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Tags: wavespotter/Oceananigans.jl

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v0.95.5

v0.95.4

[Diff since v0.95.3](CliMA/Oceananigans.jl@v0.95.3...v0.95.4)

**Merged pull requests:**
- Allow FieldTimeSeries to load data split across multiple files (CliMA#3976) (@glwagner)
- Avoid flux computations when not needed in the `IsopycnalSkewSymmetricDiffusivity` (CliMA#3992) (@simone-silvestri)
- Dont import Grids.coordinates (CliMA#4000) (@glwagner)
- Try to add plot labels automagically within Makie extension (CliMA#4001) (@glwagner)
- Generalized Checkpointing plus interface for `set!(::Simulation, pickup)` (CliMA#4003) (@glwagner)
- Add masking methods for `ConstantField`s (CliMA#4006) (@simone-silvestri)

**Closed issues:**
- Mid-Level Enzyme + Oceananigans Integration Test (CliMA#3346)
- Automatically adding labels to Makie's plots in Oceananigans (CliMA#3998)
- WARNING: could not import Grids.coordinates into ImmersedBoundaries (CliMA#3999)

v0.95.3

[Diff since v0.95.2](CliMA/Oceananigans.jl@v0.95.2...v0.95.3)

**Merged pull requests:**
- (0.95.3) Reset model clock and skip `time_step!`ing if next actuation time is tiny (CliMA#3606) (@tomchor)
- Add parameter to epsilon equation so buoyancy flux term may always be positive (CliMA#3886) (@glwagner)
- (0.95.3) Restores open boundary condition functionality (CliMA#3937) (@jagoosw)
- Actually test instantiation on GPU and also skip LagrangianAveragedDynamicSmagorinsky test (CliMA#3989) (@glwagner)
- Add support for loading data generated prior to 0.95.0 with FieldTimeSeries (CliMA#3990) (@glwagner)
- Update the docstring for `HydrostaticFreeSurfaceModel` (CliMA#3991) (@simone-silvestri)
- Remove grid requirements from a `Model` in a `Simulation` (CliMA#3993) (@simone-silvestri)

**Closed issues:**
- Pressure has extremely high gradients in random chunks of simulation using `NonhydrostaticModel` with `ImmersedBoundaryGrid` and `BuoyancyTracer` (CliMA#3593)
- Unexpected FlatExtrapolationBoundaryCondition behaviour in validation script cylinder.jl (CliMA#3975)
- Testing the instantiation of `LagrangianAveragedDynamicSmagorinsky` on GPU takes 1 hour (CliMA#3988)

v0.95.2

[Diff since v0.95.1](CliMA/Oceananigans.jl@v0.95.1...v0.95.2)

**Merged pull requests:**
- (0.95.2) Bugfix in the Polar BC (CliMA#3985) (@simone-silvestri)

v0.95.1

[Diff since v0.95.0](CliMA/Oceananigans.jl@v0.95.0...v0.95.1)

**Merged pull requests:**
- Fix horizontally `Flat` WENO advection (CliMA#3979) (@simone-silvestri)
- Fix exported names from BuoyancyFormulations module (CliMA#3984) (@glwagner)
- Bump to 0.95.1 (CliMA#3987) (@glwagner)

v0.95.0

[Diff since v0.94.3](CliMA/Oceananigans.jl@v0.94.3...v0.95.0)

**Merged pull requests:**
- Correct `AveragedTimeInterval` to use actuations (CliMA#3721) (@liuchihl)
- Adds momentum equation test for Enzyme extension (CliMA#3822) (@jlk9)
- Add test for autodifferentiating hydrostatic turbulence simulation (CliMA#3867) (@glwagner)
- Fix bug in `advect_particle` (CliMA#3923) (@simone-silvestri)
- Reinstate DynamicSmagorinsky tests (CliMA#3926) (@glwagner)
- RK3 for the HydrostaticFreeSurfaceModel version 2 (CliMA#3930) (@simone-silvestri)
- Fix `Integral` reductions on immersed grids (CliMA#3949) (@ali-ramadhan)
- Fix positivity preserving WENO (CliMA#3952) (@simone-silvestri)
- Refactor of spacings and correction of spacings-connected bugs (CliMA#3955) (@simone-silvestri)
- Allow Tuple of closures with CATKE (CliMA#3960) (@simone-silvestri)
- Polar boundary conditions (CliMA#3965) (@simone-silvestri)
- Some corrections in the timestepper constructors (CliMA#3969) (@simone-silvestri)
- advective form of the GM skew diffusivity (CliMA#3971) (@simone-silvestri)
- (0.95.0) `Buoyancy` -> `BuoyancyForce` and `BuoyancyModels` -> `BuoyancyFormulations` (CliMA#3973) (@glwagner)
- (0.95.0) Refactor grids to allow generalized vertical coordinate (CliMA#3974) (@simone-silvestri)

