[Jacob Cook (jacobcook1995)]

Description

This PR changes the way that soil enzyme classes are produced. Instead of being generated directly from the configuration, a path to a csv file is provided. This CSV file is then used in model setup to create multiple instances of SoilEnzymeClass.

Lai Hao Ran (@hrlai), I've just put down David as a reviewer for this PR as I mainly need feedback on the code at the moment. I'll put you down as a reviewer for the overall feature branch when that is being merged to main (because when that happens the input data will need to change)

Fixes #1541

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
• If this PR changes the expected model inputs, are the relevant people from the
  data science team included as reviewers?

[Codecov Comments Bot (codecov-commenter)]

Codecov Report

❌ Patch coverage is 30.07519% with 93 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (1928-not-providing-parameterisation-for-soil-microbial-groups-and-enzymes-doesnt-result-in-a-configuration-error@42b3dde). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
virtual_ecosystem/models/soil/functional_groups.py	0.00%	86 Missing ⚠️
...ation_scripts/microbial_parametrisation_example.py	0.00%	7 Missing ⚠️

Additional details and impacted files

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[David Orme (davidorme)]

Jacob Cook (@jacobcook1995) I haven't looked in detail - nothing alarming but I think it would be more robust to make more direct use of the existing pydantic models and validation. I've pushed a module showing what I mean - my feeling is that things are more DRY using this structure and it allows the pydantic validation to handle loading and validation errors.

I haven't been through to try and get parity of all the checks with your new code - thought it was worth checking which direction to take it first.

ETA

• I also have made no attempt at testing except that load_enzymes works with your new example file.
• Also, the enzyme and microbe classes can be removed from model_config.py
• The default settings on these classes forbid extra fields. I'd honestly stick with that - if you think it's worth warning, just forbid it?

[Jacob Cook (jacobcook1995)]

Jacob Cook (Jacob Cook (@jacobcook1995)) I haven't looked in detail - nothing alarming but I think it would be more robust to make more direct use of the existing pydantic models and validation. I've pushed a module showing what I mean - my feeling is that things are more DRY using this structure and it allows the pydantic validation to handle loading and validation errors.

I haven't been through to try and get parity of all the checks with your new code - thought it was worth checking which direction to take it first.

Yes that is a lot cleaner, thanks! I'll work on integrating it into the main model flow now