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Author: TorkelE

ext/CatalystHomotopyContinuationExtension/homotopy_continuation_extension.jl

@@ -67,7 +67,7 @@ function make_int_exps(expr)
     wrap(Rewriters.Postwalk(Rewriters.PassThrough(___make_int_exps))(unwrap(expr))).val
 end
 function ___make_int_exps(expr)
-    !istree(expr) && return expr
+    !iscall(expr) && return expr
     if (operation(expr) == ^)
         if isinteger(arguments(expr)[2])
             return arguments(expr)[1]^Int64(arguments(expr)[2])

src/reactionsystem.jl

@@ -1479,4 +1479,4 @@ function validate(rs::ReactionSystem, info::String = "")
 end
 
 # Checks if a unit consist of exponents with base 1 (and is this unitless).
-unitless_exp(u) = istree(u) && (operation(u) == ^) && (arguments(u)[1] == 1)
+unitless_exp(u) = iscall(u) && (operation(u) == ^) && (arguments(u)[1] == 1)

src/reactionsystem_serialisation/serialisation_support.jl

@@ -240,7 +240,7 @@ const SKIPPED_METADATA = [ModelingToolkit.MTKVariableTypeCtx, Symbolics.Variable
 # Potentially strips the call for a symbolics. E.g. X(t) becomes X (but p remains p). This is used 
 # when variables are written to files, as in code they are used without the call part.
 function strip_call(sym)
-    return istree(sym) ? Sym{Real}(Symbolics.getname(sym)) : sym
+    return iscall(sym) ? Sym{Real}(Symbolics.getname(sym)) : sym
 end
 
 # For an vector of symbolics, creates a dictionary taking each symbolics to each call-stripped form.

test/dsl/dsl_options.jl

@@ -574,8 +574,8 @@ let
         end
     end
     V,W = getfield.(observed(rn), :lhs)
-    @test isequal(arguments(ModelingToolkit.unwrap(V)), Any[Catalyst.get_iv(rs), Catalyst.get_sivs(rn)[1], Catalyst.get_sivs(rn)[2]])
-    @test isequal(arguments(ModelingToolkit.unwrap(W)), Any[Catalyst.get_iv(rs), Catalyst.get_sivs(rn)[2]])
+    @test isequal(arguments(ModelingToolkit.unwrap(V)), Any[Catalyst.get_iv(rn), Catalyst.get_sivs(rn)[1], Catalyst.get_sivs(rn)[2]])
+    @test isequal(arguments(ModelingToolkit.unwrap(W)), Any[Catalyst.get_iv(rn), Catalyst.get_sivs(rn)[2]])
 end
 
 # Checks that metadata is written properly.

test/reactionsystem_core/coupled_equation_crn_systems.jl

@@ -47,7 +47,7 @@ let
     # Checks that the correct steady state is found through ODEProblem.
     oprob = ODEProblem(coupled_rs, u0, tspan, ps)
     osol = solve(oprob, Vern7(); abstol = 1e-8, reltol = 1e-8)
-    @test osol[end] ≈ [2.0, 1.0]
+    @test osol.u[end] ≈ [2.0, 1.0]
 
     # Checks that the correct steady state is found through NonlinearProblem.
     nlprob = NonlinearProblem(coupled_rs, u0, ps)
@@ -116,7 +116,7 @@ let
     for coupled_rs in [coupled_rs_prog, coupled_rs_extended, coupled_rs_dsl]
         oprob = ODEProblem(coupled_rs, u0, tspan, ps)
         osol = solve(oprob, Vern7(); abstol = 1e-8, reltol = 1e-8)
-        osol[end] ≈ [10.0, 10.0, 11.0, 11.0]
+        osol.u[end] ≈ [10.0, 10.0, 11.0, 11.0]
     end
 end
 
@@ -160,7 +160,7 @@ let
     # Checks that the correct steady state is found through ODEProblem.
     oprob = ODEProblem(coupled_rs, u0, tspan, ps; structural_simplify = true)
     osol = solve(oprob, Rosenbrock23(); abstol = 1e-8, reltol = 1e-8)
-    @test osol[end] ≈ [2.0, 3.0]
+    @test osol.u[end] ≈ [2.0, 3.0]
 
     # Checks that the correct steady state is found through NonlinearProblem.
     nlprob = NonlinearProblem(coupled_rs, u0, ps)
@@ -207,7 +207,7 @@ let
     osol = solve(oprob, Rosenbrock23(); abstol = 1e-8, reltol = 1e-8)
     sssol = solve(ssprob, DynamicSS(Rosenbrock23()); abstol = 1e-8, reltol = 1e-8)
     nlsol = solve(nlprob; abstol = 1e-8, reltol = 1e-8)
-    @test osol[end] ≈ sssol ≈ nlsol
+    @test osol.u[end] ≈ sssol ≈ nlsol
 end
 
 

test/reactionsystem_core/reactionsystem.jl

@@ -356,7 +356,7 @@ let
     oprob1 = ODEProblem(osys, u0map, tspan, pmap)
     sts = [B, D, E, C]
     syms = [:B, :D, :E, :C]
-    ofun = ODEFunction(f!; syms)
+    ofun = ODEFunction(f!; sys = ModelingToolkit.SymbolCache(syms))
     oprob2 = ODEProblem(ofun, u0, tspan, p)
     saveat = tspan[2] / 50
     abstol = 1e-10