From c7e3866945bc21c09f45517a510f56642f0a0d2e Mon Sep 17 00:00:00 2001
From: Sam Isaacson <isaacsas@users.noreply.github.com>
Date: Tue, 6 Aug 2024 13:36:56 -0400
Subject: [PATCH 1/6] update JumpSystem for auto-alg support

---
 src/systems/jumps/jumpsystem.jl |  3 ++-
 test/jumpsystem.jl              | 10 +++++++---
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/src/systems/jumps/jumpsystem.jl b/src/systems/jumps/jumpsystem.jl
index da75b7dfd6..29f2906c6e 100644
--- a/src/systems/jumps/jumpsystem.jl
+++ b/src/systems/jumps/jumpsystem.jl
@@ -426,7 +426,8 @@ jprob = JumpProblem(complete(js), dprob, Direct())
 sol = solve(jprob, SSAStepper())
 ```
 """
-function JumpProcesses.JumpProblem(js::JumpSystem, prob, aggregator; callback = nothing,
+function JumpProcesses.JumpProblem(js::JumpSystem, prob,
+        aggregator = JumpProcesses.NullAggregator(); callback = nothing,
         eval_expression = false, eval_module = @__MODULE__, kwargs...)
     if !iscomplete(js)
         error("A completed `JumpSystem` is required. Call `complete` or `structural_simplify` on the system before creating a `JumpProblem`")
diff --git a/test/jumpsystem.jl b/test/jumpsystem.jl
index 11c9fc1cd9..2af7adfb86 100644
--- a/test/jumpsystem.jl
+++ b/test/jumpsystem.jl
@@ -69,16 +69,21 @@ parammap = [β => 0.1 / 1000, γ => 0.01]
 dprob = DiscreteProblem(js2, u₀map, tspan, parammap)
 jprob = JumpProblem(js2, dprob, Direct(), save_positions = (false, false), rng = rng)
 Nsims = 30000
-function getmean(jprob, Nsims)
+function getmean(jprob, Nsims; use_stepper = true)
     m = 0.0
     for i in 1:Nsims
-        sol = solve(jprob, SSAStepper())
+        sol = use_stepper ? solve(jprob, SSAStepper()) : solve(jprob)
         m += sol[end, end]
     end
     m / Nsims
 end
 m = getmean(jprob, Nsims)
 
+# test auto-alg selection works
+jprobb = JumpProblem(js2, dprob; save_positions = (false, false), rng)
+mb = getmean(jprobb, Nsims; use_stepper = false)
+@test abs(m - mb) / m < 0.01
+
 @variables S2(t)
 obs = [S2 ~ 2 * S]
 @named js2b = JumpSystem([j₁, j₃], t, [S, I, R], [β, γ], observed = obs)
@@ -89,7 +94,6 @@ sol = solve(jprob, SSAStepper(), saveat = tspan[2] / 10)
 @test all(2 .* sol[S] .== sol[S2])
 
 # test save_positions is working
-
 jprob = JumpProblem(js2, dprob, Direct(), save_positions = (false, false), rng = rng)
 sol = solve(jprob, SSAStepper(), saveat = 1.0)
 @test all((sol.t) .== collect(0.0:tspan[2]))

From 9103a670f8468076cd5b2c966eddab5cee093b1c Mon Sep 17 00:00:00 2001
From: Sam Isaacson <isaacsas@users.noreply.github.com>
Date: Tue, 6 Aug 2024 14:14:48 -0400
Subject: [PATCH 2/6] update Project for JumpProcesses

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 9b54b5a676..4368fc9e82 100644
--- a/Project.toml
+++ b/Project.toml
@@ -89,7 +89,7 @@ FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
 InteractiveUtils = "1"
 JuliaFormatter = "1.0.47"
-JumpProcesses = "9.1"
+JumpProcesses = "9.13"
 LabelledArrays = "1.3"
 Latexify = "0.11, 0.12, 0.13, 0.14, 0.15, 0.16"
 Libdl = "1"

From 7c05c99e0ccfd1292a3279bc25d51f410a93be05 Mon Sep 17 00:00:00 2001
From: Sam Isaacson <isaacsas@users.noreply.github.com>
Date: Tue, 6 Aug 2024 15:44:17 -0400
Subject: [PATCH 3/6] generate dep graphs

---
 src/systems/jumps/jumpsystem.jl |  3 ++-
 test/jumpsystem.jl              | 20 ++++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/src/systems/jumps/jumpsystem.jl b/src/systems/jumps/jumpsystem.jl
index 29f2906c6e..1a925922d2 100644
--- a/src/systems/jumps/jumpsystem.jl
+++ b/src/systems/jumps/jumpsystem.jl
@@ -449,7 +449,8 @@ function JumpProcesses.JumpProblem(js::JumpSystem, prob,
         error("Use continuous problems such as an ODEProblem or a SDEProblem with VariableRateJumps")
     jset = JumpSet(Tuple(vrjs), Tuple(crjs), nothing, majs)
 
-    if needs_vartojumps_map(aggregator) || needs_depgraph(aggregator)
+    if needs_vartojumps_map(aggregator) || needs_depgraph(aggregator) ||
