Improved scripts to create initial conditions files

[einola]

Improved scripts to create initial conditions files

Fixes #945

Task List

• Defined the tests that specify a complete and functioning change (It may help to create a design specification & test specification)
• Implemented the source code change that satisfies the tests
• Documented the feature by providing worked example
• Updated the README or other documentation
• Completed the pre-Request checklist below

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Change Description

Adds the functionality to make_init_base.py to make generic geographic grids, in addition to idealised ones. The user must supply lat/lon coordinates of the grid and may provide a mask and initial fields. The program can create nextsim grids from a grid of lat/lon coordinates or lat/lon coordinates of a NEMO C-grid (which also provides coordinates of the upper right corner of the grid box).

Usage:
 0. Import make_init_base
  >> from make_init_base import initMaker
 1. Create an initialiser object with a given filename, e.g.
  >> init = initMaker("test")
     2a. Create a cartesian grid from dimensions and resolution, e.g.
      >> init.make_cartesian_grid(128, 128, 3e3)
     2b. Create a geographic grid from a file containing coordinates. We need to define type of grid:
        * "p": only centre points of the grid are given
        * "ur": the centre and upper right corner of the grid is given
        * "ll": the centre and lower left corner of the grid is given
      init.make_geographic_grid("coordinates.nc", "ur", plat_name="gphit", plon_name="glamt", qlat_name="gphif", qlon_name="glamf")
 3. Modify any variables needed, e.g.
  >> init.cice = 1
  >> init.hice = 3
  >> init.hice[10:20, 10:20] = 4
 4. The init file is written when the initialiser object goes out of scope (e.g. when the program ends or at the end of a loop).

I also modified and renamed make_initNH.py to use make_init_base.py

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Test Description

I used the script to recreate the grid of the integration test, as well as the grid from our NEMO-coupled setup and a few others. All of which run successfully.

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Documentation Impact

The functionality of make_init_base.py should be documented in the usage section of the manual, but it is not.

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Other Details

N/A

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Pre-Request Checklist

• The requirements of this pull request are fully captured in an issue or design specification and are linked and summarised in the description of this PR
• No new warnings are generated
• The documentation has been updated (or an issue has been created to track the corresponding change)
• Methods and Tests are commented such that they can be understood without having to obtain additional context
• This PR/Issue is labelled as a bug/feature/enhancement/breaking change
• This change conforms to the conventions described in the README

[einola]

I got into a fight with Ruff, and this resulted in a lot of unrelated formatting changes - sorry.

I won over Ruff in the end!