/test/test-data/from-libsbml/QTPop.txt b/src/test/test-data/from-libsbml/QTPop.txt index 387f7aaa..8a10f0a1 100644 --- a/src/test/test-data/from-libsbml/QTPop.txt +++ b/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 diff --git a/src/test/test-data/from-libsbml/comp.txt b/src/test/test-data/from-libsbml/comp.txt index ebea430f..9f42f59e 100644 --- a/src/test/test-data/from-libsbml/comp.txt +++ b/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: diff --git a/src/test/test-data/from-libsbml/exchangetest.txt b/src/test/test-data/from-libsbml/exchangetest.txt index dbd88fba..6fbd97d0 100644 --- a/src/test/test-data/from-libsbml/exchangetest.txt +++ b/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: diff --git a/src/test/test-data/from-libsbml/replace_rules_and_constraints.txt b/src/test/test-data/from-libsbml/replace_rules_and_constraints.txt index 36f95ad4..89a3f1d7 100644 --- a/src/test/test-data/from-libsbml/replace_rules_and_constraints.txt +++ b/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. diff --git a/src/test/test-data/from-libsbml/test22.txt b/src/test/test-data/from-libsbml/test22.txt index 3e60b6ab..f39e8276 100644 --- a/src/test/test-data/from-libsbml/test22.txt +++ b/src/test/test-data/from-libsbml/test22.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test23.txt b/src/test/test-data/from-libsbml/test23.txt index 4091a524..08752ad4 100644 --- a/src/test/test-data/from-libsbml/test23.txt +++ b/src/test/test-data/from-libsbml/test23.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test24.txt b/src/test/test-data/from-libsbml/test24.txt index c91bd61b..2a318017 100644 --- a/src/test/test-data/from-libsbml/test24.txt +++ b/src/test/test-data/from-libsbml/test24.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test25.txt b/src/test/test-data/from-libsbml/test25.txt index 10957169..bb1e98a4 100644 --- a/src/test/test-data/from-libsbml/test25.txt +++ b/src/test/test-data/from-libsbml/test25.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test27.txt b/src/test/test-data/from-libsbml/test27.txt index 983933c8..43e7b33c 100644 --- a/src/test/test-data/from-libsbml/test27.txt +++ b/src/test/test-data/from-libsbml/test27.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Assignment Rules: diff --git a/src/test/test-data/from-libsbml/test28.txt b/src/test/test-data/from-libsbml/test28.txt index 6bd49bd0..eb93a659 100644 --- a/src/test/test-data/from-libsbml/test28.txt +++ b/src/test/test-data/from-libsbml/test28.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test39.txt b/src/test/test-data/from-libsbml/test39.txt index 583dc7d9..ad938430 100644 --- a/src/test/test-data/from-libsbml/test39.txt +++ b/src/test/test-data/from-libsbml/test39.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test44.txt b/src/test/test-data/from-libsbml/test44.txt index 5103c48e..205cae2a 100644 --- a/src/test/test-data/from-libsbml/test44.txt +++ b/src/test/test-data/from-libsbml/test44.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test45.txt b/src/test/test-data/from-libsbml/test45.txt index f0dbfbbb..359550e8 100644 --- a/src/test/test-data/from-libsbml/test45.txt +++ b/src/test/test-data/from-libsbml/test45.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Rate Rules: diff --git a/src/test/test-data/from-libsbml/test46.txt b/src/test/test-data/from-libsbml/test46.txt index 33789843..abc21468 100644 --- a/src/test/test-data/from-libsbml/test46.txt +++ b/src/test/test-data/from-libsbml/test46.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test47.txt b/src/test/test-data/from-libsbml/test47.txt index 1323c772..78fbfe00 100644 --- a/src/test/test-data/from-libsbml/test47.txt +++ b/src/test/test-data/from-libsbml/test47.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test48.txt b/src/test/test-data/from-libsbml/test48.txt index de0bf6cc..353ebd06 100644 --- a/src/test/test-data/from-libsbml/test48.txt +++ b/src/test/test-data/from-libsbml/test48.