From c317809af1068708d96de6e7c1fbe08f7ddf112c Mon Sep 17 00:00:00 2001
From: Torkel <torkel.loman@gmail.com>
Date: Tue, 4 Apr 2023 11:12:46 -0400
Subject: [PATCH 1/3] testfix

---
 src/problem.jl | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/problem.jl b/src/problem.jl
index d0bde3c3..7c07a36c 100644
--- a/src/problem.jl
+++ b/src/problem.jl
@@ -119,6 +119,12 @@ function DiffEqBase.remake(thing::JumpProblem; kwargs...)
       thing.kwargs)
 end
 
+# when setindex! is used.
+function Base.setindex!(prob::JumpProblem, args...; kwargs...)
+    ___internal_setindex!(prob.prob, args...; kwargs...)
+    update_parameters!(prob.massaction_jump, prob.dprob.p; kwargs...)
+end
+
 DiffEqBase.isinplace(::JumpProblem{iip}) where {iip} = iip
 JumpProblem(prob::JumpProblem) = prob
 

From 887e0db7c0c2e6efc4a37ccd719a0fa0b1b4c2fc Mon Sep 17 00:00:00 2001
From: Torkel <torkel.loman@gmail.com>
Date: Tue, 4 Apr 2023 11:23:01 -0400
Subject: [PATCH 2/3] getindex as well

---
 src/JumpProcesses.jl | 2 +-
 src/problem.jl       | 7 ++++++-
 2 files changed, 7 insertions(+), 2 deletions(-)

diff --git a/src/JumpProcesses.jl b/src/JumpProcesses.jl
index 7b1915f7..64273373 100644
--- a/src/JumpProcesses.jl
+++ b/src/JumpProcesses.jl
@@ -7,7 +7,7 @@ using RandomNumbers, TreeViews, LinearAlgebra, Markdown, DocStringExtensions
 using DataStructures, PoissonRandom, Random, ArrayInterface
 using FunctionWrappers, UnPack
 using Graphs
-using SciMLBase: SciMLBase
+using SciMLBase: SciMLBase, ___internal_setindex!
 using Base.FastMath: add_fast
 
 import DiffEqBase: DiscreteCallback, init, solve, solve!, plot_indices, initialize!
diff --git a/src/problem.jl b/src/problem.jl
index 7c07a36c..6b8b1bac 100644
--- a/src/problem.jl
+++ b/src/problem.jl
@@ -122,9 +122,14 @@ end
 # when setindex! is used.
 function Base.setindex!(prob::JumpProblem, args...; kwargs...)
     ___internal_setindex!(prob.prob, args...; kwargs...)
-    update_parameters!(prob.massaction_jump, prob.dprob.p; kwargs...)
+    if using_params(prob.massaction_jump)
+        update_parameters!(prob.massaction_jump, prob.prob.p)
+    end
 end
 
+# when getindex is used.
+Base.getindex(prob::JumpProblem, args...; kwargs...) = Base.getindex(prob.prob, args...; kwargs...)
+
 DiffEqBase.isinplace(::JumpProblem{iip}) where {iip} = iip
 JumpProblem(prob::JumpProblem) = prob
 

From ad4d693caf2d17898dfebc9660a7b3d25e6e14e3 Mon Sep 17 00:00:00 2001
From: Torkel <torkel.loman@gmail.com>
Date: Tue, 4 Apr 2023 11:24:34 -0400
Subject: [PATCH 3/3] formating

---
 src/problem.jl | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/problem.jl b/src/problem.jl
index 6b8b1bac..2dade240 100644
--- a/src/problem.jl
+++ b/src/problem.jl
@@ -128,7 +128,9 @@ function Base.setindex!(prob::JumpProblem, args...; kwargs...)
 end
 
 # when getindex is used.
-Base.getindex(prob::JumpProblem, args...; kwargs...) = Base.getindex(prob.prob, args...; kwargs...)
+function Base.getindex(prob::JumpProblem, args...; kwargs...)
+    Base.getindex(prob.prob, args...; kwargs...)
+end
 
 DiffEqBase.isinplace(::JumpProblem{iip}) where {iip} = iip
 JumpProblem(prob::JumpProblem) = prob