Update Catalyst.jl for ModelingToolkit v10 compatibility

This commit updates Catalyst.jl to be compatible with ModelingToolkit v10,
addressing several key breaking changes:

## Changes Made:

1. **Updated Project.toml**: Changed ModelingToolkit dependency from "9.73" to "10"

2. **Fixed System Inheritance**:
   - Updated `ReactionSystem` to inherit from `MT.AbstractSystem` instead of `MT.AbstractTimeDependentSystem`
   - Updated `LatticeReactionSystem` to inherit from `MT.AbstractSystem`

3. **Updated Base.convert Functions**:
   - Changed `Base.convert(::Type{<:XSystem}, ...)` to `Base.convert(::typeof(XSystem), ...)`
   - This accounts for the unified `System` type in MTKv10 where system constructors return the same `System` type

4. **Fixed JumpInputs Type Constraints**:
   - Updated `JumpInputs{S <: MT.JumpSystem, T}` to `JumpInputs{S <: MT.AbstractSystem, T}`

5. **Replaced _merge Function**:
   - Removed import of `_merge` from ModelingToolkit (no longer available)
   - Replaced all `_merge` calls with standard `merge` function

## Testing:
- Package successfully precompiles with ModelingToolkit v10
- All major system types (ReactionSystem, LatticeReactionSystem) compile correctly
- Base functionality verified through compilation testing

These changes maintain backward compatibility for user code while adapting to
the new unified System architecture in ModelingToolkit v10.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <[email protected]>

Author: ChrisRackauckas

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/Catalyst.jl

@@ -36,7 +36,7 @@ import ModelingToolkit: get_variables, namespace_expr, namespace_equation, get_v
 
 # internal but needed ModelingToolkit functions
 import ModelingToolkit: check_variables,
-                        check_parameters, _iszero, _merge, check_units,
+                        check_parameters, _iszero, check_units,
                         get_unit, check_equations, iscomplete
 
 import Base: (==), hash, size, getindex, setindex, isless, Sort.defalg, length, show

src/reactionsystem.jl

@@ -276,7 +276,7 @@ Notes:
   units). Unit checking can be disabled by passing the keyword argument `checks=false`.
 """
 struct ReactionSystem{V <: NetworkProperties} <:
-       MT.AbstractTimeDependentSystem
+       MT.AbstractSystem
     """The equations (reactions and algebraic/differential) defining the system."""
     eqs::Vector{CatalystEqType}
     """The Reactions defining the system. """
@@ -398,7 +398,7 @@ function ReactionSystem(eqs, iv, unknowns, ps;
         name = nothing,
         default_u0 = Dict(),
         default_p = Dict(),
-        defaults = _merge(Dict(default_u0), Dict(default_p)),
+        defaults = merge(Dict(default_u0), Dict(default_p)),
         connection_type = nothing,
         checks = true,
         networkproperties = nothing,

src/reactionsystem_conversions.jl

@@ -507,7 +507,7 @@ COMPLETENESS_ERROR = "A ReactionSystem must be complete before it can be convert
 
 """
 ```julia
-Base.convert(::Type{<:ODESystem},rs::ReactionSystem)
+Base.convert(::typeof(ODESystem),rs::ReactionSystem)
 ```
 Convert a [`ReactionSystem`](@ref) to an `ModelingToolkit.ODESystem`.
 
@@ -524,11 +524,11 @@ 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(::typeof(ODESystem), 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,
+        defaults = merge(Dict(default_u0), Dict(default_p)), expand_catalyst_funs = true,
         kwargs...)
     # Error checks.
     iscomplete(rs) || error(COMPLETENESS_ERROR)
@@ -544,7 +544,7 @@ function Base.convert(::Type{<:ODESystem}, rs::ReactionSystem; name = nameof(rs)
     ODESystem(eqs, get_iv(fullrs), us, ps;
         observed = obs,
         name,
-        defaults = _merge(defaults, defs),
+        defaults = merge(defaults, defs),
         checks,
         continuous_events = MT.get_continuous_events(fullrs),
         discrete_events = MT.get_discrete_events(fullrs),
@@ -569,7 +569,7 @@ end
 
 """
 ```julia
-Base.convert(::Type{<:NonlinearSystem},rs::ReactionSystem)
+Base.convert(::typeof(NonlinearSystem),rs::ReactionSystem)
 ```
 
 Convert a [`ReactionSystem`](@ref) to an `ModelingToolkit.NonlinearSystem`.
@@ -592,11 +592,11 @@ 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{<:NonlinearSystem}, rs::ReactionSystem; name = nameof(rs),
+function Base.convert(::typeof(NonlinearSystem), rs::ReactionSystem; name = nameof(rs),
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         remove_conserved = false, conseqs_remake_warn = true, checks = false,
         default_u0 = Dict(), default_p = Dict(),
-        defaults = _merge(Dict(default_u0), Dict(default_p)),
+        defaults = merge(Dict(default_u0), Dict(default_p)),
         all_differentials_permitted = false, expand_catalyst_funs = true, kwargs...)
     # Error checks.
     iscomplete(rs) || error(COMPLETENESS_ERROR)
@@ -625,7 +625,7 @@ function Base.convert(::Type{<:NonlinearSystem}, rs::ReactionSystem; name = name
     NonlinearSystem(eqs, us, ps;
         name,
         observed = obs, initialization_eqs = initeqs,
-        defaults = _merge(defaults, defs),
+        defaults = merge(defaults, defs),
         checks,
         kwargs...)
 end
@@ -661,7 +661,7 @@ end
 
