Merge branch 'master' into iv_property

Author: hersle

Project.toml

@@ -1,7 +1,7 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <[email protected]>", "Chris Rackauckas <[email protected]> and contributors"]
-version = "9.32.0"
+version = "9.33.1"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -96,7 +96,7 @@ Libdl = "1"
 LinearAlgebra = "1"
 MLStyle = "0.4.17"
 NaNMath = "0.3, 1"
-NonlinearSolve = "3.12"
+NonlinearSolve = "3.14"
 OrderedCollections = "1"
 OrdinaryDiffEq = "6.82.0"
 PrecompileTools = "1"
@@ -112,8 +112,8 @@ SparseArrays = "1"
 SpecialFunctions = "0.7, 0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "0.10, 0.11, 0.12, 1.0"
 SymbolicIndexingInterface = "0.3.28"
-SymbolicUtils = "2.1"
-Symbolics = "5.32"
+SymbolicUtils = "3.2"
+Symbolics = "6"
 URIs = "1"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"

docs/Project.toml

@@ -37,6 +37,6 @@ Plots = "1.36"
 SciMLStructures = "1.1"
 StochasticDiffEq = "6"
 SymbolicIndexingInterface = "0.3.1"
-SymbolicUtils = "2, 3"
-Symbolics = "5"
+SymbolicUtils = "3"
+Symbolics = "6"
 Unitful = "1.12"

docs/make.jl

@@ -1,4 +1,5 @@
 using Documenter, ModelingToolkit
+using ModelingToolkit: SciMLBase
 
 # Make sure that plots don't throw a bunch of warnings / errors!
 ENV["GKSwstype"] = "100"

docs/src/internals.md

@@ -27,11 +27,20 @@ The procedure for variable elimination inside [`structural_simplify`](@ref) is
 
 ## Preparing a system for simulation
 
-Before a simulation or optimization can be performed, the symbolic equations stored in an [`AbstractSystem`](@ref) must be converted into executable code. This step typically occurs after the simplification explained above, and is performed when an instance of a [`SciMLBase.SciMLProblem`](@ref), such as a [`ODEProblem`](@ref), is constructed.
+Before a simulation or optimization can be performed, the symbolic equations stored in an [`AbstractSystem`](@ref) must be converted into executable code. This step typically occurs after the simplification explained above, and is performed when an instance of a [`SciMLBase.AbstractSciMLProblem`](@ref), such as a [`ODEProblem`](@ref), is constructed.
 The call chain typically looks like this, with the function names in the case of an `ODESystem` indicated in parentheses
 
  1. Problem constructor ([`ODEProblem`](@ref))
  2. Build an `DEFunction` ([`process_DEProblem`](@ref) -> [`ODEFunction`](@ref)
  3. Write actual executable code ([`generate_function`](@ref) or [`generate_custom_function`](@ref))
 
 Apart from [`generate_function`](@ref), which generates the dynamics function, `ODEFunction` also builds functions for observed equations (`build_explicit_observed_function`) and Jacobians (`generate_jacobian`) etc. These are all stored in the `ODEFunction`.
+
+## Creating an `MTKParameters` object
+
+It may be useful to create a parameter object without creating the problem. For this
+purpose, the `MTKParameters` constructor is exposed as public API.
+
+```@docs
+MTKParameters
+```

ext/MTKBifurcationKitExt.jl

@@ -144,9 +144,10 @@ function BifurcationKit.BifurcationProblem(osys::ODESystem, args...; kwargs...)
     if !ModelingToolkit.iscomplete(osys)
         error("A completed `ODESystem` is required. Call `complete` or `structural_simplify` on the system before creating a `BifurcationProblem`")
     end
-    nsys = NonlinearSystem([0 ~ eq.rhs for eq in equations(osys)],
+    nsys = NonlinearSystem([0 ~ eq.rhs for eq in full_equations(osys)],
         unknowns(osys),
         parameters(osys);
+        observed = observed(osys),
         name = nameof(osys))
     return BifurcationKit.BifurcationProblem(complete(nsys), args...; kwargs...)
 end

src/ModelingToolkit.jl

@@ -275,4 +275,6 @@ export debug_system
 export Sample, Hold, Shift, ShiftIndex, sampletime, SampleTime
 export Clock, SolverStepClock, TimeDomain
 
+export MTKParameters
+
 end # module

src/debugging.jl

@@ -32,5 +32,5 @@ function debug_sub(ex)
     f = operation(ex)
     args = map(debug_sub, arguments(ex))
     f in LOGGED_FUN ? logged_fun(f, args...) :
-    maketerm(typeof(ex), f, args, symtype(t), metadata(ex))
+    maketerm(typeof(ex), f, args, metadata(ex))
 end

src/structural_transformation/utils.jl

@@ -449,6 +449,6 @@ function simplify_shifts(var)
         return simplify_shifts(ModelingToolkit.Shift(t1 === nothing ? t2 : t1, s1 + s2)(vv2))
     else
         return maketerm(typeof(var), operation(var), simplify_shifts.(arguments(var)),
-            Symbolics.symtype(var), unwrap(var).metadata)
+            unwrap(var).metadata)
     end
 end

