Merge pull request #1169 from isaacsas/enable_SI_on_1.11

Try to enable SI on 1.11

Author: TorkelE

Project.toml

@@ -34,12 +34,15 @@ GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
+StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
+
 
 [extensions]
 CatalystBifurcationKitExtension = "BifurcationKit"
 CatalystCairoMakieExtension = "CairoMakie"
 CatalystGraphMakieExtension = ["GraphMakie", "NetworkLayout", "Makie"]
 CatalystHomotopyContinuationExtension = "HomotopyContinuation"
+CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
 [compat]
 BifurcationKit = "0.4.4"
@@ -66,6 +69,7 @@ Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
 SciMLBase = "2.57.2"
 Setfield = "1"
+StructuralIdentifiability = "0.5.11"
 SymbolicUtils = "3.8.1"
 Symbolics = "6.22"
 Unitful = "1.12.4"

docs/Project.toml

@@ -42,6 +42,7 @@ SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
+StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
@@ -87,4 +88,5 @@ SpecialFunctions = "2.4"
 StaticArrays = "1.9"
 SteadyStateDiffEq = "2.2"
 StochasticDiffEq = "6.65"
+StructuralIdentifiability = "0.5.11"
 Symbolics = "6.22"

docs/pages.jl

@@ -48,7 +48,7 @@ pages = Any[
         "inverse_problems/petab_ode_param_fitting.md",
         "inverse_problems/optimization_ode_param_fitting.md",
         "inverse_problems/behaviour_optimisation.md",
-        # "inverse_problems/structural_identifiability.md",
+        "inverse_problems/structural_identifiability.md",
         "inverse_problems/global_sensitivity_analysis.md",
         "Examples" => Any[
             "inverse_problems/examples/ode_fitting_oscillation.md"

docs/unpublished/structural_identifiability.md renamed to docs/src/inverse_problems/structural_identifiability.md

@@ -113,7 +113,9 @@ function SI.assess_identifiability(rs::ReactionSystem, args...;
     funcs_to_check = make_ftc(funcs_to_check, conseqs, vars)
 
     # Computes identifiability and converts it to a easy to read form.
-    out = SI.assess_identifiability(osys, args...; measured_quantities,
+    # The `::ODESystem` designation fixes: https://github.com/SciML/StructuralIdentifiability.jl/issues/360,
+    # however, the exact mechanisms of this is still not fully clear.
+    out = SI.assess_identifiability(osys::ODESystem, args...; measured_quantities,
         funcs_to_check, kwargs...)
     return make_output(out, funcs_to_check, consconsts)
 end

ext/CatalystStructuralIdentifiabilityExtension/structural_identifiability_extension.jl

@@ -10,4 +10,4 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
-# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
+StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"

test/extensions/Project.toml

@@ -101,20 +101,20 @@ end
 # Tests `ReactionSystem`s.
 let
     @species x(t) y(t)
-    @parameters k v n 
+    @parameters k v n
     rs1 = @reaction_network rs begin
         mm(x, v, k), 0 --> x
         mmr(x, v, k), 0 --> x
         hill(x, v, k, n), 0 --> x
         hillr(x, v, k, n), 0 --> x
-        hillar(x, y, v, k, n), 0 --> x    
+        hillar(x, y, v, k, n), 0 --> x
     end
     rs2 = @reaction_network rs begin
         v * x / (x + k), 0 --> x
         v * k / (x + k), 0 --> x
         v * (x^n) / (x^n + k^n), 0 --> x
         v * (k^n) / (x^n + k^n), 0 --> x
-        v * (x^n) / (x^n + y^n + k^n), 0 --> x    
+        v * (x^n) / (x^n + y^n + k^n), 0 --> x
     end
 
     @test Catalyst.expand_registered_functions(rs1) == rs2
@@ -123,14 +123,14 @@ end
 # Tests `Reaction`s.
 let
     @species x(t) y(t)
-    @parameters k v n 
-    
+    @parameters k v n
+
     r1 = @reaction mm(x, v, k), 0 --> x
     r2 = @reaction mmr(x, v, k), 0 --> x
     r3 = @reaction hill(x, v, k, n), 0 --> x
     r4 = @reaction hillr(x, v, k, n), 0 --> x
     r5 = @reaction hillar(x, y, v, k, n), 0 --> x + y
-    
+
     @test isequal(Catalyst.expand_registered_functions(r1).rate, v * x / (x + k))
     @test isequal(Catalyst.expand_registered_functions(r2).rate, v * k / (x + k))
     @test isequal(Catalyst.expand_registered_functions(r3).rate, v * (x^n) / (x^n + k^n))
@@ -143,14 +143,14 @@ end
 let
     @parameters T
     @variables X(T) Y(T)
-    @parameters K V N 
-    
+    @parameters K V N
+
     eq1 = 0 ~ mm(X, V, K)
     eq2 = 0 ~ mmr(X, V, K)
     eq3 = 0 ~ hill(X, V, K, N)
     eq4 = 0 ~ hillr(X, V, K, N)
     eq5 = 0 ~ hillar(X, Y, V, K, N)
-    
+
     @test isequal(Catalyst.expand_registered_functions(eq1), 0 ~ V * X / (X + K))
     @test isequal(Catalyst.expand_registered_functions(eq2), 0 ~ V * K / (X + K))
     @test isequal(Catalyst.expand_registered_functions(eq3), 0 ~ V * (X^N) / (X^N + K^N))
@@ -166,7 +166,7 @@ let
     @parameters v K
     eqs = [
         Reaction(mm(X,v,K), [], [X]),
-        mm(V,v,K) ~ V + 1    
+        mm(V,v,K) ~ V + 1
     ]
     @named rs = ReactionSystem(eqs, t)
 
@@ -211,7 +211,7 @@ let
         (v * (X^n) / (X^n + K^n) > 1000.0) => [X ~ v * (K^n) / (X^n + K^n) + 2]
     ]
     continuous_events = ModelingToolkit.SymbolicContinuousCallback.(continuous_events)
-    discrete_events = ModelingToolkit.SymbolicDiscreteCallback.(discrete_events)    
+    discrete_events = ModelingToolkit.SymbolicDiscreteCallback.(discrete_events)
     @test isequal(only(Catalyst.get_rxs(rs_expanded)).rate, v0 + v * (X^n) / (X^n + Y^n + K^n))
     @test isequal(get_continuous_events(rs_expanded), continuous_events)
     @test isequal(get_discrete_events(rs_expanded), discrete_events)

test/reactionsystem_core/custom_crn_functions.jl

@@ -80,9 +80,7 @@ end
         @time @safetestset "Graph visualization" begin include("extensions/graphmakie.jl") end
         @time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end
         @time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end
-
-        # BROKEN
-        # @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
+        @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
 
         # Tests stability computation (but requires the HomotopyContinuation extension).
         #@time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end