Merge main (first version)

.github/review-checklist.md

@@ -19,7 +19,7 @@ This checklist is meant to assist creators of PRs (to let them know what reviewe
 - [ ] 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`.
+- [ ] If the PR introduces a significant change or new feature, it is documented in `NEWS.md` with its PR number.
 
 #### Testing
 - [ ] The PR passes all tests.
@@ -35,4 +35,4 @@ This checklist is meant to assist creators of PRs (to let them know what reviewe
 - [ ] 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.*
+*Created with :heart: by the Trixi.jl community.*

.github/workflows/Documenter.yml

@@ -34,9 +34,9 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
-          version: '1.9'
+          version: '1.10'
           show-versioninfo: true
       - uses: julia-actions/cache@v1
       - uses: julia-actions/julia-buildpkg@v1

.github/workflows/Downgrade.yml

@@ -64,7 +64,7 @@ jobs:
           - threaded
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}

.github/workflows/Invalidations.yml

@@ -16,7 +16,7 @@ jobs:
     if: github.base_ref == github.event.repository.default_branch
     runs-on: ubuntu-latest
     steps:
-    - uses: julia-actions/setup-julia@v1
+    - uses: julia-actions/setup-julia@v2
       with:
         version: '1'
     - uses: actions/checkout@v4

.github/workflows/SpellCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.18.2
+        uses: crate-ci/typos@v1.21.0

.github/workflows/benchmark.yml

@@ -11,7 +11,7 @@ jobs:
         os:
           - ubuntu-latest
         version:
-          - '1.9'
+          - '1.10'
         arch:
           - x64
     steps:
@@ -21,7 +21,7 @@ jobs:
       - run: |
           git fetch --tags
           git branch --create-reflog main origin/main
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}

.github/workflows/ci.yml

@@ -52,8 +52,8 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.9'
-          # - '~1.9.0-0' # including development versions
+          - '1.10'
+          # - '~1.10.0-0' # including development versions
           # - 'nightly'
         os:
           - ubuntu-latest
@@ -86,28 +86,28 @@ jobs:
             arch: x64
             trixi_test: threaded_legacy
           - version: '1.9'
-            os: macOS-latest
+            os: ubuntu-latest
             arch: x64
-            trixi_test: mpi
-          - version: '1.9'
-            os: macOS-latest
+            trixi_test: threaded_legacy
+          - version: '1.10'
+            os: macos-13
             arch: x64
+            trixi_test: mpi
+          - version: '1.10'
+            os: macos-latest
+            arch: aarch64
             trixi_test: threaded
-          - version: '1.9'
+          - version: '1.10'
             os: windows-latest
             arch: x64
             trixi_test: mpi
-          - version: '1.9'
+          - version: '1.10'
             os: windows-latest
             arch: x64
             trixi_test: threaded
-          - version: '1.9'
-            os: macos-14
-            arch: arm64
-            trixi_test: threaded
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}

.github/workflows/downstream.yml

@@ -64,7 +64,7 @@ jobs:
           - TrixiShallowWater.jl
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}

NEWS.md

@@ -8,8 +8,11 @@ for human readability.
 
 #### Added
 - Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D` and extension
-  to 1D and 3D on `TreeMesh`.
-
+  to 1D and 3D on `TreeMesh` ([#1855], [#1873]).
+- Implementation of 1D Linearized Euler Equations ([#1867]).
+- New analysis callback for 2D `P4estMesh` to compute integrated quantities along a boundary surface, e.g., pressure lift and drag coefficients ([#1812]).
+- Optional tuple parameter for `GlmSpeedCallback` called `semi_indices` to specify for which semidiscretization of a `SemidiscretizationCoupled` we need to update the GLM speed ([#1835]).
+- Subcell local one-sided limiting support for nonlinear variables in 2D for `TreeMesh` ([#1792]).
 
