Merge pull request #107 from SciML/pl/convert_promotelocals_expandfuns

use SBML converter that retains initialAssignment

Author: paulflang

Project.toml

@@ -1,7 +1,7 @@
 name = "SBMLToolkit"
 uuid = "86080e66-c8ac-44c2-a1a0-9adaadfe4a4e"
 authors = ["paulflang", "anandijain"]
-version = "0.1.19"
+version = "0.1.20"
 
 [deps]
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
@@ -12,7 +12,7 @@ SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 [compat]
 Catalyst = "12"
 MathML = "0.1"
-SBML = "1.3"
+SBML = "1.4"
 SymbolicUtils = "0.17, 0.18, 0.19"
 julia = "1.6"
 

README.md

@@ -27,7 +27,7 @@ SBML models can be simulated with the following steps (note that `sol` is in abs
   SBMLToolkit.checksupport_file("my_model.xml")
   mdl = readSBML("my_model.xml", doc -> begin
       set_level_and_version(3, 2)(doc)
-      convert_simplify_math(doc)
+      convert_promotelocals_expandfuns(doc)
   end)
 
   rs = ReactionSystem(mdl)  # If you want to create a reaction system

docs/src/index.md

@@ -22,7 +22,7 @@ using SBMLToolkit, ModelingToolkit, OrdinaryDiffEq
 SBMLToolkit.checksupport_file("my_model.xml")
 mdl = readSBML("my_model.xml", doc -> begin
     set_level_and_version(3, 2)(doc)
-    convert_simplify_math(doc)
+    convert_promotelocals_expandfuns(doc)
 end)
 rs = ReactionSystem(mdl)  # If you want to create a reaction system
 odesys = convert(ODESystem, rs)  # Alternatively: ODESystem(mdl)

src/SBMLToolkit.jl

@@ -11,7 +11,10 @@ include("rules.jl")
 include("events.jl")
 include("utils.jl")
 
+@deprecate convert_simplify_math convert_promotelocals_expandfuns
+
 export ReactionSystem, ODESystem
-export readSBML, readSBMLFromString, set_level_and_version, convert_simplify_math
+export readSBML, readSBMLFromString, set_level_and_version, convert_simplify_math,
+       convert_promotelocals_expandfuns
 
 end

test/events.jl

@@ -9,7 +9,7 @@ const IV = Catalyst.DEFAULT_IV
 function readmodel(sbml)
     SBMLToolkit.readSBMLFromString(sbml, doc -> begin
                                        set_level_and_version(3, 2)(doc)
-                                       convert_simplify_math(doc)
+                                       convert_promotelocals_expandfuns(doc)
                                    end)
 end
 

test/rules.jl

@@ -10,7 +10,7 @@ const IV = Catalyst.DEFAULT_IV
 function readmodel(sbml)
     SBMLToolkit.readSBMLFromString(sbml, doc -> begin
                                        set_level_and_version(3, 2)(doc)
-                                       convert_simplify_math(doc)
+                                       convert_promotelocals_expandfuns(doc)
                                    end)
 end
 

test/utils.jl

@@ -5,7 +5,7 @@ using Test
 function readmodel(sbml)
     SBMLToolkit.readSBMLFromString(sbml, doc -> begin
                                        set_level_and_version(3, 2)(doc)
-                                       convert_simplify_math(doc)
+                                       convert_promotelocals_expandfuns(doc)
                                    end)
 end
 

test/wuschel.jl

@@ -9,7 +9,7 @@ sbml_url = "https://www.ebi.ac.uk/biomodels/model/download/MODEL1112100000.2?fil
 sbml = String(take!(Downloads.download(sbml_url, IOBuffer())))
 m = readSBMLFromString(sbml, doc -> begin
                        # set_level_and_version(3, 2)(doc) # fails on wuschel
-                       convert_simplify_math(doc) end)
+                       convert_promotelocals_expandfuns(doc) end)
 sys = ODESystem(m)
 @test length(equations(sys)) == 1012
 @test length(states(sys)) == 1012