WIP: MTK v10

Project.toml

@@ -62,7 +62,7 @@ LaTeXStrings = "1.3.0"
 Latexify = "0.16.6"
 MacroTools = "0.5.5"
 Makie = "0.22.1"
-ModelingToolkit = "9.73"
+ModelingToolkit = "10"
 NetworkLayout = "0.4.7"
 Parameters = "0.12"
 Reexport = "1.0"

src/latexify_recipes.jl

@@ -19,7 +19,7 @@ const LATEX_DEFS = CatalystLatexParams()
         return rs
     elseif form == :ode      # Returns ODE system code.
         mult_symbol --> ""
-        return convert(ODESystem, rs)
+        return convert(System, rs)
     elseif form == :sde      # Returns SDE system code.
         mult_symbol --> ""
         return convert(SDESystem, rs)

src/reactionsystem.jl

@@ -258,7 +258,7 @@ Continuing from the example in the [`Reaction`](@ref) definition:
 Keyword Arguments:
 - `observed::Vector{Equation}`, equations specifying observed variables.
 - `systems::Vector{AbstractSystems}`, vector of sub-systems. Can be `ReactionSystem`s,
-  `ODESystem`s, or `NonlinearSystem`s.
+  `System`s, or `NonlinearSystem`s.
 - `name::Symbol`, the name of the system (must be provided, or `@named` must be used).
 - `defaults::Dict`, a dictionary mapping parameters to their default values and species to
   their default initial values.
@@ -545,7 +545,7 @@ function make_ReactionSystem_internal(rxs_and_eqs::Vector, iv, us_in, ps_in;
     # Extracts any species, variables, and parameters that occur in (non-reaction) equations.
     # Creates the new reactions + equations vector, `fulleqs` (sorted reactions first, equations next).
     if !isempty(eqs)
-        osys = ODESystem(eqs, iv; name = gensym())
+        osys = System(eqs, iv; name = gensym())
         fulleqs = CatalystEqType[rxs; equations(osys)]
         union!(us, unknowns(osys))
         union!(ps, parameters(osys))
@@ -1399,7 +1399,7 @@ Notes:
 - All `Reaction`s within subsystems are namespaced and merged into the list of `Reactions`
   of `rs`. The merged list is then available as `reactions(rs)`.
 - All algebraic and differential equations are merged in the equations of `rs`.
-- Currently only `ReactionSystem`s, `NonlinearSystem`s and `ODESystem`s are supported as
+- Currently only `ReactionSystem`s, `NonlinearSystem`s and `System`s are supported as
   sub-systems when flattening.
 - `rs.networkproperties` is reset upon flattening.
 - The default value of `combinatoric_ratelaws` will be the logical or of all
@@ -1408,11 +1408,11 @@ Notes:
 function MT.flatten(rs::ReactionSystem; name = nameof(rs))
     isempty(get_systems(rs)) && return rs
 
-    # right now only NonlinearSystems and ODESystems can be handled as subsystems
+    # right now only NonlinearSystems and Systems can be handled as subsystems
     subsys_types = getsubsystypes(rs)
-    allowed_types = (ReactionSystem, NonlinearSystem, ODESystem)
+    allowed_types = (ReactionSystem, NonlinearSystem, System)
     all(T -> any(T .<: allowed_types), subsys_types) ||
-        error("flattening is currently only supported for subsystems mixing ReactionSystems, NonlinearSystems and ODESystems.")
+        error("flattening is currently only supported for subsystems mixing ReactionSystems, NonlinearSystems and Systems.")
 
     ReactionSystem(equations(rs), get_iv(rs), unknowns(rs), parameters(rs);
         observed = MT.observed(rs),
@@ -1440,7 +1440,7 @@ end
 Compose the indicated [`ReactionSystem`](@ref) with one or more `AbstractSystem`s.
 
