Using pyrealm within the Plants model

[davidorme]

Description

This PR is to replace the placeholder internals of the Plants Model with actual pyrealm functionality. That is basically impossible to do in small steps, so this is an uncomfortably sprawling PR.

• Replaces old plants config with new setup for T model parameters
• Replaces flora structure with pyrealm Flora
• Replaces cohort structure with pyrealm Cohorts
• Replaces community structure with pyrealm Community
• Uses pyrealm demography functionality to go from cohort DBH data to allometry
• Uses PModel to estimate GPP and transpiration.

Tip

@vgro If you can look at the internals of the Plants Model setup and update to see if anything seems wrong
@sallymatson Could you look at the canopy, community and functional types to see if the way I'm using pyrealm structures is well enough described (for now, anyway).

Fixes #659
Fixes #655

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

[sallymatson]

Thanks for making the changes - LGTM!

[vgro]

Looks good to me, a few points that we might want to discuss in person. One change that is unclear at the moment is what happened to the Cohorts?

[davidorme]

@vgro Thanks for those comments - I've resolved the simple typos and doc updates and commented on the others. Could you review my responses and either resolve them if you are happy or flag them for more discussion!

I've updated the docs to give more clarity on cohorts - they are part of the pyrealm community objects.

[vgro]

This looks good to me. The only remaining issue I have is the name of the canopy_absorption which I think we should change if we include the radiation absorbed by the soil.