Merge pull request #280 from TorkelE/master

Fix ModelingTookit extension

.github/workflows/CI.yml

@@ -13,7 +13,7 @@ jobs:
       matrix:
         group:
           - Core
-          - ModelingToolkitExt
+          - ModelingToolkitSIExt
         version:
           - '1'
           - '1.6'

Project.toml

@@ -26,7 +26,7 @@ SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [extensions]
-ModelingToolkitExt = ["ModelingToolkit", "SymbolicUtils", "Symbolics"]
+ModelingToolkitSIExt = ["ModelingToolkit", "SymbolicUtils", "Symbolics"]
 
 [compat]
 AbstractAlgebra = "0.34.5, 0.35"

docs/src/tutorials/creating_ode.md

@@ -54,7 +54,7 @@ assess_identifiability(ode)
 
 ## Defining using `ModelingToolkit`
 
-`StructuralIdentifiability` has an extension `ModelingToolkitExt` which allows to use `ODESystem` from `ModelingToolkit` to describe
+`StructuralIdentifiability` has an extension `ModelingToolkitSIExt` which allows to use `ODESystem` from `ModelingToolkit` to describe
 a model. The extension is loaded automatically once `ModelingToolkit` is loaded via `using ModelingToolkit`.
 In this case, one should encode the equations for the states as `ODESystem` and specify the outputs separately.
 In order to do this, we first introduce all functions and scalars:

docs/src/tutorials/discrete_time.md

@@ -87,7 +87,7 @@ assess_local_identifiability(dds; funcs_to_check = [β * S])
 As other main functions in the package, `assess_local_identifiability` accepts an optional parameter `loglevel` (default: `Logging.Info`)
 to adjust the verbosity of logging.
 
-If one loads `ModelingToolkit` (and thus the `ModelingToolkitExt` extension), one can use `DiscreteSystem` from `ModelingToolkit` to
+If one loads `ModelingToolkit` (and thus the `ModelingToolkitSIExt` extension), one can use `DiscreteSystem` from `ModelingToolkit` to
 describe the input model (now in terms of difference!):
 
 ```@example discrete_mtk

ext/ModelingToolkitExt.jl → ext/ModelingToolkitSIExt.jl

@@ -1,4 +1,4 @@
-module ModelingToolkitExt
+module ModelingToolkitSIExt
 
 using DataStructures
 using Logging
@@ -15,9 +15,6 @@ else
     using ..ModelingToolkit
 end
 
-export mtk_to_si
-export assess_local_identifiability, assess_identifiability, find_identifiable_functions
-
 # ------------------------------------------------------------------------------
 
 function eval_at_nemo(e::Num, vals::Dict)
@@ -96,7 +93,7 @@ Output:
 - `conversion` dictionary from the symbols in the input MTK model to the variable
   involved in the produced `ODE` object
 """
-function mtk_to_si(
+function StructuralIdentifiability.mtk_to_si(
     de::ModelingToolkit.AbstractTimeDependentSystem,
     measured_quantities::Array{ModelingToolkit.Equation},
 )
@@ -106,7 +103,7 @@ function mtk_to_si(
     )
 end
 
-function mtk_to_si(
+function StructuralIdentifiability.mtk_to_si(
     de::ModelingToolkit.AbstractTimeDependentSystem,
     measured_quantities::Array{<:Symbolics.Num},
 )
@@ -116,7 +113,7 @@ function mtk_to_si(
     )
 end
 
-function mtk_to_si(
+function StructuralIdentifiability.mtk_to_si(
     de::ModelingToolkit.AbstractTimeDependentSystem,
     measured_quantities::Array{<:SymbolicUtils.BasicSymbolic},
 )

src/StructuralIdentifiability.jl

@@ -172,4 +172,10 @@ end
 using PrecompileTools
 include("precompile.jl")
 
+### Extensions ###
+
+# ModelingToolkit extension.
+function mtk_to_si end
+export mtk_to_si
+
 end

test/extensions/modelingtoolkit.jl

@@ -1,4 +1,4 @@
-if GROUP == "All" || GROUP == "ModelingToolkitExt"
+if GROUP == "All" || GROUP == "ModelingToolkitSIExt"
     @testset "Check identifiability of `ODESystem` object" begin
         using ModelingToolkit
         using ModelingToolkit: parameters
@@ -656,4 +656,48 @@ if GROUP == "All" || GROUP == "ModelingToolkitExt"
             ) == c[:res]
         end
     end
+
+    @testset "Exporting ModelingToolkit Model to SI Model" begin
+
+        # Creates MTK model and assesses its identifiability.
+        @parameters r1, r2, c1, c2, beta1, beta2, chi1, chi2
+        @variables t, x1(t), x2(t), y(t), u(t)
+        D = Differential(t)
+        eqs = [
+            D(x1) ~ r1 * x1 * (1 - c1 * x1) + beta1 * x1 * x2 / (chi1 + x2) + u,
+            D(x2) ~ r2 * x2 * (1 - c2 * x2) + beta2 * x1 * x2 / (chi2 + x1),
+        ]
+        measured_quantities = [y ~ x1]
+        ode_mtk = ODESystem(eqs, t, name = :mutualist)
+
+        global_id_1 =
+            assess_identifiability(ode_mtk, measured_quantities = measured_quantities)
+        local_id_1 =
+            assess_local_identifiability(ode_mtk, measured_quantities = measured_quantities)
+        ifs_1 =
+            find_identifiable_functions(ode_mtk, measured_quantities = measured_quantities)
+
+        # Converts mtk model to si model, and assesses its identifiability.
+        si_model, _ = mtk_to_si(ode_mtk, measured_quantities)
+        global_id_2 = assess_identifiability(si_model)
+        local_id_2 = assess_local_identifiability(si_model)
+        ifs_2 = find_identifiable_functions(si_model)
+
+        # Converts the output dicts from StructuralIdentifiability functions from "weird symbol => stuff" to "symbol => stuff" (the output have some strange meta data which prevents equality checks, this enables this).
+        # Structural identifiability also provides variables like x (rather than x(t)). This is a bug, but we have to convert to make it work (now just remove any (t) to make them all equal).
+        function sym_dict(dict_in)
+            dict_out = Dict{Symbol, Any}()
+            for key in keys(dict_in)
+                sym_key = Symbol(key)
+                sym_key = Symbol(replace(String(sym_key), "(t)" => ""))
+                dict_out[sym_key] = dict_in[key]
+            end
+            return dict_out
+        end
+
+        # Checks that the two approaches yields the same result
+        @test issetequal(sym_dict(local_id_1), sym_dict(local_id_2))
+        @test issetequal(sym_dict(local_id_1), sym_dict(local_id_2))
+        @test length(ifs_1) == length(ifs_2)
+    end
 end

test/runtests.jl

@@ -68,7 +68,7 @@ using StructuralIdentifiability:
 const GROUP = get(ENV, "GROUP", "All")
 
 @static if VERSION >= v"1.10.0"
-    if GROUP == "All" || GROUP == "ModelingToolkitExt"
+    if GROUP == "All" || GROUP == "ModelingToolkitSIExt"
         using Pkg
         Pkg.add("ModelingToolkit")
         Pkg.add("Symbolics")
@@ -123,7 +123,7 @@ function get_test_files(group)
                 if group == "All" ||
                    (group == "Core" && dir != "./extensions") ||
                    (
-                       group == "ModelingToolkitExt" &&
+                       group == "ModelingToolkitSIExt" &&
                        dir == "./extensions" &&
                        VERSION >= v"1.10.0"
                    )