renames QueueMethod to Coevolve.

Author: gzagatti

benchmarks/Jumps/Diffusion_CTRW.jmd

@@ -21,7 +21,7 @@ N = 256
 h = 1 / N
 u0 = 10 * ones(Int64, N)
 tf = .01
-methods = (Direct(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
+methods = (Direct(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 jprob = JumpProblemLibrary.prob_jump_diffnetwork
 rn = jprob.network(N)

benchmarks/Jumps/Hawkes_process.jmd

@@ -56,7 +56,7 @@ function hawkes_jump(u, g, h)
     return [hawkes_jump(i, g, h) for i in 1:length(u)]
 end
 
-function hawkes_problem(p, agg::QueueMethod; u=[0.], tspan=(0., 50.), save_positions=(false, true),
+function hawkes_problem(p, agg::Coevolve; u=[0.], tspan=(0., 50.), save_positions=(false, true),
     g = [[1]], h = [[]])
     dprob = DiscreteProblem(u, tspan, p)
     jumps = hawkes_jump(u, g, h)
@@ -80,7 +80,7 @@ end
 ```
 
 ```julia
-methods = (Direct(), QueueMethod())
+methods = (Direct(), Coevolve())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 
 V = 10
@@ -96,7 +96,7 @@ plots = []
 for (i, method) in enumerate(methods)
     jump_prob = hawkes_problem(p, method; u=u, tspan=tspan, g=g, h=h)
     reset_history!(h)
-    if typeof(method) <: QueueMethod
+    if typeof(method) <: Coevolve
         sol = solve(jump_prob, SSAStepper())
     else
         sol = solve(jump_prob, Tsit5())
@@ -131,7 +131,7 @@ for method in methods
             global _u = [0. for i in 1:nv(_G)]
             global _h = [eltype(tspan)[] for _ in 1:nv(_G)]
             global _jump_prob = hawkes_problem(p, method; u=_u, tspan=tspan, g=_g, h=_h)
-            if typeof(method) <: QueueMethod
+            if typeof(method) <: Coevolve
                 global _stepper = SSAStepper()
             else
                 global _stepper = Tsit5()

benchmarks/Jumps/Manifest.toml

@@ -724,9 +724,9 @@ version = "0.1.3"
 
 [[deps.JumpProcesses]]
 deps = ["ArrayInterfaceCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"]
-path = "../../../JumpProcesses.jl"
+path = "/home/gzagatti/.julia/dev/JumpProcesses"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-version = "9.2.2"
+version = "9.2.3"
 
 [[deps.KLU]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"]

benchmarks/Jumps/Mendes_multistate_example.jmd

@@ -21,7 +21,7 @@ reactions(rn)
 
 # Plot solutions by each method
 ```julia
-methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
+methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 tf      = 10.0 * jprob.tstop
 prob    = DiscreteProblem(rn, jprob.u0, (0.0, tf), jprob.rates)

benchmarks/Jumps/NegFeedback_GeneExpr.jmd

@@ -20,7 +20,7 @@ reactions(rn)
 # Plot solutions by each method
 
 ```julia
-methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
+methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 prob    = prob_jump_dnarepressor.discrete_prob
 tf      = prob_jump_dnarepressor.tstop

benchmarks/Jumps/NegFeedback_GeneExpr_Marchetti.jmd

@@ -33,7 +33,7 @@ plot(solution, format=fmt)
 
 ```julia
 tf = 4000.
-methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), QueueMethod())
+methods = (Direct(), FRM(), SortingDirect(), NRM(), DirectCR(), RSSA(), RSSACR(), Coevolve())
 shortlabels = [string(leg)[15:end-2] for leg in methods]
 prob = prob = DiscreteProblem(rn, u0, (0.0, tf), rnpar)
 ploth = plot(reuse=false)