From 7f2c8c15a2d1e9bf3d7055333d3f0067dbbfb7ff Mon Sep 17 00:00:00 2001
From: Sam Isaacson <isaacsas@users.noreply.github.com>
Date: Fri, 18 Oct 2024 15:58:34 -0400
Subject: [PATCH] fix tutorial again

---
 docs/Project.toml                             | 10 ++++-----
 .../examples/hodgkin_huxley_equation.md       | 21 ++++++++++++-------
 2 files changed, 19 insertions(+), 12 deletions(-)

diff --git a/docs/Project.toml b/docs/Project.toml
index d2f3fd2186..a009c89b8d 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -59,11 +59,11 @@ LinearSolve = "2.30"
 ModelingToolkit = "9.32"
 NonlinearSolve = "3.12"
 Optim = "1.9"
-Optimization = "3.25"
-OptimizationBBO = "0.3"
-OptimizationNLopt = "0.2.1"
-OptimizationOptimJL = "0.3.1"
-OptimizationOptimisers = "0.2.1"
+Optimization = "4"
+OptimizationBBO = "0.4"
+OptimizationNLopt = "0.3"
+OptimizationOptimJL = "0.4"
+OptimizationOptimisers = "0.3"
 OrdinaryDiffEq = "6.80.1"
 Plots = "1.40"
 QuasiMonteCarlo = "0.3"
diff --git a/docs/src/model_creation/examples/hodgkin_huxley_equation.md b/docs/src/model_creation/examples/hodgkin_huxley_equation.md
index 078aa0de00..e47f3ed996 100644
--- a/docs/src/model_creation/examples/hodgkin_huxley_equation.md
+++ b/docs/src/model_creation/examples/hodgkin_huxley_equation.md
@@ -171,22 +171,29 @@ hhmodel2 = @reaction_network hhmodel2 begin
 end
 ```
 Finally, we extend the `hhmodel` with the systems defining the ion channel currents
-```julia
+```@example hh1
 for sys in (IKmodel, INamodel, ILmodel)
     @named hhmodel2 = extend(sys, hhmodel2)
 end 
 hhmodel2 = complete(hhmodel2)
 ```
-Starting from the resting state, let's again solve the system when the amplitude
-of the stimulus is non-zero and check we get the same figure as above. Note, we
-now run `structural_simplify` from ModelingToolkit as part of building the
-`ODEProblem` to eliminate the algebraic equations for the currents
+Let's again solve the system for the resting state, and then solve with the same
+applied current as above (to verify we get the same figure). Note, we now
+explicitly convert to an `ODESystem` and then run `structural_simplify` from
+ModelingToolkit to eliminate the algebraic equations for the ionic currents
 
 ```@example hh1
+osys = convert(ODESystem, hhmodel2)
+osys = structural_simplify(osys)
+
 tspan = (0.0, 50.0)
+u₀ = symmap_to_varmap(osys, [:V => -70, :m => 0.0, :h => 0.0, :n => 0.0,
+	  :m′ => 1.0, :n′ => 1.0, :h′ => 1.0])
+oprob = ODEProblem(osys, u₀, tspan)
+hhsssol = solve(oprob, Rosenbrock23())
+u_ss = unknowns(osys) .=> hhsssol(tspan[2], idxs = unknowns(osys))
 @unpack I₀,V = hhmodel2
-oprob = ODEProblem(hhmodel2, u_ss, tspan, [I₀ => 10.0]; 
-    structural_simplify = true)
+oprob = ODEProblem(osys, u_ss, tspan, [I₀ => 10.0])
 sol = solve(oprob)
 plot(sol, idxs = V, legend = :outerright)
 ```