Simplified mycorrhizal uptake model

[jacobcook1995]

Description

This PR simplifies the mycorrhizal uptake model by reducing the amount of information being passed backwards and forwards between the soil and plants models.

Instead, the mycorrhizal fungi allocate a fixed (but configurable) portion of their nutrient uptake to supply the plants. And the total amount supplied is passed to the plants at the next model time step.

Getting this to work requires making an initial estimate of the amount of nutrients supplied (in the soil model init). This estimate is based on the initial state of the model with the assumption that the microbes take up nutrients at the maximum possible rate.

I've added documentation justifying the new model. Let me know if it makes sense!

Fixes #1197

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

❌ Patch coverage is 98.59155% with 1 line in your changes missing coverage. Please review.
✅ Project coverage is 95.05%. Comparing base (8368bb1) to head (3b8e05f).
⚠️ Report is 3 commits behind head on develop.

Files with missing lines	Patch %	Lines
virtual_ecosystem/models/soil/model_config.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1266      +/-   ##
===========================================
- Coverage    95.05%   95.05%   -0.01%     
===========================================
  Files           71       71              
  Lines         7298     7317      +19     
===========================================
+ Hits          6937     6955      +18     
- Misses         361      362       +1     

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[davidorme]

Yup - LGTM. I think this is cleaner code, easy to explain and a reasonable approximation, and it avoids a whole lot of unpleasantness from the previous version. One minor niggle on code.