Merge pull request #4746 from ChrisRackauckas-Claude/agent/fix-docs-example-regressions

Fix documentation examples for current dependency APIs

Author: ChrisRackauckas

docs/Project.toml

@@ -12,6 +12,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
 FMI = "14a09403-18e3-468f-ad8a-74f8dda2d9ac"
 # FMIZoo = "724179cf-c260-40a9-bd27-cccc6fe2f195"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 InfiniteOpt = "20393b10-9daf-11e9-18c9-8db751c92c57"
 Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
 JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
@@ -24,6 +25,8 @@ Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+OrdinaryDiffEqFunctionMap = "d3585ca7-f5d3-4ba6-8057-292ed1abd90f"
+OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
 SciCompDSL = "91a8cdf1-4ca6-467b-a780-87fda3fff15e"
@@ -48,6 +51,7 @@ Documenter = "1"
 DynamicQuantities = "1"
 FMI = "0.14"
 # FMIZoo = "1"
+Graphs = "1.5.2"
 InfiniteOpt = "0.6"
 Ipopt = "1"
 JumpProcesses = "9"
@@ -58,6 +62,8 @@ Optim = "1.9, 2"
 Optimization = "5"
 OptimizationOptimJL = "0.4"
 OrdinaryDiffEq = "6.31, 7"
+OrdinaryDiffEqFunctionMap = "1, 2"
+OrdinaryDiffEqRosenbrock = "1, 2"
 Plots = "1.36"
 PreallocationTools = "0.4, 1"
 SciCompDSL = "1"

docs/src/examples/tearing_parallelism.md

@@ -149,9 +149,9 @@ between the blocks. We can use the bipartite graph functionality to dig in and
 investigate what this means:
 
 ```@example tearing
-using ModelingToolkit.BipartiteGraphs
-ts = TearingState(expand_connections(big_rc))
-inc_org = BipartiteGraphs.incidence_matrix(ts.structure.graph)
+using Graphs.LinAlg: incidence_matrix
+using ModelingToolkitBase: asgraph, expand_connections
+inc_org = incidence_matrix(asgraph(expand_connections(big_rc)))
 # Note: sorted_incidence_matrix requires the system and matrix dimensions to match
 # blt_reduced = StructuralTransformations.sorted_incidence_matrix(sys)
 ```

docs/src/tutorials/bifurcation_diagram_computation.md

@@ -125,11 +125,11 @@ plot(bf;
 
 Here, the value of `x` in the steady state does not change, however, at `μ=0` a Hopf bifurcation occur and the steady state turn unstable.
 
-We compute the branch of periodic orbits which is nearby the Hopf Bifurcation. We thus provide the branch `bf.γ`, the index of the Hopf point we want to branch from: 2 in this case and a method `PeriodicOrbitOCollProblem(20, 5)` to compute periodic orbits.
+We compute the branch of periodic orbits which is nearby the Hopf Bifurcation. We thus provide the branch `bf.γ`, the index of the Hopf point we want to branch from: 2 in this case and a method `Collocation(20, 5)` to compute periodic orbits.
 
 ```@example Bif2
 br_po = continuation(bf.γ, 2, opts_br,
-    PeriodicOrbitOCollProblem(20, 5);)
+    Collocation(20, 5);)
 
 plot(bf; putspecialptlegend = false,
     markersize = 2,

docs/src/tutorials/discrete_system.md

@@ -5,7 +5,8 @@ In this example, we will use the [`System`](@ref) API to create an SIR model.
 ```@example discrete
 using ModelingToolkit
 using ModelingToolkit: t_nounits as t
-using OrdinaryDiffEq: solve, FunctionMap
+using CommonSolve: solve
+using OrdinaryDiffEqFunctionMap: FunctionMap
 
 @inline function rate_to_proportion(r, t)
     1 - exp(-r * t)

docs/src/tutorials/ode_modeling.md

@@ -291,6 +291,7 @@ still is the problem using the `connected` system above):
 
 ```@example ode2
 using BenchmarkTools
+using OrdinaryDiffEqRosenbrock: Rodas4
 @btime solve(prob, Rodas4());
 nothing # hide
 ```