Cleanup whitespaces in Breeze codebase

.github/workflows/Whitespace.yml

@@ -0,0 +1,36 @@
+name: Whitespace
+
+permissions: {}
+
+on:
+  push:
+    branches:
+      - 'main'
+  pull_request:
+
+jobs:
+  whitespace:
+    name: Check whitespace
+    runs-on: ubuntu-latest
+    timeout-minutes: 2
+    steps:
+      - name: Checkout the NumericalEarth/Breeze.jl repository
+        uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+      - name: Checkout the JuliaLang/julia repository
+        uses: actions/checkout@v6
+        with:
+          persist-credentials: false
+          repository: 'JuliaLang/julia'
+          # Clone Julia in a subdir.
+          path: '.julia'
+          # Check out a fixed revision to avoid surprises in case the script is
+          # changed in the future.
+          ref: '3b12a882e887753e4d2e9e9db65d99d3f7d9e26b'
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: '1.12.4'
+      - name: Check whitespace
+        run: |
+          .julia/contrib/check-whitespace.jl

AGENTS.md

@@ -390,7 +390,7 @@ serve(dir="docs/build")
 When implementing a simulation from a published paper:
 
 ### 1. Parameter Extraction
-- **Read the paper carefully** and extract ALL parameters: domain size, resolution, physical constants, 
+- **Read the paper carefully** and extract ALL parameters: domain size, resolution, physical constants,
   boundary conditions, initial conditions, forcing, closure parameters
 - Look for parameter tables (often "Table 1" or similar)
 - Check figure captions for additional details
@@ -433,11 +433,11 @@ Before running a long simulation:
 - Quantitative comparison: compute the same diagnostics as the paper
 
 ### 7. Common Issues
-- **NaN blowups**: Usually from timestep too large, unstable initial conditions, 
+- **NaN blowups**: Usually from timestep too large, unstable initial conditions,
   or if-else statements on GPU (use `ifelse` instead)
-- **Nothing happening**: Check that buoyancy anomaly has the right sign, 
+- **Nothing happening**: Check that buoyancy anomaly has the right sign,
   that initial conditions are actually applied, that forcing is active
-- **Wrong direction of flow**: Check coordinate conventions (is y increasing 
+- **Wrong direction of flow**: Check coordinate conventions (is y increasing
   upslope or downslope?)
 - **GPU issues**: Avoid branching, ensure type stability, use `randn()` carefully
 

docs/src/contributing.md

@@ -90,7 +90,7 @@ See [`ExplicitImports.jl` documentation](https://juliatesting.github.io/Explicit
 ## Building the documentation locally
 
 `Breeze.jl` [documentation](https://numericalearth.github.io/BreezeDocumentation/) is generated using [`Documenter.jl`](https://github.com/JuliaDocs/Documenter.jl).
-You can preview how the documentation will look like with your changes by building the documentation locally. 
+You can preview how the documentation will look like with your changes by building the documentation locally.
 From the top-level directory of your local repository run
 
 ```sh

docs/src/developer/microphysics_interface.md

@@ -34,7 +34,7 @@ a microphysics implementation in `AtmosphereModel`:
 
 ## Example implementation
 
-To illustrate the development of a new microphysics scheme, we implement a 
+To illustrate the development of a new microphysics scheme, we implement a
 simple microphysics scheme that represents droplet and ice particle nucleation
 with constant-rate relaxation of specific humidity to saturation.
 
@@ -59,7 +59,7 @@ prognostic_field_names(::ExplicitMicrophysics) = (:ρqᵛ, :ρqˡ, :ρqⁱ)
 ```
 
 !!! note
-    The names of prognostic fields defined by `prognostic_field_names` 
+    The names of prognostic fields defined by `prognostic_field_names`
     **are crucial to the user interface**, because users can interact them and
     [`set!`](https://clima.github.io/OceananigansDocumentation/stable/appendix/library/#Oceananigans.Fields.set!) their initial conditions. The names of variables should be carefully
     chosen to be concise, mathematical forms that are consistent with Breeze conventions.
@@ -78,7 +78,7 @@ function materialize_microphysical_fields(::ExplicitMicrophysics, grid, boundary
     return (; ρqˡ, ρqⁱ, ρqᵛ, qᵛ)
 end
 ```
-The tendencies for 
+The tendencies for
 
