update for diffeq syntax changes

Author: ChrisRackauckas

README.md

@@ -237,7 +237,7 @@ end
 and mutate `tis.values` in `f`. For example, we could have
 
 ```julia
-function f(t, tissue::Tissue, du)
+function f(du, tissue::Tissue, p, t)
     du .+= randn(3)
 end
 ```

test/REQUIRE

@@ -1,2 +1,2 @@
-OrdinaryDiffEq 2.29.1
-StochasticDiffEq 1.1.0
+OrdinaryDiffEq 3.0.0
+StochasticDiffEq 3.0.0

test/additional_fields_test.jl

@@ -23,7 +23,7 @@ host = construct(Host,[
         )]
     )
 
-evolve = function (t,u::Host,du)
+evolve = function (du,u::Host,p,t)
   for i in 1:length(u)
     du[i] = 2*u[i]
   end
@@ -60,7 +60,7 @@ host2 = construct(Host2,[
         :my_cell_type
     )
 
-evolve = function (t,u::Host2,du)
+evolve = function (du,u::Host2,p,t)
   for i in 1:length(u)
     du[i] = 2*u[i]
   end

test/dynamic_diffeq.jl

@@ -32,22 +32,22 @@ tissue1 = construct(Tissue, deepcopy([population, population2])) # Make a Tissue
 tissue2 = construct(Tissue, deepcopy([population2, population]))
 embryo = construct(Embryo, deepcopy([tissue1, tissue2])) # Make an embryo from Tissues
 
-cell_ode = function (t, cell, dcell)
+cell_ode = function (dcell,cell,p,t)
     m = mean(cell)
     for i in eachindex(cell)
         dcell[i] = -m*cell[i]
     end
 end
 
-f = function (t, embryo, dembryo)
+f = function (dembryo,embryo,p,t)
     for (cell, y, z) in LevelIterIdx(embryo, 2)
-        cell_ode(t, cell, @view dembryo[y:z])
+        cell_ode(@view(dembryo[y:z]),cell,p,t)
     end
 end
 
 tstop = [0.5]
 
-condition = function (t, u, integrator)
+condition = function (u, t, integrator)
     t ∈ tstop
 end
 
@@ -82,7 +82,7 @@ sol = solve(prob, Rosenbrock23(), callback=shrinking_cb, tstops=tstop)
 
 println("Do the SDE Part")
 
-g = function (t, u, du)
+g = function (du,u,p,t)
     for i in eachindex(u)
         du[i] = 0.1u[i]
     end

test/indexing_and_creation_tests.jl

@@ -143,12 +143,12 @@ p/zero(t)
 
 size(p)
 
-f = function (t, u, du)
+f = function (du,u,p,t)
     for i in eachindex(u)
         du[i] = 0.42*u[i]
     end
 end
-g = function (t, u, du)
+g = function (du,u,p,t)
     for i in eachindex(u)
         du[i] = 0.42*u[i]
     end