Fixing incorrect plant growth

[davidorme]

Description

This PR contains fixes for incorrect plant growth calculations. The culprits are:

1. The PlantsModel._setup updated the turnover traits for the time step of the model, but did so in the wrong direction. The trait values are expressed in the models as reciprocals, and so $\tau_r = \tau_r / 12$ increases the speed of turnover in the model by a factor of $12^2 = 144$ compared to the correct $\tau_r = \tau_r \times 12$.

2. The PlantsMode._setup was not updating respiration rates for the time step of the model at all - so the full annual respiration costs were being removed at each time step. These rates are straightforward factors depending on masses, so are simply divided by the number of time steps.

3. The subcanopy vegetation biomass (should be kg C) was being updated with µg C values, so implausibly then contained 10 million tons of carbon per m2. That pushed the equations in the abiotic_simple so far outside bounds that canopy temperature plummeted to -20°C and the plants then all slowly shrank to death.

There are likely to be more issues, but hopefully this gets the model into territory where we can calibrate it.

I had to update the test values in one of the stochiometry tests - I'm assuming these are code-derived values from the previous aberrant behaviour.

Fixes #961

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 94.21%. Comparing base (4278c74) to head (6cd7348).
⚠️ Report is 1502 commits behind head on develop.

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #962      +/-   ##
===========================================
- Coverage    94.27%   94.21%   -0.06%     
===========================================
  Files           79       79              
  Lines         6513     6518       +5     
===========================================
+ Hits          6140     6141       +1     
- Misses         373      377       +4     

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[sallymatson]

LGTM