Average abiotic quantities over relevant soil layers

[jacobcook1995]

Description

This PR changes the soil model so that it averages abiotic quantities over the relevant soil layers. The temperature and matric potential averaging works the same as in the litter model. The soil moisture "averaging" is something I just added, so sanity checking that would be really appreciated!

Fixes #533

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

All modified and coverable lines are covered by tests ✅

Project coverage is 94.65%. Comparing base (606cff7) to head (509a671).
Report is 495 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #803   +/-   ##
========================================
  Coverage    94.64%   94.65%           
========================================
  Files           74       74           
  Lines         5120     5127    +7     
========================================
+ Hits          4846     4853    +7     
  Misses         274      274           

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[vgro]

I think you might need to use the soil layer depth instead of the soil layer thickness here. If both layers are 1m thick, the depth of the first on is 1m, the depth of the second is 2m. if your microbial depth is then 1.2 m, you want all of the first layer but only 0.2 of the second layer, right? At the moment it looks like it always starts from zero?

[jacobcook1995]

Okay, I'll add a note explaining what layer_structure.soil_layer_active_thickness is as that isn't really clear from the name alone

[vgro]

LGTM