From 933bde3b46106b73fe7328b3f0bccfa787f9a661 Mon Sep 17 00:00:00 2001 From: Abhro <5664668+abhro@users.noreply.github.com> Date: Thu, 20 Nov 2025 17:30:50 -0500 Subject: [PATCH 1/6] Fix inter-document cross-ref link --- docs/src/features/dae_initialization.md | 4 ++-- docs/src/tutorials/dae_example.md | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/src/features/dae_initialization.md b/docs/src/features/dae_initialization.md index 6f8acd647..4cf10deb7 100644 --- a/docs/src/features/dae_initialization.md +++ b/docs/src/features/dae_initialization.md @@ -1,4 +1,4 @@ -# DAE Initialization +# [DAE Initialization](@id dae_initialization) DAE (Differential-Algebraic Equation) problems often require special initialization procedures to ensure that the initial conditions are consistent with the algebraic constraints. The DifferentialEquations.jl ecosystem provides several initialization algorithms to handle this automatically or to verify that your provided initial conditions are already consistent. @@ -213,4 +213,4 @@ sol = solve(prob, IDA(), initializealg = CheckInit()) # Sundials ## References - Brown, P. N., Hindmarsh, A. C., & Petzold, L. R. (1998). Consistent initial condition calculation for differential-algebraic systems. SIAM Journal on Scientific Computing, 19(5), 1495-1512. -- Shampine, L. F. (2002). Consistent initial condition for differential-algebraic systems. SIAM Journal on Scientific Computing, 22(6), 2007-2026. \ No newline at end of file +- Shampine, L. F. (2002). Consistent initial condition for differential-algebraic systems. SIAM Journal on Scientific Computing, 22(6), 2007-2026. diff --git a/docs/src/tutorials/dae_example.md b/docs/src/tutorials/dae_example.md index 06daf85a4..1b236ba4e 100644 --- a/docs/src/tutorials/dae_example.md +++ b/docs/src/tutorials/dae_example.md @@ -165,7 +165,7 @@ sol_check = DE.solve(prob, Sundials.IDA(), initializealg = DiffEqBase.CheckInit( ``` For more details on DAE initialization options, see the -[DAE Initialization documentation](@ref dae_initialization). +[DAE Initialization documentation](@ref "dae_initialization"). In order to clearly see all the features of this solution, it should be plotted on a logarithmic scale. We'll also plot each on a different subplot, to allow From e425bf82a78dee15f966c78d5d52fe418c0e51a3 Mon Sep 17 00:00:00 2001 From: Abhro <5664668+abhro@users.noreply.github.com> Date: Thu, 20 Nov 2025 17:31:16 -0500 Subject: [PATCH 2/6] Remove `xlims` and `ylims` keyword args from `Plots.plot()` Kept throwing errors when building docs --- docs/src/examples/classical_physics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/src/examples/classical_physics.md b/docs/src/examples/classical_physics.md index 8cfc8f67d..dfe00ee01 100644 --- a/docs/src/examples/classical_physics.md +++ b/docs/src/examples/classical_physics.md @@ -152,7 +152,7 @@ p = Plots.plot(sol, vars = (1, 2), xlims = (-9, 9), title = "Phase Space Plot", function phase_plot(prob, u0, p, tspan = 2pi) _prob = ODE.ODEProblem(prob.f, u0, (0.0, tspan)) sol = ODE.solve(_prob, ODE.Vern9()) # Use Vern9 solver for higher accuracy - Plots.plot!(p, sol, idxs = (1, 2), xlims = nothing, ylims = nothing) + Plots.plot!