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SciML · Jan 8, 2025 · e9d1e87 · e9d1e87
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diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,6 @@
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
+BoundaryValueDiffEq = "764a87c0-6b3e-53db-9096-fe964310641d"
 BoundaryValueDiffEqAscher = "7227322d-7511-4e07-9247-ad6ff830280e"
 BoundaryValueDiffEqCore = "56b672f2-a5fe-4263-ab2d-da677488eb3a"
 BoundaryValueDiffEqFIRK = "85d9eb09-370e-4000-bb32-543851f73618"
@@ -19,6 +20,7 @@ SimpleBoundaryValueDiffEq = "be0294bd-f90f-4760-ac4e-3421ce2b2da0"
 
 [compat]
 ADTypes = "1.9"
+BoundaryValueDiffEq = "5.12.0"
 BoundaryValueDiffEqCore = "1.1"
 BoundaryValueDiffEqFIRK = "1.1"
 BoundaryValueDiffEqMIRK = "1.1"

diff --git a/docs/make.jl b/docs/make.jl
@@ -16,6 +16,11 @@ cp(joinpath(@__DIR__, "Project.toml"),
 
 include("pages.jl")
 
+bib = CitationBibliography(joinpath(@__DIR__, "src", "refs.bib"))
+
+interlinks = InterLinks("ADTypes" => "https://sciml.github.io/ADTypes.jl/stable/",
+    "LineSearch" => "https://sciml.github.io/LineSearch.jl/dev/")
+
 makedocs(; sitename = "BoundaryValueDiffEq.jl",
     authors = "SciML",
     modules = [BoundaryValueDiffEqCore, BoundaryValueDiffEqMIRK, BoundaryValueDiffEqFIRK,
@@ -25,6 +30,7 @@ makedocs(; sitename = "BoundaryValueDiffEq.jl",
     doctest = false,
     checkdocs = :exports,
     warnonly = [:missing_docs],
+    plugins = [bib, interlinks],
     format = Documenter.HTML(assets = ["assets/favicon.ico"],
         canonical = "https://docs.sciml.ai/BoundaryValueDiffEq/stable/"),
     pages)
diff --git a/docs/src/assets/Project.toml b/docs/src/assets/Project.toml
@@ -0,0 +1,37 @@
+[deps]
+ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
+BoundaryValueDiffEq = "764a87c0-6b3e-53db-9096-fe964310641d"
+BoundaryValueDiffEqAscher = "7227322d-7511-4e07-9247-ad6ff830280e"
+BoundaryValueDiffEqCore = "56b672f2-a5fe-4263-ab2d-da677488eb3a"
+BoundaryValueDiffEqFIRK = "85d9eb09-370e-4000-bb32-543851f73618"
+BoundaryValueDiffEqMIRK = "1a22d4ce-7765-49ea-b6f2-13c8438986a6"
+BoundaryValueDiffEqMIRKN = "9255f1d6-53bf-473e-b6bd-23f1ff009da4"
+BoundaryValueDiffEqShooting = "ed55bfe0-3725-4db6-871e-a1dc9f42a757"
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
+LineSearch = "87fe0de2-c867-4266-b59a-2f0a94fc965b"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+SimpleBoundaryValueDiffEq = "be0294bd-f90f-4760-ac4e-3421ce2b2da0"
+
+[compat]
+ADTypes = "1.9"
+BoundaryValueDiffEq = "5.12.0"
+BoundaryValueDiffEqCore = "1.1"
+BoundaryValueDiffEqFIRK = "1.1"
+BoundaryValueDiffEqMIRK = "1.1"
+BoundaryValueDiffEqShooting = "1.1"
+DiffEqBase = "6.158.3"
+Documenter = "1"
+DocumenterCitations = "1"
+DocumenterInterLinks = "1.0.0"
+LineSearch = "0.1.4"
+LinearAlgebra = "1.10"
+LinearSolve = "2.36.2"
+OrdinaryDiffEq = "6.90.1"
+SciMLBase = "2.60.0"
+SimpleBoundaryValueDiffEq = "1.1.0"
diff --git a/docs/src/basics/autodiff.md b/docs/src/basics/autodiff.md
@@ -1,4 +1,4 @@
-# # Automatic Differentiation Backends
+# Automatic Differentiation Backends
 
