Format source code based on ˋSciMLˋ style (4 spaces) (#1513)

* Format source code based on ˋSciMLˋ style (4 spaces)

* Make JuliaFormatter consume the two-layer SWE files again

* Remove files from ignore list

* Format two-layer SWE files

* Fix recursive_length formatting

* Find accceptable formatting for SemiHypMeshBCSolver

* Slightly improve semi_hyp_par formatting

* Variant on TrixiODESolution type formatting

* add FormatCheck CI job

* Allow alignment in struct definitions

* Fix formatting abomination

* Remove useless spam

* Sanitize type alias

* Fix using statement

* Update src/auxiliary/mpi.jl

Co-authored-by: Hendrik Ranocha <[email protected]>

* Update src/callbacks_stage/positivity_zhang_shu.jl

Co-authored-by: Hendrik Ranocha <[email protected]>

* Update src/callbacks_step/amr_dg2d.jl

Co-authored-by: Hendrik Ranocha <[email protected]>

* Update src/callbacks_step/analysis.jl

Co-authored-by: Hendrik Ranocha <[email protected]>

* Format the formatter

* substituted non-ascii lambda (#1521)

* rename format-check job name

* fix bad formatting

* improve some bad formatting

* align some struct fields

* align some struct fields

* align some struct fields

* begin end blocks for some at-trixi_timeit

* Update src/visualization/utilities.jl

* Update src/solvers/fdsbp_tree/fdsbp.jl

* Update src/meshes/p4est_mesh.jl

* Update src/meshes/p4est_mesh.jl

* comments on pssing nothing as mortar

* comment on passing nothing as mortar

* formatting on/off blocks

* Copy JuliaFormatter.toml from TrixiParticles.jl

* Add info on automated source code formatting

* Format `ext/`

* Format `benchmark/`

* Format `utils/`

---------

Co-authored-by: Hendrik Ranocha <[email protected]>
Co-authored-by: Joshua Lampert <[email protected]>
Co-authored-by: Hendrik Ranocha <[email protected]>
Co-authored-by: Jesse Chan <[email protected]>

.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/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'

benchmark/benchmark_ec.jl

@@ -1,50 +1,50 @@
 using Printf, BenchmarkTools, Trixi
 
-function run_benchmarks(benchmark_run; levels=0:5, polydeg=3)
-  runtimes = zeros(length(levels))
-  for (idx,initial_refinement_level) in enumerate(levels)
-    result = benchmark_run(; initial_refinement_level, polydeg)
-    display(result)
-    runtimes[idx] = result |> median |> time # in nanoseconds
-  end
-  return (; levels, runtimes, polydeg)
+function run_benchmarks(benchmark_run; levels = 0:5, polydeg = 3)
+    runtimes = zeros(length(levels))
+    for (idx, initial_refinement_level) in enumerate(levels)
+        result = benchmark_run(; initial_refinement_level, polydeg)
+        display(result)
+        runtimes[idx] = result |> median |> time # in nanoseconds
+    end
+    return (; levels, runtimes, polydeg)
 end
 
 function tabulate_benchmarks(args...; kwargs...)
-  result = run_benchmarks(args...; kwargs...)
-  println("#Elements | Runtime in seconds")
-  for (level,runtime) in zip(result.levels, result.runtimes)
-    @printf("%9d | %.2e\n", 4^level, 1.0e-9 * runtime)
-  end
-  for (level,runtime) in zip(result.levels, result.runtimes)
-    @printf("%.16e\n", 1.0e-9 * runtime)
-  end
+    result = run_benchmarks(args...; kwargs...)
+    println("#Elements | Runtime in seconds")
+    for (level, runtime) in zip(result.levels, result.runtimes)
+        @printf("%9d | %.2e\n", 4^level, 1.0e-9*runtime)
+    end
+    for (level, runtime) in zip(result.levels, result.runtimes)
+        @printf("%.16e\n", 1.0e-9*runtime)
+    end
 end
 
