Feature/update atlas 0.38.1

[twsearle]

Description

Changes to update tests for compatibility with atlas 0.38.1 Disable tests of halo resize until we get the new atlas-orca mesh generator halo = 1.

Issue(s) addressed

• Part of Add halo > 0 support for ORCA meshes ecmwf/atlas-orca#19
• Fixes MPI parallelism produces different interpolation outputs #53
• Fixes Update to atlas v0.38.1 #109
• related to OOPS PR #2670 requires Atlas tagged version 0.38 JCSDA/spack-stack#1155

Dependencies

• jjdocs change for testing in sith https://github.com/MetOffice/jjdocs/pull/167
• Fix to properly wrap periodic cells during interpolation Wrap out-of-bounds source cells into the domain ecmwf/atlas#211
• ci/Update container to atlas v0.38.1 #114
• MetOffice/mo-bundle/pull/533

Impact

Enable merging of the atlas-orca changes to enable domain distributed MPI for improved performance of high resolution models.

Testing

• 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
• 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 (the ci is passing because it uses a container containing the updated atlas version in ci/Update container to atlas v0.38.1 #114)
• I have run mo-bundle to check integration with the rest of JEDI and run the unit tests under all environments

[matthewrmshin]

Tested in my environment. Works as expected.

[matthewrmshin]

See also MetOffice/mo-bundle#533.