Merge branch 'main' into ap/p4est_mesh_ns

.github/dependabot.yml

@@ -4,4 +4,4 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "monthly"

.github/review-checklist.md

@@ -0,0 +1,38 @@
+### Review checklist
+
+This checklist is meant to assist creators of PRs (to let them know what reviewers will typically look for) and reviewers (to guide them in a structured review process). Items do not need to be checked explicitly for a PR to be eligible for merging.
+
+#### Purpose and scope
+- [ ] The PR has a single goal that is clear from the PR title and/or description.
+- [ ] All code changes represent a single set of modifications that logically belong together.
+- [ ] No more than 500 lines of code are changed or there is no obvious way to split the PR into multiple PRs.
+
+#### Code quality
+- [ ] The code can be understood easily.
+- [ ] Newly introduced names for variables etc. are self-descriptive and consistent with existing naming conventions.
+- [ ] There are no redundancies that can be removed by simple modularization/refactoring.
+- [ ] There are no leftover debug statements or commented code sections.
+- [ ] The code adheres to our [conventions](https://trixi-framework.github.io/Trixi.jl/stable/conventions/) and [style guide](https://trixi-framework.github.io/Trixi.jl/stable/styleguide/), and to the [Julia guidelines](https://docs.julialang.org/en/v1/manual/style-guide/).
+
+#### Documentation
+- [ ] New functions and types are documented with a docstring or top-level comment.
+- [ ] Relevant publications are referenced in docstrings (see [example](https://github.com/trixi-framework/Trixi.jl/blob/7f83a1a938eecd9b841efe215a6e482e67cfdcc1/src/equations/compressible_euler_2d.jl#L601-L615) for formatting).
+- [ ] Inline comments are used to document longer or unusual code sections.
+- [ ] Comments describe intent ("why?") and not just functionality ("what?").
+- [ ] If the PR introduces a significant change or new feature, it is documented in `NEWS.md`.
+
+#### Testing
+- [ ] The PR passes all tests.
+- [ ] New or modified lines of code are covered by tests.
+- [ ] New or modified tests run in less then 10 seconds.
+
+#### Performance
+- [ ] There are no type instabilities or memory allocations in performance-critical parts.
+- [ ] If the PR intent is to improve performance, before/after [time measurements](https://trixi-framework.github.io/Trixi.jl/stable/performance/#Manual-benchmarking) are posted in the PR.
+
+#### Verification
+- [ ] The correctness of the code was verified using appropriate tests.
+- [ ] If new equations/methods are added, a convergence test has been run and the results
+  are posted in the PR.
+
+*Created with :heart: by the Trixi.jl community.*

.github/workflows/CacheNotebooks.yml

@@ -11,7 +11,7 @@ jobs:
     steps:
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
       - name: Checkout caching branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: tutorial_notebooks
 

.github/workflows/DocPreviewCleanup.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout gh-pages branch
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: gh-pages
 

.github/workflows/Documenter.yml

@@ -33,7 +33,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: '1.9'

.github/workflows/FormatCheck.yml

@@ -20,7 +20,7 @@ jobs:
         with:
           version: ${{ matrix.julia-version }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install JuliaFormatter and format
         # This will use the latest version by default but you can set the version like so:
         #

.github/workflows/Invalidations.yml

@@ -19,12 +19,12 @@ jobs:
     - uses: julia-actions/setup-julia@v1
       with:
         version: '1'
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - uses: julia-actions/julia-buildpkg@v1
     - uses: julia-actions/julia-invalidations@v1
       id: invs_pr
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ github.event.repository.default_branch }}
     - uses: julia-actions/julia-buildpkg@v1

.github/workflows/ReviewChecklist.yml

@@ -0,0 +1,20 @@
+name: Add review checklist
+
+on:
+  pull_request_target:
+    types: [opened]
+
+permissions:
+  pull-requests: write
+
+jobs:
+  add-review-checklist:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Add review checklist
+        uses: trixi-framework/add-pr-review-checklist@v1
+        with:
+          file: '.github/review-checklist.md'
+          no-checklist-keyword: '[no checklist]'

