updates

Author: TorkelE

ext/CatalystStructuralIdentifiabilityExtension/structural_identifiability_extension.jl

@@ -157,7 +157,8 @@ end
 function make_osys(rs::ReactionSystem; remove_conserved=true)
     # Creates the ODESystem corresponding to the ReactionSystem (expanding functions and flattening it).
     # Creates a list of the systems all symbols (unknowns and parameters).
-    rs = complete(Catalyst.expand_registered_functions(flatten(rs)))
+    iscomplete(rs) || error(COMPLETENESS_ERROR)
+    rs = Catalyst.expand_registered_functions(flatten(rs))
     osys = complete(convert(ODESystem, rs; remove_conserved))
     vars = [unknowns(rs); parameters(rs)]
 

src/reaction_network.jl

@@ -148,9 +148,6 @@ emptyrn = @reaction_network
 
 ReactionSystems generated through `@reaction_network` are complete.
 """
-# macro reaction_network(args...)
-#     return :(complete(@network_component $(args... )))
-# end
 macro reaction_network(name::Symbol, ex::Expr)
     :(complete($(make_reaction_system(MacroTools.striplines(ex); name = :($(QuoteNode(name)))))))
 end
@@ -179,6 +176,9 @@ macro reaction_network(name::Symbol = gensym(:ReactionSystem))
                 :(complete(ReactionSystem(Reaction[], t, [], []; name = $(QuoteNode(name))))))
 end
 
+# Ideally, it would have been possible to combine the @reaction_network and @network_component macros.
+# However, this issue: https://github.com/JuliaLang/julia/issues/37691 causes problem with interpolations
+# if we make the @reaction_network macro call the @network_component macro.
 """
     @network_component
 

src/reactionsystem.jl

@@ -544,7 +544,7 @@ struct ReactionSystem{V <: NetworkProperties} <:
     # inner constructor is considered private and may change between non-breaking releases.
     function ReactionSystem(eqs, rxs, iv, sivs, unknowns, spcs, ps, var_to_name, observed,
                             name, systems, defaults, connection_type, nps, cls, cevs, devs,
-                            metadata, complete; checks::Bool = true)
+                            metadata = nothing, complete = false; checks::Bool = true)
 
         # unit checks are for ODEs and Reactions only currently
         nonrx_eqs = Equation[eq for eq in eqs if eq isa Equation]
@@ -680,7 +680,7 @@ function ReactionSystem(eqs, iv, unknowns, ps;
 
     ReactionSystem(eqs′, rxs, iv′, sivs′, unknowns′, spcs, ps′, var_to_name, observed, name,
                    systems, defaults, connection_type, nps, combinatoric_ratelaws,
-                   ccallbacks, dcallbacks, metadata, false; checks = checks)
+                   ccallbacks, dcallbacks, metadata; checks = checks)
 end
 
 function ReactionSystem(rxs::Vector, iv = Catalyst.DEFAULT_IV; kwargs...)

test/dsl/custom_functions.jl

@@ -138,8 +138,9 @@ let
 end
 
 # Tests `Equation`s.
+# Tests using non-default independent variable.
 let
-    @variables X(t) Y(t)
+    @variables T X(T) Y(T)
     @parameters K V N 
 
     eq1 = 0 ~ mm(X, V, K)

test/extensions/bifurcation_kit.jl

@@ -7,7 +7,8 @@ using BifurcationKit, Catalyst, Test
 using StableRNGs
 rng = StableRNG(12345)
 
-### Run Tests ###
+
+### Basic Tests ###
 
 # Brusselator extended with conserved species.
 # Runs full computation, checks values corresponds to known values.
@@ -174,4 +175,20 @@ let
 
     # Checks that there is an error if information for conserved quantities computation is not provided.
     @test_throws Exception bprob = BifurcationProblem(rn, u_guess, p_start, k1; plot_var = X1)
+end
+
+
+### Other Tests ###
+
+# Checks that `BifurcationProblem`s cannot be generated from non-complete `ReactionSystems`s.
+let 
+    # Create model.
+    incomplete_network = @network_component begin
+        (p, d), 0 <--> X
+    end
+    u0_guess = [:X => 1.0]
+    p_start = [p => 1.0, d => 0.2]
+    
+    # Computes bifurcation diagram.
+    @test_throws Exception BifurcationProblem(incomplete_network, u0_guess, p_start, :p)
 end

test/extensions/homotopy_continuation.jl

@@ -7,7 +7,7 @@ import HomotopyContinuation
 # Fetch test functions.
 include("../test_functions.jl")
 
-### Run Tests ###
+### Basic Tests ###
 
 # Tests for network without conservation laws.
 # Tests for Symbol parameter input.
@@ -104,4 +104,19 @@ let
     end
 
     @test_throws Exception hc_steady_states(rs, [:v => 5.0, :K => 2.5, :n => 2.7, :d => 1.0]; show_progress=false)
+end
+
+
+### Other Tests ###
+
+# Checks that `hc_steady_states` cannot be applied to non-complete `ReactionSystems`s.
+let 
+    # Create model.
+    incomplete_network = @network_component begin
+        (p, d), 0 <--> X
+    end
+    p_start = [p => 1.0, d => 0.2]
+    
+    # Computes bifurcation diagram.
+    @test_throws Exception hc_steady_states(incomplete_network, p_start)
 end

test/extensions/structural_identifiability.jl

@@ -17,7 +17,7 @@ function sym_dict(dict_in)
 end
 
 
-### Run Tests ###
+### Basic Tests ###
 
 # Tests for Goodwin model (model with both global, local, and non identifiable components).
 # Tests for system using Catalyst function (in this case, Michaelis-Menten function)
@@ -306,4 +306,21 @@ let
         :x3 => :globally,
     )
     @test length(find_identifiable_functions(rs, measured_quantities = [:x3])) == 1
+end
+
+
+### Other Tests ###
+
+# Checks that identifiability functions cannot be applied to non-complete `ReactionSystems`s.
+let 
+    # Create model.
+    incomplete_network = @network_component begin
+        (p, d), 0 <--> X
+    end
+    measured_quantities = [:X]
+    
+    # Computes bifurcation diagram.
+    @test_throws Exception assess_identifiability(incomplete_network; measured_quantities)
+    @test_throws Exception assess_local_identifiability(incomplete_network; measured_quantities)
+    @test_throws Exception find_identifiable_functions(incomplete_network; measured_quantities)
 end