fix problem symbolic indexing

Project.toml

@@ -19,6 +19,7 @@ RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [weakdeps]
@@ -28,18 +29,19 @@ FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 JumpProcessFastBroadcastExt = "FastBroadcast"
 
 [compat]
-ArrayInterface = "7"
+ArrayInterface = "7.9"
 DataStructures = "0.18"
-DiffEqBase = "6.122"
+DiffEqBase = "6.148"
 DocStringExtensions = "0.9"
-FunctionWrappers = "1.0"
-Graphs = "1.4"
+FunctionWrappers = "1.1"
+Graphs = "1.9"
 PoissonRandom = "0.4"
-RandomNumbers = "1.3"
-RecursiveArrayTools = "3"
+RandomNumbers = "1.5"
+RecursiveArrayTools = "3.12"
 Reexport = "1.0"
-SciMLBase = "1.51, 2"
-StaticArrays = "1.0"
+SciMLBase = "2.30.1"
+StaticArrays = "1.9"
+SymbolicIndexingInterface = "0.3.11"
 UnPack = "1.0.2"
 julia = "1.10"
 

src/JumpProcesses.jl

@@ -17,6 +17,7 @@ import Graphs: neighbors, outdegree
 
 import RecursiveArrayTools: recursivecopy!
 using StaticArrays, Base.Threads
+import SymbolicIndexingInterface as SII
 
 abstract type AbstractJump end
 abstract type AbstractMassActionJump <: AbstractJump end

src/problem.jl

@@ -122,12 +122,15 @@ end
 # when setindex! is used.
 function Base.setindex!(prob::JumpProblem, args...; kwargs...)
     SciMLBase.___internal_setindex!(prob.prob, args...; kwargs...)
+end
+
+# for updating parameters in JumpProblems to update MassActionJumps
+function SII.set_parameter!(prob::JumpProblem, val, idx)
+    ans = SII.set_parameter!(SII.parameter_values(prob), val, idx)
 
-    # since parameters are no longer allowed to be mutated and the preceding will error this
-    # isn't needed
-    # if using_params(prob.massaction_jump)
-    #     update_parameters!(prob.massaction_jump, prob.prob.p)
-    # end
+    if using_params(prob.massaction_jump)
+        update_parameters!(prob.massaction_jump, prob.prob.p)
+    end
 end
 
 # when getindex is used.

test/jprob_symbol_indexing.jl

@@ -1,21 +1,36 @@
 # prepares the problem
-using JumpProcesses, Test
+using JumpProcesses, Test, SymbolicIndexingInterface
 rate1(u, p, t) = p[1]
 rate2(u, p, t) = p[2]
 affect1!(integ) = (integ.u[1] += 1)
 affect2!(integ) = (integ.u[2] += 1)
 crj1 = ConstantRateJump(rate1, affect1!)
 crj2 = ConstantRateJump(rate2, affect2!)
-g = DiscreteFunction((du, u, p, t) -> nothing; sys = SymbolicIndexingInterface.SymbolCache([:a, :b], [:p1, :p2], :t))
+maj = MassActionJump([[1 => 1], [1 => 1]], [[1 => -1], [1 => -1]]; param_idxs = [1,2])
+g = DiscreteFunction((du, u, p, t) -> nothing;
+    sys = SymbolicIndexingInterface.SymbolCache([:a, :b], [:p1, :p2], :t))
 dprob = DiscreteProblem(g, [0, 10], (0.0, 10.0), [1.0, 2.0])
-jprob = JumpProblem(dprob, Direct(), crj1, crj2)
+jprob = JumpProblem(dprob, Direct(), crj1, crj2, maj)
 
-# runs the tests
+# test basic querying of u0 and p
 @test jprob[:a] == 0
 @test jprob[:b] == 10
-
-# these are no longer supported by SciMLBase
 @test getp(jprob,:p1)(jprob) == 1.0
 @test getp(jprob,:p2)(jprob) == 2.0
 @test jprob.ps[:p1] == 1.0
 @test jprob.ps[:p2] == 2.0
+
+# test updating u0
+jprob[:a] = 20
+@test jprob[:a] == 20
+
+# test mass action jumps update with parameter mutation in problems
+@test jprob.massaction_jump.scaled_rates[1] == 1.0
+jprob.ps[:p1] = 3.0
+@test jprob.ps[:p1] == 3.0
+@test jprob.massaction_jump.scaled_rates[1] == 3.0
+p1setter = setp(jprob, [:p1, :p2])
+p1setter(jprob, [4.0, 10.0])
+@test jprob.ps[:p1] == 4.0
+@test jprob.ps[:p2] == 10.0
+@test jprob.massaction_jump.scaled_rates == [4.0, 10.0]