Adding organic phosphorus flows

[jacobcook1995]

Description

This pull request adds organic flows of phosphorus to the soil model. This involved extending the functionality developed to track the organic nitrogen cycle to also track the organic phosphorus cycle. The scientific content is a bit dense here, but would be good to get feedback on the code structure/clarity.

Type of change

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist

• Make sure you've run the pre-commit checks: $ pre-commit run -a
• All tests pass: $ poetry run pytest

Further checks

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works
• Relevant documentation reviewed and updated

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 90.47619% with 4 lines in your changes missing coverage. Please review.

Project coverage is 94.57%. Comparing base (bf33499) to head (41d5f1b).
Report is 15 commits behind head on develop.

Files with missing lines	Patch %	Lines
...ample_data/generation_scripts/soil_example_data.py	0.00%	4 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #653      +/-   ##
===========================================
- Coverage    94.63%   94.57%   -0.06%     
===========================================
  Files           73       73              
  Lines         4619     4645      +26     
===========================================
+ Hits          4371     4393      +22     
- Misses         248      252       +4     

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[dalonsoa]

The code itself looks OK - it pretty much follows what nitrogen is doing, as far as I can tell.

However, I've seen that now there are several functions returning dictionaries rather than tuples that can be unpacked, which is less readable. I wonder if it would be better to create dataclasses, as it is done for MicrobialChanges, to contain those outputs.

The same might apply to pools, which is a very large dict and that could be more more readable if it were a dataclass.

None of this is a request for a change, just observations.

[jacobcook1995]

@dalonsoa yes I did wonder whether returning dataclasses rather than dictionaries would be better practice. Good to know!

The next thing I'm working on will be adding inorganic nitrogen and phosphorus pools in, which will involve altering some of functions added/changed here. With that in mind I will merge this now and switch outputs to dataclasses when I'm working on the new code