Error in High Level Example from GitHub front page

[TorkelE]

Hello,
I try to run this, simply the code copied from the GitHub front page:

using ModelingToolkit, OrdinaryDiffEq

@parameters t σ ρ β
@variables x(t) y(t) z(t)
@derivatives D'~t

eqs = [D(D(x)) ~ σ*(y-x),
       D(y) ~ x*(ρ-z)-y,
       D(z) ~ x*y - β*z]

sys = ODESystem(eqs)
sys = ode_order_lowering(sys)

u0 = [D(x) => 2.0,
      x => 1.0,
      y => 0.0,
      z => 0.0]

p  = [σ => 28.0,
      ρ => 10.0,
      β => 8/3]

tspan = (0.0,100.0)
prob = ODEProblem(sys,u0,tspan,p,jac=true)
sol = solve(prob,Tsit5())
using Plots; plot(sol,vars=(x,y))

everything works well, until the line prob = ODEProblem(sys,u0,tspan,p,jac=true) which generates an error:

MethodError: no method matching ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ODESystem, ::Array{Variable,1}, ::Array{Variable,1}; analytic=nothing, tgrad=Base.RefValue{Array{Expression,1}}(Expression[]), jac=Base.RefValue{Array{Expression,2}}(Array{Expression}(undef,0,0)), jvp=nothing, vjp=nothing, Wfact=Base.RefValue{Array{Expression,2}}(Array{Expression}(undef,0,0)), Wfact_t=Base.RefValue{Array{Expression,2}}(Array{Expression}(undef,0,0)), paramjac=nothing, syms=nothing, colorvec=nothing)
Closest candidates are:
  ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ModelingToolkit.AbstractODESystem, ::Any, ::Any; version, tgrad, jac, Wfact) where iip at /home/torkelloman/.julia/packages/ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125 got unsupported keyword arguments "analytic", "jvp", "vjp", "Wfact_t", "paramjac", "syms", "colorvec"
  ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ModelingToolkit.AbstractODESystem, ::Any) where iip at /home/torkelloman/.julia/packages/ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125 got unsupported keyword arguments "analytic", "tgrad", "jac", "jvp", "vjp", "Wfact", "Wfact_t", "paramjac", "syms", "colorvec"
  ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ModelingToolkit.AbstractODESystem) where iip at /home/torkelloman/.julia/packages/ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125 got unsupported keyword arguments "analytic", "tgrad", "jac", "jvp", "vjp", "Wfact", "Wfact_t", "paramjac", "syms", "colorvec"
  ...
in top-level scope at test.jl:24
in  at DiffEqBase/jMOwn/src/problems/ode_problems.jl:76
in #ODEProblem#214 at DiffEqBase/jMOwn/src/problems/ode_problems.jl:76
in convert at DiffEqBase/jMOwn/src/diffeqfunction.jl:989
in  at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:111
in #ODEFunction#79 at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:111 
in  at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125
in  at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125
in kwerr at base/error.jl:157

Next, I try the second example:

using ModelingToolkit, OrdinaryDiffEq

@parameters t σ ρ β
@variables x(t) y(t) z(t)
@derivatives D'~t

eqs = [D(x) ~ σ*(y-x),
       D(y) ~ x*(ρ-z)-y,
       D(z) ~ x*y - β*z]

lorenz1 = ODESystem(eqs,name=:lorenz1)
lorenz2 = ODESystem(eqs,name=:lorenz2)

@variables a
@parameters γ
connections = [0 ~ lorenz1.x + lorenz2.y + a*γ]
connected = ODESystem(connections,t,[a],[γ],systems=[lorenz1,lorenz2])

u0 = [lorenz1.x => 1.0,
      lorenz1.y => 0.0,
      lorenz1.z => 0.0,
      lorenz2.x => 0.0,
      lorenz2.y => 1.0,
      lorenz2.z => 0.0,
      a => 2.0]

p  = [lorenz1.σ => 10.0,
      lorenz1.ρ => 28.0,
      lorenz1.β => 8/3,
      lorenz2.σ => 10.0,
      lorenz2.ρ => 28.0,
      lorenz2.β => 8/3,
      γ => 2.0]

tspan = (0.0,100.0)
prob = ODEProblem(connected,u0,tspan,p)
sol = solve(prob,Rodas5())

using Plots; plot(sol,vars=(a,lorenz1.x,lorenz2.z))

and again I run into an error on the line prob = ODEProblem(connected,u0,tspan,p):