-function benchmark_euler(; initial_refinement_level=1, polydeg=3)
+function benchmark_euler(; initial_refinement_level = 1, polydeg = 3)
+    γ = 1.4
+    equations = CompressibleEulerEquations2D(γ)
 
-  γ = 1.4
-  equations = CompressibleEulerEquations2D(γ)
+    surface_flux = flux_ranocha
+    volume_flux = flux_ranocha
+    solver = DGSEM(polydeg, surface_flux, VolumeIntegralFluxDifferencing(volume_flux))
 
-  surface_flux = flux_ranocha
-  volume_flux  = flux_ranocha
-  solver = DGSEM(polydeg, surface_flux, VolumeIntegralFluxDifferencing(volume_flux))
+    coordinates_min = (-2.0, -2.0)
+    coordinates_max = (2.0, 2.0)
+    mesh = TreeMesh(coordinates_min, coordinates_max,
+                    initial_refinement_level = initial_refinement_level,
+                    n_cells_max = 100_000)
 
-  coordinates_min = (-2.0, -2.0)
-  coordinates_max = ( 2.0,  2.0)
-  mesh = TreeMesh(coordinates_min, coordinates_max,
-                  initial_refinement_level=initial_refinement_level,
-                  n_cells_max=100_000)
+    semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_weak_blast_wave,
+                                        solver)
 
-  semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_weak_blast_wave, solver)
+    t0 = 0.0
+    u0 = compute_coefficients(t0, semi)
+    du = similar(u0)
 
-  t0 = 0.0
-  u0 = compute_coefficients(t0, semi)
-  du = similar(u0)
-
-  @benchmark Trixi.rhs!($du, $u0, $semi, $t0)
+    @benchmark Trixi.rhs!($du, $u0, $semi, $t0)
 end
 
 # versioninfo(verbose=true)
 @show Threads.nthreads()
-tabulate_benchmarks(benchmark_euler, levels=0:8)
+tabulate_benchmarks(benchmark_euler, levels = 0:8)

benchmark/benchmarks.jl

@@ -1,3 +1,6 @@
+# Disable formatting this file since it contains highly unusual formatting for better
+# readability
+#! format: off
 
