init

Author: TorkelE

ext/CatalystHomotopyContinuationExtension/homotopy_continuation_extension.jl

@@ -104,4 +104,27 @@ 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
+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

src/reactionsystem.jl

@@ -1296,6 +1296,11 @@ 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 && for eq in eqs
+        eq.rhs = expand_registered_functions!(eq.rhs)
+    end
 
     ODESystem(eqs, get_iv(fullrs), sts, ps;
               observed = obs,
@@ -1404,6 +1409,11 @@ 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).
+    expand_functions && for eq in eqs
+        eq.rhs = expand_registered_functions!(eq.rhs)
+    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