780 abiotic model account properly for time step and area in particular with energy fluxes

[vgro]

This PR aims to sort out the time intervals for the energy balance. The equations really only make sense in a short time interval, an hour or so, so I did a very clumsy for loop implementation as a first step and would appreciate feedback on how to better handle it. At the moment we cannot have hourly input data, so it does not make sense to run it for more than 1 average hour, this is a separate problem.

I have also deleted a lot of bits that are handled by the plant model now (related to absorbed radiation).

Fixes #780

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

[davidorme]

@vgro Could you walk through the logic of the time interval value to run_microclimate? At the moment AbioticModel._update is pinning that value at 3600? So what are the different time interval cases that the logic is intended to handle?

[vgro]

I want the timestep that goes in the functions (delta t) to be one hour, the update interval of the model will most likely always be larger than that, so I divide the model update interval by 3600 to get the number of hours per model time interval. If the model time interval is a day or shorter, run for every hour (this will be the option with hourly input data), if not than do only one step

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 94.22%. Comparing base (486672f) to head (e613726).

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #933   +/-   ##
========================================
  Coverage    94.22%   94.22%           
========================================
  Files           79       79           
  Lines         6320     6308   -12     
========================================
- Hits          5955     5944   -11     
+ Misses         365      364    -1     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

• ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

[dalonsoa]

I've made a comment about a potential error, but other than that, I do not see any other, more elegant way of doing this if the equations being solved require smaller timesteps. To be honest, inner loops to handle shorter timesteps is something that I was expecting to happen given the different timescales of the processes you are handling.

[davidorme]

Looks good - thanks for clarifying the timing stuff. I do find the setup within run_microclimate a bit confusing - it seems like the running mode (iterated vs equilibrium) might be something that is an argument to the function. Having said that - there's a lot of stuff still to come when the hourly data becomes available - so I think that's polishing for later.

[vgro]

Looks good - thanks for clarifying the timing stuff. I do find the setup within run_microclimate a bit confusing - it seems like the running mode (iterated vs equilibrium) might be something that is an argument to the function. Having said that - there's a lot of stuff still to come when the hourly data becomes available - so I think that's polishing for later.

Thanks for the feedback. I will definitely revisit the setup; at the moment the model just returns the final state and I would like to treat this more like the hydrology model where monthly means/stats will be returned. I just didn't want to complicate this PR any further (initially only intended to make sure everything has the same unit). Will consider #517 in this context.