 using BenchmarkTools
 using Trixi

benchmark/elixir_2d_euler_vortex_p4est.jl

@@ -17,43 +17,42 @@ The classical isentropic vortex test case of
   [NASA/CR-97-206253](https://ntrs.nasa.gov/citations/19980007543)
 """
 function initial_condition_isentropic_vortex(x, t, equations::CompressibleEulerEquations2D)
-  # needs appropriate mesh size, e.g. [-10,-10]x[10,10]
-  # make sure that the inicenter does not exit the domain, e.g. T=10.0
-  # initial center of the vortex
-  inicenter = SVector(0.0, 0.0)
-  # size and strength of the vortex
-  iniamplitude = 0.2
-  # base flow
-  rho = 1.0
-  v1 = 1.0
-  v2 = 1.0
-  vel = SVector(v1, v2)
-  p = 10.0
-  rt = p / rho                  # ideal gas equation
-  cent = inicenter + vel*t      # advection of center
-  cent = x - cent               # distance to centerpoint
-  #cent=cross(iniaxis,cent)     # distance to axis, tangent vector, length r
-  # cross product with iniaxis = [0,0,1]
-  cent = SVector(-cent[2], cent[1])
-  r2 = cent[1]^2 + cent[2]^2
-  du = iniamplitude/(2*π)*exp(0.5*(1-r2)) # vel. perturbation
-  dtemp = -(equations.gamma-1)/(2*equations.gamma*rt)*du^2            # isentrop
-  rho = rho * (1+dtemp)^(1\(equations.gamma-1))
-  vel = vel + du*cent
-  v1, v2 = vel
-  p = p * (1+dtemp)^(equations.gamma/(equations.gamma-1))
-  prim = SVector(rho, v1, v2, p)
-  return prim2cons(prim, equations)
+    # needs appropriate mesh size, e.g. [-10,-10]x[10,10]
+    # make sure that the inicenter does not exit the domain, e.g. T=10.0
+    # initial center of the vortex
+    inicenter = SVector(0.0, 0.0)
+    # size and strength of the vortex
+    iniamplitude = 0.2
+    # base flow
+    rho = 1.0
+    v1 = 1.0
+    v2 = 1.0
+    vel = SVector(v1, v2)
+    p = 10.0
+    rt = p / rho                  # ideal gas equation
+    cent = inicenter + vel * t      # advection of center
+    cent = x - cent               # distance to centerpoint
+    #cent=cross(iniaxis,cent)     # distance to axis, tangent vector, length r
+    # cross product with iniaxis = [0,0,1]
+    cent = SVector(-cent[2], cent[1])
+    r2 = cent[1]^2 + cent[2]^2
+    du = iniamplitude / (2 * π) * exp(0.5 * (1 - r2)) # vel. perturbation
+    dtemp = -(equations.gamma - 1) / (2 * equations.gamma * rt) * du^2            # isentrop
+    rho = rho * (1 + dtemp)^(1 \ (equations.gamma - 1))
+    vel = vel + du * cent
+    v1, v2 = vel
+    p = p * (1 + dtemp)^(equations.gamma / (equations.gamma - 1))
+    prim = SVector(rho, v1, v2, p)
+    return prim2cons(prim, equations)
 end
 initial_condition = initial_condition_isentropic_vortex
-solver = DGSEM(polydeg=3, surface_flux=flux_lax_friedrichs)
+solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 
 coordinates_min = (-10.0, -10.0)
-coordinates_max = ( 10.0,  10.0)
-mesh = P4estMesh((1, 1), polydeg=Trixi.polydeg(solver),
-                 coordinates_min=coordinates_min, coordinates_max=coordinates_max,
-                 initial_refinement_level=4)
-
+coordinates_max = (10.0, 10.0)
+mesh = P4estMesh((1, 1), polydeg = Trixi.polydeg(solver),
+                 coordinates_min = coordinates_min, coordinates_max = coordinates_max,
+                 initial_refinement_level = 4)
 
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
 
@@ -66,19 +65,20 @@ ode = semidiscretize(semi, tspan)
 summary_callback = SummaryCallback()
 
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, save_analysis=true,
-                                     extra_analysis_errors=(:conservation_error,),
-                                     extra_analysis_integrals=(entropy, energy_total,
-                                                               energy_kinetic, energy_internal))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval,
+                                     save_analysis = true,
+                                     extra_analysis_errors = (:conservation_error,),
+                                     extra_analysis_integrals = (entropy, energy_total,
+                                                                 energy_kinetic,
+                                                                 energy_internal))
 
-alive_callback = AliveCallback(analysis_interval=analysis_interval)
+alive_callback = AliveCallback(analysis_interval = analysis_interval)
 
 callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback)
 
-
 ###############################################################################
 # run the simulation
 
 sol = solve(ode, BS3(),
-            save_everystep=false, callback=callbacks);
+            save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary

