Merge branch 'main' into subcell-limiting-visualization

Project.toml

@@ -1,7 +1,7 @@
 name = "Trixi"
 uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb"
 authors = ["Michael Schlottke-Lakemper <[email protected]>", "Gregor Gassner <[email protected]>", "Hendrik Ranocha <[email protected]>", "Andrew R. Winters <[email protected]>", "Jesse Chan <[email protected]>"]
-version = "0.5.42-pre"
+version = "0.5.45-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"

README.md

@@ -7,6 +7,7 @@
 [![Build Status](https://github.com/trixi-framework/Trixi.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/Trixi.jl/actions?query=workflow%3ACI)
 [![Codecov](https://codecov.io/gh/trixi-framework/Trixi.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/Trixi.jl)
 [![Coveralls](https://coveralls.io/repos/github/trixi-framework/Trixi.jl/badge.svg?branch=main)](https://coveralls.io/github/trixi-framework/Trixi.jl?branch=main)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3996439.svg)](https://doi.org/10.5281/zenodo.3996439)
 [![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/Trixi)](https://pkgs.genieframework.com?packages=Trixi)
@@ -17,16 +18,6 @@
   <img width="300px" src="https://trixi-framework.github.io/assets/logo.png">
 </p>
 
-***
-**Trixi.jl at JuliaCon 2023**<br/>
-At this year's JuliaCon, we will be present with an online contribution that involves Trixi.jl:
-
-* [Scaling Trixi.jl to more than 10,000 cores using MPI](https://pretalx.com/juliacon2023/talk/PC8PZ8/),
-  27th July 2023, 10:30–11:30 (US/Eastern), 32-G449 (Kiva)
-
-We are looking forward to seeing you there ♥️
-***
-
 **Trixi.jl** is a numerical simulation framework for hyperbolic conservation
 laws written in [Julia](https://julialang.org). A key objective for the
 framework is to be useful to both scientists and students. Therefore, next to

docs/Project.toml

@@ -13,7 +13,7 @@ Trixi2Vtk = "bc1476a1-1ca6-4cc3-950b-c312b255ff95"
 
 [compat]
 CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
-Documenter = "0.27"
+Documenter = "1"
 ForwardDiff = "0.10"
 HOHQMesh = "0.1, 0.2"
 LaTeXStrings = "1.2"

docs/literate/make.jl

@@ -51,12 +51,25 @@ function create_tutorials(files)
     # Run tests on all tutorial files
     @testset "TrixiTutorials" begin
         for (i, (title, filename)) in enumerate(files)
+            # Evaluate each tutorial in its own module to avoid leaking of
+            # function/variable names, polluting the namespace of later tutorials
+            # by stuff defined in earlier tutorials.
             if filename isa Vector # Several files of one topic
                 for j in eachindex(filename)
-                    @testset "$(filename[j][2][2])" begin include(joinpath(repo_src, filename[j][2][1], filename[j][2][2])) end
+                    mod = gensym(filename[j][2][2])
+                    @testset "$(filename[j][2][2])" begin
+                        @eval module $mod
+                            include(joinpath($repo_src, $(filename[j][2][1]), $(filename[j][2][2])))
+                        end
+                    end
                 end
             else # Single files
-                @testset "$title" begin include(joinpath(repo_src, filename)) end
+                mod = gensym(title)
+                @testset "$title" begin
+                    @eval module $mod
+                        include(joinpath($repo_src, $filename))
+                    end
+                end
             end
         end
     end

docs/literate/src/files/DGMulti_1.jl

@@ -194,3 +194,15 @@ plot(pd["rho"])
 plot!(getmesh(pd))
 
 # For more information, please have a look in the [StartUpDG.jl documentation](https://jlchan.github.io/StartUpDG.jl/stable/).
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "StartUpDG", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/DGMulti_2.jl

@@ -38,3 +38,15 @@ D = couple_continuously(legendre_derivative_operator(xmin=0.0, xmax=1.0, N=4),
 
 # For more information and other SBP operators, see the documentations of [StartUpDG.jl](https://jlchan.github.io/StartUpDG.jl/dev/)
 # and [SummationByPartsOperators.jl](https://ranocha.de/SummationByPartsOperators.jl/stable/).
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "StartUpDG", "SummationByPartsOperators"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/DGSEM_FluxDiff.jl

@@ -236,3 +236,15 @@ plot(sol)
 # [`flux_chandrashekar`](@ref), [`flux_kennedy_gruber`](@ref).
 # As surface flux you can use all volume fluxes and additionally for instance [`flux_lax_friedrichs`](@ref),
 # [`flux_hll`](@ref), [`flux_hllc`](@ref).
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/adaptive_mesh_refinement.jl

@@ -202,3 +202,15 @@ plot!(getmesh(pd))
 # Source: Trixi.jl's YouTube channel [`Trixi Framework`](https://www.youtube.com/channel/UCpd92vU2HjjTPup-AIN0pkg)
 
 # For more information, please have a look at the respective links.
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/adding_new_parabolic_terms.jl

@@ -158,3 +158,15 @@ sol = solve(ode, RDPK3SpFSAL49(); abstol=time_int_tol, reltol=time_int_tol,
 using Plots
 plot(sol)
 
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)
+

docs/literate/src/files/adding_new_scalar_equations.jl

@@ -211,3 +211,15 @@ semi = remake(semi, solver=DGSEM(3, flux_godunov, VolumeIntegralFluxDifferencing
 ode = semidiscretize(semi, (0.0, 0.5))
 sol = solve(ode, SSPRK43(); ode_default_options()...)
 plot(sol)
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)

docs/literate/src/files/adding_nonconservative_equation.jl

@@ -288,3 +288,15 @@ sol = solve(ode, Tsit5(), abstol=1.0e-6, reltol=1.0e-6,
 ## Plot the numerical solution at the final time
 using Plots: plot
 plot(sol);
+
+
+# ## Package versions
+
+# These results were obtained using the following versions.
+
+using InteractiveUtils
+versioninfo()
+
+using Pkg
+Pkg.status(["Trixi", "OrdinaryDiffEq", "Plots"],
+           mode=PKGMODE_MANIFEST)