MethodError: no method matching ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ODESystem, ::Array{Variable,1}, ::Array{Variable,1}; analytic=nothing, tgrad=Base.RefValue{Array{Expression,1}}(Expression[]), jac=Base.RefValue{Array{Expression,2}}(Array{Expression}(undef,0,0)), jvp=nothing, vjp=nothing, Wfact=Base.RefValue{Array{Expression,2}}(Array{Expression}(undef,0,0)), Wfact_t=Base.RefValue{Array{Expression,2}}(Array{Expression}(undef,0,0)), paramjac=nothing, syms=nothing, colorvec=nothing)
Closest candidates are:
  ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ModelingToolkit.AbstractODESystem, ::Any, ::Any; version, tgrad, jac, Wfact) where iip at /home/torkelloman/.julia/packages/ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125 got unsupported keyword arguments "analytic", "jvp", "vjp", "Wfact_t", "paramjac", "syms", "colorvec"
  ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ModelingToolkit.AbstractODESystem, ::Any) where iip at /home/torkelloman/.julia/packages/ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125 got unsupported keyword arguments "analytic", "tgrad", "jac", "jvp", "vjp", "Wfact", "Wfact_t", "paramjac", "syms", "colorvec"
  ODEFunction{true,F,TMM,Ta,Tt,TJ,JVP,VJP,JP,TW,TWt,TPJ,S,TCV} where TCV where S where TPJ where TWt where TW where JP where VJP where JVP where TJ where Tt where Ta where TMM where F(::ModelingToolkit.AbstractODESystem) where iip at /home/torkelloman/.julia/packages/ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125 got unsupported keyword arguments "analytic", "tgrad", "jac", "jvp", "vjp", "Wfact", "Wfact_t", "paramjac", "syms", "colorvec"
  ...
in top-level scope at test.jl:36
in ODEProblem at DiffEqBase/jMOwn/src/problems/ode_problems.jl:76
in #ODEProblem#214 at DiffEqBase/jMOwn/src/problems/ode_problems.jl:76
in convert at DiffEqBase/jMOwn/src/diffeqfunction.jl:989
in  at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:111
in #ODEFunction#79 at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:111 
in  at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125
in  at ModelingToolkit/N4mo2/src/systems/diffeqs/abstractodesystem.jl:125
in kwerr at base/error.jl:157

I am running this in atom. This is the list of package versions of possibly relevant packages:

  [c52e3926] Atom v0.12.10
  [2b5f629d] DiffEqBase v6.10.2
  [0c46a032] DifferentialEquations v6.9.0
  [e5e0dc1b] Juno v0.8.1
  [961ee093] ModelingToolkit v2.0.0
  [1dea7af3] OrdinaryDiffEq v5.26.8

Hope this is not a too embarrassing issue, that I should have caught myself.

[ChrisRackauckas]

MTK should be version 3, not 2.

[TorkelE]

Thanks. In my defence I tried running Pkg 'update' and Pkg update ModelingToolkit, but it doesn't seem to get me later versions, however, that is probably some issue I should be able to fix.

[ChrisRackauckas]

DiffEqBio might be the issue? I know that the homotopycontinuation bound tends to cause some problems.

[TorkelE]

That seems like a good track, thanks for the lead.

[TorkelE]

Actually it seems to have been StochasticDelayDiffEq. Removing it allowed the update (as well as another update to Plots). Re-adding StochasticDelayDiffEq then downgrade ModellingToolkit back to v2.

[ChrisRackauckas]

Yeah we need to update that.