 ```@example microphysics_interface
 import Breeze.AtmosphereModels: microphysical_tendency

examples/boussinesq_bomex.jl

@@ -143,7 +143,7 @@ set!(Fθ_field, z -> dTdt_bomex(1, z))
 θ_forcing = (θ_radiation_forcing, θ_subsidence_forcing)
 
 model = NonhydrostaticModel(; grid, buoyancy, coriolis,
-                            advection = WENO(order=5), 
+                            advection = WENO(order=5),
                             tracers = (:θ, :qᵗ),
                             forcing = (; qᵗ=qᵗ_forcing, u=u_forcing, v=v_forcing, θ=θ_forcing),
                             boundary_conditions = (θ=θ_bcs, qᵗ=qᵗ_bcs, u=u_bcs, v=v_bcs))

examples/cloudy_thermal_bubble.jl

@@ -149,7 +149,7 @@ nothing #hide
 # following the methodology described by Bryan and Fritsch (2002). This simulation
 # includes moisture processes, where excess water vapor condenses to liquid water,
 # releasing latent heat that enhances the buoyancy of the rising bubble.
-# 
+#
 # For pedagogical purposes, we build a new model with warm-phase saturation adjustment microphysics.
 # (We coudl have also used this model for the dry simulation):
 

examples/prescribed_sea_surface_temperature.jl

@@ -111,9 +111,9 @@ Uᵍ = 1e-2  # Minimum wind speed (m/s)
 #
 # For `BulkVaporFlux`, the saturation specific humidity is computed from the surface
 # temperature. Surface temperature can be provided as a `Field`, a `Function`, or a `Number`.
-# 
+#
 # In this example, we specify the sea surface temperature as a top hat function
-# i.e. representing a pair of ocean fronts in a periodic domain, with a 
+# i.e. representing a pair of ocean fronts in a periodic domain, with a
 # difference of 4 degrees K,
 
 ΔT = 4 # K

examples/rico.jl

@@ -148,7 +148,7 @@ set!(∂t_ρqᵗ_large_scale, ρᵣ * ∂t_ρqᵗ_large_scale)
 # This is the key simplification that allows us to avoid interactive radiation.
 
 ∂t_ρθ_large_scale = Field{Nothing, Nothing, Center}(grid)
-∂t_θ_large_scale = - 2.5 / day # K / day
+∂t_θ_large_scale = - 2.5 / day # K / day
 set!(∂t_ρθ_large_scale, ρᵣ * ∂t_θ_large_scale)
 ρθ_large_scale_forcing = Forcing(∂t_ρθ_large_scale)
 

ext/BreezeCloudMicrophysicsExt/one_moment_helpers.jl

@@ -92,7 +92,7 @@ Adapt.adapt_structure(to, k::SurfacePrecipitationFluxKernel) =
     # wʳ < 0 (downward), so -wʳ * ρqʳ > 0 represents flux out of domain
     @inbounds wʳ = kernel.terminal_velocity[i, j, 1]
     @inbounds ρqʳ = kernel.rain_density[i, j, 1]
-    
+
     # Return positive flux for rain leaving domain (downward)
     return -wʳ * ρqʳ
 end

ext/BreezeCloudMicrophysicsExt/two_moment_helpers.jl

@@ -138,4 +138,3 @@ function Base.show(io::IO, bμp::BulkMicrophysics{<:Any, <:CM2MCategories})
 end
 
 Base.summary(bμp::TwoMomentCloudMicrophysics) = "TwoMomentCloudMicrophysics"
-

ext/BreezeRRTMGPExt/BreezeRRTMGPExt.jl

@@ -15,7 +15,7 @@ using Oceananigans.Fields: ZFaceField
 
 # RRTMGP imports (external types - cannot modify)
 #   GrayAtmosphericState: atmospheric state arrays (t_lay, p_lay, t_lev, p_lev, z_lev, t_sfc)
-#   NoScatLWRTE, NoScatSWRTE: longwave/shortwave RTE solvers  
+#   NoScatLWRTE, NoScatSWRTE: longwave/shortwave RTE solvers
 #   FluxLW, FluxSW: flux storage (flux_up, flux_dn, flux_net, flux_dn_dir)
 #   RRTMGPParameters: physical constants for RRTMGP
 
