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Merge branch 'main' into feature-t8code-3d
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jmark authored Dec 18, 2023
2 parents 1421434 + 6bef107 commit af06ee9
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2 changes: 1 addition & 1 deletion .github/workflows/CacheNotebooks.yml
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion .github/workflows/DocPreviewCleanup.yml
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Expand Up @@ -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

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2 changes: 1 addition & 1 deletion .github/workflows/Documenter.yml
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Expand Up @@ -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'
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4 changes: 2 additions & 2 deletions .github/workflows/FormatCheck.yml
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Expand Up @@ -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:
#
Expand All @@ -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 '
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4 changes: 2 additions & 2 deletions .github/workflows/Invalidations.yml
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion .github/workflows/ReviewChecklist.yml
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Expand Up @@ -12,7 +12,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out repository
uses: actions/checkout@v3
uses: actions/checkout@v4
- name: Add review checklist
uses: trixi-framework/add-pr-review-checklist@v1
with:
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4 changes: 2 additions & 2 deletions .github/workflows/SpellCheck.yml
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Expand Up @@ -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].5
uses: crate-ci/[email protected].23
2 changes: 1 addition & 1 deletion .github/workflows/benchmark.yml
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Expand Up @@ -15,7 +15,7 @@ jobs:
arch:
- x64
steps:
- uses: actions/checkout@v3
- uses: actions/checkout@v4
with:
fetch-depth: 0
- run: |
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4 changes: 2 additions & 2 deletions .github/workflows/ci.yml
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Expand Up @@ -102,7 +102,7 @@ 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 }}
Expand Down Expand Up @@ -176,7 +176,7 @@ 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
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94 changes: 94 additions & 0 deletions .github/workflows/downstream.yml
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@@ -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
2 changes: 1 addition & 1 deletion .zenodo.json
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Expand Up @@ -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"
},
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2 changes: 1 addition & 1 deletion AUTHORS.md
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Expand Up @@ -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),
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35 changes: 34 additions & 1 deletion NEWS.md
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Expand Up @@ -4,6 +4,31 @@ 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
Expand All @@ -12,7 +37,12 @@ for human readability.
- 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`
- 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

Expand All @@ -29,6 +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

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17 changes: 11 additions & 6 deletions Project.toml
Original file line number Diff line number Diff line change
@@ -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 = "0.5.40-pre"
version = "0.6.5-pre"

[deps]
CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949"
FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
Expand Down Expand Up @@ -52,37 +53,41 @@ TrixiMakieExt = "Makie"
[compat]
CodeTracking = "1.0.5"
ConstructionBase = "1.3"
DataStructures = "0.18.15"
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"
TimerOutputs = "0.5"
T8code = "0.4.3, 0.5"
TimerOutputs = "0.5.7"
Triangulate = "2.0"
TriplotBase = "0.1"
TriplotRecipes = "0.1"
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