Merge branch 'main' into sc/p4est_coupling

.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:
         #
@@ -30,7 +30,7 @@ jobs:
         #       format(".")
         run: |
           julia  -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))'
-          julia  -e 'using JuliaFormatter; format(["benchmark", "ext", "src", "utils"])'
+          julia  -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])'
       - name: Format check
         run: |
           julia -e '

.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].1
+        uses: crate-ci/[email protected].21

.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

.github/workflows/downstream.yml

@@ -0,0 +1,94 @@
+# Note: this file is inspired by the downstream testing facilities in the SciML ecosystem
+# x-ref: https://github.com/SciML/SciMLBase.jl/blob/ffe68aebedee5915190623cb08160d7ef1fbcce0/.github/workflows/Downstream.yml
+
+name: Downstream
+on:
+  push:
+    branches:
+      - main
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'CITATION.bib'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE.md'
+      - 'NEWS.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/benchmark.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'benchmark/**'
+      # - 'docs/**'
+      - 'utils/**'
+  pull_request:
+    paths-ignore:
+      - 'AUTHORS.md'
+      - 'CITATION.bib'
+      - 'CONTRIBUTING.md'
+      - 'LICENSE.md'
+      - 'NEWS.md'
+      - 'README.md'
+      - '.zenodo.json'
+      - '.github/workflows/benchmark.yml'
+      - '.github/workflows/CompatHelper.yml'
+      - '.github/workflows/TagBot.yml'
+      - 'benchmark/**'
+      # - 'docs/**'
+      - 'utils/**'
+  workflow_dispatch:
+
+# Cancel redundant CI tests automatically
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    # We could also include the Julia version as in
+    # name: ${{ matrix.trixi_test }} - ${{ matrix.os }} - Julia ${{ matrix.version }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    # to be more specific. However, that requires us updating the required CI tests whenever we update Julia.
+    name: ${{ matrix.package }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.9'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+        package:
+          - Trixi2Vtk.jl
+          - TrixiShallowWater.jl
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)'
+      - uses: julia-actions/cache@v1
+      - uses: julia-actions/julia-buildpkg@v1
+      - name: Retrieve downstream package
+        # Note: we retrieve the current `main` branch of the downstream package to ensure
+        # that compatibility errors we make in Trixi.jl are detected already here
+        # See also https://github.com/trixi-framework/Trixi.jl/pull/1707#discussion_r1382938895
+        uses: actions/checkout@v4
+        with:
+          repository: trixi-framework/${{ matrix.package }}
+          path: downstream
+      - name: Load upstream package into downstream environment
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          Pkg.develop(PackageSpec(path="."))
+          Pkg.update()
+      - name: Run downstream tests (without coverage)
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          Pkg.test(coverage=false)
+        env:
+          TRIXI_TEST: upstream

.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

@@ -4,13 +4,45 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju
 used in the Julia ecosystem. Notable changes will be documented in this file
 for human readability.
 
+## Changes when updating to v0.6 from v0.5.x
+
+#### Added
+- AMR for hyperbolic-parabolic equations on 2D `P4estMesh`
+
+#### Changed
+
+- The wave speed estimates for `flux_hll`, `FluxHLL()` are now consistent across equations.
+  In particular, the functions `min_max_speed_naive`, `min_max_speed_einfeldt` are now 
+  conceptually identical across equations.
+  Users, who have been using `flux_hll` for MHD have now to use `flux_hlle` in order to use the
+  Einfeldt wave speed estimate.
+- Parabolic diffusion terms are now officially supported and not marked as experimental
+  anymore.
+
+#### Deprecated
+
+#### Removed
+
+- The neural network-based shock indicators have been migrated to a new repository
+  [TrixiSmartShockFinder.jl](https://github.com/trixi-framework/TrixiSmartShockFinder.jl).
+  To continue using the indicators, you will need to use both Trixi.jl and
+  TrixiSmartShockFinder.jl, as explained in the latter packages' `README.md`.
+
+
 ## Changes in the v0.5 lifecycle
 
 #### 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
+- Implementation of the polytropic Euler equations in 2D
+- Implementation of the quasi-1D shallow water equations
+- Subcell (positivity and local min/max) limiting support for conservative variables
+  in 2D for `TreeMesh`
+- AMR for hyperbolic-parabolic equations on 2D/3D `TreeMesh`
+- Added `GradientVariables` type parameter to `AbstractEquationsParabolic`
 
 #### Changed
 
@@ -27,6 +59,9 @@ for human readability.
 
 #### Removed
 
+- Migrate neural network-based shock indicators to a new repository
+  [TrixiSmartShockFinder.jl](https://github.com/trixi-framework/TrixiSmartShockFinder.jl).
+
 
 ## Changes when updating to v0.5 from v0.4.x
 

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 = "0.5.37-pre"
+version = "0.6.3-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
@@ -56,32 +56,35 @@ 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"
+LinearAlgebra = "1"
 LinearMaps = "2.7, 3.0"
 LoopVectorization = "0.12.118"
 MPI = "0.20"
 Makie = "0.19"
 MuladdMacro = "0.2.2"
 Octavian = "0.3.5"
 OffsetArrays = "1.3"
-P4est = "0.4"
+P4est = "0.4.9"
 Polyester = "0.7.5"
 PrecompileTools = "1.1"
+Printf = "1"
 RecipesBase = "1.1"
 Reexport = "1.0"
 Requires = "1.1"
-SciMLBase = "1.90"
+SciMLBase = "1.90, 2"
 Setfield = "0.8, 1"
 SimpleUnPack = "1.1"
+SparseArrays = "1"
 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"
 SummationByPartsOperators = "0.5.41"
-T8code = "0.4.1"
+T8code = "0.4.3"
 TimerOutputs = "0.5"
 Triangulate = "2.0"
 TriplotBase = "0.1"