Fix remaining issues with datetime conversions and coordinate naming for iris/xarray compatibility

[w-k-jones]

This PR has expanded to cover a number of remaining issues with iris/xarray compatibility in RC_v1.6.0:

Datetime conversion:

Feature times are always converted to cftime if not using min_distance parameter with 2d data, and add_coordinates is called multiple times. This was likely caused by a merge conflict, when add_coordinates was moved to before distance filtering the preserve_iris_datetime_types parameter was missing.

https://github.com/tobac-project/tobac/blame/f05da214511da70e0ee54dcdec892d08f7f8f6be/tobac/feature_detection.py#L1423

This PR fixes this bug, removes the duplicate add_coordinates call and adds test for various datetime outputs.

I also fixed test_feature_detection_coords, as it turned out that this wasn't actually testing anything as the input dataset had no coords...

Coordinate naming:

Implements the previously unused use_standard_name parameter for coordinate interpolation in feature detection. Now the default behaviour is to use standard names for iris cube input and variable names for xarray dataarrays, but either can be chosen by the user by setting use_standard_name to True or False.

This resulted in a couple of issues, as a number of utils/analysis functions in tobac currently expect dataframe columns to always have standard names (e.g. projection_x_coordinate). To avoid this, I added new functionality to find horizontal coordinate names from dataframes in the same manner as the existing find_dataframe_vertical_coord

Internal utils

At some point during RC_v1.6.0, tobac.utils.general_utils was added to the branch along with tobac.utils.basic. These contained both duplicate functions to each other, as well as duplicate, outdated versions of functions now in other modules. I have resolved this issue, and also split basic into two modules coordinates and label_props to clarify what these module are used for

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[codecov]

Codecov Report

Attention: Patch coverage is 99.54955% with 1 line in your changes missing coverage. Please review.

Project coverage is 63.52%. Comparing base (f05da21) to head (d231cb3).

Files with missing lines	Patch %	Lines
tobac/utils/internal/coordinates.py	98.48%	1 Missing ⚠️

Additional details and impacted files

@@              Coverage Diff              @@
##           RC_v1.6.0     #489      +/-   ##
=============================================
+ Coverage      59.14%   63.52%   +4.38%     
=============================================
  Files             25       27       +2     
  Lines           3892     3836      -56     
=============================================
+ Hits            2302     2437     +135     
+ Misses          1590     1399     -191     

Flag	Coverage Δ
unittests	63.52% <99.54%> (+4.38%)	⬆️

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[github-actions]

Linting results by Pylint:

Your code has been rated at 8.21/10 (previous run: 8.21/10, +0.00)
_{The linting score is an indicator that reflects how well your code version follows Pylint’s coding standards and quality metrics with respect to the RC_v1.6.0 branch.
A decrease usually indicates your new code does not fully meet style guidelines or has potential errors.}

[w-k-jones]

@freemansw1 @JuliaKukulies @kelcyno This fixes the bug with datetime conversions in feature detection that I mentioned earlier, hopefully it should be a quick change to review :)

edit: Fixing the datetime issues found in #490 ended up being a bigger job. I've created two new utils submodules:

• datetime handles datetime conversion functions used to transform between numpy, pydatetime, pandas and cftime datetimes which should make these issues easier to handle in future
• generators includes (for now) a single generator used to iterate through the time slices of a dataarray and find the matching features. It replaces the two different implementations previously in segmentation and bulk statistics, and should be more resilient to different datetime formats

In addition, datetime conversions are fully handled in the iris to xarray conversion decorator now, rather than being sorted by the coordinate interpolation function, which helps ensure that time coordinates remain in the same format as the input

[w-k-jones]

Right, I think all the issues that have cropped up have been resolved and that this is now ready for review. Hopefully this should make the v1.6 release more stable and make future development easier

[freemansw1]

Fantastic work, @w-k-jones. Honestly, that datetime utility would be extremely useful for the broader community, not even just tobac internally.

[freemansw1]

Happy with the new changes!

[fsenf]

@w-k-jones : Great development!

From the first impression I noticed that some docstrings are missing:

1. could you add short descriptive texts to your new tests consistent with the other tests.
2. complete numpydoc docstrings are needed in the datetime.py module.

Could you update everything accordingly? Thanks!

[w-k-jones]

Thanks for flagging this @fsenf , I'll work on fixing those asap

[fsenf]

@w-k-jones : Do you need support for finishing the docstrings?

[w-k-jones]

@fsenf I should have addressed your points now

[fsenf]

Great achievement! I am happy with the PR!

@w-k-jones : Please go ahead and merge.