Adding nitrogen mineralisation

[jacobcook1995]

Description

This pull request adds two new pools to track nitrogen in the soil "soil_n_pool_don" and "soil_n_pool_particulate". These pools both receive input from litter mineralisation, and the DON (dissolved organic nitrogen) pool also leaches. Both pools are organic nitrogen pools, so effectively track the nitrogen stoichiometry of their corresponding carbon pools (the low molecular weight carbon (LMWC) pool and the particulate organic matter (POM) pool). The breakdown rate of POM to LMWC therefore determines the rate at which nitrogen goes from the particulate to the dissolved pool.

I've also tried to restructure the code a bit. I've added a new SoilPools class, which has method to calculate updates for all soil pools. I still feel like the contents of this method is a bit messy, but I couldn't see an obvious way to group the function steps that would make it clearer. I'm leaving this as is for now, but intended to refactor as further pools are added

Fixes #605

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 96.07843% with 2 lines in your changes missing coverage. Please review.

Project coverage is 95.16%. Comparing base (a7efd83) to head (06e6b61).
Report is 10 commits behind head on develop.

Files with missing lines	Patch %	Lines
...ample_data/generation_scripts/soil_example_data.py	0.00%	2 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #616      +/-   ##
===========================================
- Coverage    95.18%   95.16%   -0.02%     
===========================================
  Files           74       74              
  Lines         4380     4409      +29     
===========================================
+ Hits          4169     4196      +27     
- Misses         211      213       +2     

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[dalonsoa]

I've made a couple of comments/suggestions, but it looks good, otherwise.

[jacobcook1995]

@dalonsoa, I've tried to address all your suggestions. Let me know whether the changes look okay. Cheers!

[dalonsoa]

All looks good!