Merge pull request #578 from ChrisRackauckas-Claude/agent/mirkn-explicit-public-api

Remove MIRKN blanket reexports

Author: ChrisRackauckas

lib/BoundaryValueDiffEqMIRKN/Project.toml

@@ -14,7 +14,6 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 PreallocationTools = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
 Preferences = "21216c6a-2e73-6563-6e65-726566657250"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
-Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 
@@ -32,7 +31,6 @@ PreallocationTools = "1.2"
 Preferences = "1.4"
 Random = "1.10"
 RecursiveArrayTools = "3.27.0, 4"
-Reexport = "1.2"
 SciMLBase = "3.30"
 SciMLTesting = "2.4"
 Setfield = "1.1.1"

lib/BoundaryValueDiffEqMIRKN/src/BoundaryValueDiffEqMIRKN.jl

@@ -1,6 +1,6 @@
 module BoundaryValueDiffEqMIRKN
 
-using ADTypes: ADTypes, AutoSparse, AutoForwardDiff
+using ADTypes: ADTypes, AutoSparse
 using BoundaryValueDiffEqCore: BoundaryValueDiffEqCore,
     AbstractBoundaryValueDiffEqAlgorithm,
     AbstractBoundaryValueDiffEqCache, BVPJacobianAlgorithm,
@@ -29,15 +29,12 @@ using LinearAlgebra: LinearAlgebra
 using PreallocationTools: PreallocationTools, get_tmp
 using Preferences: Preferences
 using RecursiveArrayTools: AbstractVectorOfArray, ArrayPartition
-using Reexport: @reexport
 using SciMLBase: SciMLBase, ReturnCode, SecondOrderBVProblem,
     StandardSecondOrderBVProblem, TwoPointSecondOrderBVProblem, isinplace, remake
 using Setfield: @set!
 
 const DI = DifferentiationInterface
 
-@reexport using ADTypes, BoundaryValueDiffEqCore, SciMLBase
-
 include("types.jl")
 include("algorithms.jl")
 include("mirkn.jl")

lib/BoundaryValueDiffEqMIRKN/src/algorithms.jl

@@ -6,37 +6,51 @@ for order in (4, 6)
 
     @eval begin
         """
-            $($alg)(; nlsolve = NewtonRaphson(), optimize = nothing, jac_alg = BVPJacobianAlgorithm(),
+            $($alg)(; nlsolve = nothing, optimize = nothing, jac_alg = BVPJacobianAlgorithm(),
                     defect_threshold = 0.1, max_num_subintervals = 3000)
 
         $($order)th order Monotonic Implicit Runge Kutta Nyström method.
 
+        ## Fields
+
+        - `nlsolve`: Optional nonlinear solver algorithm. `nothing` selects the package default.
+        - `optimize`: Optional optimization solver algorithm. `nothing` disables optimization-based
+          initialization.
+        - `jac_alg`: Jacobian construction configuration used by the nonlinear solver.
+        - `defect_threshold`: Defect-control threshold used to refine the mesh.
+        - `max_num_subintervals`: Maximum number of mesh subintervals permitted during refinement.
+
         ## Keyword Arguments
 
-        - `nlsolve`: Internal Nonlinear solver. Any solver which conforms to the SciML
-          `NonlinearProblem` interface can be used. Note that any autodiff argument for
-          the solver will be ignored and a custom jacobian algorithm will be used.
-        - `optimize`: Internal Optimization solver. Any solver which conforms to the SciML
-          `OptimizationProblem` interface can be used. Note that any autodiff argument for
-          the solver will be ignored and a custom jacobian algorithm will be used. Optimization
-          solvers should first be loaded to allow this functionality.
-        - `jac_alg`: Jacobian Algorithm used for the nonlinear solver. Defaults to
-          `BVPJacobianAlgorithm()`, which automatically decides the best algorithm to
-          use based on the input types and problem type.
+        - `nlsolve = nothing`: Internal nonlinear solver. Any solver that conforms to the SciML
+          `NonlinearProblem` interface can be used. Its autodiff setting is ignored because MIRKN
+          uses `jac_alg` to construct the Jacobian.
+        - `optimize = nothing`: Internal optimization solver. Any solver that conforms to the
+          SciML `OptimizationProblem` interface can be used for initialization. Load the solver
+          package before constructing the algorithm.
+        - `jac_alg = BVPJacobianAlgorithm()`: Jacobian algorithm used for the nonlinear solver.
+          It automatically selects an algorithm from the problem and input types.
           - For `TwoPointBVProblem`, only `diffmode` is used (defaults to
             `AutoSparse(AutoForwardDiff())` if possible else `AutoSparse(AutoFiniteDiff())`).
           - For `BVProblem`, `bc_diffmode` and `nonbc_diffmode` are used. For
             `nonbc_diffmode` defaults to `AutoSparse(AutoForwardDiff())` if possible else
             `AutoSparse(AutoFiniteDiff())`. For `bc_diffmode`, defaults to `AutoForwardDiff` if
             possible else `AutoFiniteDiff`.
-        - `defect_threshold`: Threshold for defect control.
-        - `max_num_subintervals`: Number of maximal subintervals, default as 3000.
+        - `defect_threshold = 0.1`: Threshold for defect control.
+        - `max_num_subintervals = 3000`: Maximum number of mesh subintervals.
 
         !!! note
 
             For type-stability, the chunksizes for ForwardDiff ADTypes in
             `BVPJacobianAlgorithm` must be provided.
 
+        ## Examples
+
+        ```jldoctest
+        julia> MIRKN$($order)().max_num_subintervals
+        3000
+        ```
+
         ## References
 
         ```bibtex

lib/BoundaryValueDiffEqMIRKN/test/Core/mirkn_basic_tests.jl

@@ -1,7 +1,9 @@
 using BoundaryValueDiffEqMIRKN
+using SciMLBase: DynamicalBVPFunction, SecondOrderBVProblem, TwoPointSecondOrderBVProblem,
+    solve
 using Test
 
-using BoundaryValueDiffEqMIRKN
+import SciMLBase
 
 for order in (4, 6)
     s = Symbol("MIRKN$(order)")
@@ -85,8 +87,6 @@ end
 # JET tests have been moved to the separate QA test group (test/qa/)
 
 @testset "Example problem from paper" begin
-    using BoundaryValueDiffEqMIRKN
-
     for order in (4, 6)
         s = Symbol("MIRKN$(order)")
         @eval mirkn_solver(::Val{$order}, args...; kwargs...) = $(s)(args...; kwargs...)

lib/BoundaryValueDiffEqMIRKN/test/qa/qa.jl

@@ -2,9 +2,6 @@ using SciMLTesting
 using BoundaryValueDiffEqMIRKN
 using Test
 
-const DOCS_SRC = normpath(joinpath(@__DIR__, "..", "..", "..", "..", "docs", "src"))
-include(joinpath(@__DIR__, "..", "..", "..", "..", "test", "qa", "reexports.jl"))
-
 run_qa(
     BoundaryValueDiffEqMIRKN;
     ei_kwargs = (;
@@ -15,9 +12,4 @@ run_qa(
             ignore = (:StandardSecondOrderBVProblem, :pickchunksize),
         ),
     ),
-    reexports_allow = MIRKN_REEXPORTS,
-    api_docs_kwargs = (;
-        docs_src = DOCS_SRC, ignore = MIRKN_REEXPORTS,
-        rendered_ignore = MIRKN_REEXPORTS,
-    ),
 )