src/systems/abstractsystem.jl

@@ -1098,7 +1098,7 @@ function _apply_to_variables(f::F, ex) where {F}
     iscall(ex) || return ex
     maketerm(typeof(ex), _apply_to_variables(f, operation(ex)),
         map(Base.Fix1(_apply_to_variables, f), arguments(ex)),
-        symtype(ex), metadata(ex))
+        metadata(ex))
 end
 
 abstract type SymScope end
@@ -1110,7 +1110,7 @@ function LocalScope(sym::Union{Num, Symbolic, Symbolics.Arr{Num}})
             args = arguments(sym)
             a1 = setmetadata(args[1], SymScope, LocalScope())
             maketerm(typeof(sym), operation(sym), [a1, args[2:end]...],
-                symtype(sym), metadata(sym))
+                metadata(sym))
         else
             setmetadata(sym, SymScope, LocalScope())
         end
@@ -1127,7 +1127,7 @@ function ParentScope(sym::Union{Num, Symbolic, Symbolics.Arr{Num}})
             a1 = setmetadata(args[1], SymScope,
                 ParentScope(getmetadata(value(args[1]), SymScope, LocalScope())))
             maketerm(typeof(sym), operation(sym), [a1, args[2:end]...],
-                symtype(sym), metadata(sym))
+                metadata(sym))
         else
             setmetadata(sym, SymScope,
                 ParentScope(getmetadata(value(sym), SymScope, LocalScope())))
@@ -1146,7 +1146,7 @@ function DelayParentScope(sym::Union{Num, Symbolic, Symbolics.Arr{Num}}, N)
             a1 = setmetadata(args[1], SymScope,
                 DelayParentScope(getmetadata(value(args[1]), SymScope, LocalScope()), N))
             maketerm(typeof(sym), operation(sym), [a1, args[2:end]...],
-                symtype(sym), metadata(sym))
+                metadata(sym))
         else
             setmetadata(sym, SymScope,
                 DelayParentScope(getmetadata(value(sym), SymScope, LocalScope()), N))
@@ -1162,7 +1162,7 @@ function GlobalScope(sym::Union{Num, Symbolic, Symbolics.Arr{Num}})
             args = arguments(sym)
             a1 = setmetadata(args[1], SymScope, GlobalScope())
             maketerm(typeof(sym), operation(sym), [a1, args[2:end]...],
-                symtype(sym), metadata(sym))
+                metadata(sym))
         else
             setmetadata(sym, SymScope, GlobalScope())
         end
@@ -1180,13 +1180,13 @@ function renamespace(sys, x)
         if iscall(x) && operation(x) isa Operator
             return maketerm(typeof(x), operation(x),
                 Any[renamespace(sys, only(arguments(x)))],
-                symtype(x), metadata(x))::T
+                metadata(x))::T
         end
         if iscall(x) && operation(x) === getindex
             args = arguments(x)
             return maketerm(
                 typeof(x), operation(x), vcat(renamespace(sys, args[1]), args[2:end]),
-                symtype(x), metadata(x))::T
+                metadata(x))::T
         end
         let scope = getmetadata(x, SymScope, LocalScope())
             if scope isa LocalScope
@@ -1271,13 +1271,12 @@ function namespace_expr(
             # metadata from the rescoped variable
             rescoped = renamespace(n, O)
             maketerm(typeof(rescoped), operation(rescoped), renamed,
-                symtype(rescoped),
                 metadata(rescoped))
         elseif Symbolics.isarraysymbolic(O)
             # promote_symtype doesn't work for array symbolics
-            maketerm(typeof(O), operation(O), renamed, symtype(O), metadata(O))
+            maketerm(typeof(O), operation(O), renamed, metadata(O))
         else
-            maketerm(typeof(O), operation(O), renamed, symtype(O), metadata(O))
+            maketerm(typeof(O), operation(O), renamed, metadata(O))
         end
     elseif isvariable(O)
         renamespace(n, O)
@@ -2275,14 +2274,13 @@ function linearization_function(sys::AbstractSystem, inputs,
     end
     x0 = merge(defaults_and_guesses(sys), op)
     if has_index_cache(sys) && get_index_cache(sys) !== nothing
-        sys_ps = MTKParameters(sys, p, x0; eval_expression, eval_module)
+        sys_ps = MTKParameters(sys, p, x0)
     else
         sys_ps = varmap_to_vars(p, parameters(sys); defaults = x0)
     end
     p[get_iv(sys)] = NaN
     if has_index_cache(initsys) && get_index_cache(initsys) !== nothing
-        oldps = MTKParameters(initsys, p, merge(guesses(sys), defaults(sys), op);
-            eval_expression, eval_module)
+        oldps = MTKParameters(initsys, p, merge(guesses(sys), defaults(sys), op))
         initsys_ps = parameters(initsys)
         p_getter = build_explicit_observed_function(
             sys, initsys_ps; eval_expression, eval_module)

src/systems/clock_inference.jl

@@ -63,7 +63,7 @@ function substitute_sample_time(ex, dt)
             end
             new_args[i] = ex_arg
         end
-        maketerm(typeof(ex), op, new_args, symtype(ex), metadata(ex))
+        maketerm(typeof(ex), op, new_args, metadata(ex))
     end
 end