Adopt extended LayerStructure functionality

[davidorme]

Description

This PR is taking the code in develop and applying the new API for the LayerStructure from #452, which has been merged down into this.

The main changes are:

• In the models, replacing locally calculated vertical indices with the core LayerStructure indices.
• Replacing the LayerStructure.role_indices['canopy'] approach from the first pass in Amending vertical layer structure #441, which has been deprecated in favour of explicit per role attributes (LayerStructure.index_canopy).
• In the tests, updating tests to accept the central fixture_core_components and then systematically using the from_template and index attributes to generate expected and test values, replacing hard coded integer layer indices with layer specific indices from the fixture_core_components.LayerStructure instance.

Fixes #451 and #458

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 97.56098% with 4 lines in your changes missing coverage. Please review.

Project coverage is 94.95%. Comparing base (94e29ca) to head (998e0ac).

Files	Patch %	Lines
virtual_ecosystem/core/core_components.py	96.72%	4 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #459      +/-   ##
===========================================
- Coverage    94.96%   94.95%   -0.01%     
===========================================
  Files           70       70              
  Lines         3792     3869      +77     
===========================================
+ Hits          3601     3674      +73     
- Misses         191      195       +4     

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[jacobcook1995]

LGTM (though I only looked at the soil related stuff)!

[vgro]

LGTM, a few comments that are probably for another PR.