**Closed issues:**
- Add Multi GPU testing (CliMA#2526)
- Should we make `Conjugate Gradient` + `FFTBased-preconditioner` the default for `HydrostaticFreeSurfaceModel`? (CliMA#2635)
- Is `Architectures.next_stream()` redundant? (CliMA#2748)
- Problem using immersed boundary with `PartialCellBottom` and Flat horizontal dimensions (CliMA#2798)
- `with_halo` is broken for `ImmersedBoundaryGrid` (CliMA#2988)
- Boundary condition ordering (CliMA#3342)
- `xspacings` is broken for `ImmersedBoundaryGrid` (CliMA#3701)
- Implementing AB2 for variable time-step size (CliMA#3738)
- `SplitExplicitFreeSurface` code improvements (CliMA#3873)
- Why do we only build distributed `test_architectures` if `MPI.Initialized`? (CliMA#3879)
- Some Lagrangian particles like to travel Southwest on an immersed lat-lon grid + hydrostatic model (CliMA#3917)
- Error when constructing `Integral` of a field on an immersed rectilinear grid: `Azᶜᶜᵃ` not defined  (CliMA#3948)
- `minimum_xspacing` does not account for the immersed boundary (CliMA#3954)
- Duplicate `ψspacing` and `Δψ` (CliMA#3957)
- Why are the prognostic fields deep-copied in the constructor for `HydrostaticFreeSurfaceModel`? (CliMA#3967)

v0.94.3

[Diff since v0.94.2](CliMA/Oceananigans.jl@v0.94.2...v0.94.3)

**Merged pull requests:**
- Reduce parameter space for velocity tendency kernels (CliMA#3924) (@simone-silvestri)
- Leftover from split explicit refactor (CliMA#3931) (@simone-silvestri)
- CompatHelper: bump compat for StructArrays to 0.7, (keep existing compat) (CliMA#3934) (@github-actions[bot])
- (0.94.3) Vector rotation for immersed boundary grids (CliMA#3939) (@simone-silvestri)
- Bugfix in compute bottom height (CliMA#3940) (@simone-silvestri)
- Better message for `regularize_immersed_boundary_condition` (CliMA#3942) (@navidcy)
- Fix a typo in `show(io, Simulation)` (CliMA#3944) (@glwagner)

v0.94.2

[Diff since v0.94.1](CliMA/Oceananigans.jl@v0.94.1...v0.94.2)

**Merged pull requests:**
- (0.94.2) Support interpolation from triple-Flat grids (CliMA#3928) (@glwagner)

v0.94.1

v0.94.0

[Diff since v0.93.3](CliMA/Oceananigans.jl@v0.93.3...v0.94.0)

**Merged pull requests:**
- Implement scale-invariant dynamic Smagorinsky (CliMA#3642) (@tomchor)
- Open halo filling on Windowed fields (CliMA#3834) (@simone-silvestri)
- `static_column_depth` interface and numerical bottom height in `AbstractGridFittedBottom` (CliMA#3841) (@simone-silvestri)
- (0.94.0) Refactor exported names (CliMA#3872) (@glwagner)
- Bugfix in distributed GPU tests and Distributed `set!` (CliMA#3880) (@simone-silvestri)
- Correct error message in `validate_lat_lon_grid_args` (CliMA#3887) (@simone-silvestri)
- Fix fft_poisson_solver constructor (CliMA#3890) (@glwagner)
- Use launch! for particle advection (CliMA#3891) (@glwagner)
- Mask `ReducedFields` accounting the immersed column (CliMA#3900) (@simone-silvestri)
- For output readers, make `reader_kw` default to an empty `NamedTuple` (CliMA#3902) (@ali-ramadhan)
- Fix equation rendering in `boundary_conditions.md` (CliMA#3906) (@jbisits)
- Dont adapt Flat direction advection scheme plus better summary for FluxFormAdvection (CliMA#3908) (@glwagner)
- Remove redundant advection aliases (CliMA#3912) (@simone-silvestri)
- Remove `fill_halo_regions!` specific kwargs from `launch!` (CliMA#3922) (@simone-silvestri)

**Closed issues:**
- More / more flexible Smagorinsky models (CliMA#3637)
- Open boundary conditions do not work for windowed fields (CliMA#3833)
- Error in ConjugateGradientPoissonSolver for nonuniform grids (CliMA#3889)
- The MPI we use in the distributed tests is not CUDA-aware (CliMA#3897)
- Use default `reader_kw=nothing` to make `FieldTimeSeries` concretely typed (CliMA#3898)
- Plotting a reduced field on an `ImmersedBoundaryGrid` fills in NaNs incorrectly (CliMA#3899)
- LaTeX not rendering in `boundary_conditions.md` (CliMA#3905)
- MakieExt having trouble with sliced fields? (CliMA#3921)