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model moddef1() // Compartments and Species: diff --git a/src/test/test-data/from-libsbml/test54.txt b/src/test/test-data/from-libsbml/test54.txt index 8876355b..168df5c8 100644 --- a/src/test/test-data/from-libsbml/test54.txt +++ b/src/test/test-data/from-libsbml/test54.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Warnings from automatic translation: // Unable to process deletion from submodel B in model baz. Deletions of Deletion elements have not been added as a concept in Antimony. diff --git a/src/test/test-data/from-libsbml/test58.txt b/src/test/test-data/from-libsbml/test58.txt index 946af420..6de80f75 100644 --- a/src/test/test-data/from-libsbml/test58.txt +++ b/src/test/test-data/from-libsbml/test58.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Warnings from automatic translation: // Cannot replace stoichiometries in Antimony: all replacedElements and replacedBy children of z in reaction J2 will be ignored. diff --git a/src/test/test-data/from-libsbml/test59.txt b/src/test/test-data/from-libsbml/test59.txt index 7a7d4585..01cb3d1a 100644 --- a/src/test/test-data/from-libsbml/test59.txt +++ b/src/test/test-data/from-libsbml/test59.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Warnings from automatic translation: // Cannot replace stoichiometries in Antimony: all replacedElements and replacedBy children of z in reaction J2 will be ignored. diff --git a/src/test/test-data/from-libsbml/test61.txt b/src/test/test-data/from-libsbml/test61.txt index d4a16b03..80efd40e 100644 --- a/src/test/test-data/from-libsbml/test61.txt +++ b/src/test/test-data/from-libsbml/test61.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Warnings from automatic translation: // Cannot replace stoichiometries in Antimony: all replacedElements and replacedBy children of S1 in reaction R1 will be ignored. diff --git a/src/test/test-data/function_name_rt.txt b/src/test/test-data/function_name_rt.txt index 4888c4ed..95f109b5 100644 --- a/src/test/test-data/function_name_rt.txt +++ b/src/test/test-data/function_name_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 function foo() 3; end diff --git a/src/test/test-data/hasPart_rt.txt b/src/test/test-data/hasPart_rt.txt index c6bd49ee..708dbaac 100644 --- a/src/test/test-data/hasPart_rt.txt +++ b/src/test/test-data/hasPart_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/hasProperty_rt.txt b/src/test/test-data/hasProperty_rt.txt index 970c2f58..89558ca7 100644 --- a/src/test/test-data/hasProperty_rt.txt +++ b/src/test/test-data/hasProperty_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/hasTaxon_rt.txt b/src/test/test-data/hasTaxon_rt.txt index e07c8879..69aca9d9 100644 --- a/src/test/test-data/hasTaxon_rt.txt +++ b/src/test/test-data/hasTaxon_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/hasVersion_rt.txt b/src/test/test-data/hasVersion_rt.txt index db1bcc11..9abf9423 100644 --- a/src/test/test-data/hasVersion_rt.txt +++ b/src/test/test-data/hasVersion_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/identity_rt.txt b/src/test/test-data/identity_rt.txt index c8a7f550..d75a812b 100644 --- a/src/test/test-data/identity_rt.txt +++ b/src/test/test-data/identity_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/interquartileRange_rt.txt b/src/test/test-data/interquartileRange_rt.txt index 06a280ab..f407cba9 100644 --- a/src/test/test-data/interquartileRange_rt.txt +++ b/src/test/test-data/interquartileRange_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; x = ; diff --git a/src/test/test-data/isDescribedBy_rt.txt b/src/test/test-data/isDescribedBy_rt.txt index de92bed1..bb83ee8c 100644 --- a/src/test/test-data/isDescribedBy_rt.txt +++ b/src/test/test-data/isDescribedBy_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isEncodedBy_rt.txt b/src/test/test-data/isEncodedBy_rt.txt index c3566e1e..61f646cf 100644 --- a/src/test/test-data/isEncodedBy_rt.txt +++ b/src/test/test-data/isEncodedBy_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isHomologTo_rt.txt