benchmark/elixir_2d_euler_vortex_structured.jl

@@ -17,43 +17,42 @@ The classical isentropic vortex test case of
   [NASA/CR-97-206253](https://ntrs.nasa.gov/citations/19980007543)
 """
 function initial_condition_isentropic_vortex(x, t, equations::CompressibleEulerEquations2D)
-  # needs appropriate mesh size, e.g. [-10,-10]x[10,10]
-  # make sure that the inicenter does not exit the domain, e.g. T=10.0
-  # initial center of the vortex
-  inicenter = SVector(0.0, 0.0)
-  # size and strength of the vortex
-  iniamplitude = 0.2
-  # base flow
-  rho = 1.0
-  v1 = 1.0
-  v2 = 1.0
-  vel = SVector(v1, v2)
-  p = 10.0
-  rt = p / rho                  # ideal gas equation
-  cent = inicenter + vel*t      # advection of center
-  cent = x - cent               # distance to centerpoint
-  #cent=cross(iniaxis,cent)     # distance to axis, tangent vector, length r
-  # cross product with iniaxis = [0,0,1]
-  cent = SVector(-cent[2], cent[1])
-  r2 = cent[1]^2 + cent[2]^2
-  du = iniamplitude/(2*π)*exp(0.5*(1-r2)) # vel. perturbation
-  dtemp = -(equations.gamma-1)/(2*equations.gamma*rt)*du^2            # isentrop
-  rho = rho * (1+dtemp)^(1\(equations.gamma-1))
-  vel = vel + du*cent
-  v1, v2 = vel
-  p = p * (1+dtemp)^(equations.gamma/(equations.gamma-1))
-  prim = SVector(rho, v1, v2, p)
-  return prim2cons(prim, equations)
+    # needs appropriate mesh size, e.g. [-10,-10]x[10,10]
+    # make sure that the inicenter does not exit the domain, e.g. T=10.0
+    # initial center of the vortex
+    inicenter = SVector(0.0, 0.0)
+    # size and strength of the vortex
+    iniamplitude = 0.2
+    # base flow
+    rho = 1.0
+    v1 = 1.0
+    v2 = 1.0
+    vel = SVector(v1, v2)
+    p = 10.0
+    rt = p / rho                  # ideal gas equation
+    cent = inicenter + vel * t      # advection of center
+    cent = x - cent               # distance to centerpoint
+    #cent=cross(iniaxis,cent)     # distance to axis, tangent vector, length r
+    # cross product with iniaxis = [0,0,1]
+    cent = SVector(-cent[2], cent[1])
+    r2 = cent[1]^2 + cent[2]^2
+    du = iniamplitude / (2 * π) * exp(0.5 * (1 - r2)) # vel. perturbation
+    dtemp = -(equations.gamma - 1) / (2 * equations.gamma * rt) * du^2            # isentrop
+    rho = rho * (1 + dtemp)^(1 \ (equations.gamma - 1))
+    vel = vel + du * cent
+    v1, v2 = vel
+    p = p * (1 + dtemp)^(equations.gamma / (equations.gamma - 1))
+    prim = SVector(rho, v1, v2, p)
+    return prim2cons(prim, equations)
 end
 initial_condition = initial_condition_isentropic_vortex
-solver = DGSEM(polydeg=3, surface_flux=flux_lax_friedrichs)
+solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs)
 
 coordinates_min = (-10.0, -10.0)
-coordinates_max = ( 10.0,  10.0)
+coordinates_max = (10.0, 10.0)
 cells_per_dimension = (16, 16)
 mesh = StructuredMesh(cells_per_dimension, coordinates_min, coordinates_max)
 
-
 semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver)
 
 ###############################################################################
@@ -65,19 +64,20 @@ ode = semidiscretize(semi, tspan)
 summary_callback = SummaryCallback()
 
 analysis_interval = 100
-analysis_callback = AnalysisCallback(semi, interval=analysis_interval, save_analysis=true,
-                                     extra_analysis_errors=(:conservation_error,),
-                                     extra_analysis_integrals=(entropy, energy_total,
-                                                               energy_kinetic, energy_internal))
+analysis_callback = AnalysisCallback(semi, interval = analysis_interval,
+                                     save_analysis = true,
+                                     extra_analysis_errors = (:conservation_error,),
+                                     extra_analysis_integrals = (entropy, energy_total,
+                                                                 energy_kinetic,
+                                                                 energy_internal))
 
-alive_callback = AliveCallback(analysis_interval=analysis_interval)
+alive_callback = AliveCallback(analysis_interval = analysis_interval)
 
 callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback)
 
-
 ###############################################################################
 # run the simulation
 
 sol = solve(ode, BS3(),
-            save_everystep=false, callback=callbacks);
+            save_everystep = false, callback = callbacks);
 summary_callback() # print the timer summary