 !!! note
 

diff --git a/docs/src/basics/bvp_functions.md b/docs/src/basics/bvp_functions.md
@@ -6,7 +6,5 @@ The SciML ecosystem provides an extensive interface for declaring extra function
 
 ```@docs
 SciMLBase.BVPFunction
-SciMLBase.TwoPointBVPFunction
-SciMLBase.SecondOrderBVPFunction
-SciMLBase.TwoPointSecondOrderBVPFunction
+SciMLBase.DynamicalBVPFunction
 ```
diff --git a/docs/src/basics/solve.md b/docs/src/basics/solve.md
@@ -1,9 +1,5 @@
 # [Common Solver Options (Solve Keyword Arguments)](@id solver_options)
 
-```@docs
-solve(::AbstractBVProblem, args...; kwargs...)
-```
-
 ## Iteration Controls
 
   - `maxiters::Int`: The maximum number of iterations to perform. Defaults to `1000`.

diff --git a/docs/src/devdocs/internal_interfaces.md b/docs/src/devdocs/internal_interfaces.md
@@ -2,6 +2,6 @@
 
 ## Solvers
 
-```@docs
-BoundaryValueDiffEqCore.BuondaryValueDiffEqAlgorithm
+```julia
+BoundaryValueDiffEqCore.BoundaryValueDiffEqAlgorithm
 ```
diff --git a/docs/src/refs.bib b/docs/src/refs.bib
@@ -0,0 +1,8 @@
+@article{Muir2001MonoImplicitRM,
+  title={Mono-Implicit Runge-Kutta-Nystr{\"o}m Methods with Application to Boundary Value Ordinary Differential Equations},
+  author={Paul H. Muir and Mark F. Adams},
+  journal={BIT Numerical Mathematics},
+  year={2001},
+  volume={41},
+  pages={776-799},
+}
diff --git a/docs/src/solvers/ascher.md b/docs/src/solvers/ascher.md
@@ -1,4 +1,4 @@
-# [BoundaryValueDiffEqAscher.jl](@id ascher)
+# [BoundaryValueDiffEqAscher](@id ascher)
 
 Gauss Legendre collocation methods with Ascher's error control adaptivity and mesh refinement routines. To be able to access the solvers in BoundaryValueDiffEqFIRK, you must first install them use the Julia package manager:
 
@@ -15,12 +15,12 @@ solve(prob::TwoPointBVProblem, alg; kwargs...)
 ## Full List of Methods
 
   - `Ascher1`: 1 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
-  - `Ascher2`: 1 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
-  - `Ascher3`: 1 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
-  - `Ascher4`: 1 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
-  - `Ascher5`: 1 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
-  - `Ascher6`: 1 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
-  - `Ascher7`: 1 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
+  - `Ascher2`: 2 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
+  - `Ascher3`: 3 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
+  - `Ascher4`: 4 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
+  - `Ascher5`: 5 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
+  - `Ascher6`: 6 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
+  - `Ascher7`: 7 stage Gauss Legendre collocation method with Ascher's error control adaptivity and mesh refinement.
 
 ## Detailed Solvers Explanation
 

diff --git a/docs/src/solvers/firk.md b/docs/src/solvers/firk.md
@@ -1,4 +1,4 @@
-# [BoundaryValueDiffEqFIRK.jl](@id firk)
+# [BoundaryValueDiffEqFIRK](@id firk)
 
 Fully Implicit Runge Kutta(FIRK) Methods. To be able to access the solvers in BoundaryValueDiffEqFIRK, you must first install them use the Julia package manager:
 

diff --git a/docs/src/solvers/mirk.md b/docs/src/solvers/mirk.md
@@ -1,4 +1,4 @@
-# [BoundaryValueDiffEqMIRK.jl](@id mirk)
+# [BoundaryValueDiffEqMIRK](@id mirk)
 
 Monotonic Implicit Runge Kutta(MIRK) Methods. To only use the MIRK methods form BoundaryVaueDiffEq.jl, you need to install them use the Julia package manager:
 

diff --git a/docs/src/solvers/mirkn.md b/docs/src/solvers/mirkn.md
@@ -1,4 +1,4 @@
-# [BoundaryValueDiffEqMIRKN.jl](@id mirkn)
+# [BoundaryValueDiffEqMIRKN](@id mirkn)
 
 Monotonic Implicit Runge Kutta Nyström(MIRKN) Methods. To only use the MIRKN methods form BoundaryVaueDiffEq.jl, you need to install them use the Julia package manager:
 
@@ -12,8 +12,9 @@ solve(prob::SecondOrderBVProblem, alg; kwargs...)
 solve(prob::TwoPointSecondOrderBVProblem, alg; kwargs...)
 ```
 
