v0.103.1

Oceananigans v0.103.1

Diff since v0.103.0

Merged pull requests:

• Lock Exchange Example (#4968) (@surbhidhiman)
• Update docs for turbulence closures (#5069) (@glwagner)
• Update references in index.md (#5070) (@navidcy)
• Update coordinate system information in physics documentation (#5071) (@glwagner)
• Adds linkcheck=true in makedocs + fixes a bunch of broken urls (#5074) (@navidcy)
• Implement TabulatedFunction (#5077) (@glwagner)

Closed issues:

• Make use of CUDA.versioninfo() (#874)
• Update Coord system and Notation page in docs (#1779)
• Document the fact that you can pass a Tuple as closure to models (#1879)
• Should we use Base.TwicePrecision to align_time_step? (#2321)
• Support Nz = 1 with DistributedFFTPoissonSolver (#2533)
• Highlighting important breaking changes in releases (#3147)
• Doing better than overwriting_existing=true with output? (#3543)
• Oddly-written halo filling code for the cubed sphere (#4855)
• Possible error in computing Cs² of dynamic Smagorinsky-Lilly model (#4880)

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)

v0.102.5

Oceananigans v0.102.5

Diff since v0.102.4

Merged pull requests:

• Extending DistributedField and DistributedFFTBasedPoissonSolver functionality to allow for distributed FFT preconditioner for ConjugateGradientPoissonSolver (#4555) (@xkykai)
• Change default minimum buffer upwind order to 3 (#5009) (@glwagner)
• Resolve warnings when importing symbols already usinged (#5041) (@giordano)
• [docs] Include info about computing environment in Literate examples (#5043) (@giordano)
• Add znodes docstring (copied back from v0.94.3) (#5045) (@briochemc)
• Add with_number_type function for distributed grids for correct reconstruction (#5050) (@xkykai)
• Change default to hydrostatic_pressure_anomaly = nothing for vertically periodic topologies (#5052) (@xkykai)
• Correct field constructor to work with OffsetArrays (#5053) (@simone-silvestri)

Closed issues:

• Laplacian on ImmersedBoundaryGrid is incorrect if using ∂x, ∂y, and ∂z composition (#2915)
• Differences of reduced fields seem to not be defined? (#5040)
• Missing znodes docstrings + broken links in docs (#5042)
• DistributedFFTBasedPoissonSolver on reduced precision grid doesn't work as preconditioner for ConjugateGradientPoissonSolver in distributed settings (#5044)

v0.102.4

Oceananigans v0.102.4

Diff since v0.102.3

Merged pull requests:

• Generalize bounded WENO advection (#5002) (@glwagner)
• Fix flaky test: test_chunked_abstraction (#5038) (@ali-ramadhan)
• Support vertical plots with custom coordinates (#5039) (@glwagner)

Closed issues:

• Flaky test: test_chunked_abstraction in test_output_readers.jl (#5037)

v0.102.3

Oceananigans v0.102.3

Diff since v0.102.2

Merged pull requests:

• Explicit imports in more modules (#5015) (@giordano)
• (v0.102.3) Fix NetCDF outputs on vertically stretched lat-lon grids, test non-hydrostatic η output, and fix non-hydrostatic free surface time stepping (#5030) (@ali-ramadhan)
• [docs] Use PNG format for CairoMakie images (#5031) (@giordano)
• Update horizontal_convection.jl (#5034) (@navidcy)
• [docs] Use PNG figures in more places (#5036) (@giordano)

Closed issues:

• Implicit free surface implementation in NonhydrostaticModel (#4715)
• Cannot output η via a NetCDFWriter on a vertically stretched lat-lon grid (#5029)
• Cannot time step a NonhydrostaticModel with an ImplicitFreeSurface on a CUDA GPU (#5032)

v0.102.2

Oceananigans v0.102.2

Diff since v0.102.1

Merged pull requests:

• SphericalCoriolis which supports nonhydrostatic and hydrostatic formulations (#4695) (@francispoulin)
• Fix clock argument in TriadIsopycnalSkewSymmetricDiffusivity's explicit_R₃₃_∂z_c function (#4780) (@xkykai)
• Support ImmersedBoundaryGrid reconstruction using NetCDF (#4848) (@tomchor)
• Allow arbitrary fluxes across immersed boundaries and test this with AdvectiveForcing (#4987) (@tomchor)
• Check undefined exports with Aqua (#4992) (@giordano)
• Implement minimum_buffer_upwind_order for WENO and UpwindBiased (#5003) (@glwagner)
• Move prettysummary to Utils (#5006) (@giordano)
• Fix location was not passed in configure_kernel (#5007) (@simone-silvestri)
• Disambiguate binary operations on Numbers (#5010) (@glwagner)
• Link prominently to jobs working on or with Oceananigans (#5011) (@glwagner)
• Fix small typo in validation script (#5012) (@tomchor)
• Reorganize test_output_readers.jl (#5016) (@tomchor)
• Add NORi paper (#5020) (@navidcy)
• Update community resource links in README (#5022) (@glwagner)
• (0.102.2) Fix NaNs in halo regions due to division by zero in split-explicit free surface (#5025) (@ali-ramadhan)

Closed issues:

• CUDA/KA circular dependancy (#3964)
• clock argument missing in TriadIsopycnalSkewSymmetricDiffusivity's explicit_R₃₃_∂z_c function (#4779)
• Different behavior of AdvectiveForcing when tracers encounter a domain boundary and an immersed boundary (#4812)
• Calling nodes on integral of field on LatitudeLongitudeGrid raises error (#5014)
• NaNs in the halo regions when running a hydrostatic model with land (#5024)

v0.102.1

Oceananigans v0.102.1

Diff since v0.102.0

Merged pull requests:

• Add a test for CATKE with DateTime clock and fix (#4885) (@glwagner)
• Oceananigans-local FFTW num threads setting (#4958) (@milankl)
• Use julia v1.12 for CI (#4961) (@navidcy)
• Bump actions/checkout from 5 to 6 (#4973) (@dependabot[bot])
• Fix typo in internal_wave.jl comment (#4983) (@navidcy)
• Remove all remaining unused imports (#4993) (@giordano)
• Remove all self-qualified accesses (#4994) (@giordano)
• Remove duplicate hack_cosd/hack_sind definitions (#4995) (@giordano)
• Do not import Base.sum! from Statistics (#4996) (@giordano)
• Use explicit imports in more modules (#4997) (@giordano)
• Bump version from 0.102.0 to 0.102.1 (#5005) (@navidcy)

v0.102.0

Oceananigans v0.102.0

Diff since v0.101.3

Breaking changes

• This release fixes the non-standard style of BuoyancyField, which is renamed to buoyancy_field
• It also adds ExplicitImports to testing which will affect in which modules certain names are available.

Other changes

• Finally, it implements a buoyancy_force and buoyancy_tracers interface for TurbulenceClosures. This is not a breaking change.

Merged pull requests:

• Improvements and fixes to NetCDFWriter (#4890) (@tomchor)
• fix tapering function in diffusive GM (#4909) (@xkykai)
• Update CPU architecture reference in OutputReaders.jl (#4963) (@simone-silvestri)
• Fix typo in models_overview.md (#4964) (@awiteck)
• Update warning message format in split_hydrostatic_runge_kutta_3.jl (#4965) (@navidcy)
• Add set! for FieldTimeSeries that can take in functions of time (#4966) (@glwagner)
• Clean up; implement buoyancy_force interface for TurbulenceClosures (#4967) (@glwagner)
• Use Julia v1.12.2 for CI (#4970) (@navidcy)
• Fix typos in internal wave comments (#4974) (@navidcy)
• Add adapt method for AMD plus closure coeff for functions (#4976) (@glwagner)
• Run Aqua tests (#4979) (@giordano)
• Improve testing coverage for AdvectiveForcing (and other forcings too) (#4980) (@tomchor)
• Start running ExplicitImports checks (#4985) (@giordano)
• Bump to 0.102.1 (#4986) (@glwagner)
• Add Brenner et al. (2025) paper to documentation (#4988) (@navidcy)
• Downgrade version from 0.102.1 to 0.102.0 (#4991) (@glwagner)

v0.101.3

Oceananigans v0.101.3

Diff since v0.101.2

Merged pull requests:

• Make nodes() return the correct indices when passed a view of a Field (#4814) (@tomchor)
• Refactor the buffer system and add methods for synchronize_communication! (#4939) (@simone-silvestri)
• Three dimensional column_depth methods (#4940) (@simone-silvestri)
• Refactor SplitExplicitFreeSurface to compute transport barotropic velocities (#4941) (@simone-silvestri)
• Remove redundant FT definition in fields tests (#4942) (@giordano)
• Remove integrated areas in ImplicitFreeSurface and refactor solver (#4943) (@simone-silvestri)
• Properly set status for computed fields (#4945) (@erin-atkinson)
• Add AGENTS.md for agent-assisted coding (#4946) (@glwagner)
• Fix bug in multi-region SplitExplicitFreeSurface (#4947) (@simone-silvestri)
• Add DJ4Earth paper (#4950) (@navidcy)
• Run benchmarks on julia 1.12 (#4951) (@simone-silvestri)
• Remove unused cubed spheres module (#4953) (@simone-silvestri)
• Fix formatting and punctuation in references (#4955) (@navidcy)
• Fix typo in grids doc (#4956) (@awiteck)
• Add "it" to operations doc for clarity (#4957) (@awiteck)
• Remove duplicate citation for DJ4Earth paper (#4959) (@navidcy)
• Update MakieExt for Makie v0.24 + add tests (#4960) (@navidcy)

Closed issues:

• nodes() returns the full grid when given a smaller view of a Field (#4729)
• compute!(field, time) doesn't update status of field (#4944)
• [doc] Add README-zh-CN.md (#4948)

v0.101.2

Oceananigans v0.101.2

Diff since v0.101.1

Merged pull requests:

• Try reusing the julia path for distributed tests (#4783) (@simone-silvestri)
• Change regularize_forcing to materialize_forcing, plus refine model_forcing interface (#4930) (@glwagner)
• import OutputReaders in Reactant extension (#4935) (@simone-silvestri)
• Introduce Abstract formulation types for FourierTridiagonalPoissonSolver (#4936) (@glwagner)