 ## Changes when updating to v0.7 from v0.6.x
 
@@ -187,9 +190,8 @@ for human readability.
 #### Added
 
 - Experimental support for artificial neural network-based indicators for shock capturing and
-  adaptive mesh refinement ([#632](https://github.com/trixi-framework/Trixi.jl/pull/632))
-- Experimental support for direct-hybrid aeroacoustics simulations
-  ([#712](https://github.com/trixi-framework/Trixi.jl/pull/712))
+  adaptive mesh refinement ([#632])
+- Experimental support for direct-hybrid aeroacoustics simulations ([#712])
 - Implementation of shallow water equations in 2D
 - Experimental support for interactive visualization with [Makie.jl](https://makie.juliaplots.org/)
 
@@ -225,7 +227,7 @@ for human readability.
   - acoustic perturbation equations
   - Lattice-Boltzmann equations
 - Composable `FluxPlusDissipation` and `FluxLaxFriedrichs()`, `FluxHLL()` with adaptable
-  wave speed estimates were added in [#493](https://github.com/trixi-framework/Trixi.jl/pull/493)
+  wave speed estimates were added in [#493]
 - New structured, curvilinear, conforming mesh type `StructuredMesh`
 - New unstructured, curvilinear, conforming mesh type `UnstructuredMesh2D` in 2D
 - New unstructured, curvilinear, adaptive (non-conforming) mesh type `P4estMesh` in 2D and 3D
@@ -238,13 +240,13 @@ for human readability.
 - `flux_lax_friedrichs(u_ll, u_rr, orientation, equations::LatticeBoltzmannEquations2D)` and
   `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
+  in [#493]. This is considered a bugfix
   (released in Trixi.jl v0.3.22).
 - The required Julia version is updated to v1.6.
 
 #### Deprecated
 
-- `calcflux` → `flux` ([#463](https://github.com/trixi-framework/Trixi.jl/pull/463))
+- `calcflux` → `flux` ([#463])
 - `flux_upwind` → `flux_godunov`
 - `flux_hindenlang` → `flux_hindenlang_gassner`
 - Providing the keyword argument `solution_variables` of `SaveSolutionCallback`
@@ -256,6 +258,6 @@ for human readability.
   only a single two-point numerical flux for nonconservative is deprecated. The new
   interface is described in a tutorial. Now, a tuple of two numerical fluxes of the
   form `(conservative_flux, nonconservative_flux)` needs to be passed for
-  nonconservative equations, see [#657](https://github.com/trixi-framework/Trixi.jl/pull/657).
+  nonconservative equations, see [#657].
 
 #### Removed

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 = "0.7.6-pre"
+version = "0.7.12-pre"
 
 [deps]
 CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"

docs/.gitignore

@@ -1,3 +1,4 @@
+src/changelog.md
 src/code_of_conduct.md
 src/contributing.md
 

docs/Project.toml

@@ -1,5 +1,6 @@
 [deps]
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Changelog = "5217a498-cd5d-4ec6-b8c2-9b85a09b6e3e"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 HOHQMesh = "e4f4c7b8-17cb-445a-93c5-f69190ed6c8c"
@@ -14,6 +15,7 @@ TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284"
 
 [compat]
 CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10, 0.11"
+Changelog = "1.1"
 Documenter = "1"
 ForwardDiff = "0.10"
 HOHQMesh = "0.1, 0.2"

docs/literate/make.jl

@@ -75,7 +75,17 @@ function create_tutorials(files)
     end
 
     # Generate markdown file for introduction page
-    Literate.markdown(joinpath(repo_src, "index.jl"), pages_dir; name="introduction")
+    # Preprocessing introduction file: Generate consecutive tutorial numbers by replacing
+    # each occurrence of `{index}` with an integer incremented by 1, starting at 1.
+    function preprocess_introduction(content)
+        counter = 1
+        while occursin("{index}", content)
+            content = replace(content, "{index}" => "$counter", count = 1)
+            counter += 1
+        end
+        return content
+    end
+    Literate.markdown(joinpath(repo_src, "index.jl"), pages_dir; name="introduction", preprocess=preprocess_introduction)
     # Navigation system for makedocs
     pages = Any["Introduction" => "tutorials/introduction.md",]
 

docs/literate/src/files/first_steps/changing_trixi.jl

@@ -4,6 +4,14 @@
 # the cloned directory.
 
