Improved microbial enzyme secretion model

[jacobcook1995]

Description

This PR changes how the calculation of enzyme secretion by microbes so that microbes have an allocate a certain fraction of new biomass to extracellular enzymes (previously it was a fraction of cellular maintenance). The reason behind this change is that it allows enzymes to have different stochiometries to the microbes producing them. This is something that needs to be added before fungi can be split between mycorrhizal and saprotrophic.

The main structural change arises because the microbial groups now need information about the enzyme classes (so that the average stoichiometry of the synthesised biomass can be found). So now a set of EnzymeConstants has to be provided for the creation of a MicrobialGroupConstants data class. Feedback on this would be appreciated!

I also fixed a bug I noticed with the calculation of microbial pH suitability.

Fixes #760 #779

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 94.64%. Comparing base (4c03507) to head (9a5c71a).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #801      +/-   ##
===========================================
+ Coverage    94.62%   94.64%   +0.01%     
===========================================
  Files           74       74              
  Lines         5102     5120      +18     
===========================================
+ Hits          4828     4846      +18     
  Misses         274      274              

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[dalonsoa]

I've just made a small, maths-related comment, but all looks good otherwise. Quite an interesting business!

[dalonsoa]

Please, let someone check my maths, but I think that you can take the dividing total_enzyme_allocation out of the sums, in which case it will cancel with the multiplying one below:

Suggested change

	enzyme_c_n_weighted = sum(
	enzyme_classes[f"{name}_{substrate}"].c_n_ratio
	* allocation
	/ total_enzyme_allocation
	for substrate, allocation in enzyme_production.items()
	)
	enzyme_c_p_weighted = sum(
	enzyme_classes[f"{name}_{substrate}"].c_p_ratio
	* allocation
	/ total_enzyme_allocation
	for substrate, allocation in enzyme_production.items()
	)
	return {
	"nitrogen": (c_n_ratio + enzyme_c_n_weighted * total_enzyme_allocation)
	/ (1.0 + total_enzyme_allocation),
	"phosphorus": (c_p_ratio + enzyme_c_p_weighted * total_enzyme_allocation)
	/ (1.0 + total_enzyme_allocation),
	}
	enzyme_c_n_weighted = sum(
	enzyme_classes[f"{name}_{substrate}"].c_n_ratio
	* allocation
	for substrate, allocation in enzyme_production.items()
	)
	enzyme_c_p_weighted = sum(
	enzyme_classes[f"{name}_{substrate}"].c_p_ratio
	* allocation
	for substrate, allocation in enzyme_production.items()
	)
	return {
	"nitrogen": (c_n_ratio + enzyme_c_n_weighted)
	/ (1.0 + total_enzyme_allocation),
	"phosphorus": (c_p_ratio + enzyme_c_p_weighted)
	/ (1.0 + total_enzyme_allocation),
	}

[jacobcook1995]

Yes, you are right! I think I was overly focused on the line-by-line logic so I lost the big picture