Merge branch 'master' into qqy/bvp_opt

ErikQQY · web-flow · commit 19bb198e1318 · 2025-07-30T20:26:19.000+08:00
diff --git a/.github/workflows/CI_BoundaryValueDiffEq.yml b/.github/workflows/CI_BoundaryValueDiffEq.yml
@@ -39,7 +39,7 @@ jobs:
         version:
           - "1"
           - "lts"
-          #- "pre"
+          - "pre"
         os:
           - ubuntu-latest
     steps:
@@ -102,7 +102,7 @@ jobs:
             ${{ runner.os }}-test-${{ env.cache-name }}-
             ${{ runner.os }}-test-
             ${{ runner.os }}-
-      - uses: julia-actions/julia-downgrade-compat@v1
+      - uses: julia-actions/julia-downgrade-compat@v2
         with:
           skip: BoundaryValueDiffEqCore, BoundaryValueDiffEqMIRK, BoundaryValueDiffEqMIRKN, BoundaryValueDiffEqFIRK, BoundaryValueDiffEqShooting, BoundaryValueDiffEqAscher
       - name: "Install Dependencies and Run Tests"
diff --git a/.github/workflows/CI_BoundaryValueDiffEqCore.yml b/.github/workflows/CI_BoundaryValueDiffEqCore.yml
@@ -78,7 +78,7 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: julia-actions/julia-downgrade-compat@v1
+      - uses: julia-actions/julia-downgrade-compat@v2
       - name: "Install Dependencies and Run Tests"
         run: |
           import Pkg
diff --git a/.github/workflows/CI_BoundaryValueDiffEqFIRK.yml b/.github/workflows/CI_BoundaryValueDiffEqFIRK.yml
@@ -92,7 +92,7 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: julia-actions/julia-downgrade-compat@v1
+      - uses: julia-actions/julia-downgrade-compat@v2
         with:
           skip: BoundaryValueDiffEqCore, BoundaryValueDiffEqFIRK
       - name: "Install Dependencies and Run Tests"
diff --git a/.github/workflows/CI_BoundaryValueDiffEqMIRK.yml b/.github/workflows/CI_BoundaryValueDiffEqMIRK.yml
@@ -86,7 +86,7 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: julia-actions/julia-downgrade-compat@v1
+      - uses: julia-actions/julia-downgrade-compat@v2
         with:
           skip: BoundaryValueDiffEqCore, BoundaryValueDiffEqMIRK
       - name: "Install Dependencies and Run Tests"
diff --git a/.github/workflows/CI_BoundaryValueDiffEqMIRKN.yml b/.github/workflows/CI_BoundaryValueDiffEqMIRKN.yml
@@ -86,7 +86,7 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: julia-actions/julia-downgrade-compat@v1
+      - uses: julia-actions/julia-downgrade-compat@v2
         with:
           skip: BoundaryValueDiffEqCore, BoundaryValueDiffEqMIRKN
       - name: "Install Dependencies and Run Tests"
diff --git a/.github/workflows/CI_BoundaryValueDiffEqShooting.yml b/.github/workflows/CI_BoundaryValueDiffEqShooting.yml
@@ -86,7 +86,7 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
-      - uses: julia-actions/julia-downgrade-compat@v1
+      - uses: julia-actions/julia-downgrade-compat@v2
         with:
           skip: BoundaryValueDiffEqCore, BoundaryValueDiffEqShooting
       - name: "Install Dependencies and Run Tests"
diff --git a/.github/workflows/Downgrade.yml b/.github/workflows/Downgrade.yml
@@ -0,0 +1,31 @@
+name: Downgrade
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        downgrade_mode: ['alldeps']
+        julia-version: ['1.10']
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: julia-actions/julia-downgrade-compat@v2
+        with:
+          skip: Pkg,TOML
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          ALLOW_RERESOLVE: false
diff --git a/.github/workflows/DowngradeSublibraries.yml b/.github/workflows/DowngradeSublibraries.yml
@@ -0,0 +1,43 @@
+name: Downgrade Sublibraries
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        downgrade_mode: ['alldeps']
+        julia-version: ['1.10']
+        project:
+          - 'lib/BoundaryValueDiffEqAscher'
+          - 'lib/BoundaryValueDiffEqCore'
+          - 'lib/BoundaryValueDiffEqFIRK'
+          - 'lib/BoundaryValueDiffEqMIRK'
+          - 'lib/BoundaryValueDiffEqMIRKN'
+          - 'lib/BoundaryValueDiffEqShooting'
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.julia-version }}
+      - uses: julia-actions/julia-downgrade-compat@v2
+        with:
+          project: ${{ matrix.project }}
+          skip: Pkg,TOML
+      - uses: julia-actions/julia-buildpkg@v1
+        with:
+          project: ${{ matrix.project }}
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          project: ${{ matrix.project }}
+          ALLOW_RERESOLVE: false
diff --git a/.github/workflows/Invalidations.yml b/.github/workflows/Invalidations.yml
diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml
@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request]
+
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout Actions Repository
+        uses: actions/checkout@v4
+      - name: Check spelling
+        uses: crate-ci/typos@v1.18.0
diff --git a/.typos.toml b/.typos.toml
@@ -0,0 +1,77 @@
+[default.extend-words]
+# BVP-specific functions 
+Comput = "Comput"
+ABD = "ABD"
+
+# Julia-specific functions
+indexin = "indexin"
+findfirst = "findfirst"
+findlast = "findlast"
+eachindex = "eachindex"
+setp = "setp"
+getp = "getp"
+setu = "setu"
+getu = "getu"
+
+# Mathematical/scientific terms
+jacobian = "jacobian"
+hessian = "hessian" 
+eigenvalue = "eigenvalue"
+eigenvector = "eigenvector"
+discretization = "discretization"
+linearization = "linearization"
+parameterized = "parameterized"
+discretized = "discretized"
+vectorized = "vectorized"
+
+# Common variable patterns in Julia/SciML
+ists = "ists"
+ispcs = "ispcs"
+osys = "osys"
+rsys = "rsys"
+usys = "usys"
+fsys = "fsys"
+eqs = "eqs"
+rhs = "rhs"
+lhs = "lhs"
+ode = "ode"
+pde = "pde"
+sde = "sde"
+dde = "dde"
+bvp = "bvp"
+ivp = "ivp"
+
+# Common abbreviations
+tol = "tol"
+rtol = "rtol"
+atol = "atol"
+idx = "idx"
+jdx = "jdx"
+prev = "prev"
+curr = "curr"
+init = "init"
+tmp = "tmp"
+vec = "vec"
+arr = "arr"
+dt = "dt"
+du = "du"
+dx = "dx"
+dy = "dy"
+dz = "dz"
+
+# Algorithm/type suffixes
+alg = "alg"
+prob = "prob"
+sol = "sol"
+cb = "cb"
+opts = "opts"
+args = "args"
+kwargs = "kwargs"
+
+# Scientific abbreviations
+ND = "ND"
+nd = "nd"
+MTK = "MTK"
+ODE = "ODE"
+PDE = "PDE"
+SDE = "SDE"
diff --git a/docs/src/basics/autodiff.md b/docs/src/basics/autodiff.md
@@ -6,7 +6,7 @@
     the [backends page](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterface/stable/explanation/backends/)
     for more information.
 
