Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs

Oceananigans v0.36.0

Diff since v0.35.0

This release coincides with the publication of the Oceananigans.jl Journal of Open Source Software (JOSS) paper.

Changelog:

• Simplified boundary condition interface, types, and constructors. See the "boundary conditions" section under "Model setup" in the documentation for updated examples.
• Support for a NonTraditionalBetaPlane Coriolis force implementation.
• The AnisotropicBiharmonicDiffusivity closure now works properly in closed domains with zero Flux boundary conditions, as higher-order boundary conditions are enforced.
• Bug fix: Appending to NetCDF files with NetCDFOutputWriter works now.
• Bug fix: Computations of abstract operations compute the right end point of face-centered fields along bounded dimensions.
• Bug fix: Averages with_halos=false return results with the correct dimensions for face-centered results along bounded dimensions.
• Small bug fixes for show methods.

Breaking changes:

• When constructing a NetCDFOutputWriter, use mode="c" instead of clobber=true and mode="a" instead of clobber=false.

Closed issues:

• More streamlined interface for boundary functions? (#769)
• Return of the multiple of 16 bug (#780)
• When printing an AbstractOperation, the tree should be indented for readability (and without newline separation) (#893)
• Is the warning "This simulation will recalculate the time step every iteration which can be slow" correct? (#903)
• Wrong size for averages with halos of face-centered fields along bounded dimensions (#906)
• Computations do not compute the right end point faces of bounded dimensions (#908)
• Cannot append to NetCDF file even with clobber=false (#913)
• Docs for 0.35.0 seem to be missing (#917)

Merged pull requests:

• Journal of Open Source Software paper (#564) (@ali-ramadhan)
• Output writer "diagnostic dependencies" (#886) (@glwagner)
• Convenience kwargs in JLD2OutputWriter constructor for averaging output (#887) (@glwagner)
• Simplifies boundary condition interface, types, and constructors (#894) (@glwagner)
• Non-traditional β plane (#899) (@ali-ramadhan)
• Generalizes halo filling for flux boundary conditions (#904) (@glwagner)
• Nicer Base.show for abstract operations (#905) (@ali-ramadhan)
• Fix size for averages with halos of face-centered fields along bounded dimensions (#907) (@ali-ramadhan)
• Update test to also catch multiple of 16 bug (#909) (@ali-ramadhan)
• Fix computation work layout for faces along bounded dimensions (#910) (@ali-ramadhan)
• Fix typo in AnisotropicBiharmonicDiffusivity docstring (#911) (@navidcy)
• Fix appending to NetCDF file (#915) (@ali-ramadhan)
• Bump v0.36.0 (JOSS release) (#916) (@ali-ramadhan)