compelteness error for SI

Author: TorkelE

ext/CatalystStructuralIdentifiabilityExtension/structural_identifiability_extension.jl

@@ -157,7 +157,7 @@ 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).
-    iscomplete(rs) || error(COMPLETENESS_ERROR)
+    ModelingToolkit.iscomplete(rs) || error("Identifiability should only be computed for complete systems. A ReactionSystem can be marked as complete using the `complete` function.")
     rs = Catalyst.expand_registered_functions(flatten(rs))
     osys = complete(convert(ODESystem, rs; remove_conserved))
     vars = [unknowns(rs); parameters(rs)]

test/model_simulation/simulate_SDEs.jl

@@ -282,7 +282,7 @@ let
 end
 
 # Tests  using complicated noise scaling expressions.
-@time let
+let
     noise_scaling_network = @reaction_network begin
         @parameters η1 η2 η3 η4
         @species N1(t) N2(t)=0.5

test/runtests.jl

@@ -3,58 +3,6 @@ using SafeTestsets
 
 ### Run the tests ###
 @time begin
-
-    ### Tests the properties of ReactionSystems. ###
-    @time @safetestset "Reactions" begin include("reactionsystem_structure/reactions.jl") end
-    @time @safetestset "ReactionSystem" begin include("reactionsystem_structure/reactionsystem.jl") end
-    @time @safetestset "Higher Order Reactions" begin include("reactionsystem_structure/higher_order_reactions.jl") end
-
-    ### Tests model creation via the @reaction_network DSL. ###
-    @time @safetestset "Basic DSL" begin include("dsl/dsl_basics.jl") end
-    @time @safetestset "DSL Model Construction" begin include("dsl/dsl_model_construction.jl") end
-    @time @safetestset "Custom CRN Functions" begin include("dsl/custom_functions.jl") end
-    @time @safetestset "DSL Options" begin include("dsl/dsl_options.jl") end
-
-    ### Non-DSL model creation and modification. ###
-    @time @safetestset "ReactionSystem Components Based Creation" begin include("programmatic_model_creation/component_based_model_creation.jl") end
-    @time @safetestset "Programmatic Model Expansion" begin include("programmatic_model_creation/programmatic_model_expansion.jl") end
-
-    # Runs various miscellaneous tests.
-    @time @safetestset "API" begin include("miscellaneous_tests/api.jl") end
-    @time @safetestset "Symbolic Stoichiometry" begin include("miscellaneous_tests/symbolic_stoichiometry.jl") end
-    @time @safetestset "NonlinearProblems and Steady State Solving" begin include("miscellaneous_tests/nonlinear_solve.jl") end
-    @time @safetestset "Events" begin include("miscellaneous_tests/events.jl") end
-    @time @safetestset "Compound species" begin include("miscellaneous_tests/compound_macro.jl") end
-    @time @safetestset "Reaction balancing" begin include("miscellaneous_tests/reaction_balancing.jl") end
-    @time @safetestset "Units" begin include("miscellaneous_tests/units.jl") end
-
-    ### Reaction network analysis. ###
-    @time @safetestset "Conservation Laws" begin include("network_analysis/conservation_laws.jl") end
-    @time @safetestset "Network Properties" begin include("network_analysis/network_properties.jl") end
-
-    ### Tests ODE, SDE, PDE, and Gillespie Simulations. ###
-    @time @safetestset "ODE System Simulations" begin include("model_simulation/simulate_ODEs.jl") end
-    @time @safetestset "Automatic Jacobian Construction" begin include("model_simulation/make_jacobian.jl") end
-    @time @safetestset "U0 and Parameters Input Variants" begin include("model_simulation/u0_n_parameter_inputs.jl") end
-    @time @safetestset "SDE System Simulations" begin include("model_simulation/simulate_SDEs.jl") end
-    @time @safetestset "Jump System Simulations" begin include("model_simulation/simulate_jumps.jl") end
-
-    ### Tests Spatial Network Simulations. ###
-    @time @safetestset "PDE Systems Simulations" begin include("spatial_reaction_systems/simulate_PDEs.jl") end
-    @time @safetestset "Lattice Reaction Systems" begin include("spatial_reaction_systems/lattice_reaction_systems.jl") end
-    @time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_reaction_systems/lattice_reaction_systems_ODEs.jl") end
-
-    ### Tests network visualization. ###
-    @time @safetestset "Latexify" begin include("visualization/latexify.jl") end
-    # @time @safetestset "Basic Plotting" begin include("visualization/plotting.jl") end
-    # Disable on Macs as can't install GraphViz via jll
-    if !Sys.isapple()
-        @time @safetestset "Graphs" begin include("visualization/graphs.jl") end
-    end
-    
-    ### Tests extensions. ###
-    @time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end
-    @time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end
     @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
 
 end # @time