Merge branch 'Muladd_for_NavierStokes' of github.com:DanielDoehring/T…

…rixi.jl into Muladd_for_NavierStokes
trixi-framework · Sep 20, 2023 · 19c7415 · 19c7415
2 parents 939c17c + 5122b78
commit 19c7415
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diff --git a/README.md b/README.md
@@ -7,6 +7,7 @@
 [![Build Status](https://github.com/trixi-framework/Trixi.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/Trixi.jl/actions?query=workflow%3ACI)
 [![Codecov](https://codecov.io/gh/trixi-framework/Trixi.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/Trixi.jl)
 [![Coveralls](https://coveralls.io/repos/github/trixi-framework/Trixi.jl/badge.svg?branch=main)](https://coveralls.io/github/trixi-framework/Trixi.jl?branch=main)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3996439.svg)](https://doi.org/10.5281/zenodo.3996439)
 [![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/Trixi)](https://pkgs.genieframework.com?packages=Trixi)

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -13,7 +13,7 @@ Trixi2Vtk = "bc1476a1-1ca6-4cc3-950b-c312b255ff95"
 
 [compat]
 CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
-Documenter = "0.27"
+Documenter = "1"
 ForwardDiff = "0.10"
 HOHQMesh = "0.1, 0.2"
 LaTeXStrings = "1.2"

diff --git a/docs/make.jl b/docs/make.jl
@@ -77,15 +77,16 @@ makedocs(
     # Specify modules for which docstrings should be shown
     modules = [Trixi, Trixi2Vtk],
     # Set sitename to Trixi.jl
-    sitename="Trixi.jl",
+    sitename = "Trixi.jl",
     # Provide additional formatting options
     format = Documenter.HTML(
         # Disable pretty URLs during manual testing
         prettyurls = get(ENV, "CI", nothing) == "true",
         # Explicitly add favicon as asset
         assets = ["assets/favicon.ico"],
         # Set canonical URL to GitHub pages URL
-        canonical = "https://trixi-framework.github.io/Trixi.jl/stable"
+        canonical = "https://trixi-framework.github.io/Trixi.jl/stable",
+        size_threshold_ignore = ["reference-trixi.md"]
     ),
     # Explicitly specify documentation structure
     pages = [
@@ -124,9 +125,8 @@ makedocs(
         "Authors" => "authors.md",
         "Contributing" => "contributing.md",
         "Code of Conduct" => "code_of_conduct.md",
-        "License" => "license.md"
-    ],
-    strict = true # to make the GitHub action fail when doctests fail, see https://github.com/neuropsychology/Psycho.jl/issues/34
+        "License" => "license.md",
+    ]
 )
 
 deploydocs(

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -7,6 +7,7 @@
 [![Build Status](https://github.com/trixi-framework/Trixi.jl/workflows/CI/badge.svg)](https://github.com/trixi-framework/Trixi.jl/actions?query=workflow%3ACI)
 [![Codecov](https://codecov.io/gh/trixi-framework/Trixi.jl/branch/main/graph/badge.svg)](https://codecov.io/gh/trixi-framework/Trixi.jl)
 [![Coveralls](https://coveralls.io/repos/github/trixi-framework/Trixi.jl/badge.svg?branch=main)](https://coveralls.io/github/trixi-framework/Trixi.jl?branch=main)
+[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 [![License: MIT](https://img.shields.io/badge/License-MIT-success.svg)](https://opensource.org/licenses/MIT)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3996439.svg)](https://doi.org/10.5281/zenodo.3996439)
 

diff --git a/src/solvers/dgsem_unstructured/dg_2d.jl b/src/solvers/dgsem_unstructured/dg_2d.jl
@@ -357,9 +357,9 @@ function calc_boundary_flux_by_type!(cache, t, BCs::Tuple{}, BC_indices::Tuple{}
     nothing
 end
 
-function calc_boundary_flux!(cache, t, boundary_condition, boundary_indexing,
+function calc_boundary_flux!(cache, t, boundary_condition::BC, boundary_indexing,
                              mesh::UnstructuredMesh2D, equations,
-                             surface_integral, dg::DG)
+                             surface_integral, dg::DG) where {BC}
     @unpack surface_flux_values = cache.elements
     @unpack element_id, element_side_id = cache.boundaries
 

diff --git a/test/Project.toml b/test/Project.toml
@@ -1,13 +1,5 @@
-[compat]
-BSON = "0.3.3"
-CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
-Flux = "0.13 - 0.13.12" # TODO: Return to "0.13" once https://github.com/FluxML/Flux.jl/issues/2204 is resolved
-ForwardDiff = "0.10"
-MPI = "0.20"
-OrdinaryDiffEq = "6.49.1"
-Plots = "1.16"
-
 [deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
@@ -21,6 +13,16 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
+[compat]
+Aqua = "0.7"
+BSON = "0.3.3"
+CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10"
+Flux = "0.13.15, 0.14"
+ForwardDiff = "0.10"
+MPI = "0.20"
+OrdinaryDiffEq = "6.49.1"
+Plots = "1.16"
+
 [preferences.OrdinaryDiffEq]
 PrecompileAutoSpecialize = false
 PrecompileAutoSwitch = false

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -109,6 +109,7 @@ const TRIXI_NTHREADS = clamp(Sys.CPU_THREADS, 2, 3)
 
     @time if TRIXI_TEST == "all" || TRIXI_TEST == "misc_part2"
         include("test_special_elixirs.jl")
+        include("test_aqua.jl")
     end
 
     @time if TRIXI_TEST == "all" || TRIXI_TEST == "performance_specializations_part1"

diff --git a/test/test_aqua.jl b/test/test_aqua.jl
@@ -0,0 +1,18 @@
+module TestAqua
+
+using Aqua
+using Test
+using Trixi
+
+include("test_trixi.jl")
+
+@timed_testset "Aqua.jl" begin
+    Aqua.test_all(Trixi,
+                  ambiguities = false,
+                  # exceptions necessary for adding a new method `StartUpDG.estimate_h`
+                  # in src/solvers/dgmulti/sbp.jl
+                  piracy = (treat_as_own = [Trixi.StartUpDG.RefElemData,
+                                            Trixi.StartUpDG.MeshData],))
+end
+
+end #module
diff --git a/test/test_threaded.jl b/test/test_threaded.jl
@@ -312,11 +312,7 @@ Trixi.mpi_isroot() && isdir(outdir) && rm(outdir, recursive=true)
         t = sol.t[end]
         u_ode = sol.u[end]
         du_ode = similar(u_ode)
-        if (Threads.nthreads() < 2) || (VERSION < v"1.9")
-          @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 5000
-        else
-          @test_broken (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 5000
-        end
+        @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 5000
       end
     end
 

diff --git a/test/test_tree_2d_euler.jl b/test/test_tree_2d_euler.jl
@@ -140,7 +140,7 @@ EXAMPLES_DIR = pkgdir(Trixi, "examples", "tree_2d_dgsem")
   @trixi_testset "elixir_euler_sedov_blast_wave_neuralnetwork_perssonperaire.jl" begin
     @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_sedov_blast_wave_neuralnetwork_perssonperaire.jl"),
       l2   = [0.0845430093623868, 0.09271459184623232, 0.09271459184623232, 0.4377291875101709],
-      linf = [1.3608553480069898, 1.6822884847136004, 1.6822884847135997, 4.220147414536653],
+      linf = [1.3608553480069898, 1.6822884847136004, 1.6822884847135997, 4.2201475428867035],
       maxiters = 30,
       coverage_override = (maxiters=6,))
   end