(p, sol, idxs = (1, 2)) end for i in (-4pi):(pi / 2):(4π) for j in (-4pi):(pi / 2):(4π) From c4747c1755e4dfd72a8f4597aa3dc1db3f011f4b Mon Sep 17 00:00:00 2001 From: Abhro <5664668+abhro@users.noreply.github.com> Date: Thu, 20 Nov 2025 17:32:32 -0500 Subject: [PATCH 3/6] Ignore StochasticDiffEq doc copies Files generated when running docs/make.jl --- .gitignore | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.gitignore b/.gitignore index 0b2114508..92ec2f779 100644 --- a/.gitignore +++ b/.gitignore @@ -4,7 +4,9 @@ docs/build docs/site docs/src/api/ordinarydiffeq +docs/src/api/stochasticdiffeq docs/ordinarydiffeq_pages.jl +docs/stochasticdiffeq_pages.jl docs/common_first_steps.jl /Manifest.toml From f3ebbaf31c6bdd032945038632419a9e0a4ea2ab Mon Sep 17 00:00:00 2001 From: Abhro <5664668+abhro@users.noreply.github.com> Date: Thu, 20 Nov 2025 17:36:40 -0500 Subject: [PATCH 4/6] Remove duplicate gitignore lines --- .gitignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.gitignore b/.gitignore index 92ec2f779..e2236d15e 100644 --- a/.gitignore +++ b/.gitignore @@ -8,7 +8,6 @@ docs/src/api/stochasticdiffeq docs/ordinarydiffeq_pages.jl docs/stochasticdiffeq_pages.jl docs/common_first_steps.jl -/Manifest.toml # vscode stuff .vscode From 85f8f57752da318412806085ea4492957bd45b57 Mon Sep 17 00:00:00 2001 From: Abhro <5664668+abhro@users.noreply.github.com> Date: Thu, 20 Nov 2025 17:36:50 -0500 Subject: [PATCH 5/6] Ignore copied Project.toml file Created during doc building --- .gitignore | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index e2236d15e..6089b27ef 100644 --- a/.gitignore +++ b/.gitignore @@ -13,4 +13,5 @@ docs/common_first_steps.jl .vscode .vscode/* -Manifest.toml \ No newline at end of file +docs/src/assets/Project.toml +Manifest.toml From db1a54e5990ae985ec75a7dd703194121b18733b Mon Sep 17 00:00:00 2001 From: Abhro <5664668+abhro@users.noreply.github.com> Date: Thu, 20 Nov 2025 18:02:02 -0500 Subject: [PATCH 6/6] Copy over common_imex_first_steps.jl from OrdinaryDiffEq.jl --- .gitignore | 1 + docs/make.jl | 10 ++++++---- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index 6089b27ef..18e9a4249 100644 --- a/.gitignore +++ b/.gitignore @@ -8,6 +8,7 @@ docs/src/api/stochasticdiffeq docs/ordinarydiffeq_pages.jl docs/stochasticdiffeq_pages.jl docs/common_first_steps.jl +docs/common_imex_first_steps.jl # vscode stuff .vscode diff --git a/docs/make.jl b/docs/make.jl index 717425c60..0f3ca294f 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -28,10 +28,12 @@ if isdir(ordinartdiffeq_docs_path) ordinary_diffeq_pages_file = joinpath(ordinartdiffeq_docs_root, "pages.jl") cp(ordinary_diffeq_pages_file, ordinary_diffeq_pages_dest, force = true) - # Copy the common_first_steps.jl file from OrdinaryDiffEq.jl - common_first_steps_dest = joinpath(@__DIR__, "common_first_steps.jl") - common_first_steps_file = joinpath(ordinartdiffeq_docs_root, "common_first_steps.jl") - cp(common_first_steps_file, common_first_steps_dest, force = true) + # Copy the common_first_steps.jl and common_imex_first_steps.jl files from OrdinaryDiffEq.jl + for fname in ["common_first_steps.jl", "common_imex_first_steps.jl"] + common_first_steps_dest = joinpath(@__DIR__, fname) + common_first_steps_file = joinpath(ordinartdiffeq_docs_root, fname) + cp(common_first_steps_file, common_first_steps_dest, force = true) + end end # Copy StochasticDiffEq.jl documentation