Fixes to Biomass draft

[davidorme]

Description

This PR:

• Fixes a stupid mistake: the new BiomassTissue classes should not extract turnover - the biomass carbon is untouched by turnover, that's the whole point. So the tissue_turnover and extract_turnover methods are removed and collapse back into a single get_turnover method that returns the nutrient turnover losses for inclusion in the whole stem nutrient balancing.

  ETA: To clarify - I had setup the BiomassTissue.extract_turnover abstract method description and then the implementations in the subclasses to actually remove carbon and nutrient masses from the Tissue. This isn't what happens in turnover - a quantity of carbon is allocated to replace old tissue but the tissue mass is maintained. We need to know those masses to pass turnover into the correct pools but the tissue biomasses are unchanged. The method does also need to record the nutrient loss so that the stoichiometric balance of the individual can be resolved after all allocation has occurred.

• Updates the functionality of elements_needed_for_growth. Back in Stoichiometry this just reported the elemental masses for nutrient balancing - however with Biomasses it makes more sense for this function to also be responsible for adding growth allocation to the carbon biomasses and similarly increasing nutrient allocations to tissues. This function also returns the new nutrient allocation for inclusion in whole stem element balancing. The method is renamed apply_growth.

These new BiomassTissue methods are now called by the relevant functions in the Biomasses class and the tests are updated to cover the new functionality and naming.

Fixes #1493

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

[davidorme]

@sallymatson I think there are some things about the internal representations that can be made more efficient, but this feels to me like it's shaking down into something fairly solid. I also think some of the code repetition can be reduced, but I'm going to worry about that later.

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 94.99%. Comparing base (47f5007) to head (df77892).

Additional details and impacted files

@@                                    Coverage Diff                                    @@
##           1482-feature-branch-for-biomass-related-functionality    #1494      +/-   ##
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- Coverage                                                  94.99%   94.99%   -0.01%     
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  Files                                                         72       72              
  Lines                                                       7790     7787       -3     
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- Hits                                                        7400     7397       -3     
  Misses                                                       390      390              

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[sallymatson]

All looks sensible to me.

A bit hard to get my head around everything to give a 100% full review, but I trust the details etc and I agree that it's moving in a great direction.

[sallymatson]

Can you just clarify what you mean by this? "Fixes a stupid mistake: the new BiomassTissue classes should not extract turnover - the biomass carbon is untouched by turnover, that's the whole point."

[davidorme]

Yup - I've updated the PR description.