Feature/soil trophic piping

[TaranRallings]

Description

I have made a separate PR for the whole soil foraging system. The new plant piping will be done separately. This portion was expedited as Jacob is going on holiday.

There shouldn't be anything actually new here, just new versions of existing things to handle the integration of mushrooms, soil fungi, pom, and bacteria. I have gone with mushrooms as the diet name for fruiting bodies because underscores don't work with my naming system.

New Traits

• specific diets for for fungal fruiting (mushrooms), soil fungi, pom, and bacteria

New methods:

• delta_mass methods for fungal fruiting, soil fungi, pom, and bacteria
• get_pools methods for those same resources

Modified methods

• forage cohort
• forage community

Fixes # (issue)

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 95.69892% with 4 lines in your changes missing coverage. Please review.
✅ Project coverage is 95.11%. Comparing base (61f557a) to head (7a93eb0).
⚠️ Report is 7 commits behind head on develop.

Files with missing lines	Patch %	Lines
virtual_ecosystem/models/animal/animal_model.py	66.66%	4 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1012      +/-   ##
===========================================
+ Coverage    94.93%   95.11%   +0.18%     
===========================================
  Files           80       80              
  Lines         6631     6693      +62     
===========================================
+ Hits          6295     6366      +71     
+ Misses         336      327       -9     

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[jacobcook1995]

This seems to be completely consistent with how the previous litter model piping is done. (so there might still be issues, but if there are they will be broader than this PR).

Happy for this to be merged once tests are added

[jacobcook1995]

Is it worth calling this diet type something more specific like SOIL_FUNGI, to really differentiate it from MUSHROOMS?

[TaranRallings]

I think this is a solid idea but I'll need to do a passthrough later on to clean up the diet language and can do it then, if that works for you.

[jacobcook1995]

Yep that works for me (I guess this is mainly something that will cause you confusion, as I doubt I will be looking at this code)

[jacobcook1995]

love the name!