b/src/test/test-data/isHomologTo_rt.txt index 2d172407..9310eabc 100644 --- a/src/test/test-data/isHomologTo_rt.txt +++ b/src/test/test-data/isHomologTo_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isPartOf_rt.txt b/src/test/test-data/isPartOf_rt.txt index 97c28497..7df39f3e 100644 --- a/src/test/test-data/isPartOf_rt.txt +++ b/src/test/test-data/isPartOf_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isPropertyOf_rt.txt b/src/test/test-data/isPropertyOf_rt.txt index 9c8351d7..5d1cdd68 100644 --- a/src/test/test-data/isPropertyOf_rt.txt +++ b/src/test/test-data/isPropertyOf_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/isVersionOf_rt.txt b/src/test/test-data/isVersionOf_rt.txt index 24f4dd8a..72bc9d78 100644 --- a/src/test/test-data/isVersionOf_rt.txt +++ b/src/test/test-data/isVersionOf_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/kurtosis_rt.txt b/src/test/test-data/kurtosis_rt.txt index 5a9c766d..f5dd58f1 100644 --- a/src/test/test-data/kurtosis_rt.txt +++ b/src/test/test-data/kurtosis_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/mean_rt.txt b/src/test/test-data/mean_rt.txt index 8ef2f246..9c7dbafa 100644 --- a/src/test/test-data/mean_rt.txt +++ b/src/test/test-data/mean_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/median_rt.txt b/src/test/test-data/median_rt.txt index df9d48db..a8298eb1 100644 --- a/src/test/test-data/median_rt.txt +++ b/src/test/test-data/median_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/mode_rt.txt b/src/test/test-data/mode_rt.txt index b4bcdde7..a5867670 100644 --- a/src/test/test-data/mode_rt.txt +++ b/src/test/test-data/mode_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/modified_element_rt.txt b/src/test/test-data/modified_element_rt.txt index d24c9152..99bade4f 100644 --- a/src/test/test-data/modified_element_rt.txt +++ b/src/test/test-data/modified_element_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/modified_model_parts_rt.txt b/src/test/test-data/modified_model_parts_rt.txt index 57b3cc32..3ff85392 100644 --- a/src/test/test-data/modified_model_parts_rt.txt +++ b/src/test/test-data/modified_model_parts_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/modified_model_rt.txt b/src/test/test-data/modified_model_rt.txt index 57b3cc32..3ff85392 100644 --- a/src/test/test-data/modified_model_rt.txt +++ b/src/test/test-data/modified_model_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/module_name_rt.txt b/src/test/test-data/module_name_rt.txt index 10418abe..76b84be3 100644 --- a/src/test/test-data/module_name_rt.txt +++ b/src/test/test-data/module_name_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/namedstoich_assignment_rt.txt b/src/test/test-data/namedstoich_assignment_rt.txt index f042c67b..44d659a6 100644 --- a/src/test/test-data/namedstoich_assignment_rt.txt +++ b/src/test/test-data/namedstoich_assignment_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Compartments and Species: species a; diff --git a/src/test/test-data/namedstoich_basic_rt.txt b/src/test/test-data/namedstoich_basic_rt.txt index 0effeed8..9fa3f7f4 100644 --- a/src/test/test-data/namedstoich_basic_rt.txt +++ b/src/test/test-data/namedstoich_basic_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Compartments and Species: species a; diff --git a/src/test/test-data/namedstoich_rate_rt.txt b/src/test/test-data/namedstoich_rate_rt.txt index 44f6a8bf..d096db1b 100644 --- a/src/test/test-data/namedstoich_rate_rt.txt +++ b/src/test/test-data/namedstoich_rate_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Compartments and Species: species a; diff --git a/src/test/test-data/namedstoich_value_rt.txt b/src/test/test-data/namedstoich_value_rt.txt index 8b3c7cd7..e4559210 100644 --- a/src/test/test-data/namedstoich_value_rt.txt +++ b/src/test/test-data/namedstoich_value_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Compartments and Species: species a; diff --git a/src/test/test-data/negparen_rt.txt