Switch to writing files in CDF5 (NETCDF3_64BIT_DATA) format

[xylar]

This is E3SM's preferred fromat for large files. Since E3SM can't support NETCDF4 format, it is the only option that we
can be sure will work for both small and large meshes, and saves us the hassle of having different fromats for different mesh sizes.

Good performance does require first writing a NETCDF4 file from xarray and then converting to NETCDF3_64BIT_DATA. This is handled by a new version of mpas_tools, see MPAS-Dev/MPAS-Tools#633.

Copilot summary

This pull request introduces changes to improve NetCDF file handling and streamline the codebase in polaris. Key updates include modifying the default NetCDF format, refactoring imports for clarity, and adding functionality to set default I/O types for streams. Below is a breakdown of the most important changes:

NetCDF File Handling Improvements:

• Updated the default NetCDF format to NETCDF3_64BIT_DATA in polaris/default.cfg to align with improved compatibility and performance. The output engine was also switched from scipy to netcdf4.
• Added logic in polaris/model_step.py to set the default I/O type for streams when the format is NETCDF3_64BIT_DATA.
• Introduced the set_default_io_type function in polaris/streams.py to set the io_type attribute for streams and immutable streams, except for immutable streams named 'mesh'.

Codebase Refactoring:

• Refactored imports in polaris/mesh/spherical.py, replacing xarray with an alias xr and adding write_netcdf for improved readability and functionality.
• Updated instances of xarray.DataArray and xarray.open_dataset to use the alias xr for consistency in polaris/mesh/spherical.py. [1] [2]
• Enhanced the run method in polaris/mesh/spherical.py to rewrite temporary mesh files in the desired NetCDF format using write_netcdf.

Checklist

• User's Guide has been updated
• Developer's Guide has been updated
• API documentation in the Developer's Guide (api.md) has any new or modified class, method and/or functions listed
• Documentation has been built locally and changes look as expected
• Testing comment in the PR documents testing used to verify the changes

[xylar]

Testing

I ran the pr suite and could show that all tests were BFB with a recent pr suite before this functionality was added. (The overflow test was added after I generated the baseline, I could not check that test.)

[xylar]

I'm going to merged this. If it turns out to be a problem, we can move back to NETCDF3_64BIT for files that aren't too large. But I would like to at least try to have a consistent format for now.