(0.2.5) Update compat to Oceananigans 0.95 (#297)

glwagner · simone-silvestri · web-flow · commit 07af260e8fc0 · 2024-12-13T16:20:22.000-07:00
* Update to Oceananigans 0.95

* Bump to 0.2.5

* update orthogonalsphericalshellgrids

* Update Project.toml

* adapt to new syntax

* correct the formulation

* last one

* Update Project.toml

* Update docs Project compat

* Bump docs compat for OrthogonalSphericalShellGrids

---------

Co-authored-by: Simone Silvestri &lt;silvestri.simone0@gmail.com&gt;
diff --git a/Project.toml b/Project.toml
@@ -2,7 +2,7 @@ name = "ClimaOcean"
 uuid = "0376089a-ecfe-4b0e-a64f-9c555d74d754"
 license = "MIT"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.2.4"
+version = "0.2.5"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -42,9 +42,9 @@ JLD2 = "0.4, 0.5"
 KernelAbstractions = "0.9"
 MPI = "0.20"
 NCDatasets = "0.12, 0.13, 0.14"
-Oceananigans = "0.94.3 - 0.99" # This needs to be 0.94.4 when PolarBoundaryCondition is implemented
+Oceananigans = "0.95.2 - 0.99"
 OffsetArrays = "1.14"
-OrthogonalSphericalShellGrids = "0.1.9"
+OrthogonalSphericalShellGrids = "0.2.0"
 Scratch = "1"
 SeawaterPolynomials = "0.3.4"
 StaticArrays = "1"
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -11,5 +11,5 @@ OrthogonalSphericalShellGrids = "c2be9673-fb75-4747-82dc-aa2bb9f4aed0"
 CairoMakie = "0.10.12, 0.11, 0.12"
 DataDeps = "0.7"
 Documenter = "1"
-Oceananigans = "0.94.3"
-OrthogonalSphericalShellGrids = "0.1.8"
+Oceananigans = "0.95.2 - 0.99"
+OrthogonalSphericalShellGrids = "0.2.0"
diff --git a/examples/single_column_os_papa_simulation.jl b/examples/single_column_os_papa_simulation.jl
@@ -17,7 +17,7 @@
 using ClimaOcean
 using Oceananigans
 using Oceananigans.Units
-using Oceananigans.BuoyancyModels: buoyancy_frequency
+using Oceananigans.BuoyancyFormulations: buoyancy_frequency
 using Oceananigans.Units: Time
 using Printf
 
diff --git a/experiments/one_degree_calibration/distributed_perfect_one_degree_model_calibration.jl b/experiments/one_degree_calibration/distributed_perfect_one_degree_model_calibration.jl
@@ -2,7 +2,7 @@ using Oceananigans
 using Oceananigans.Architectures: arch_array
 using Oceananigans.Units
 using Oceananigans.Utils: WallTimeInterval
-using Oceananigans.BuoyancyModels: buoyancy
+using Oceananigans.BuoyancyFormulations: buoyancy
 using Oceananigans.Models.HydrostaticFreeSurfaceModels: VerticalVorticityField
 using ClimaOcean.NearGlobalSimulations: one_degree_near_global_simulation
 using ParameterEstimocean
diff --git a/experiments/one_degree_calibration/gm_one_degree_model_calibration.jl b/experiments/one_degree_calibration/gm_one_degree_model_calibration.jl
@@ -3,7 +3,7 @@ using Oceananigans.Architectures: arch_array
 using Oceananigans.Units
 using Oceananigans.Grids: on_architecture
 using Oceananigans.Utils: WallTimeInterval
-using Oceananigans.BuoyancyModels: buoyancy
+using Oceananigans.BuoyancyFormulations: buoyancy
 using Oceananigans.Models.HydrostaticFreeSurfaceModels: VerticalVorticityField
 using ClimaOcean.NearGlobalSimulations: one_degree_near_global_simulation
 using ParameterEstimocean
diff --git a/experiments/one_degree_calibration/inspect_one_degree_near_global_simulation.jl b/experiments/one_degree_calibration/inspect_one_degree_near_global_simulation.jl
@@ -1,5 +1,5 @@
 using Oceananigans
-using Oceananigans.BuoyancyModels: ∂z_b, buoyancy_perturbation
+using Oceananigans.BuoyancyFormulations: ∂z_b, buoyancy_perturbation
 using SeawaterPolynomials.TEOS10: TEOS10EquationOfState
 using JLD2
 using CairoMakie
diff --git a/experiments/one_degree_calibration/one_degree_near_global_simulation.jl b/experiments/one_degree_calibration/one_degree_near_global_simulation.jl
@@ -3,7 +3,7 @@ using ClimaOcean.NearGlobalSimulations: one_degree_near_global_simulation
 using Oceananigans
 using Oceananigans.Units
 using Oceananigans.Utils: WallTimeInterval
-using Oceananigans.BuoyancyModels: buoyancy
+using Oceananigans.BuoyancyFormulations: buoyancy
 using Oceananigans.Models.HydrostaticFreeSurfaceModels: VerticalVorticityField
 using Oceananigans.TurbulenceClosures.CATKEVerticalDiffusivities:
     MixingLength, TurbulentKineticEnergyEquation, CATKEVerticalDiffusivity
diff --git a/experiments/one_degree_calibration/perfect_one_degree_model_calibration.jl b/experiments/one_degree_calibration/perfect_one_degree_model_calibration.jl
@@ -2,7 +2,7 @@ using Oceananigans
 using Oceananigans.Architectures: arch_array
 using Oceananigans.Units
 using Oceananigans.Utils: WallTimeInterval
-using Oceananigans.BuoyancyModels: buoyancy
+using Oceananigans.BuoyancyFormulations: buoyancy
 using Oceananigans.Models.HydrostaticFreeSurfaceModels: VerticalVorticityField
 using ClimaOcean.NearGlobalSimulations: one_degree_near_global_simulation
 using ParameterEstimocean
diff --git a/src/Diagnostics.jl b/src/Diagnostics.jl
@@ -3,7 +3,7 @@ module Diagnostics
 export MixedLayerDepthField
 
