Merge pull request #1674 from isaacsas/rename-diffeqjump

Rename DiffEqJump to JumpProcesses

Author: ChrisRackauckas

Project.toml

@@ -11,7 +11,6 @@ ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-DiffEqJump = "c894b116-72e5-5b58-be3c-e6d8d4ac2b12"
 DiffRules = "b552c78f-8df3-52c6-915a-8e097449b14b"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
@@ -21,6 +20,7 @@ Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
+JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
@@ -50,14 +50,14 @@ ConstructionBase = "1"
 DataStructures = "0.17, 0.18"
 DiffEqBase = "6.83.0"
 DiffEqCallbacks = "2.16"
-DiffEqJump = "7.0, 8"
 DiffRules = "0.1, 1.0"
 Distributions = "0.23, 0.24, 0.25"
 DocStringExtensions = "0.7, 0.8, 0.9"
 DomainSets = "0.5"
 Graphs = "1.5.2"
 IfElse = "0.1"
 JuliaFormatter = "1"
+JumpProcesses = "9"
 LabelledArrays = "1.3"
 Latexify = "0.11, 0.12, 0.13, 0.14, 0.15"
 MacroTools = "0.5"

src/ModelingToolkit.jl

@@ -12,7 +12,7 @@ using Latexify, Unitful, ArrayInterfaceCore
 using MacroTools
 @reexport using UnPack
 using Setfield, ConstructionBase
-using DiffEqJump
+using JumpProcesses
 using DataStructures
 using SpecialFunctions, NaNMath
 using RuntimeGeneratedFunctions

src/systems/jumps/jumpsystem.jl

@@ -212,7 +212,7 @@ and no SDEs associated with the system.
 
 Continuing the example from the [`JumpSystem`](@ref) definition:
 ```julia
-using DiffEqBase, DiffEqJump
+using DiffEqBase, JumpProcesses
 u₀map = [S => 999, I => 1, R => 0]
 parammap = [β => .1/1000, γ => .01]
 tspan = (0.0, 250.0)
@@ -264,7 +264,7 @@ and no SDEs associated with the system.
 
 Continuing the example from the [`JumpSystem`](@ref) definition:
 ```julia
-using DiffEqBase, DiffEqJump
+using DiffEqBase, JumpProcesses
 u₀map = [S => 999, I => 1, R => 0]
 parammap = [β => .1/1000, γ => .01]
 tspan = (0.0, 250.0)
@@ -305,7 +305,7 @@ jprob = JumpProblem(js, dprob, Direct())
 sol = solve(jprob, SSAStepper())
 ```
 """
-function DiffEqJump.JumpProblem(js::JumpSystem, prob, aggregator; kwargs...)
+function JumpProcesses.JumpProblem(js::JumpSystem, prob, aggregator; kwargs...)
     statetoid = Dict(value(state) => i for (i, state) in enumerate(states(js)))
     eqs = equations(js)
     invttype = prob.tspan[1] === nothing ? Float64 : typeof(1 / prob.tspan[2])
@@ -421,6 +421,6 @@ function (ratemap::JumpSysMajParamMapper{U, V, W})(maj::MassActionJump, newparam
                                       value(substitute(ratemap.paramexprs[i],
                                                        ratemap.subdict)))
     end
-    scale_rates && DiffEqJump.scalerates!(maj.scaled_rates, maj.reactant_stoch)
+    scale_rates && JumpProcesses.scalerates!(maj.scaled_rates, maj.reactant_stoch)
     nothing
 end

test/dep_graphs.jl

@@ -1,5 +1,5 @@
 using Test
-using ModelingToolkit, Graphs, DiffEqJump
+using ModelingToolkit, Graphs, JumpProcesses
 
 import ModelingToolkit: value
 

test/jumpsystem.jl

@@ -1,4 +1,4 @@
-using ModelingToolkit, DiffEqBase, DiffEqJump, Test, LinearAlgebra
+using ModelingToolkit, DiffEqBase, JumpProcesses, Test, LinearAlgebra
 MT = ModelingToolkit
 
 # basic MT SIR model with tweaks

test/units.jl

@@ -1,4 +1,4 @@
-using ModelingToolkit, Unitful, OrdinaryDiffEq, DiffEqJump, IfElse
+using ModelingToolkit, Unitful, OrdinaryDiffEq, JumpProcesses, IfElse
 using Test
 MT = ModelingToolkit
 @parameters τ [unit = u"ms"] γ
@@ -88,7 +88,7 @@ noiseeqs = [0.1u"MW" 0.1u"MW"
             0.1u"MW" 0.1u"MW"]
 @named sys = SDESystem(eqs, noiseeqs, t, [P, E], [τ, Q])
 
-# Invalid noise matrix 
+# Invalid noise matrix
 noiseeqs = [0.1u"MW" 0.1u"MW"
             0.1u"MW" 0.1u"s"]
 @test !MT.validate(eqs, noiseeqs)