b/src/test/test-data/negparen_rt.txt index 4e4f0714..97fdbd24 100644 --- a/src/test/test-data/negparen_rt.txt +++ b/src/test/test-data/negparen_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = -(x + 2); x = ; diff --git a/src/test/test-data/notes_element_noxml_rt.txt b/src/test/test-data/notes_element_noxml_rt.txt index ea6b053d..99f0dec3 100644 --- a/src/test/test-data/notes_element_noxml_rt.txt +++ b/src/test/test-data/notes_element_noxml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/notes_element_xml_rt.txt b/src/test/test-data/notes_element_xml_rt.txt index 3c5747c7..2950affa 100644 --- a/src/test/test-data/notes_element_xml_rt.txt +++ b/src/test/test-data/notes_element_xml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/notes_model_noxml_rt.txt b/src/test/test-data/notes_model_noxml_rt.txt index 4496b732..ddcb7b45 100644 --- a/src/test/test-data/notes_model_noxml_rt.txt +++ b/src/test/test-data/notes_model_noxml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model *foo() // Variable initializations: diff --git a/src/test/test-data/notes_model_xml_internal_rt.txt b/src/test/test-data/notes_model_xml_internal_rt.txt index 48c8b9d3..ff12db49 100644 --- a/src/test/test-data/notes_model_xml_internal_rt.txt +++ b/src/test/test-data/notes_model_xml_internal_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model *MorrisonAllegra() // Variable initializations: diff --git a/src/test/test-data/notes_model_xml_rt.txt b/src/test/test-data/notes_model_xml_rt.txt index 955bb6eb..8b1ac7b9 100644 --- a/src/test/test-data/notes_model_xml_rt.txt +++ b/src/test/test-data/notes_model_xml_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model *MorrisonAllegra() // Variable initializations: diff --git a/src/test/test-data/occursIn_rt.txt b/src/test/test-data/occursIn_rt.txt index e9558086..b016da03 100644 --- a/src/test/test-data/occursIn_rt.txt +++ b/src/test/test-data/occursIn_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = 3; diff --git a/src/test/test-data/range_rt.txt b/src/test/test-data/range_rt.txt index d5f618f7..ba4632f0 100644 --- a/src/test/test-data/range_rt.txt +++ b/src/test/test-data/range_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/same_unit_name.txt b/src/test/test-data/same_unit_name.txt index 50b17945..0adcabae 100644 --- a/src/test/test-data/same_unit_name.txt +++ b/src/test/test-data/same_unit_name.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 model *same_units() // Variable initializations: diff --git a/src/test/test-data/sampleSize_rt.txt b/src/test/test-data/sampleSize_rt.txt index c7129fed..2fe03860 100644 --- a/src/test/test-data/sampleSize_rt.txt +++ b/src/test/test-data/sampleSize_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/skewness_rt.txt b/src/test/test-data/skewness_rt.txt index 73ac89eb..7413d906 100644 --- a/src/test/test-data/skewness_rt.txt +++ b/src/test/test-data/skewness_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/standardDeviation_rt.txt b/src/test/test-data/standardDeviation_rt.txt index 5a2f63cc..5ca7f1c3 100644 --- a/src/test/test-data/standardDeviation_rt.txt +++ b/src/test/test-data/standardDeviation_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/standardError_rt.txt b/src/test/test-data/standardError_rt.txt index e538ec45..6cbc1d99 100644 --- a/src/test/test-data/standardError_rt.txt +++ b/src/test/test-data/standardError_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/variance_rt.txt b/src/test/test-data/variance_rt.txt index ce006dbe..6dc3baa3 100644 --- a/src/test/test-data/variance_rt.txt +++ b/src/test/test-data/variance_rt.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: a = ; diff --git a/src/test/test-data/volume.txt b/src/test/test-data/volume.txt index 4ed0951c..7e8942d0 100644 --- a/src/test/test-data/volume.txt +++ b/src/test/test-data/volume.txt @@ -1,4 +1,4 @@ -// Created by libAntimony v2.14.0 +// Created by libAntimony v2.15.0 // Variable initializations: volume_ = 1; A = volume_*5;