-!!! note "MIRKN don't have defect control adaptivity"
+!!! note "Defect control adaptivity"
 
+    MIRKN don't have defect control adaptivity
 
 ## Full List of Methods
 

diff --git a/docs/src/solvers/shooting.md b/docs/src/solvers/shooting.md
@@ -1,4 +1,4 @@
-# [BoundaryValueDiffEqShooting.jl](@id shooting)
+# [BoundaryValueDiffEqShooting](@id shooting)
 
 Single shooting method and multiple shooting method. To only use the Shooting methods form BoundaryVaueDiffEq.jl, you need to install them use the Julia package manager:
 

diff --git a/docs/src/solvers/simple_solvers.md b/docs/src/solvers/simple_solvers.md
@@ -1,8 +1,8 @@
-# [SimpleBoundaryValueDiffEq.jl](@id simpleboundaryvaluediffeq)
+# [SimpleBoundaryValueDiffEq](@id simpleboundaryvaluediffeq)
 
 ## Full List of Methods
 
-```@docs
+```julia
 SimpleBoundaryValueDiffEq.SimpleMIRK4
 SimpleBoundaryValueDiffEq.SimpleMIRK5
 SimpleBoundaryValueDiffEq.SimpleMIRK6

diff --git a/docs/src/tutorials/getting_started.md b/docs/src/tutorials/getting_started.md
@@ -2,18 +2,18 @@
 
 When ordinary differential equations has constraints over the time span, we should model the ordinary differential equations as a boundary value problem which has the form of:
 
-$$
+```math
 \frac{du}{dt}=f(u, p, t)\\
 g(u(a),u(b))=0
-$$
+```
 
 BoundaryValueDiffEq.jl address three types of BVProblem.
 
  1. General boundary value problems:, i.e., differential equations with constraints applied over the time span. This is a system where you would like to obtain the solution of the differential equations and make sure the solution satisfy the boundary conditions simutanously.
  2. General second order boundary value problems, i.e., differential equations with constraints for both solution and derivative of solution applied over time span. This is a system where you would like to obtain the solution of the differential equations and make sure the solution satisfy the boundary conditions simutanously.
  3. Boundary value differential algebraic equations, i.e., apart from constraints applied over the time span, BVDAE has additional algebraic equations which state the algebraic relationship of different states in BVDAE.
 
-## Linear two-point boundary value problem
+## Solving Linear two-point boundary value problem
 
 Consider the linear two-point boundary value problem from [standard BVP test problem](https://archimede.uniba.it/%7Ebvpsolvers/testsetbvpsolvers/?page_id=29).
 
@@ -58,20 +58,20 @@ sol = solve(prob, MIRK4(), dt = 0.01)
 
 Consirder the test problem from example problems in MIRKN paper.
 
-$$
+```math
 \begin{cases}
 y_1'(x)= y_2(x),\\
 \epsilon y_2'(x)=-y_1(x)y_2'(x)- y_3(x)y_3'(x),\\
 \epsilon y_3'(x)=y_1'(x) y_3(x)- y_1(x) y_3 '(x)
 \end{cases}
-$$
+```
 
 with initial conditions:
 
-$$
+```math
 y_1(0) = y_1'(0)= y_1(1)=y_1'(1)=0,y_3(0)=
 -1, y_3(1)=1
-$$
+```
 
 ```julia
 function f!(ddu, du, u, p, t)
@@ -98,20 +98,20 @@ sol = solve(prob, MIRKN4(), dt = 0.01)
 
 Consider the nonlinear semi-explicit DAE of index at most 2
 
-$$
+```math
 \begin{cases}
 x_1'=(\epsilon+x_2-p_2(t))y+p_1'(t) \\
 x_2'=p_2'(t) \\
 x_3'=y \\
 0=(x_1-p_1(t))(y-e^t)
 \end{cases}
-$$
+```
 
 with boundary conditions
 
-$$
+```math
 x_1(0)=0,x_3(0)=1,x_2(1)=\sin(1)
-$$
+```
 
 ```julia
 function f!(du, u, p, t)
@@ -121,7 +121,7 @@ function f!(du, u, p, t)
     du[3] = u[4]
     du[4] = (u[1] - sin(t)) * (u[4] - e^t)
 end
-function bc1!(res, u, p, t)
+function bc!(res, u, p, t)
     res[1] = u[1]
     res[2] = u[3] - 1
     res[3] = u[2] - sin(1.0)