@@ -76,4 +76,3 @@ include("clear_sky_radiative_transfer_model.jl")
 include("all_sky_radiative_transfer_model.jl")
 
 end # module
-

ext/BreezeRRTMGPExt/all_sky_radiative_transfer_model.jl

@@ -51,7 +51,7 @@ RRTMGP loads lookup tables from netCDF via an extension.
 # Keyword Arguments
 - `background_atmosphere`: Background atmospheric gas composition (default: `BackgroundAtmosphere{FT}()`).
 - `surface_temperature`: Surface temperature in Kelvin (required).
-- `coordinate`: Tuple of (longitude, latitude) in degrees. If `nothing` (default), 
+- `coordinate`: Tuple of (longitude, latitude) in degrees. If `nothing` (default),
                 extracted from grid coordinates.
 - `epoch`: Optional epoch for computing time with floating-point clocks.
 - `surface_emissivity`: Surface emissivity, 0-1 (default: 0.98). Scalar.

ext/BreezeRRTMGPExt/clear_sky_radiative_transfer_model.jl

@@ -34,7 +34,7 @@ RRTMGP loads lookup tables from netCDF via an extension.
 # Keyword Arguments
 - `background_atmosphere`: Background atmospheric gas composition (default: `BackgroundAtmosphere{FT}()`).
 - `surface_temperature`: Surface temperature in Kelvin (required).
-- `coordinate`: Tuple of (longitude, latitude) in degrees. If `nothing` (default), 
+- `coordinate`: Tuple of (longitude, latitude) in degrees. If `nothing` (default),
                 extracted from grid coordinates.
 - `epoch`: Optional epoch for computing time with floating-point clocks.
 - `surface_emissivity`: Surface emissivity, 0-1 (default: 0.98). Scalar.

ext/BreezeRRTMGPExt/gray_radiative_transfer_model.jl

@@ -42,11 +42,11 @@ Construct a gray atmosphere radiative transfer model for the given grid.
 # Keyword Arguments
 - `optical_thickness`: Optical thickness parameterization (default: `GrayOpticalThicknessOGorman2008(FT)`).
 - `surface_temperature`: Surface temperature in Kelvin (required).
-- `coordinate`: Tuple of (longitude, latitude) in degrees. If `nothing` (default), 
+- `coordinate`: Tuple of (longitude, latitude) in degrees. If `nothing` (default),
                 extracted from grid coordinates.
 - `epoch`: Optional epoch for computing time with floating-point clocks.
 - `surface_emissivity`: Surface emissivity, 0-1 (default: 0.98). Scalar.
-- `surface_albedo`: Surface albedo, 0-1. Can be scalar or 2D field. 
+- `surface_albedo`: Surface albedo, 0-1. Can be scalar or 2D field.
                     Alternatively, provide both `direct_surface_albedo` and `diffuse_surface_albedo`.
 - `direct_surface_albedo`: Direct surface albedo, 0-1. Can be scalar or 2D field.
 - `diffuse_surface_albedo`: Diffuse surface albedo, 0-1. Can be scalar or 2D field.

ext/BreezeRRTMGPExt/rrtmgp_shared_utilities.jl

@@ -134,4 +134,3 @@ end
         ℐ_sw_dn[i, j, k] = -sw_flux_dn[k, col]
     end
 end
-

src/AnelasticEquations/AnelasticEquations.jl

@@ -45,4 +45,3 @@ const AnelasticModel = AtmosphereModel{<:AnelasticDynamics}
 include("anelastic_time_stepping.jl")
 
 end # module
-

src/AnelasticEquations/anelastic_buoyancy.jl

@@ -47,4 +47,3 @@ where `pᵣ` is the reference pressure, `Rᵐ` is the mixture gas constant, and
 
