complete converted sys and get u0 and p from oprob

Author: isaacsas

benchmarks/Bio/BCR.jmd

@@ -30,7 +30,7 @@ show(to)
 rn    = complete(prnbng.rn)
 obs = [eq.lhs for eq in observed(rn)]
 
-@timeit to "Create ODESys" osys = convert(ODESystem, rn)
+@timeit to "Create ODESys" osys = complete(convert(ODESystem, rn))
 show(to)
 
 tspan = (0.,tf)
@@ -56,12 +56,12 @@ As compiling the ODE derivative functions has in the past taken longer than
 running a simulation, we first force compilation by evaluating these functions
 one time.
 ```julia
-u  = ModelingToolkit.varmap_to_vars(nothing, species(rn); defaults=ModelingToolkit.defaults(rn))
+u = oprob.u0
 du = copy(u)
-p  = ModelingToolkit.varmap_to_vars(nothing, parameters(rn); defaults=ModelingToolkit.defaults(rn))
+p = oprob.p
 @timeit to "ODE rhs Eval1" oprob.f(du,u,p,0.)
-@timeit to "ODE rhs Eval2" oprob.f(du,u,p,0.)
-sparsejacprob.f(du,u,p,0.)
+@timeit to "ODE rhs spjac Eval1" sparsejacprob.f(du,u,p,0.)
+show(to)
 ```
 
 We also time the ODE rhs function with BenchmarkTools as it is more accurate