Merge branch 'multi_ion_mhd' into multi_ion_collision_sources

.JuliaFormatter.toml

@@ -0,0 +1,8 @@
+# Use SciML style: https://github.com/SciML/SciMLStyle
+style = "sciml"
+
+# Python style alignment. See https://github.com/domluna/JuliaFormatter.jl/pull/732.
+yas_style_nesting = true
+
+# Align struct fields for better readability of large struct definitions
+align_struct_field = true

.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

@@ -33,10 +33,10 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.8'
+          version: '1.9'
           show-versioninfo: true
       - uses: julia-actions/julia-buildpkg@v1
         env:

.github/workflows/FormatCheck.yml

@@ -0,0 +1,44 @@
+name: format-check
+
+on:
+  push:
+    branches:
+      - 'main'
+    tags: '*'
+  pull_request:
+
+jobs:
+  check-format:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - 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:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version = "0.13.0"))'
+        #
+        # TODO: Change the call below to
+        #       format(".")
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "utils"])'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff --name-only`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'

.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

@@ -0,0 +1,13 @@
+name: Spell Check
+
+on: [pull_request, workflow_dispatch]
+
+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/[email protected]

.github/workflows/benchmark.yml

@@ -11,11 +11,11 @@ jobs:
         os:
           - ubuntu-latest
         version:
-          - '1.8'
+          - '1.9'
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - run: |

.github/workflows/ci.yml

@@ -52,7 +52,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.8'
+          - '1.9'
+          # - '~1.9.0-0' # including development versions
           # - 'nightly'
         os:
           - ubuntu-latest
@@ -68,33 +69,39 @@ jobs:
           - structured
           - p4est_part1
           - p4est_part2
+          - t8code_part1
           - unstructured_dgmulti
           - parabolic
           - paper_self_gravitating_gas_dynamics
           - misc_part1
           - misc_part2
-          - misc_part3
+          - performance_specializations_part1
+          - performance_specializations_part2
           - mpi
           - threaded
         include:
           - version: '1.8'
+            os: ubuntu-latest
+            arch: x64
+            trixi_test: threaded_legacy
+          - version: '1.9'
             os: macOS-latest
             arch: x64
             trixi_test: mpi
-          - version: '1.8'
+          - version: '1.9'
             os: macOS-latest
             arch: x64
             trixi_test: threaded
-          - version: '1.8'
+          - version: '1.9'
             os: windows-latest
             arch: x64
             trixi_test: mpi
-          - version: '1.8'
+          - version: '1.9'
             os: windows-latest
             arch: x64
             trixi_test: threaded
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
@@ -120,7 +127,7 @@ jobs:
           TRIXI_TEST: ${{ matrix.trixi_test }}
       - uses: julia-actions/julia-processcoverage@v1
         with:
-          directories: src,examples
+          directories: src,examples,ext
       - uses: codecov/codecov-action@v3
         with:
           file: ./lcov.info
@@ -168,7 +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

.gitignore

@@ -26,3 +26,8 @@ coverage_report/
 .vscode/
 
 .DS_Store
+
+run
+run/*
+
+LocalPreferences.toml

.typos.toml

@@ -0,0 +1,4 @@
+[default.extend-words]
+rcall = "rcall"
+claus = "claus"
+dum = "dum"

.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

@@ -1,38 +1,42 @@
 # Authors
 
-Trixi's development is coordinated by a group of *principal developers*,
+Trixi.jl's development is coordinated by a group of *principal developers*,
 who are also its main contributors and who can be contacted in case of
-questions about Trixi. In addition, there are *contributors* who have
+questions about Trixi.jl. In addition, there are *contributors* who have
 provided substantial additions or modifications. Together, these two groups form
-"The Trixi Authors" as mentioned in the [LICENSE.md](LICENSE.md) file.
+"The Trixi.jl Authors" as mentioned in the [LICENSE.md](LICENSE.md) file.
 
 ## Principal Developers
 * [Michael Schlottke-Lakemper](https://lakemper.eu),
-  RWTH Aachen University, Germany
+  RWTH Aachen University/High-Performance Computing Center Stuttgart (HLRS), Germany
 * [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),
   Rice University, US
 
 ## Contributors
-The following people contributed major additions or modifications to Trixi and
+The following people contributed major additions or modifications to Trixi.jl and
 are listed in alphabetical order:
 
 * Maximilian D. Bertrand
 * Benjamin Bolm
+* Simon Candelaresi
 * Jesse Chan
 * Lars Christmann
 * Christof Czernik
+* Daniel Doehring
+* Patrick Ersing
 * Erik Faulhaber
 * Gregor Gassner
 * Lucas Gemein
 * Sven Goldberg
 * Joshua Lampert
 * Julia Odenthal
+* Sigrun Ortleb
 * Hendrik Ranocha
 * Andrés M. Rueda-Ramírez
 * Felipe Santillan

CONTRIBUTING.md

@@ -1,12 +1,12 @@
 # Contributing
 
-Trixi is an open-source project and we are very happy to accept contributions
+Trixi.jl is an open-source project and we are very happy to accept contributions
 from the community. Please feel free to open issues or submit patches (preferably
-as merge requests) any time. For planned larger contributions, it is often
+as pull requests) any time. For planned larger contributions, it is often
 beneficial to get in contact with one of the principal developers first (see
 [AUTHORS.md](AUTHORS.md)).
 
-Trixi and its contributions are licensed under the MIT license (see
+Trixi.jl and its contributions are licensed under the MIT license (see
 [LICENSE.md](LICENSE.md)). As a contributor, you certify that all your
 contributions are in conformance with the *Developer Certificate of Origin
 (Version 1.1)*, which is reproduced below.

LICENSE.md

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2020-present The Trixi Authors (see [AUTHORS.md](AUTHORS.md))
+Copyright (c) 2020-present The Trixi.jl Authors (see [AUTHORS.md](AUTHORS.md))
 
 Permission is hereby granted, free of charge, to any person obtaining a copy  
 of this software and associated documentation files (the "Software"), to deal  

NEWS.md

@@ -9,6 +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
 
@@ -19,6 +23,9 @@ for human readability.
 - The macro `@unpack` (re-exported originally from UnPack.jl) is deprecated and
   will be removed. Consider using Julia's standard destructuring syntax
   `(; a, b) = stuff` instead of `@unpack a, b = stuff`.
+- The constructor `DGMultiMesh(dg; cells_per_dimension, kwargs...)` is deprecated
+  and will be removed. The new constructor `DGMultiMesh(dg, cells_per_dimension; kwargs...)`
+  does not have `cells_per_dimesion` as a keyword argument.
 
 #### Removed
 
@@ -164,7 +171,7 @@ for human readability.
   `flux_lax_friedrichs(u_ll, u_rr, orientation, equations::LatticeBoltzmannEquations3D)`
   were actually using the logic of `flux_godunov`. Thus, they were renamed accordingly
   in [#493](https://github.com/trixi-framework/Trixi.jl/pull/493). This is considered a bugfix
-  (released in Trixi v0.3.22).
+  (released in Trixi.jl v0.3.22).
 - The required Julia version is updated to v1.6.
 
 #### Deprecated