     return - g * ρ′
 end
-

src/AnelasticEquations/anelastic_dynamics.jl

@@ -164,4 +164,3 @@ function AtmosphereModels.materialize_momentum_and_velocities(dynamics::Anelasti
 
     return momentum, velocities
 end
-

src/AnelasticEquations/anelastic_pressure_solver.jl

@@ -102,4 +102,3 @@ end
     δ = divᶜᶜᶜ(i, j, k, grid, ρu, ρv, ρw)
     @inbounds rhs[i, j, k] = active * Δzᶜᶜᶜ(i, j, k, grid) * δ / Δt
 end
-

src/AnelasticEquations/anelastic_time_stepping.jl

@@ -75,4 +75,3 @@ function TimeSteppers.make_pressure_correction!(model::AnelasticModel, Δt)
 
     return nothing
 end
-

src/AtmosphereModels/Diagnostics/saturation_specific_humidity.jl

@@ -131,4 +131,3 @@ end
 
 const SaturationSpecificHumidityField = Field{C, C, C, <:SaturationSpecificHumidity}
 SaturationSpecificHumidityField(model, flavor_symbol=:prognostic) = Field(SaturationSpecificHumidity(model, flavor_symbol))
-

src/AtmosphereModels/Diagnostics/static_energy.jl

@@ -118,4 +118,3 @@ function (d::StaticEnergyKernelFunction)(i, j, k, grid)
         return ρᵣ * e
     end
 end
-

src/AtmosphereModels/dynamics_interface.jl

@@ -140,7 +140,7 @@ function validate_velocity_boundary_conditions(dynamics, user_boundary_condition
     velocity_names = (:u, :v, :w)
     user_bc_names = keys(user_boundary_conditions)
     provided_velocity_bcs = filter(name -> name ∈ user_bc_names, velocity_names)
-    
+
     if !isempty(provided_velocity_bcs)
         throw(ArgumentError(
             "Boundary conditions for velocity components $(provided_velocity_bcs) are not supported " *

src/Breeze.jl

@@ -34,7 +34,7 @@ export
     mixture_heat_capacity,
     dynamics_density,
     dynamics_pressure,
-    
+
     # Diagnostics
     compute_hydrostatic_pressure!,
     PotentialTemperature,

src/CompressibleEquations/compressible_buoyancy.jl

@@ -34,4 +34,3 @@ in the momentum equation without subtraction of a reference state.
 
     return -g * ρ
 end
-

src/CompressibleEquations/compressible_dynamics.jl

@@ -179,4 +179,3 @@ function AtmosphereModels.materialize_momentum_and_velocities(dynamics::Compress
 
     return momentum, velocities
 end
-

src/CompressibleEquations/compressible_time_stepping.jl

@@ -150,4 +150,3 @@ end
 
     return T, p
 end
-

src/Forcings/subsidence_forcing.jl

@@ -111,7 +111,7 @@ end
 # Strip the ρ prefix from density variable names
 # e.g., :ρu → :u, :ρθ → :θ, :ρe → :e
 function strip_density_prefix(name::Symbol)
-    chars = string(name) |> collect 
+    chars = string(name) |> collect
     prefix = popfirst!(chars)
     return Symbol(chars...)
 end

src/KinematicDriver/kinematic_driver_time_stepping.jl

@@ -34,11 +34,11 @@ AtmosphereModels.set_velocity!(model::KinematicModel, name::Symbol, value) =
 set_velocity!(velocity::AbstractField, value) = set!(velocity, value)
 
 # FunctionFields (from PrescribedVelocityFields): cannot be set
-set_velocity!(::FunctionField, value) = 
+set_velocity!(::FunctionField, value) =
     throw(ArgumentError("Cannot set velocity component of PrescribedVelocityFields."))
 
 # No momentum in kinematic models
-AtmosphereModels.set_momentum!(::KinematicModel, name::Symbol, value) = 
+AtmosphereModels.set_momentum!(::KinematicModel, name::Symbol, value) =
     throw(ArgumentError("Cannot set momentum component '$name' of a KinematicModel."))
 
