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Adding a particulate organic matter pool #253

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merged 10 commits into from
Jul 12, 2023
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Description

This pull request adds an extra carbon pool to the soil carbon model. The pool added is the particulate organic matter (POM) pool. This pool is for organic matter that is too complex to be immediately taken up by microbes but that isn't protected through mineral association. The motivation for adding this pool is that the carbon transfers from litter to soil go to this pool, so adding it is a prerequisite for setting up a litter model/module.

I've just added @vgro as a reviewer here, as this PR just extends existing functionality and doesn't really add anything novel, so I don't feel it needs a really thorough going over. If others want to add comments that's completely fine.

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 jacobcook1995 requested a review from vgro July 11, 2023 09:29
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codecov-commenter commented Jul 11, 2023

Codecov Report

Merging #253 (17a06bd) into develop (67ac3f3) will increase coverage by 0.04%.
The diff coverage is 100.00%.

@@             Coverage Diff             @@
##           develop     #253      +/-   ##
===========================================
+ Coverage    95.04%   95.08%   +0.04%     
===========================================
  Files           42       42              
  Lines         1694     1708      +14     
===========================================
+ Hits          1610     1624      +14     
  Misses          84       84              
Impacted Files Coverage Δ
virtual_rainforest/models/soil/carbon.py 100.00% <100.00%> (ø)
virtual_rainforest/models/soil/constants.py 100.00% <100.00%> (ø)
virtual_rainforest/models/soil/soil_model.py 100.00% <100.00%> (ø)

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@vgro vgro left a comment

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LGTM.
The only thing I noticed is that a lot of functions operate with float which I guess assumes that this is the same across all grid cells. Are you planning on extending this to account for all cell_ids?

@jacobcook1995 jacobcook1995 merged commit 437b8ee into develop Jul 12, 2023
@jacobcook1995 jacobcook1995 deleted the feature/add_POM_pool branch July 24, 2023 10:23
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3 participants