Merge branch 'main' into compathelper/new_version/2023-03-10-00-06-48…

…-222-01498339475

.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/workflows/Documenter.yml

@@ -36,7 +36,7 @@ jobs:
       - uses: actions/checkout@v3
       - 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@v3
+      - 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/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@v3
+      - name: Check spelling
+        uses: crate-ci/[email protected]

.github/workflows/benchmark.yml

@@ -11,7 +11,7 @@ jobs:
         os:
           - ubuntu-latest
         version:
-          - '1.8'
+          - '1.9'
         arch:
           - x64
     steps:

.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
@@ -73,23 +74,28 @@ jobs:
           - 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
@@ -120,7 +126,7 @@ 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

.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"

AUTHORS.md

@@ -1,14 +1,14 @@
 # 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),
@@ -19,20 +19,22 @@ provided substantial additions or modifications. Together, these two groups form
   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
 * Jesse Chan
 * Lars Christmann
 * Christof Czernik
+* 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 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

@@ -167,7 +167,7 @@ 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

Project.toml

@@ -1,11 +1,12 @@
 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 = "0.5.17-pre"
+version = "0.5.29-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
 FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -20,6 +21,7 @@ Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 P4est = "7d669430-f675-4ae7-b43e-fab78ec5a902"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -30,6 +32,7 @@ SimpleUnPack = "ce78b400-467f-4804-87d8-8f486da07d0a"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StartUpDG = "472ebc20-7c99-4d4b-9470-8fde4e9faa0f"
 Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
+StaticArrayInterface = "0d7ed370-da01-4f52-bd93-41d350b8b718"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StrideArrays = "d1fa6d79-ef01-42a6-86c9-f7c551f8593b"
 StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
@@ -39,30 +42,40 @@ Triangulate = "f7e6ffb2-c36d-4f8f-a77e-16e897189344"
 TriplotBase = "981d1d27-644d-49a2-9326-4793e63143c3"
 TriplotRecipes = "808ab39a-a642-4abf-81ff-4cb34ebbffa3"
 
+[weakdeps]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
+
+[extensions]
+TrixiMakieExt = "Makie"
+
 [compat]
 CodeTracking = "1.0.5"
 ConstructionBase = "1.3"
+DiffEqCallbacks = "2.25"
 EllipsisNotation = "1.0"
 FillArrays = "0.13.2, 1"
 ForwardDiff = "0.10.18"
 HDF5 = "0.14, 0.15, 0.16"
 IfElse = "0.1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"
+Makie = "0.19"
 MPI = "0.20"
 MuladdMacro = "0.2.2"
 Octavian = "0.3.5"
 OffsetArrays = "1.3"
 P4est = "0.4"
 Polyester = "0.3.4, 0.5, 0.6, 0.7"
+PrecompileTools = "1.1"
 RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
 SciMLBase = "1.90"
 Setfield = "0.8, 1"
 SimpleUnPack = "1.1"
-StartUpDG = "0.15, 0.16"
+StartUpDG = "0.17"
 Static = "0.3, 0.4, 0.5, 0.6, 0.7, 0.8"
+StaticArrayInterface = "1.4"
 StaticArrays = "1"
 StrideArrays = "0.1.18"
 StructArrays = "0.6"
@@ -72,3 +85,6 @@ Triangulate = "2.0"
 TriplotBase = "0.1"
 TriplotRecipes = "0.1"
 julia = "1.8"
+
+[extras]
+Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"