+            (aggregator isa JumpProcesses.NullAggregator)
         jdeps = asgraph(js)
         vdeps = variable_dependencies(js)
         vtoj = jdeps.badjlist
diff --git a/test/jumpsystem.jl b/test/jumpsystem.jl
index 2af7adfb86..a730c87bfa 100644
--- a/test/jumpsystem.jl
+++ b/test/jumpsystem.jl
@@ -274,3 +274,23 @@ affect = [X ~ X - 1]
 
 j1 = ConstantRateJump(k, [X ~ X - 1])
 @test_nowarn @mtkbuild js1 = JumpSystem([j1], t, [X], [k])
+
+
+# test correct autosolver is selected
+let
+    @parameters k
+    @variables X(t)
+    rate = k
+    affect = [X ~ X - 1]
+    j1 = ConstantRateJump(k, [X ~ X - 1])
+
+    Nv = [1, JumpProcesses.USE_DIRECT_THRESHOLD + 1, JumpProcesses.USE_RSSA_THRESHOLD + 1]
+    algtypes = [Direct, RSSA, RSSACR]
+    for (N, algtype) in zip(Nv, algtypes)
+        @named jsys = JumpSystem([deepcopy(j1) for _ in 1:N], t, [X], [k])
+        jsys = complete(jsys)
+        dprob = DiscreteProblem(jsys, [X => 10], (0.0, 10.0), [k => 1])
+        jprob = JumpProblem(jsys, dprob)
+        @test jprob.aggregator isa algtype
+    end
+end
\ No newline at end of file

From 55a1f940ad56388dd22bd0d49aca123ba0d59d1f Mon Sep 17 00:00:00 2001
From: Sam Isaacson <isaacsas@users.noreply.github.com>
Date: Tue, 6 Aug 2024 15:44:41 -0400
Subject: [PATCH 4/6] comment

---
 test/jumpsystem.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/test/jumpsystem.jl b/test/jumpsystem.jl
index a730c87bfa..21e660d16e 100644
--- a/test/jumpsystem.jl
+++ b/test/jumpsystem.jl
@@ -276,7 +276,7 @@ j1 = ConstantRateJump(k, [X ~ X - 1])
 @test_nowarn @mtkbuild js1 = JumpSystem([j1], t, [X], [k])
 
 
-# test correct autosolver is selected
+# test correct autosolver is selected, which implies appropriate dep graphs are available
 let
     @parameters k
     @variables X(t)

From 10489f508fba5a59bfc26dc17a9edd8603334344 Mon Sep 17 00:00:00 2001
From: Sam Isaacson <isaacsas@users.noreply.github.com>
Date: Tue, 6 Aug 2024 15:45:34 -0400
Subject: [PATCH 5/6] format

---
 src/systems/jumps/jumpsystem.jl | 2 +-
 test/jumpsystem.jl              | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/src/systems/jumps/jumpsystem.jl b/src/systems/jumps/jumpsystem.jl
index 1a925922d2..0ad1a009eb 100644
--- a/src/systems/jumps/jumpsystem.jl
+++ b/src/systems/jumps/jumpsystem.jl
@@ -450,7 +450,7 @@ function JumpProcesses.JumpProblem(js::JumpSystem, prob,
     jset = JumpSet(Tuple(vrjs), Tuple(crjs), nothing, majs)
 
     if needs_vartojumps_map(aggregator) || needs_depgraph(aggregator) ||
-            (aggregator isa JumpProcesses.NullAggregator)
+       (aggregator isa JumpProcesses.NullAggregator)
         jdeps = asgraph(js)
         vdeps = variable_dependencies(js)
         vtoj = jdeps.badjlist
diff --git a/test/jumpsystem.jl b/test/jumpsystem.jl
index 21e660d16e..d14fa8b545 100644
--- a/test/jumpsystem.jl
+++ b/test/jumpsystem.jl
@@ -275,7 +275,6 @@ affect = [X ~ X - 1]
 j1 = ConstantRateJump(k, [X ~ X - 1])
 @test_nowarn @mtkbuild js1 = JumpSystem([j1], t, [X], [k])
 
-
 # test correct autosolver is selected, which implies appropriate dep graphs are available
 let
     @parameters k
@@ -293,4 +292,4 @@ let
         jprob = JumpProblem(jsys, dprob)
         @test jprob.aggregator isa algtype
     end
-end
\ No newline at end of file
+end

From 4ef25cbbde3dc11a2a090388bee5a468450a7d46 Mon Sep 17 00:00:00 2001
From: Sam Isaacson <isaacsas@users.noreply.github.com>
Date: Tue, 6 Aug 2024 15:52:04 -0400
Subject: [PATCH 6/6] bump JumpProcesses

---
 Project.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Project.toml b/Project.toml
index 4368fc9e82..5245347838 100644
--- a/Project.toml
+++ b/Project.toml
@@ -89,7 +89,7 @@ FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
 InteractiveUtils = "1"
 JuliaFormatter = "1.0.47"
-JumpProcesses = "9.13"
+JumpProcesses = "9.13.1"
 LabelledArrays = "1.3"
 Latexify = "0.11, 0.12, 0.13, 0.14, 0.15, 0.16"
 Libdl = "1"