Submodules for grids, solvers, diagnostics, and output writers

[ali-ramadhan]

This PR refactors each of grids.jl, poisson_solvers.jl, diagnostics.jl and output_writers.jl into their own submodules.

Moving stuff into modules is a pretty disruptive change that introduces tough merge conflicts into other PRs so I also created a Grids and a Solvers submodule in preparation for the vertically stretched grid as I didn't want to include them with vertically stretched PRs that could sit open for days.

The whole code still feels a bit messy to me but I think working on #497 will help a lot.

Helps with #456 and #495

[glwagner]

It's hard to wrap my head around this but scanning the new source structure, it looks like a move in the right direction.

[glwagner]

Looks like there are some issues with examples, and that's why the doc builds failed.

[glwagner]

As a side note: I think it's ok to include "shared utils" at the top level within a submodule prior to importing logically-distinct functionality contained in separate files. Sometimes this can improve code-readability if there are a small number of utils. The need for a separate "utils.jl" file should decrease when the code structure is more modular and separated into logical subunits, I think.

We can also have single-file submodules, as in Documenter.jl (I think their file structure looks very sane and manageable):

https://github.com/JuliaDocs/Documenter.jl/tree/master/src

There's still a bit of work we need to do to understand inter-submodule dependencies; once that's sorted out I think the top-level Oceananigans.jl file will clean up.

[glwagner]

By the way, with a Grids submodule we can rename RegularCartesianGrid to Grids.RegularCartesian (and Grids.VerticallyStretchedCartesian). This may help with script readability and script-writing. We may even eventually have a subsubmodule Grids.Cartesian.Regular; Grids.Cartesian.VerticallyStretched.

[codecov]

Codecov Report

Merging #512 into master will decrease coverage by 2.01%.
The diff coverage is 68.94%.

@@            Coverage Diff             @@
##           master     #512      +/-   ##
==========================================
- Coverage   67.68%   65.66%   -2.02%     
==========================================
  Files          49       65      +16     
  Lines        1838     1896      +58     
==========================================
+ Hits         1244     1245       +1     
- Misses        594      651      +57

Impacted Files	Coverage Δ
src/Operators/ops_regular_cartesian_grid.jl	84.21% <ø> (ø)	⬆️
src/AbstractOperations/AbstractOperations.jl	33.33% <ø> (ø)	⬆️
src/Oceananigans.jl	75% <ø> (ø)	⬆️
src/TurbulenceClosures/TurbulenceClosures.jl	100% <ø> (ø)	⬆️
src/Solvers/poisson_solver_gpu.jl	0% <0%> (ø)
src/Grids/Grids.jl	100% <100%> (ø)
src/Solvers/poisson_solver_cpu.jl	100% <100%> (ø)
src/Diagnostics/Diagnostics.jl	100% <100%> (ø)
src/TimeSteppers/TimeSteppers.jl	74.35% <100%> (ø)	⬆️
src/Solvers/Solvers.jl	100% <100%> (ø)
... and 36 more

---

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 4b8ff03...9060a5f. Read the comment docs.

[ali-ramadhan]

As a side note: I think it's ok to include "shared utils" at the top level within a submodule prior to importing logically-distinct functionality contained in separate files. Sometimes this can improve code-readability if there are a small number of utils. The need for a separate "utils.jl" file should decrease when the code structure is more modular and separated into logical subunits, I think.

Hmmm, I like having separate utils.jl files because it gives me a default place to put utility functions and look for them. I also like keeping the top-level module file strictly for import/export statements and include statements.

Been thinking that the main Oceananigans.jl module file could be cleaned up quite a bit, especially if it becomes just import/export/include statements.

At some point we should discuss how to structure the package code then everything should become much cleaner.