 #####

src/Microphysics/dcmip2016_kessler.jl

@@ -418,7 +418,7 @@ end
 
     # Temperature offset for saturation adjustment (from TetensFormula)
     δT = constants.saturation_vapor_pressure.liquid_temperature_offset
-    
+
     # Microphysics parameters
     cfl    = microphysics.substep_cfl
     Cᵨ     = microphysics.density_scale
@@ -448,7 +448,7 @@ end
             qˡ_sum = qᶜˡ + qʳ
             qᵗ = max(qᵗ, qˡ_sum)
             qᵛ = qᵗ - qˡ_sum
-            
+
             # Convert to mixing ratios for Kessler physics
             q = MoistureMassFractions(qᵛ, qˡ_sum)
             r = MoistureMixingRatio(q)

src/PotentialTemperatureFormulations/potential_temperature_formulation.jl

@@ -124,4 +124,3 @@ function Base.show(io::IO, formulation::LiquidIcePotentialTemperatureFormulation
         print(io, "└── potential_temperature: ", prettysummary(formulation.potential_temperature))
     end
 end
-

src/StaticEnergyFormulations/static_energy_formulation.jl

@@ -124,4 +124,3 @@ function Base.show(io::IO, formulation::StaticEnergyFormulation)
         print(io, "└── specific_energy: ", prettysummary(formulation.specific_energy))
     end
 end
-

src/Thermodynamics/dynamic_states.jl

@@ -54,7 +54,7 @@ end
     qˡ = q.liquid
     qⁱ = q.ice
 
-    return Π * θ + (ℒˡᵣ * qˡ + ℒⁱᵣ * qⁱ) / cᵖᵐ 
+    return Π * θ + (ℒˡᵣ * qˡ + ℒⁱᵣ * qⁱ) / cᵖᵐ
 end
 
 @inline function with_temperature(𝒰::LiquidIcePotentialTemperatureState, T, constants)
@@ -125,4 +125,4 @@ end
     e = cᵖᵐ * T + g * z - ℒˡᵣ * qˡ - ℒⁱᵣ * qⁱ
 
     return StaticEnergyState(e, q, z, 𝒰.reference_pressure)
-end
+end

src/Thermodynamics/thermodynamics_constants.jl

@@ -423,7 +423,7 @@ end
 
 #####
 ##### Moisture mixing ratios
-##### 
+#####
 
 struct MoistureMixingRatio{FT}
     vapor :: FT
@@ -517,4 +517,3 @@ Converts mixing ratios to mass fractions and calls `mixture_heat_capacity(q::MMF
 @inline function mixture_heat_capacity(r::MR, constants::TC)
     return mixture_heat_capacity(MoistureMassFractions(r), constants)
 end
-

src/Thermodynamics/vapor_saturation.jl

@@ -107,7 +107,7 @@ Compute the supersaturation ``𝒮 = pᵛ/pᵛ⁺ - 1`` over a given `surface`.
 
 # Arguments
 - `T`: Temperature
-- `ρ`: Total air density  
+- `ρ`: Total air density
 - `q`: `MoistureMassFractions` containing vapor, liquid, and ice mass fractions
 - `constants`: `ThermodynamicConstants`
 - `surface`: Surface type (e.g., `PlanarLiquidSurface()`, `PlanarIceSurface()`)

test/advection_schemes.jl

@@ -15,7 +15,7 @@ using Test
     @testset "Default advection schemes" begin
         static_energy_model = AtmosphereModel(grid; thermodynamic_constants=constants, dynamics,
                                               formulation=:StaticEnergy)
-        potential_temperature_model = AtmosphereModel(grid; thermodynamic_constants=constants, dynamics, 
+        potential_temperature_model = AtmosphereModel(grid; thermodynamic_constants=constants, dynamics,
                                                       formulation=:LiquidIcePotentialTemperature)
 
         @test static_energy_model.advection.ρe isa Centered
@@ -119,4 +119,3 @@ using Test
         end
     end
 end
-

test/all_sky_radiative_transfer.jl

@@ -156,4 +156,3 @@ using RRTMGP
         @test all(isfinite, interior(radiation.upwelling_longwave_flux))
     end
 end
-

test/atmosphere_model_construction.jl

@@ -122,4 +122,3 @@ end
         @test model.clock.iteration == 1
     end
 end
-