Merge pull request #84 from sys-bio/develop

Update version number.

CMakeLists.txt

@@ -12,7 +12,7 @@ project(libantimony)
 #
 SET(LIBANTIMONY_VERSION_MAJOR 2)
 SET(LIBANTIMONY_VERSION_MINOR 13)
-SET(LIBANTIMONY_VERSION_PATCH ".3")
+SET(LIBANTIMONY_VERSION_PATCH ".4")
 SET(LIBANTIMONY_VERSION_RELEASE "")
 
 

src/test/test-data/BIOMD0000000118.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 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 v2.13.3
+// Created by libAntimony v2.13.4
 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 v2.13.3
+// Created by libAntimony v2.13.4
 // Compartments and Species:
 compartment a;
 

src/test/test-data/SBO_event_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Events:
 E0: at time > 3: b = 4;
 

src/test/test-data/SBO_function_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 function foo()
   3;
 end

src/test/test-data/SBO_localvar_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model *foo()
 
   // Variable initializations:

src/test/test-data/SBO_module_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model *foo()
 end
 

src/test/test-data/SBO_param2_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/SBO_param_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/SBO_reaction_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Compartments and Species:
 species A;
 

src/test/test-data/SBO_species_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Compartments and Species:
 species a;
 

src/test/test-data/SBO_submodel_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model foo()
 end
 

src/test/test-data/SBO_submodel_shadowed_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model foo()
 
   // Variable initializations:

src/test/test-data/coefficientOfVariation_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/confidenceInterval_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/credibleInterval_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/default_compartment.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model *def_comp()
 
   // Compartments and Species:

src/test/test-data/distribution_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/encodes_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/externalParameter1_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/externalParameter2_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/externalParameter3_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 x = ;

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

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 
 // 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 v2.13.3
+// Created by libAntimony v2.13.4
 function get2DArrayElement(a, b, c)
   a;
 end

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

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

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

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model *testmod()
 
   // Compartments and Species:

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

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 
 // 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.

src/test/test-data/from-libsbml/test22.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test23.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test24.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test25.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test27.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Assignment Rules:

src/test/test-data/from-libsbml/test28.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test39.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test44.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test45.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Rate Rules:

src/test/test-data/from-libsbml/test46.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test47.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test48.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model moddef1()
 
   // Compartments and Species:

src/test/test-data/from-libsbml/test54.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 
 // 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.

src/test/test-data/from-libsbml/test58.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 
 // Warnings from automatic translation:
 //    Cannot replace stoichiometries in Antimony:  all replacedElements and replacedBy children of z in reaction J2 will be ignored.

src/test/test-data/from-libsbml/test59.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 
 // Warnings from automatic translation:
 //    Cannot replace stoichiometries in Antimony:  all replacedElements and replacedBy children of z in reaction J2 will be ignored.

src/test/test-data/from-libsbml/test61.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 
 // Warnings from automatic translation:
 //    Cannot replace stoichiometries in Antimony:  all replacedElements and replacedBy children of S1 in reaction R1 will be ignored.

src/test/test-data/function_name_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 function foo()
   3;
 end

src/test/test-data/hasPart_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/hasProperty_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/hasTaxon_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/hasVersion_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/identity_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/interactionActivationDashO.xml

@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!-- Created by libAntimony version v2.13.3 with libSBML version 5.19.5. -->
+<!-- Created by libAntimony version v2.13.4 with libSBML version 5.19.5. -->
 <sbml xmlns="http://www.sbml.org/sbml/level3/version2/core" level="3" version="2">
   <model metaid="__main" id="__main">
     <listOfCompartments>

src/test/test-data/interquartileRange_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 x = ;

src/test/test-data/isDescribedBy_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/isEncodedBy_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/isHomologTo_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/isPartOf_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/isPropertyOf_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/isVersionOf_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = 3;
 

src/test/test-data/kurtosis_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/mean_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/median_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/mode_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Variable initializations:
 a = ;
 

src/test/test-data/module_name_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 model *foo()
 
   // Variable initializations:

src/test/test-data/namedstoich_assignment_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Compartments and Species:
 species a;
 

src/test/test-data/namedstoich_basic_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Compartments and Species:
 species a;
 

src/test/test-data/namedstoich_rate_rt.txt

@@ -1,4 +1,4 @@
-// Created by libAntimony v2.13.3
+// Created by libAntimony v2.13.4
 // Compartments and Species:
 species a;