Update MeshXY's .filters method to work with coordinates that do not have a standard name and allow the mesh to be saved

[pt331]

Description

closes #4863

In investgating the issue, we found that when saving a Mesh and converting them to MeshCoords had root a root problem in Mesh.filters(), where it was ultimately trying to guess the coord's axis, which relies on the standard_name.

This pull request addresses the issue by adding mesh_filters, which directly pulls the coordinates out of the mesh, without needing to consider their names. The construction of the mesh already gave us the information needed to do this. The original filters function calls mesh_filters before sending it to the metadata_filter like before, but removing the axis from the call because it is already accounted for.

To make the filter slightly more intelligent and to avoid the hasattr(self, "face_coords") line, _Mesh2DCoordinateManager implements its own mesh_filters to deal with face coordinates separately. It also gave the added benefit of raising a ValueError specific to the _Mesh1DCoordinateManager case, where it mentions that it only expects node and edge locations (not face). This also results in a slight change in behaviour, which is now reflected in the tests.

In the case for saving coordinates without a standard_name, we decided that naming it as "unknown" should be suffice, like what is done for cubes. In the case of using ncdump with the MWE:

ncdump -h ~/mesh_new.nc 
netcdf mesh_new {
dimensions:
        Mesh2d_node = 3 ;
        Mesh2d_face = 1 ;
        Mesh_2d_face_N_nodes = 3 ;
variables:
        int Mesh_2d ;
                Mesh_2d:cf_role = "mesh_topology" ;
                Mesh_2d:topology_dimension = 2 ;
                Mesh_2d:node_coordinates = "unknown unknown_0" ;
                Mesh_2d:face_coordinates = "unknown_1 unknown_2" ;
                Mesh_2d:face_node_connectivity = "mesh2d_face" ;
        int64 unknown(Mesh2d_node) ;
        int64 unknown_0(Mesh2d_node) ;
        int64 unknown_1(Mesh2d_face) ;
        int64 unknown_2(Mesh2d_face) ;
        int64 mesh2d_face(Mesh2d_face, Mesh_2d_face_N_nodes) ;
                mesh2d_face:cf_role = "face_node_connectivity" ;
                mesh2d_face:start_index = 0LL ;

// global attributes:
                :Conventions = "CF-1.7" ;
}

There may be some way to give a more meaningful name, but it will involve making assumptions which may not apply to everyone.

I have tried my hand at adding types as I go along, but most areas are beyond my knowledge and needed input from the team.

Checklist

Important

The Iris core developers are here to help! If anything below is unclear, just post a comment asking for help 😊

• Included a What's New entry
• Incorporated type hints in any changed code
• Checked if tests need updating
• Checked if benchmarks need updating
• Checked if documentation needs updating
  • Docstrings (we love code examples!)
  • User Manual pages
• Checked if dependencies need updating
• Confirmed that the GitHub 'checks' on this PR are passing ✅
  (further reading)

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 90.16%. Comparing base (5d7ca14) to head (11d6072).

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #7185      +/-   ##
==========================================
+ Coverage   90.15%   90.16%   +0.01%     
==========================================
  Files          91       91              
  Lines       24990    25026      +36     
  Branches     4687     4695       +8     
==========================================
+ Hits        22529    22565      +36     
  Misses       1683     1683              
  Partials      778      778              

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[trexfeathers]

This looks lovely!

I imagine you're looking into the test failures. I don't know what to make of the docs failure though; I'll look into that.

[trexfeathers]

Explanation for the docs failure: #7191 (comment)

Our docs builds on Readthedocs are vulnerable because we have not yet managed to lock the dependency versions there - unlike all our tests, which is why the rest of the CI on this PR is still fine. See SciTools/workflows#38

[trexfeathers]

I have confirmed:

• Benchmarks don't need updating
• Documentation doesn't need updating

[trexfeathers]

• Type-checking adds plenty of imports, and we discovered yesterday that at least one new import might have been harming performance or introducing circularity. I've double-checked to confirm that this is all OK now 👍
• The docs render nicely 👍
  • What's New entries
  • Type hints in public operations
• Up to you want you want to happen with the remaining open conversation.

[pp-mo]

Discussed the test skip question with @pt331, and agreed to our satisfaction!
Rescanned the discussions. Checked the WhatsNew build reads OK.
All good for me!