Initial plants model draft

[davidorme]

Description

This PR provides the first steps in setting up the plants model. The functionality in this PR is purely focussed on the initial setup of the plant community:

• Classes are defined to define plant functional types and generate those from the configuration.
• A Plants class is defined to hold lists of PlantCohorts by grid cell and to populate that from provided init data, which is basically just a data frame of plant cohort details.

The next steps for future PRs are to:

1. generate canopy model from the community data and insert canopy leaf area index and height into the data object.
2. implement an update method to estimate productivity, allocation to growth and hence a new canopy model, but this is not likely to happen soon.
3. Work out how to modify leaf area index in response to herbivory.

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

[jacobcook1995]

LGTM! I just had a few minor comments

[vgro]

This looks overall very good, I added a few minor comments.
It would be useful if you could give your variables longer, more descriptive names. Please add tests for the plant_model.

[codecov-commenter]

Codecov Report

Merging #296 (9c2e25f) into develop (bd86d67) will decrease coverage by 0.53%.
The diff coverage is 88.09%.

@@             Coverage Diff             @@
##           develop     #296      +/-   ##
===========================================
- Coverage    97.55%   97.03%   -0.53%     
===========================================
  Files           47       51       +4     
  Lines         2171     2293     +122     
===========================================
+ Hits          2118     2225     +107     
- Misses          53       68      +15     

Files Changed	Coverage Δ
...rtual_rainforest/models/plants/functional_types.py	67.56% <67.56%> (ø)
virtual_rainforest/models/plants/plants_model.py	91.89% <91.89%> (ø)
virtual_rainforest/models/plants/__init__.py	100.00% <100.00%> (ø)
virtual_rainforest/models/plants/community.py	100.00% <100.00%> (ø)
virtual_rainforest/models/plants/constants.py	100.00% <100.00%> (ø)

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[davidorme]

@vgro I was holding off on the PlantModel tests until there was something to test, but actually even the minimal tests have caught a couple of issues 😄 Can you have a quick double check of the requested changes?

[vgro]

LGTM! A few minor comments :-)

[vgro]

@vgro I was holding off on the PlantModel tests until there was something to test, but actually even the minimal tests have caught a couple of issues 😄

Haha, yes, annoyingly (and luckily) it always does ;-)