Complete implementation of T model functions

[davidorme]

Description

This PR:

• Completes the suite of functions needed for running the T Model within the new demography module. It is basically unpacking the current pyrealm.tmodel.TModel.calculate_growth method for estimating growth increments into standalone functions with proper docstrings etc. following @AmyOctoCat 's similar treatment of pyrealm.tmodel.TModel.reset_diameters for the allometric scaling.
• Updates the regression test datasets from the rtmodel.r implementation to include predictions from more than one plant functional type.
• Adds regression tests for all of the functions in pyrealm.demography.t_model_functions against those new regression golden outputs.

Does not add any user-facing documentation yet.

Fixes #284

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

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.17%. Comparing base (1f315ba) to head (1db5cc2).
Report is 75 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #285      +/-   ##
===========================================
- Coverage    95.29%   95.17%   -0.12%     
===========================================
  Files           28       32       +4     
  Lines         1720     2093     +373     
===========================================
+ Hits          1639     1992     +353     
- Misses          81      101      +20     

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[MarionBWeinzierl]

When putting in assertions, would it make sense to set a tolerance for allclose ? As, I assume, it can be quite different what an acceptable deviation for the expected value is in a each case.

[davidorme]

When putting in assertions, would it make sense to set a tolerance for allclose ? As, I assume, it can be quite different what an acceptable deviation for the expected value is in a each case.

These ones are purely deterministic and should be precise - or at least to the high default tolerance of allclose. They more or less should be identical to machine precision.

[j-emberton]

Is there a citation for this approach?

[davidorme]

No - it's a "new" approach but only in the pretty trivial sense that the foliage respiration rate can be tuned. I'll clarify that.

[j-emberton]

Looks fine to me aside from the queries on citations. Happy to approve and let you update the docstrings as you wish.

[j-emberton]

LGTM