Adding subcanopy transpiration to transpiration

[davidorme]

Description

Before this PR, we had two transpiration variables in data:

• transpiration, created and updated in PlantsModel.estimate_gpp.
• subcanopy_transpiration created and updated by Subcanopy.calculate_dynamics

With this PR:

• A data["transpiration"] array (layers x cells) is added to the reset_update_vars() method, so is initialised centrally by update
• The appropriate rows in that array are then updated by the two methods above.
• The subcanopy_transpiration array is removed.

Fixes #1182

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 95.00%. Comparing base (031afce) to head (2578340).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop    #1192   +/-   ##
========================================
  Coverage    95.00%   95.00%           
========================================
  Files           71       71           
  Lines         7269     7271    +2     
========================================
+ Hits          6906     6908    +2     
  Misses         363      363           

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[sallymatson]

LGTM

[davidorme]

@vgro I think this fixes the problem - can you just look and see if anything seems problematic?

[vgro]

LGTM