Merge remote-tracking branch 'origin/main' into ss/omip-prototype

Author: simone-silvestri

.buildkite/examples_build.yml

@@ -29,7 +29,7 @@ steps:
   - label: "Run documentation"
     key: "build_documentation"
     commands:
-      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ -e 'using Pkg; Pkg.add(url=\"https://github.com/CliMA/Oceananigans.jl\", rev=\"ss/fix-zstar-bc\"); Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate(); Pkg.precompile(; strict=true)'"
+      - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate(); Pkg.precompile(; strict=true)'"
       - "$TARTARUS_HOME/julia-$JULIA_VERSION/bin/julia --color=yes -O0 --project=docs/ docs/make.jl"
     agents:
       queue: ClimaOcean-docs

CondaPkg.toml

@@ -0,0 +1,7 @@
+
+[pip.deps]
+copernicusmarine = ">=2.0.0"
+xarray = ">=2024.7.0"
+numpy = ">=2.0.0"
+jax = ">=0.6"
+tensorflow = ">=2.17"

Project.toml

@@ -2,7 +2,7 @@ name = "ClimaOcean"
 uuid = "0376089a-ecfe-4b0e-a64f-9c555d74d754"
 license = "MIT"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.8.0"
+version = "0.8.1"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -44,7 +44,7 @@ ClimaOceanReactantExt = "Reactant"
 Adapt = "4"
 CFTime = "0.1, 0.2"
 CUDA = "4, 5"
-ClimaSeaIce = "0.3.1"
+ClimaSeaIce = "0.3.3"
 CondaPkg = "0.2.28"
 CubicSplines = "0.2"
 DataDeps = "0.7"
@@ -55,7 +55,7 @@ JLD2 = "0.4, 0.5"
 KernelAbstractions = "0.9"
 MPI = "0.20"
 NCDatasets = "0.12, 0.13, 0.14"
-Oceananigans = "0.97.3"
+Oceananigans = "0.97.4"
 OffsetArrays = "1.14"
 PrecompileTools = "1"
 PythonCall = "0.9"

README.md

@@ -105,7 +105,7 @@ Note that though ClimaOcean is currently focused on hydrostatic modeling with `O
 If you use ClimaOcean for your research, teaching, or fun 🤩, everyone in our community will be grateful
 if you give credit by citing the corresponding Zenodo record, e.g.,
 
-> Wagner, G. L. et al. (2025). CliMA/ClimaOcean.jl: v0.7.0 (v0.7.0). Zenodo. https://doi.org/10.5281/zenodo.7677442
+> Wagner, G. L. et al. (2025). CliMA/ClimaOcean.jl: v0.8.1 (v0.8.1). Zenodo. https://doi.org/10.5281/zenodo.7677442
 
 and also the recent [preprint submitted to the Journal of Advances in Modeling Earth Systems](https://arxiv.org/abs/2502.14148) that presents an overview of all the things that make Oceananigans unique:
 

examples/one_degree_simulation.jl

@@ -29,7 +29,6 @@ Nz = 40
 depth = 4000meters
 z = ExponentialCoordinate(Nz, -depth, 0; scale = 0.85*depth)
 z = Oceananigans.Grids.MutableVerticalDiscretization(z)
-
 underlying_grid = TripolarGrid(arch; size = (Nx, Ny, Nz), halo = (5, 5, 4), z)
 
 # Next, we build bathymetry on this grid, using interpolation passes to smooth the bathymetry.

experiments/arctic_simulation.jl

@@ -15,7 +15,7 @@ arch = GPU()
 
 depth = 2000meters
 Nz = 30
-z = ExponentialCoordinate(Nz, depth, 0; scale=depth/3)
+z = ExponentialCoordinate(Nz, -depth, 0; scale=depth/3)
 z = MutableVerticalDiscretization(z)
 
 Nx = 180 # longitudinal direction -> 250 points is about 1.5ᵒ resolution

experiments/flux_climatology/flux_climatology.jl

@@ -133,10 +133,10 @@ function PrescribedOcean(timeseries;
     Jᵀ = Field{Center, Center, Nothing}(grid)
     Jˢ = Field{Center, Center, Nothing}(grid)
 
-    u = XFaceField(grid,  boundary_conditions=FieldBoundaryConditions(grid, (Face,   Center, Center), top = FluxBoundaryCondition(τx)))
-    v = YFaceField(grid,  boundary_conditions=FieldBoundaryConditions(grid, (Center, Face,   Center), top = FluxBoundaryCondition(τy)))
-    T = CenterField(grid, boundary_conditions=FieldBoundaryConditions(grid, (Center, Center, Center), top = FluxBoundaryCondition(Jᵀ)))
-    S = CenterField(grid, boundary_conditions=FieldBoundaryConditions(grid, (Center, Center, Center), top = FluxBoundaryCondition(Jˢ)))
+    u = XFaceField(grid,  boundary_conditions=FieldBoundaryConditions(grid, (Face(),   Center(), Center()), top = FluxBoundaryCondition(τx)))
+    v = YFaceField(grid,  boundary_conditions=FieldBoundaryConditions(grid, (Center(), Face(),   Center()), top = FluxBoundaryCondition(τy)))
+    T = CenterField(grid, boundary_conditions=FieldBoundaryConditions(grid, (Center(), Center(), Center()), top = FluxBoundaryCondition(Jᵀ)))
+    S = CenterField(grid, boundary_conditions=FieldBoundaryConditions(grid, (Center(), Center(), Center()), top = FluxBoundaryCondition(Jˢ)))
 
     PrescribedOcean(architecture(grid), grid, clock, (; u, v, w=ZeroField()), (; T, S), timeseries)
 end

ext/ClimaOceanPythonCallExt.jl

@@ -31,7 +31,7 @@ function download_dataset(meta::CopernicusMetadata, grid=nothing; skip_existing
     output_path = joinpath(output_directory, output_filename)
     isfile(output_path) && return output_path
 
-    toolbox = try 
+    toolbox = try
         pyimport("copernicusmarine")
     catch
         install_copernicusmarine()
@@ -97,4 +97,4 @@ function depth_bounds_kw(z)
     return (; minimum_depth, maximum_depth)
 end
 
-end # module ClimaOceanPythonCallExt 
+end # module ClimaOceanPythonCallExt

src/DataWrangling/JRA55/JRA55_field_time_series.jl

@@ -433,7 +433,7 @@ function JRA55FieldTimeSeries(metadata::JRA55Metadata, architecture=CPU(), FT=Fl
                                               latitude = φr,
                                               topology = (TX, Bounded, Flat))
 
-    boundary_conditions = FieldBoundaryConditions(JRA55_native_grid, (Center, Center, Nothing))
+    boundary_conditions = FieldBoundaryConditions(JRA55_native_grid, (Center(), Center(), nothing))
     start_time = first_date(metadata.dataset, metadata.name)
     times = native_times(metadata; start_time)
 

src/DataWrangling/metadata_field_time_series.jl

@@ -120,7 +120,7 @@ function FieldTimeSeries(metadata::Metadata, grid::AbstractGrid;
 
     times = native_times(metadata)
     loc = LX, LY, LZ = location(metadata)
-    boundary_conditions = FieldBoundaryConditions(grid, loc)
+    boundary_conditions = FieldBoundaryConditions(grid, instantiate.(loc))
     fts = FieldTimeSeries{LX, LY, LZ}(grid, times; backend, time_indexing, boundary_conditions)
     set!(fts)