CliMA/Oceananigans.jl: v0.40.0

Oceananigans v0.40.0 Diff since v0.39.0 Support for Flat dimensions. See the grid section of the model setup documentation for more details and examples. New advection schemes: UpwindBiasedThirdOrder and UpwindBiasedFifthOrder. Grid halos are automatically adjusted on model construction depending on advection scheme and turbulence closure used. Improved two-dimensional turbulence example. Fixed Langmuir turbulence example. Numerous bug fixes. Closed issues: Only perform operations as needed depending on model dimension. (#35) Float32 tracer conservation test not actually Float32 (#487) Utilities for calculating buoyancy and density offline (#516) Floating point equality checking in 2D Leith (#535) Model not enforcing zero vertical shear at top and bottom (do we expect this?) (#540) Deepening mixed layer verification experiment (#547) NetCDFOutputWriter output does not include global attributes (#576) Incompressibility and pressure projection step test (#673) ERROR: LoadError: UndefVarError: SolutionBoundaryConditions not defined (#686) Cubic lattice grid with missing nodes (#743) An example with stable mixed layer depth? (#749) questions relating to Oceananigans.jl (#770) Possible bug in checkpointing? (#778) test Oceananigans returns CUDA error depsite being able to run examples on CPU and GPU (#788) Is any way to simulate the hydrodynamic behaviour of a bioreactor with Oceananigans.jl? (#830) Test failing on GPU (#882) Eliding differences, interpolation, and fill_halo_regions for Flat dimensions (#902) Stop simulation when output is NaN (#938) Model immediately turns to NaN after 1 time step when grid length is zero along Flat dimensions (#940) Model constructor should check that halos are big enough for chosen advection scheme and turbulence closure (#941) Bug(s) somewhere in UpwindBiasedThirdOrder left-biased interpolation functions (#986) Requiring Lz and Nz for two-dimensional grids is a bit counterintuitive (#1001) Langmuir example broken (#1004) Passing a Clock to restore_from_checkpoint gets overwritten by clock from checkpoint file (#1008) Cannot use Forcings with field_dependencies on GPU with Oceananigans v0.39.0 (#1010) Merged pull requests: Fixes bug in UpwindBiasedThirdOrder advection scheme (#993) (@glwagner) Adds naive (non-WENO) fifth order advection scheme (#994) (@glwagner) Better two-dimensional turbulence Docs example (#1000) (@navidcy) More support for Flat dimensions (#1003) (@glwagner) Update langmuir_turbulence.jl (#1005) (@glwagner) Add Buildkite CI pipeline (#1006) (@ali-ramadhan) Fix bug in restore_from_checkpoint (#1009) (@ali-ramadhan) Adjust halos according to advection scheme and turbulence closure (#1012) (@glwagner) Adds adapt_structure for ContinuousForcing (#1016) (@glwagner) Add Dev in Docs versions menu (#1017) (@navidcy) Build and test but do not deploy docs on Buildkite (#1018) (@ali-ramadhan) Fixes tests with AveragedField and BuoyancyField (#1020) (@glwagner) Bump v0.40.0 (#1021) (@ali-ramadhan