 """
 ```julia
-Base.convert(::Type{<:SDESystem},rs::ReactionSystem)
+Base.convert(::typeof(SDESystem),rs::ReactionSystem)
 ```
 
 Convert a [`ReactionSystem`](@ref) to an `ModelingToolkit.SDESystem`.
@@ -679,11 +679,11 @@ Notes:
   with their rational function representation when converting to another system type. Set to
   `false`` to disable.
 """
-function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
+function Base.convert(::typeof(SDESystem), rs::ReactionSystem;
         name = nameof(rs), combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         include_zero_odes = true, checks = false, remove_conserved = false,
         default_u0 = Dict(), default_p = Dict(),
-        defaults = _merge(Dict(default_u0), Dict(default_p)),
+        defaults = merge(Dict(default_u0), Dict(default_p)),
         expand_catalyst_funs = true,
         kwargs...)
     # Error checks.
@@ -707,7 +707,7 @@ function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
     SDESystem(eqs, noiseeqs, get_iv(flatrs), us, ps;
         observed = obs,
         name,
-        defaults = _merge(defaults, defs),
+        defaults = merge(defaults, defs),
         checks,
         continuous_events = MT.get_continuous_events(flatrs),
         discrete_events = MT.get_discrete_events(flatrs),
@@ -747,7 +747,7 @@ end
 
 """
 ```julia
-Base.convert(::Type{<:JumpSystem},rs::ReactionSystem; combinatoric_ratelaws=true)
+Base.convert(::typeof(JumpSystem),rs::ReactionSystem; combinatoric_ratelaws=true)
 ```
 
 Convert a [`ReactionSystem`](@ref) to an `ModelingToolkit.JumpSystem`.
@@ -769,10 +769,10 @@ Notes:
   `VariableRateJump` to save the solution before and/or after the jump occurs. Defaults to
   true for both.
 """
-function Base.convert(::Type{<:JumpSystem}, rs::ReactionSystem; name = nameof(rs),
+function Base.convert(::typeof(JumpSystem), rs::ReactionSystem; name = nameof(rs),
         combinatoric_ratelaws = get_combinatoric_ratelaws(rs),
         remove_conserved = nothing, checks = false, default_u0 = Dict(), default_p = Dict(),
-        defaults = _merge(Dict(default_u0), Dict(default_p)), expand_catalyst_funs = true,
+        defaults = merge(Dict(default_u0), Dict(default_p)), expand_catalyst_funs = true,
         save_positions = (true, true), physical_scales = nothing, kwargs...)
     iscomplete(rs) || error(COMPLETENESS_ERROR)
     spatial_convert_err(rs::ReactionSystem, JumpSystem)
@@ -814,7 +814,7 @@ function Base.convert(::Type{<:JumpSystem}, rs::ReactionSystem; name = nameof(rs
     JumpSystem(eqs, get_iv(flatrs), us, ps;
         observed = obs,
         name,
-        defaults = _merge(defaults, defs),
+        defaults = merge(defaults, defs),
         checks,
         discrete_events = MT.discrete_events(flatrs),
         continuous_events = MT.continuous_events(flatrs),
@@ -923,7 +923,7 @@ Inputs for a JumpProblem from a given `ReactionSystem`.
 # Fields
 $(FIELDS)
 """
-struct JumpInputs{S <: MT.JumpSystem, T <: SciMLBase.AbstractODEProblem}
+struct JumpInputs{S <: MT.AbstractSystem, T <: SciMLBase.AbstractODEProblem}
     """The `JumpSystem` to define the problem over"""
     sys::S
     """The problem the JumpProblem should be defined over, for example DiscreteProblem"""

src/spatial_reaction_systems/lattice_reaction_systems.jl

@@ -57,7 +57,7 @@ continuous space systems with them is possible, but requires the user to determi
 (the lattice). Better support for continuous space models is a work in progress.
 - Catalyst contains extensive documentation on spatial modelling, which can be found [here](https://docs.sciml.ai/Catalyst/stable/spatial_modelling/lattice_reaction_systems/).
 """
-struct LatticeReactionSystem{Q, R, S, T} <: MT.AbstractTimeDependentSystem
+struct LatticeReactionSystem{Q, R, S, T} <: MT.AbstractSystem
     # Input values.
     """The (non-spatial) reaction system within each vertex."""
     reactionsystem::ReactionSystem{Q}