 
+# ## Forking Trixi.jl
+
+# To create your own fork of Trixi.jl, log in to your GitHub account, visit the
+# [Trixi.jl GitHub repository](https://github.com/trixi-framework/Trixi.jl) and click the `Fork`
+# button located in the upper-right corner of the page. Then, click on `Create fork` in the opened
+# window to complete the forking process.
+
+
 # ## Cloning Trixi.jl
 
 
@@ -15,8 +23,10 @@
 # - Download and install [GitHub Desktop](https://desktop.github.com/) and then log in to
 #   your account.
 # - Open GitHub Desktop, press `Ctrl+Shift+O`.
-# - In the opened window, paste `trixi-framework/Trixi.jl` and choose the path to the folder where
-#   you want to save Trixi.jl. Then click `Clone` and Trixi.jl will be cloned to your computer. 
+# - In the opened window, navigate to the `URL` tab and paste `trixi-framework/Trixi.jl` or
+#   `YourGitHubUserName/Trixi.jl` to clone your own fork of Trixi.jl, and choose the
+#   path to the folder where you want to save Trixi.jl. Then click `Clone` and Trixi.jl will be
+#   cloned to your computer. 
 
 # Now you cloned Trixi.jl and only need to tell Julia to use the local clone as the package sources:
 # - Open a terminal using `Win+r` and `cmd`. Navigate to the folder with the cloned Trixi.jl using `cd`.
@@ -54,6 +64,9 @@
 # julia --project=. -e 'using Pkg; Pkg.develop(PackageSpec(path=".."))' # Tell Julia to use the local Trixi.jl clone
 # julia --project=. -e 'using Pkg; Pkg.add(["OrdinaryDiffEq", "Plots"])' # Install additional packages
 # ```
+# Alternatively, you can clone your own fork of Trixi.jl by replacing the link
+# `[email protected]:trixi-framework/Trixi.jl.git` with `[email protected]:YourGitHubUserName/Trixi.jl.git`.
+
 # Note that if you installed Trixi.jl this way,
 # you always have to start Julia with the `--project` flag set to your `run` directory, e.g.,
 # ```shell
@@ -62,9 +75,32 @@
 # if already inside the `run` directory.
 
 
+# ## Developing Trixi.jl
+
+# If you've created and cloned your own fork of Trixi.jl, you can make local changes to Trixi.jl
+# and propose them as a Pull Request (PR) to be merged into `trixi-framework/Trixi.jl`.
+
+# Linux and MacOS utilize the `git` version control system to manage changes between your local and
+# remote repositories. The most commonly used commands include `add`, `commit`, `push` and `pull`.
+# You can find detailed information about these functions in the
+# [Git documentation](https://git-scm.com/docs).
+
+# For Windows and GitHub Desktop users, refer to the
+# [documentation of GitHub Desktop](https://docs.github.com/en/desktop/overview/getting-started-with-github-desktop#making-changes-in-a-branch).
+
+# After making local changes to Trixi.jl and pushing them to the remote repository, you can open a
+# Pull Request (PR) from your branch to the main branch of `trixi-framework/Trixi.jl`. Then, follow
+# the Review checklist provided in the Pull Request to streamline the review process.
+
+
 # ## Additional reading
 
 # To further delve into Trixi.jl, you may have a look at the following introductory tutorials.
+# - [Behind the scenes of a simulation setup](@ref behind_the_scenes_simulation_setup) will guide
+#   you through a simple Trixi.jl setup ("elixir"), giving an overview of what happens in the
+#   background during the initialization of a simulation. It clarifies some of the more
+#   fundamental, technical concepts that are applicable to a variety of (also more complex)
+#   configurations.
 # - [Introduction to DG methods](@ref scalar_linear_advection_1d) will teach you how to set up a
 #   simple way to approximate the solution of a hyperbolic partial differential equation. It will
 #   be especially useful to learn about the