-In BoundaryValueDiffEq.jl, automatic differentiation backend should only be wrapped in `BVPJacobianAlgorithm(diffmode, bc_diffmode, nonbc_diffmode)`. `BVPJacobianAlgorithm(diffmode, bc_diffmode, nonbc_diffmode)` supports user-specified mixed automatic differentiation backends in differrent part of a boundary value problem, and AD choice should depended on the type of boundary value problem:
+In BoundaryValueDiffEq.jl, automatic differentiation backend should only be wrapped in `BVPJacobianAlgorithm(diffmode, bc_diffmode, nonbc_diffmode)`. `BVPJacobianAlgorithm(diffmode, bc_diffmode, nonbc_diffmode)` supports user-specified mixed automatic differentiation backends in different part of a boundary value problem, and AD choice should depended on the type of boundary value problem:
 
   - [`BVProblem`](@ref SciMLBase.BVProblem): Differentiation mode for boundary condition part and non boundary condition part should be specified, for example, `BVPJacobianAlgorithm(; bc_diffmode, nonbc_diffmode)`, default to `BVPJacobianAlgorithm(; bc_diffmode = AutoForwardDiff(), nonbc_diffmode = AutoSparse(AutoForwardDiff()))`.
   - [`TwoPointBVProblem`](@ref SciMLBase.TwoPointBVProblem): Differentiation mode for overall solving should be specified, for example, `BVPJacobianAlgorithm(; diffmode)`, default to `BVPJacobianAlgorithm(; diffmode = AutoSparse(AutoForwardDiff()))`.
diff --git a/docs/src/basics/error_control.md b/docs/src/basics/error_control.md
@@ -2,15 +2,15 @@
 
 Adaptivity helps ensure the quality of the our numerical solution, and when our solution exhibits significant estimating errors, adaptivity automatically refine the mesh based on the error distribution, and providing a final satisfying solution.
 