 using Oceananigans
-using Oceananigans.BuoyancyModels: buoyancy
+using Oceananigans.BuoyancyFormulations: buoyancy
 using Oceananigans.BoundaryConditions: fill_halo_regions!
 using Oceananigans.ImmersedBoundaries: ImmersedBoundaryGrid
 using Oceananigans.Architectures: device, architecture
diff --git a/src/OceanSeaIceModels/CrossRealmFluxes/ocean_sea_ice_surface_fluxes.jl b/src/OceanSeaIceModels/CrossRealmFluxes/ocean_sea_ice_surface_fluxes.jl
@@ -77,7 +77,7 @@ function OceanSeaIceSurfaceFluxes(ocean, sea_ice=nothing;
     if !isnothing(atmosphere)
         # It's the "thermodynamics gravitational acceleration"
         # (as opposed to the one used for the free surface)
-        gravitational_acceleration = ocean.model.buoyancy.model.gravitational_acceleration
+        gravitational_acceleration = ocean.model.buoyancy.formulation.gravitational_acceleration
 
         if isnothing(similarity_theory)
             similarity_theory = SimilarityTheoryTurbulentFluxes(ocean_grid; gravitational_acceleration)
diff --git a/src/OceanSeaIceModels/ocean_sea_ice_model.jl b/src/OceanSeaIceModels/ocean_sea_ice_model.jl
@@ -1,7 +1,7 @@
 using Oceananigans
 using Oceananigans.Models: update_model_field_time_series!
 using Oceananigans.TimeSteppers: Clock
-using Oceananigans.BuoyancyModels: SeawaterBuoyancy
+using Oceananigans: SeawaterBuoyancy
 
 using SeawaterPolynomials: TEOS10EquationOfState
 
@@ -57,12 +57,12 @@ reference_density(unsupported) =
 heat_capacity(unsupported) =
     throw(ArgumentError("Cannot deduce the heat capacity from $(typeof(unsupported))"))
 
-reference_density(ocean::Simulation) = reference_density(ocean.model.buoyancy.model)
-reference_density(buoyancy_model::SeawaterBuoyancy) = reference_density(buoyancy_model.equation_of_state)
+reference_density(ocean::Simulation) = reference_density(ocean.model.buoyancy.formulation)
+reference_density(buoyancy_formulation::SeawaterBuoyancy) = reference_density(buoyancy_formulation.equation_of_state)
 reference_density(eos::TEOS10EquationOfState) = eos.reference_density
 
-heat_capacity(ocean::Simulation) = heat_capacity(ocean.model.buoyancy.model)
-heat_capacity(buoyancy_model::SeawaterBuoyancy) = heat_capacity(buoyancy_model.equation_of_state)
+heat_capacity(ocean::Simulation) = heat_capacity(ocean.model.buoyancy.formulation)
+heat_capacity(buoyancy_formulation::SeawaterBuoyancy) = heat_capacity(buoyancy_formulation.equation_of_state)
 
 function heat_capacity(eos::TEOS10EquationOfState{FT}) where FT
     cₚ⁰ = SeawaterPolynomials.TEOS10.teos10_reference_heat_capacity
diff --git a/src/OceanSimulations/OceanSimulations.jl b/src/OceanSimulations/OceanSimulations.jl
@@ -18,7 +18,7 @@ using Oceananigans.TurbulenceClosures.TKEBasedVerticalDiffusivities:
 
 using SeawaterPolynomials.TEOS10: TEOS10EquationOfState
 
-using Oceananigans.BuoyancyModels: g_Earth
+using Oceananigans.BuoyancyFormulations: g_Earth
 using Oceananigans.Coriolis: Ω_Earth
 using Oceananigans.Operators
 
diff --git a/test/test_ecco.jl b/test/test_ecco.jl
@@ -96,7 +96,7 @@ end
         φ₂ = @allowscalar grid.φᵃᶜᵃ[21]
         φ₃ = @allowscalar grid.φᵃᶜᵃ[80]
         φ₄ = @allowscalar grid.φᵃᶜᵃ[100]
-        z₁ = @allowscalar grid.zᵃᵃᶜ[6]
+        z₁ = @allowscalar grid.z.cᵃᵃᶜ[6]
 
         mask = LinearlyTaperedPolarMask(northern = (φ₃, φ₄),
                                         southern = (φ₁, φ₂),
