refactor: recursively check for parameter dependencies everywhere

Co-authored-by: Aayush Sabharwal <aayush.sabharwal@juliahub.com>

Author: SebastianM-C

src/systems/abstractsystem.jl

@@ -970,7 +970,7 @@ function parameters(sys::AbstractSystem)
     result = unique(isempty(systems) ? ps :
                     [ps; reduce(vcat, namespace_parameters.(systems))])
     if has_parameter_dependencies(sys) &&
-       (pdeps = get_parameter_dependencies(sys)) !== nothing
+       (pdeps = parameter_dependencies(sys)) !== nothing
         filter(result) do sym
             !haskey(pdeps, sym)
         end
@@ -2391,8 +2391,8 @@ function extend(sys::AbstractSystem, basesys::AbstractSystem; name::Symbol = nam
     eqs = union(get_eqs(basesys), get_eqs(sys))
     sts = union(get_unknowns(basesys), get_unknowns(sys))
     ps = union(get_ps(basesys), get_ps(sys))
-    base_deps = get_parameter_dependencies(basesys)
-    deps = get_parameter_dependencies(sys)
+    base_deps = parameter_dependencies(basesys)
+    deps = parameter_dependencies(sys)
     dep_ps = isnothing(base_deps) ? deps :
              isnothing(deps) ? base_deps : union(base_deps, deps)
     obs = union(get_observed(basesys), get_observed(sys))

src/systems/diffeqs/sdesystem.jl

@@ -291,7 +291,7 @@ function stochastic_integral_transform(sys::SDESystem, correction_factor)
     end
 
     SDESystem(deqs, get_noiseeqs(sys), get_iv(sys), unknowns(sys), parameters(sys),
-        name = name, parameter_dependencies = get_parameter_dependencies(sys), checks = false)
+        name = name, parameter_dependencies = parameter_dependencies(sys), checks = false)
 end
 
 """
@@ -399,7 +399,7 @@ function Girsanov_transform(sys::SDESystem, u; θ0 = 1.0)
     # return modified SDE System
     SDESystem(deqs, noiseeqs, get_iv(sys), unknown_vars, parameters(sys);
         defaults = Dict(θ => θ0), observed = [weight ~ θ / θ0],
-        name = name, parameter_dependencies = get_parameter_dependencies(sys),
+        name = name, parameter_dependencies = parameter_dependencies(sys),
         checks = false)
 end
 

src/systems/parameter_buffer.jl

@@ -136,7 +136,7 @@ function MTKParameters(
     nonnumeric_buffer = nonnumeric_buffer
 
     if has_parameter_dependencies(sys) &&
-       (pdeps = get_parameter_dependencies(sys)) !== nothing
+       (pdeps = parameter_dependencies(sys)) !== nothing
         pdeps = Dict(k => fixpoint_sub(v, pdeps) for (k, v) in pdeps)
         dep_exprs = ArrayPartition((Any[missing for _ in 1:length(v)] for v in dep_buffer)...)
         for (sym, val) in pdeps