-When comes to solving ill-conditioned BVP, for example the singular pertubation problem where the small parameters become extremally small leading to the layers phonemona, the error control adaptivity becomes even more critical, because the minor pertubations can lead to large deviation in the solution. In such cases, adaptivity autimatically figure out where to use refined mesh and where to use coarse mesh to achieve the balance of computational efficiency and accuracy.
+When comes to solving ill-conditioned BVP, for example the singular perturbation problem where the small parameters become extremely small leading to the layers phonemona, the error control adaptivity becomes even more critical, because the minor perturbations can lead to large deviation in the solution. In such cases, adaptivity automatically figure out where to use refined mesh and where to use coarse mesh to achieve the balance of computational efficiency and accuracy.
 
 BoundaryValuDiffEq.jl support error control adaptivity for collocation methods, and the adaptivity is default as defect control adaptivity when using adaptive collocation solvers:
 
 ```julia
 sol = solve(prob, MIRK4(), dt = 0.01, adaptive = true)
 ```
 
-Actually, BoundaryValueDiffEq.jl supports both defect and global error control adaptivity(while the defect control is the default controller) [boisvert2013runge](@Citet), to specify different error control metods, we simply need to specify the `controller` keyword in `solve`:
+Actually, BoundaryValueDiffEq.jl supports both defect and global error control adaptivity(while the defect control is the default controller) [boisvert2013runge](@Citet), to specify different error control methods, we simply need to specify the `controller` keyword in `solve`:
 
 ```julia
 sol = solve(prob, MIRK4(), dt = 0.01, controller = GlobalErrorControl()) # Use global error control
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,4 +1,4 @@
-# BoundaryValueDiffEq.jl: High-Performance Bounday Value Problem Solvers
+# BoundaryValueDiffEq.jl: High-Performance Boundary Value Problem Solvers
 
 BoundaryValueDiffEq.jl is a component package in the DifferentialEquations.jl ecosystem.
 The package includes its own high-performance BVP solvers which covers wide range of different kinds boundary value problems, includes the ability to swap out to fast direct and iterative nonlinear solvers, along with the ability to use sparse
diff --git a/docs/src/tutorials/continuation.md b/docs/src/tutorials/continuation.md
@@ -6,7 +6,7 @@ Continuation is a commonly used technique for solving numerically difficult boun
 \epsilon y'' + xy' = \epsilon \pi^2\cos(\pi x) - \pi x\sin(\pi x)
 ```
 
-for $\epsilon=10^{-4}$, on $t\in[-1,1]$ with two point boundary conditions $y(-1)=-2, y(1)=0$. With analitical solution of $y(x)=\cos(\pi x)+\text{erf}(\frac{x}{\sqrt{2\epsilon}})/\text{erf}(\frac{1}{\sqrt{2\epsilon}})$, this problem has a rapid transition layer at $x=0$, making it difficult to solve numerically. In this tutorial, we will showcase how to use continuation with BoundaryValueDiffEq.jl to solve this BVP.
+for $\epsilon=10^{-4}$, on $t\in[-1,1]$ with two point boundary conditions $y(-1)=-2, y(1)=0$. With analytical solution of $y(x)=\cos(\pi x)+\text{erf}(\frac{x}{\sqrt{2\epsilon}})/\text{erf}(\frac{1}{\sqrt{2\epsilon}})$, this problem has a rapid transition layer at $x=0$, making it difficult to solve numerically. In this tutorial, we will showcase how to use continuation with BoundaryValueDiffEq.jl to solve this BVP.
 
 We use the substitution to transform this problem into a first order BVP system:
 
diff --git a/docs/src/tutorials/extremum.md b/docs/src/tutorials/extremum.md
@@ -1,6 +1,6 @@
 # Solve BVP with Extremum Boundary Conditions
 
-In many physical systems, boundary conditions are not always defined at fixed points such as intitial or terminal ends of the domain. Instead, we may encounter scenarios where constraints are imposed on the maximum or minimum values that the solution must attain somewhere within the domain. In such cases, we can use the `maxsol` and `minsol` functions provided by BoundaryValueDiffEq.jl to specify such extremum boundary conditions.
+In many physical systems, boundary conditions are not always defined at fixed points such as initial or terminal ends of the domain. Instead, we may encounter scenarios where constraints are imposed on the maximum or minimum values that the solution must attain somewhere within the domain. In such cases, we can use the `maxsol` and `minsol` functions provided by BoundaryValueDiffEq.jl to specify such extremum boundary conditions.
 
