don't automatically complete systems on read

docs/src/index.md

@@ -45,7 +45,7 @@ mdl = readSBML("my_model.xml", doc -> begin
     set_level_and_version(3, 2)(doc)
     convert_promotelocals_expandfuns(doc)
 end)
-rs = ReactionSystem(mdl)  # If you want to create a reaction system
+rs = complete(ReactionSystem(mdl))  # If you want to create a reaction system
 odesys = convert(ODESystem, rs)  # Alternatively: ODESystem(mdl)
 
 tspan = (0.0, 1.0)

src/systems.jl

@@ -41,7 +41,6 @@ function SBML.readSBML(sbmlfile::String, ::ODESystemImporter;
         include_zero_odes::Bool = true, kwargs...)  # Returns an MTK.ODESystem
     odesys = convert(ODESystem, readSBML(sbmlfile, ReactionSystemImporter(), kwargs...),
         include_zero_odes = include_zero_odes)
-    complete(odesys)
 end
 
 """
@@ -96,7 +95,7 @@ function Catalyst.ReactionSystem(model::SBML.Model; kwargs...)  # Todo: requires
         defaults = defs, name = gensym(:SBML),
         continuous_events = get_events(model),
         combinatoric_ratelaws = false, kwargs...)
-    return complete(rs)  # Todo: maybe add a `complete=True` kwarg
+    return rs
 end
 
 """
@@ -110,7 +109,6 @@ function ModelingToolkit.ODESystem(model::SBML.Model; include_zero_odes::Bool =
         kwargs...)
     rs = ReactionSystem(model; kwargs...)
     odesys = convert(ODESystem, rs; include_zero_odes = include_zero_odes)
-    complete(odesys)
 end
 
 function get_mappings(model::SBML.Model)

test/rules.jl

@@ -16,26 +16,26 @@ end
 
 # Test get_rules
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00029")  # assignmentRule
-m = readmodel(sbml)
+m = complete(readmodel(sbml))
 a, o, r = SBMLToolkit.get_rules(m)
 o_true = [S1 ~ 7 * compartment]
 @test isequal(o, o_true)
 
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00031")  # rateRule
-m = readmodel(sbml)
+m = complete(readmodel(sbml))
 a, o, r = SBMLToolkit.get_rules(m)
 r_true = [default_time_deriv()(S1) ~ 7 * compartment]
 @test isequal(r, r_true)
 
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00039")  # algebraicRule
-m = readmodel(sbml)
+m = complete(readmodel(sbml))
 a, o, r = SBMLToolkit.get_rules(m)
 a_true = [0 ~ S1 + S2 - k1]
 @test isequal(a, a_true)
 
 # Test get_var_and_assignment
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00031")
-m = readmodel(sbml)
+m = complete(readmodel(sbml))
 var, assignment = SBMLToolkit.get_var_and_assignment(m, m.rules[1])
 var_true = S1
 assignment_true = 7 * compartment
@@ -55,20 +55,20 @@ vc = SBMLToolkit.get_volume_correction(m, "S1")
 @test isequal(vc, "compartment")
 
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00060")  # hOSU="true" species
-m = readmodel(sbml)
+m = complete(readmodel(sbml))
 vc = SBMLToolkit.get_volume_correction(m, "S1")
 @test isnothing(vc)
 
 # tests that non-constant parameters become variables
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00033")
-m = readmodel(sbml)
+m = complete(readmodel(sbml))
 @named sys = ODESystem(m)
 @species k1(IV)
 @test isequal(k1, unknowns(sys)[end])
 
 # tests that non-constant compartments become variables
 sbml, _, _ = SBMLToolkitTestSuite.read_case("00051")  # hOSU="true" species
-m = readmodel(sbml)
+m = complete(readmodel(sbml))
 @named sys = ODESystem(m)
 @species C(IV)
 @test isequal(C, unknowns(sys)[end])

test/wuschel.jl

@@ -11,9 +11,9 @@ m = readSBMLFromString(sbml, doc -> begin
     # set_level_and_version(3, 2)(doc) # fails on wuschel
     convert_promotelocals_expandfuns(doc)
 end)
-sys = ODESystem(m)
+sys = ODESystem(complete(m))
 @test length(equations(sys)) == 1012
 @test length(unknowns(sys)) == 1012
-#ssys = structural_simplify(sys)  # Todo: Figure out why this complains about ExtraVariablesSystemException
-prob = ODEProblem(sys, [], (0, 10.0))
+ssys = structural_simplify(sys)  # Todo: Figure out why this complains about ExtraVariablesSystemException
+prob = ODEProblem(ssys, [], (0, 10.0))
 solve(prob, Tsit5(), save_everystep = false)