v0.103.0

Oceananigans v0.103.0

Diff since v0.102.5

Breaking changes

• This PR changes the interface for using turbulence closures that have prognostic tracers. Instead of adding these tracers manually, the tracers are added implicitly. As a result, any attempt to manually add closure tracers will result in an error.
• For example:

Before this PR

closure = CATKEVerticalDiffusivity()
tracers = (:T, :S, :e)
model = HydrostaticFreeSurfaceModel(; grid, closure, tracers)

After this PR

it should now be built with

closure = CATKEVerticalDiffusivity()
tracers = (:T, :S)
model = HydrostaticFreeSurfaceModel(; grid, closure, tracers)

Merged pull requests:

• Fix cubed sphere corner vorticity (restore 4/3 scaling) (#4741) (@siddharthabishnu)
• Change the user interface so that closure tracers are automatically added (#4788) (@glwagner)
• Fill vertical halos for conformal cubed sphere fields (#5018) (@siddharthabishnu)
• Add conservative regridding extension (#5028) (@glwagner)
• update spot_tracer_diffusion (#5046) (@briochemc)
• Show bounds in WENO summary plus validation (#5054) (@glwagner)
• Fix formatting in ConjugateGradientSolver function (#5055) (@glwagner)
• Fix boundary gradient operators on extended conformal cubed sphere grids (#5056) (@siddharthabishnu)
• Update formatting for forcings summary output (#5057) (@glwagner)
• Add info to docs about using the TEST_GROUP env variable (#5058) (@glwagner)
• Fix immersed cell when bottom = top z (#5062) (@briochemc)
• Validate location input in FieldBoundaryConditions constructor (#5065) (@glwagner)
• Tweak show and summary for Distributed grids and LatitudeLongitudeGrid (#5066) (@glwagner)
• Fix distributed CI (#5067) (@navidcy)
• Bump version from 0.102.5 to 0.103.0 (#5068) (@glwagner)

Closed issues:

• More robust method for specifying fluxes across boundaries (#1400)
• Should grids and clocks have units? (#1462)
• Bug for distributed output when with_halos=false (but only for some fields) (#2352)
• Emit a summary of model data in set!(model, ...) ? (#2462)
• Longitude values are not correctly defined on every panel of the conformal cubed sphere (#3217)
• Face-Face-Any metrics and horizontal coordinates are not filled in the halo regions for ConformalCubedSphereGrid (#3246)
• Clock and QuasiAdamsBashforth2 both have a property representing the previous time-step (#3564)
• Call it "Simulation setup" in the docs, not "Model setup" (#3584)
• Documentation 2.0 (#3672)
• Re-licensing Oceananigans under Apache 2.0 (#3708)
• Out of memory error with Docs tests (#3779)
• Does the show method for OrthogonalSphericalShellGrid make sense? (#3808)
• Segmentation fault filling halo regions with Partition(y=2) (#3878)
• Support for using set! on FieldTimeSeries with functions of time (#3929)
• Free surface for non-hydrostatic model? (#3946)
• Throwing a nice error if CUDA-aware MPI is not configured (#3983)
• Unexpected collapse of stratification in convecting_plankton.jl example with Julia v1.11 (#4613)
• Internal wave example blowing up with Julia v1.11 (#4618)
• no method matching default_prognostic_bc error when building FieldBoundaryConditions (#4759)
• compute_numerical_bottom_height is incorrect for PartialCellBottom (#5061)