 Let's walk through this functionality with an intuitive example. We still revisit the simple pendulum example here, but this time, suppose we need to impose the maximum and minimum value to our boundary conditions, specified as:
 
diff --git a/docs/src/tutorials/getting_started.md b/docs/src/tutorials/getting_started.md
@@ -33,7 +33,7 @@ prob = BVProblem(f!, bc!, u0, tspan)
 sol = solve(prob, MIRK4(), dt = 0.01)
 ```
 
-Since this proble only has constraints at the start and end of the time span, we can directly use `TwoPointBVProblem`:
+Since this problem only has constraints at the start and end of the time span, we can directly use `TwoPointBVProblem`:
 
 ```@example getting_started
 function f!(du, u, p, t)
@@ -94,7 +94,7 @@ prob = SecondOrderBVProblem(f!, bc!, u0, tspan)
 sol = solve(prob, MIRKN4(), dt = 0.01)
 ```
 
-## Solving semi-expicit boundary value differential-algebraic equations
+## Solving semi-explicit boundary value differential-algebraic equations
 
 Consider the nonlinear semi-explicit DAE of index at most 2 in COLDAE paper [ascher1994collocation](@Citet)
 
diff --git a/docs/src/tutorials/solve_nlls_bvp.md b/docs/src/tutorials/solve_nlls_bvp.md
@@ -39,7 +39,7 @@ sol = solve(prob, MIRK4(), dt = 0.01, abstol = 1e-3)
 plot(sol)
 ```
 
-Since this BVP imposes constaints only at the two endpoints, we can use `TwoPointBVProlem` to handle such cases.
+Since this BVP imposes constraints only at the two endpoints, we can use `TwoPointBVProlem` to handle such cases.
 
 ```@example nlls_overdetermined
 function f!(du, u, p, t)
diff --git a/docs/src/tutorials/unknown_parameters.md b/docs/src/tutorials/unknown_parameters.md
@@ -29,7 +29,7 @@ with boundary conditions of
 y_2(0)=0,\ y_2(\pi)=0
 ```
 
-It is worthnoting that in this system, while we have two differetial equations, it isn't enough to estimate the unknown parameters and gurantee a unique numerical solution with only two given boundary conditions. While under the hood, the parameters are estimated simultanously with the numerical solution, it makes the boundary value problem an underconstrained BVP if the number of constraints are equal to the number of states, which may result in more than one solution. So we should provide additional constraint $y(0)=1$ from the original equation to make sure unique numerical solution and the estimated parameters are we actually wanted.
+It is worthnoting that in this system, while we have two differetial equations, it isn't enough to estimate the unknown parameters and guarantee a unique numerical solution with only two given boundary conditions. While under the hood, the parameters are estimated simultaneously with the numerical solution, it makes the boundary value problem an underconstrained BVP if the number of constraints are equal to the number of states, which may result in more than one solution. So we should provide additional constraint $y(0)=1$ from the original equation to make sure unique numerical solution and the estimated parameters are we actually wanted.
 
 With BoundaryValueDiffEq.jl, it's easy to solve boundary value problems with unknown parameters, we can just specify `fit_parameters=true` when constructing the BVP and provide the guess of the unknown parameters in `prob.p`, for example, to estimate the unknown parameters in the above BVP system:
 
diff --git a/ext/BoundaryValueDiffEqODEInterfaceExt.jl b/ext/BoundaryValueDiffEqODEInterfaceExt.jl
@@ -172,7 +172,7 @@ function SciMLBase.__solve(prob::BVProblem, alg::BVPSOL; maxiters = 1000,
         elseif retcode == -5
             @warn "Given initial values inconsistent with separable linear bc"
         elseif retcode == -6
-            @warn "Iterative refinement faild to converge for `sol_method=0` \
+            @warn "Iterative refinement failed to converge for `sol_method=0` \
                    Termination since multiple shooting condition or \
                    condition of Jacobian is too bad for `sol_method=1`"
         elseif retcode == -8
diff --git a/lib/BoundaryValueDiffEqAscher/src/ascher_tableaus.jl b/lib/BoundaryValueDiffEqAscher/src/ascher_tableaus.jl
@@ -154,7 +154,7 @@ function vmonde!(rho, coef, k)
 end
 
