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Author: TorkelE

ext/CatalystHomotopyContinuationExtension/homotopy_continuation_extension.jl

@@ -104,27 +104,4 @@ function filter_negative_f(sols; neg_thres=-1e-20)
         (neg_thres < sol[idx] < 0) && (sol[idx] = 0)
     end
     return filter(sol -> all(>=(0), sol), sols)
-end
-
-### Archived ###
-
-# # Unfolds a function (like mm or hill). 
-# function deregister(fs::Vector{T}, expr) where T
-#     for f in fs
-#         expr = deregister(f, expr) 
-#     end
-#     return expr
-# end
-# # Provided by Shashi Gowda.
-# deregister(f, expr) = wrap(Rewriters.Postwalk(Rewriters.PassThrough(___deregister(f)))(unwrap(expr)))
-# function ___deregister(f)
-#     (expr) ->
-#     if istree(expr) && operation(expr) == f
-#         args = arguments(expr)
-#         invoke_with = map(args) do a
-#             t = typeof(a)
-#             issym(a) || istree(a) ? wrap(a) => symtype(a) : a => typeof(a)
-#         end 
-#         invoke(f, Tuple{last.(invoke_with)...}, first.(invoke_with)...)
-#     end
-# end
+end

src/reactionsystem.jl

@@ -538,11 +538,6 @@ struct ReactionSystem{V <: NetworkProperties} <:
         checks && validate(rs)
         rs
     end
-
-    # Copies a reaction system, but with the option of having some fields replaced
-    function ReactionSystem(rs::ReactionSystem; eqs = rs.eqs, rxs = rs.rxs, iv = rs.iv, sivs = rs.sivs, states = rs.states, species = rs.species, ps = rs.ps, var_to_name = rs.var_to_name, observed = rs.observed, name = rs.name, systems = rs.systems, defaults = rs.defaults, connection_type = rs.connection_type, networkproperties = rs.networkproperties, combinatoric_ratelaws = rs.combinatoric_ratelaws, continuous_events = rs.continuous_events, discrete_events = rs.discrete_events, complete = rs.complete)
-        new{typeof(networkproperties)}(eqs, rxs, ModelingToolkit.unwrap(iv), ModelingToolkit.unwrap.(sivs), ModelingToolkit.unwrap.(states), ModelingToolkit.unwrap.(species), ModelingToolkit.unwrap.(ps), var_to_name, observed, name, systems, defaults, connection_type, networkproperties, combinatoric_ratelaws, continuous_events, discrete_events, complete)
-    end
 end
 
 function get_speciestype(iv, states, systems)
@@ -1301,9 +1296,6 @@ function Base.convert(::Type{<:ODESystem}, rs::ReactionSystem; name = nameof(rs)
     eqs = assemble_drift(fullrs, ispcs; combinatoric_ratelaws, remove_conserved,
                          include_zero_odes)
     eqs, sts, ps, obs, defs = addconstraints!(eqs, fullrs, ists, ispcs; remove_conserved)
-    
-    # Converts expressions like mm(X,v,K) to v*X/(X+K).
-    expand_functions  && (eqs = [eq.lhs ~ expand_registered_functions!(eq.rhs) for eq in eqs])
 
     ODESystem(eqs, get_iv(fullrs), sts, ps;
               observed = obs,
@@ -1412,12 +1404,6 @@ function Base.convert(::Type{<:SDESystem}, rs::ReactionSystem;
     eqs, sts, ps, obs, defs = addconstraints!(eqs, flatrs, ists, ispcs; remove_conserved)
     ps = (noise_scaling === nothing) ? ps : vcat(ps, toparam(noise_scaling))
 
-    # Converts expressions like mm(X,v,K) to v*X/(X+K).
-    if expand_functions
-        eqs = [eq.lhs ~ expand_registered_functions!(eq.rhs) for eq in eqs]
-        noiseeqs = [expand_registered_functions!(neq) for neq in noiseeqs]
-    end
-
     if any(isbc, get_states(flatrs))
         @info "Boundary condition species detected. As constraint equations are not currently supported when converting to SDESystems, the resulting system will be undetermined. Consider using constant species instead."
     end