.github/workflows/SpellCheck.yml

@@ -8,6 +8,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Actions Repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/[email protected].2
+        uses: crate-ci/[email protected].15

.github/workflows/benchmark.yml

@@ -15,7 +15,7 @@ jobs:
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - run: |

.github/workflows/ci.yml

@@ -101,7 +101,7 @@ jobs:
             arch: x64
             trixi_test: threaded
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
@@ -175,7 +175,7 @@ jobs:
       # Instead, we use the more tedious approach described above.
       # At first, we check out the repository and download all artifacts
       # (and list files for debugging).
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/download-artifact@v3
       - run: ls -R
       # Next, we merge the individual coverage files and upload

.zenodo.json

@@ -15,7 +15,7 @@
             "orcid": "0000-0002-1752-1158"
         },
         {
-            "affiliation": "Applied Mathematics, University of Hamburg, Germany",
+            "affiliation": "Numerical Mathematics, Johannes Gutenberg University Mainz, Germany",
             "name": "Ranocha, Hendrik",
             "orcid": "0000-0002-3456-2277"
         },

AUTHORS.md

@@ -12,7 +12,7 @@ provided substantial additions or modifications. Together, these two groups form
 * [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner),
   University of Cologne, Germany
 * [Hendrik Ranocha](https://ranocha.de),
-  University of Hamburg, Germany
+  Johannes Gutenberg University Mainz, Germany
 * [Andrew Winters](https://liu.se/en/employee/andwi94),
   Linköping University, Sweden
 * [Jesse Chan](https://jlchan.github.io),
@@ -28,6 +28,7 @@ are listed in alphabetical order:
 * Jesse Chan
 * Lars Christmann
 * Christof Czernik
+* Daniel Doehring
 * Patrick Ersing
 * Erik Faulhaber
 * Gregor Gassner

NEWS.md

@@ -9,8 +9,10 @@ for human readability.
 #### Added
 
 - Experimental support for 3D parabolic diffusion terms has been added.
+- Non-uniform `TreeMesh` available for hyperbolic-parabolic equations.
 - Capability to set truly discontinuous initial conditions in 1D.
 - Wetting and drying feature and examples for 1D and 2D shallow water equations
+- Subcell positivity limiting support for conservative variables in 2D for `TreeMesh`
 
 #### Changed
 

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 = "0.5.38-pre"
+version = "0.5.45-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -56,7 +56,7 @@ DiffEqCallbacks = "2.25"
 EllipsisNotation = "1.0"
 FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.18"
-HDF5 = "0.14, 0.15, 0.16"
+HDF5 = "0.14, 0.15, 0.16, 0.17"
 IfElse = "0.1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"
@@ -71,7 +71,7 @@ PrecompileTools = "1.1"
 RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
-SciMLBase = "1.90"
+SciMLBase = "1.90, 2"
 Setfield = "0.8, 1"
 SimpleUnPack = "1.1"
 StartUpDG = "0.17"

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
@@ -247,7 +238,7 @@ Schlottke-Lakemper](https://lakemper.eu)
 (RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany) and
 [Gregor Gassner](https://www.mi.uni-koeln.de/NumSim/gregor-gassner)
 (University of Cologne, Germany). Together with [Hendrik Ranocha](https://ranocha.de)
-(University of Hamburg, Germany), [Andrew Winters](https://liu.se/en/employee/andwi94)
+(Johannes Gutenberg University Mainz, Germany), [Andrew Winters](https://liu.se/en/employee/andwi94)
 (Linköping University, Sweden), and [Jesse Chan](https://jlchan.github.io) (Rice University, US),
 they are the principal developers of Trixi.jl.
 The full list of contributors can be found in [AUTHORS.md](AUTHORS.md).

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)