 function rkbas!(s, coef, k::Integer, rkb, dm)
-    # for more guass collocation points per subinterval
+    # for more gauss collocation points per subinterval
     if k == 1
         rkb[1] = 1.0
         dm[1] = 1.0
@@ -178,7 +178,7 @@ function rkbas!(s, coef, k::Integer, rkb, dm)
 end
 
 function rkbas!(s, coef, k::Integer, rkb)
-    # for more guass collocation points per subinterval
+    # for more gauss collocation points per subinterval
     if k == 1
         rkb[1] = 1.0
         return
diff --git a/lib/BoundaryValueDiffEqAscher/src/collocation.jl b/lib/BoundaryValueDiffEqAscher/src/collocation.jl
@@ -76,7 +76,7 @@ function Φ!(cache::AscherCache{iip, T}, z, res, pt::StandardBVProblem) where {i
 
     # assembly process completed
     # solve the linear system
-    # ABD matrix decomposition
+    # AND matrix decomposition
     @views AlmostBlockDiagonals.factor_shift(g, ipvtg, df)
 
     # perform forward and backward substitution.
@@ -733,7 +733,7 @@ function approx(cache::AscherCache{iip, T}, x, zval, yval, dmval) where {iip, T}
 end
 
 # construct a group of ncomp rows of the matrices wi and
-# corrsponding to an interior collocation point
+# corresponding to an interior collocation point
 # jj=1...k
 function vwblok(cache::AscherCache{iip, T}, xcol, hrho, jj, wi,
         vi, ipvtw, zyval, df, acol, dmzo) where {iip, T}
diff --git a/lib/BoundaryValueDiffEqCore/src/solution_utils.jl b/lib/BoundaryValueDiffEqCore/src/solution_utils.jl
@@ -1,4 +1,4 @@
-# Intermidiate solution evaluation
+# Intermediate solution evaluation
 @concrete struct EvalSol{C}
     u
     t
diff --git a/lib/BoundaryValueDiffEqCore/src/types.jl b/lib/BoundaryValueDiffEqCore/src/types.jl
@@ -167,7 +167,7 @@ function __maybe_allocate_diffcache(x, chunksize, jac_alg)
 end
 __maybe_allocate_diffcache(x::DiffCache, chunksize) = DiffCache(zero(x.du), chunksize)
 
-## get_tmp shows a warning as it should on cache exapansion, this behavior however is
+## get_tmp shows a warning as it should on cache expansion, this behavior however is
 ## expected for adaptive BVP solvers so we write our own `get_tmp` and drop the warning logs
 
 @inline function get_tmp(dc, u)
diff --git a/lib/BoundaryValueDiffEqFIRK/src/interpolation.jl b/lib/BoundaryValueDiffEqFIRK/src/interpolation.jl
diff --git a/lib/BoundaryValueDiffEqFIRK/test/expanded/firk_basic_tests.jl b/lib/BoundaryValueDiffEqFIRK/test/expanded/firk_basic_tests.jl
diff --git a/lib/BoundaryValueDiffEqFIRK/test/nested/firk_basic_tests.jl b/lib/BoundaryValueDiffEqFIRK/test/nested/firk_basic_tests.jl
diff --git a/lib/BoundaryValueDiffEqMIRK/src/adaptivity.jl b/lib/BoundaryValueDiffEqMIRK/src/adaptivity.jl
diff --git a/lib/BoundaryValueDiffEqMIRK/src/interpolation.jl b/lib/BoundaryValueDiffEqMIRK/src/interpolation.jl
diff --git a/lib/BoundaryValueDiffEqMIRK/test/mirk_basic_tests.jl b/lib/BoundaryValueDiffEqMIRK/test/mirk_basic_tests.jl
diff --git a/lib/BoundaryValueDiffEqMIRKN/src/interpolation.jl b/lib/BoundaryValueDiffEqMIRKN/src/interpolation.jl
diff --git a/lib/BoundaryValueDiffEqShooting/test/orbital_tests.jl b/lib/BoundaryValueDiffEqShooting/test/orbital_tests.jl
diff --git a/src/extension_algs.jl b/src/extension_algs.jl
diff --git a/test/misc/bigfloat_test.jl b/test/misc/bigfloat_test.jl
