Merge branch 'master' into mtkv_v10_try

Author: TorkelE

.gitignore

@@ -10,4 +10,8 @@ Manifest.toml
 .vscode
 .vscode/*
 
-LocalPreferences.toml
+LocalPreferences.toml
+
+# claude
+.claude
+.claude/*

docs/Project.toml

@@ -71,7 +71,7 @@ ModelingToolkit = "9.69"
 NetworkLayout = "0.4"
 NonlinearSolve = "3.12, 4"
 Optim = "1.9"
-Optimization = "4"
+Optimization = "4, 5"
 OptimizationBBO = "0.4"
 OptimizationEvolutionary = "0.4"
 OptimizationNLopt = "0.3"

test/upstream/mtk_structure_indexing.jl

@@ -50,7 +50,7 @@ begin
     sint = init(sprob, ImplicitEM(); save_everystep = false)
     jint = init(jprob, SSAStepper())
     nint = init(nprob, NewtonRaphson(); save_everystep = false)
-    @test_broken ssint = init(ssprob, DynamicSS(Tsit5()); save_everystep = false) # https://github.com/SciML/SciMLBase.jl/issues/660
+    ssint = init(ssprob, DynamicSS(Tsit5()); save_everystep = false)
     integrators = [oint, sint, jint, nint]
 
     # Creates solutions.
@@ -152,8 +152,7 @@ end
 
 # Test integrator indexing.
 let
-    @test_broken false # NOTE: Cannot even create a `ssint` (https://github.com/SciML/SciMLBase.jl/issues/660).
-    for int in deepcopy([oint, sint, jint, nint])
+    for int in deepcopy([oint, sint, jint, nint, ssint])
         # Get u values.
         @test int[X] == int[model.X] == int[:X] == 4
         @test int[XY] == int[model.XY] == int[:XY] == 9