Moving soil model to new configuration

[davidorme]

Description

This PR:

• Moves the SoilModel and all of its methods functions etc over to the new configuration classes.
• Updates the prototype soil.model_config to add docstrings and then move a bunch of validation (ordering of pH values, required enzyme and microbial group classes) out of the model methods and into field and model validators.
• Moves the find_microbial_stoichiometries helper function over to the animal.cnp module, since it now has access to the full configuration directly and doesn't need soil to look up the data for it.
• Retires soil.microbial_groups.EnzymeConstants and the make_full_set_of_enzymes completely, since the old dataclass is functionally identical to the new validator class soil.model_config.SoilEnzymeClass and the function is basically identical to the custom validation on that pydantic model. It's basically a straight swap of things that are dict[str, EnzymeConstants] for dict[str, SoilEnzymeClass].

Note

There is similarly a huge amount of overlap between the new validator class soil.model_config.SoilMicrobialGroup and soil.microbial_groups.MicrobialGroupConstants, but that has an extra factory method. I'm sure we can combine the two, but maybe leave this for another day - lets get configuration up and running first.

• Moves all of the testing over to use the new configuration and model constants. I've added some new fixtures to get constants classes - cuts down on importing the constant classes all the time, since I'd have had to swap SoilConsts to SoilConstants etc. anyway.
• Retires a couple of model config tests and moves some of their functionality into a couple of additional soil.model_config tests.

Fixes #1108

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 94.63%. Comparing base (e435fbf) to head (eaa3233).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1109      +/-   ##
===========================================
- Coverage    94.64%   94.63%   -0.01%     
===========================================
  Files           90       90              
  Lines         7896     7887       -9     
===========================================
- Hits          7473     7464       -9     
  Misses         423      423              

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[jacobcook1995]

LGTM!

[jacobcook1995]

Very happy for this monstrosity to die

[jacobcook1995]

Probably slightly easier to understand if these are called "thresholds" rather than "values" (apologies if this is just copied directly from something I previously wrote 🫠)

[OpenDev-StockholmUni]

Hi @jacobcook1995, we're researchers from Stockholm University studying communication on GitHub.

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very happy for this monstrosity to die

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[davidorme]

@OpenDev-StockholmUni

Interesting. I guess it is a good thing to try and encourage polite discourse on GitHub - lack of moderation is a serious issue in online platforms. Having said that - what's the false positive rate like on what your tool flags? The context here is that @jacobcook1995 is commenting on his own code - without that context it's very difficult to triage comments, particularly such short ones.