[Refactor]: CDAT Migration - Update dependencies and remove `Dataset._add_cf_attrs_to_z_axes()`

[tomvothecoder]

Is your feature request related to a problem?

xCDAT bug #707 resulted in #863 in e3sm_diags.

As a temporary workaround, we added Dataset._add_cf_attrs_to_z_axes() which adds the CF axis attribute to the Z axis if it is missing in order for xCDAT to retrieve the relevant Z axis bounds for downstream operations (e.g., vertical regridding).

Describe the solution you'd like

• Update dependencies in dev.yml and ci.yml as shown below

  - numpy >=2.0.0,<3.0.0
  - shapely >=2.0.0,<3.0.0
  - xarray >=2024.03.0
  - xcdat >=0.7.3,<1.0.0
  - xesmf >=0.8.7

• Remove lines of code below
  

  e3sm_diags/e3sm_diags/driver/utils/dataset_xr.py

  Lines 422 to 425 in 3406bf2

  	# Add CF attributes to Z axes if they are missing.
  	# NOTE: This is a temporary workaround for xCDAT.
  	# Refer to https://github.com/xCDAT/xcdat/pull/708
  	ds = self._add_cf_attrs_to_z_axes(ds)

• Verify xCDAT v0.7.3 resolves this issue

Describe alternatives you've considered

No response

Additional context

No response

[tomvothecoder]

Closed by #891