read and write regular lat/lon atlas grids

[twsearle]

Description

Add reading and writing of regular latitude/longitude grid data.

• Move to factory pattern abstraction for AtlasIndex classes
• Support indexing regular grids.
• Read server can read structured grids.
• extend Write server to structured grids.

Also includes:

• a new low resolution synthetic dataset for the purposes of testing.

• a new set of jedi observations in the AMM region for testing.

Issue(s) addressed

Resolves #101

Dependencies

None at this time.

Impact

Enables multiple regional ocean model configurations in JOPA.

Testing checklist

• I have updated the unit tests to cover the change
• New functions are documented briefly via Doxygen comments in the code
• I have linted my code using cpplint
• I have run the unit tests
• I have run mo-bundle to check integration with the rest of JEDI and run the unit tests under all environments
• spice_ostia configuration on spice
• spice_ocnd configuration on spice
• spice_gl_ocn configuration on spice
• xc_ostia configuration on xc
• xc_ocnd configuration on xc
• xc_gl_ocn configuration on xc

[twsearle]

Note, this PR is guaranteed to fail CI at this time. The change has been introduced to share and discuss issues with the results of the tests. When the tests pass, the PR will come out of draft.

[twsearle]

I took out the failing integration test and this looks to pass now so I have put it in review. I will shortly add links to sith comparison workflow runs for this change.

[twsearle]

Looks like there might be some issues with AtlasIndex.h. I am getting some issues with orcamodel::OrcaIndexToBufferIndex::ij in the sith comparisons, so I won't merge until those issues are resolved. I think I could still benefit from a review though

[twsearle]

I think I have fixed the issue with the testing - I was accidentally using the atlas v0.38.1 KGO for my sith comparison tests. I also found the issue with the AMM tests - I was reading in the wrong observation file input! Apologies it took me so long to spot this (a lot of uncessary print statements) but on the bright side, I have interpolated a couple of the observations by hand so I am now quite convinced that this is working correctly.

[s-good]

Looks great, thanks. I just left a few comments for you to consider.

[s-good]

Thanks for making the change and responding to my comments.