 Notes:
-- The `AbstractSystem` being added in must be an `ODESystem`, `NonlinearSystem`,
+- The `AbstractSystem` being added in must be an `System`, `NonlinearSystem`,
   or `ReactionSystem` currently.
 - Returns a new `ReactionSystem` and does not modify `rs`.
 - By default, the new `ReactionSystem` will have the same name as `sys`.
@@ -1479,7 +1479,7 @@ end
 Extends the indicated [`ReactionSystem`](@ref) with another `AbstractSystem`.
 
 Notes:
-- The `AbstractSystem` being added in must be an `ODESystem`, `NonlinearSystem`,
+- The `AbstractSystem` being added in must be an `System`, `NonlinearSystem`,
   or `ReactionSystem` currently.
 - Returns a new `ReactionSystem` and does not modify `rs`.
 - By default, the new `ReactionSystem` will have the same name as `sys`.
@@ -1490,8 +1490,8 @@ function ModelingToolkit.extend(sys::MT.AbstractSystem, rs::ReactionSystem;
     complete_check(sys, "ModelingToolkit.extend")
     complete_check(rs, "ModelingToolkit.extend")
 
-    any(T -> sys isa T, (ReactionSystem, ODESystem, NonlinearSystem)) ||
-        error("ReactionSystems can only be extended with ReactionSystems, ODESystems and NonlinearSystems currently. Received a $(typeof(sys)) system.")
+    any(T -> sys isa T, (ReactionSystem, System, NonlinearSystem)) ||
+        error("ReactionSystems can only be extended with ReactionSystems, Systems and NonlinearSystems currently. Received a $(typeof(sys)) system.")
 
     t = get_iv(rs)
     if MT.has_iv(sys)

src/reactionsystem_conversions.jl

@@ -466,7 +466,7 @@ function addconstraints!(eqs, rs::ReactionSystem, ists, ispcs; remove_conserved
                   conservation laws. Catalyst does not check that the conserved equations
                   still hold for the final coupled system of equations. Consider using
                   `remove_conserved = false` and instead calling
-                  ModelingToolkit.structural_simplify to simplify any generated ODESystem or
+                  ModelingToolkit.structural_simplify to simplify any generated System or
                   NonlinearSystem.
                   """
         end
@@ -509,9 +509,9 @@ COMPLETENESS_ERROR = "A ReactionSystem must be complete before it can be convert
 
 """
 ```julia
-Base.convert(::Type{<:ODESystem},rs::ReactionSystem)
+Base.convert(::Type{<:System},rs::ReactionSystem)
 ```
-Convert a [`ReactionSystem`](@ref) to an `ModelingToolkit.ODESystem`.
+Convert a [`ReactionSystem`](@ref) to an `ModelingToolkit.System`.
 
 Keyword args and default values:
 - `combinatoric_ratelaws=true` uses factorial scaling factors in calculating the rate law,
@@ -526,15 +526,15 @@ Keyword args and default values:
   with their rational function representation when converting to another system type. Set to
   `false`` to disable.
 """
-function Base.convert(::Type{<:ODESystem}, rs::ReactionSystem; name = nameof(rs),
+function Base.convert(::Type{<:System}, rs::ReactionSystem; name = nameof(rs),
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         include_zero_odes = true, remove_conserved = false, checks = false, 
         default_u0 = Dict(), default_p = Dict(), 
         defaults = _merge(Dict(default_u0), Dict(default_p)), expand_catalyst_funs = true, 
         kwargs...)
     # Error checks.
     iscomplete(rs) || error(COMPLETENESS_ERROR)
-    spatial_convert_err(rs::ReactionSystem, ODESystem)
+    spatial_convert_err(rs::ReactionSystem, System)
 
     fullrs = Catalyst.flatten(rs)
     remove_conserved && conservationlaws(fullrs)
@@ -543,7 +543,7 @@ function Base.convert(::Type{<:ODESystem}, rs::ReactionSystem; name = nameof(rs)
         include_zero_odes, expand_catalyst_funs)
     eqs, us, ps, obs, defs = addconstraints!(eqs, fullrs, ists, ispcs; remove_conserved)
 
