fix test/dep_graphs.jl

Co-authored-by: "Yingbo Ma" <[email protected]>

Author: shashi

src/systems/jumps/jumpsystem.jl

@@ -289,7 +289,7 @@ function get_variables!(dep, jump::Union{ConstantRateJump,VariableRateJump}, var
 end
 
 function get_variables!(dep, jump::MassActionJump, variables)
-    sr = jump.scaled_rates
+    sr = value(jump.scaled_rates)
     (sr isa Symbolic) && get_variables!(dep, sr, variables)
     for varasop in jump.reactant_stoch
         any(isequal(varasop[1]), variables) && push!(dep, varasop[1])

src/systems/reaction/reactionsystem.jl

@@ -260,11 +260,11 @@ Notes:
 function jumpratelaw(rx; rxvars=get_variables(rx.rate), combinatoric_ratelaw=true)
     @unpack rate, substrates, substoich, only_use_rate = rx
     rl = rate
-    rl = substitute(rl, Dict(rxvars .=> var2op.(rxvars)))
+    #rl = substitute(rl, Dict(rxvars .=> var2op.(rxvars)))
     if !only_use_rate
         coef = one(eltype(substoich))
         for (i,stoich) in enumerate(substoich)
-            s   = var2op(substrates[i])
+            s   = substrates[i]
             rl *= s
             isone(stoich) && continue
             for i in one(stoich):(stoich-one(stoich))

test/dep_graphs.jl

@@ -100,4 +100,4 @@ eqs = [0 ~ σ*(y-x),
 ns = NonlinearSystem(eqs, [x,y,z],[σ,ρ,β])
 deps = equation_dependencies(ns)
 eq_sdeps = [[x,y],[y],[y,z]]
-@test all(i -> isequal(Set(deps[i]),Set(convert.(Variable,eq_sdeps[i]))), 1:length(deps))
+@test all(i -> isequal(Set(deps[i]),Set(value.(eq_sdeps[i]))), 1:length(deps))