-    ODESystem(eqs, get_iv(fullrs), us, ps;
+    System(eqs, get_iv(fullrs), us, ps;
         observed = obs,
         name,
         defaults = _merge(defaults, defs),
@@ -828,7 +828,7 @@ function DiffEqBase.ODEProblem(rs::ReactionSystem, u0, tspan,
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         include_zero_odes = true, remove_conserved = false, checks = false, 
         expand_catalyst_funs = true, structural_simplify = false, kwargs...)
-    osys = convert(ODESystem, rs; name, combinatoric_ratelaws, include_zero_odes, checks,
+    osys = convert(System, rs; name, combinatoric_ratelaws, include_zero_odes, checks,
         remove_conserved, expand_catalyst_funs)
 
     # Handles potential differential algebraic equations (which requires `structural_simplify`).
@@ -1058,7 +1058,7 @@ function DiffEqBase.SteadyStateProblem(rs::ReactionSystem, u0,
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         remove_conserved = false, include_zero_odes = true, checks = false, 
         expand_catalyst_funs = true, structural_simplify = false, kwargs...)
-    osys = convert(ODESystem, rs; name, combinatoric_ratelaws, include_zero_odes, checks,
+    osys = convert(System, rs; name, combinatoric_ratelaws, include_zero_odes, checks,
         remove_conserved, expand_catalyst_funs)
 
     # Handles potential differential algebraic equations (which requires `structural_simplify`).

src/reactionsystem_serialisation/serialise_reactionsystem.jl

@@ -28,7 +28,7 @@ rn = include("rn.jls")
 Notes:
 - `ReactionSystem`s with the `connection_type` field has this ignored (saving of this field has not
   been implemented yet).
-- `ReactionSystem`s with non-`ReactionSystem` sub-systems (e.g. `ODESystem`s) cannot be saved.
+- `ReactionSystem`s with non-`ReactionSystem` sub-systems (e.g. `System`s) cannot be saved.
 - Reaction systems with components that have units cannot currently be saved.
 - The `ReactionSystem` is saved using *programmatic* (not DSL) format for model creation.
 """

src/spatial_reaction_systems/lattice_sim_struct_interfacing.jl

@@ -455,7 +455,7 @@ function rebuild_lat_internals!(lt_ofun::LatticeTransportODEFunction, ps_new,
 
     # Updating the `MTKParameters` structure is a bit more complicated.
     p_dict = Dict(ps_new)
-    osys = complete(convert(ODESystem, reactionsystem(lrs)))
+    osys = complete(convert(System, reactionsystem(lrs)))
     for p in parameters(osys)
         MT.setp(osys, p)(lt_ofun.mtk_ps, (p_dict[p] isa Number) ? p_dict[p] : p_dict[p][1])
     end

src/spatial_reaction_systems/spatial_ODE_systems.jl

@@ -95,7 +95,7 @@ end
 # the vertex parameter values during the simulations).
 function make_mtk_ps_structs(ps, lrs, heterogeneous_vert_p_idxs)
     p_dict = Dict(ps)
-    nonspatial_osys = complete(convert(ODESystem, reactionsystem(lrs)))
+    nonspatial_osys = complete(convert(System, reactionsystem(lrs)))
     p_init = [p => p_dict[p][1] for p in parameters(nonspatial_osys)]
     mtk_ps = MT.MTKParameters(nonspatial_osys, p_init)
     p_setters = [MT.setp(nonspatial_osys, p)
@@ -220,7 +220,7 @@ function build_odefunction(lrs::LatticeReactionSystem, vert_ps::Vector{Pair{R, V
     end
 
     # Prepares the inputs to the `LatticeTransportODEFunction` functor. 
-    osys = complete(convert(ODESystem, reactionsystem(lrs);
+    osys = complete(convert(System, reactionsystem(lrs);
         name, combinatoric_ratelaws, include_zero_odes, checks))
     ofunc_dense = ODEFunction(osys; jac = true, sparse = false)
     ofunc_sparse = ODEFunction(osys; jac = true, sparse = true)