Feature/calculate conductivities

[vgro]

This PR adds the energy balance to the process-based abiotic model. I apologize for the size of the request, the processes are all very interconnected and I missed the point to stop. It should however not be too complicated (please let me know if you need smaller chunks to review). Renaming everything added to the number of files that were changed, and all abiotic files seem completely new, but it should be very easy to filter out.

Here the main changes:

• added abiotic model
• added abiotic_tools submodule
• added soil_energy_balance submodule
• added conductivities submodule
• added energy_balance above ground submodule
• expanded and reorganised dummy_climate_data
• added wind_speed_ref to example data

There are currently a number of unresolved/not implemented processes which require further advancement in other models of the Virtual Ecosystem or potentially some changes to the vertical layer structure (see abiotic_model):

• add process based update of soil temperature
• change temperatures to Kelvin
• adjust for soil moisture default in mm (once updated in hydrology model)
• coordinate latent heat flux/evapotranspiration processes between plants and abiotic
• add soil fluxes to lower atmosphere (might need to drop 'subcanopy' layer)
• return updated fluxes to data object
• introduce 'metaconstants' to support sharing of constants between models
• add self.model_timing.update_interval in seconds as input to soil balance
• expand tests to cover different atmospheric conditions

Type of change

• [x] New feature (non-breaking change which adds functionality)
• [x] Optimization (back-end change that speeds up the code)
• [ ] Bug fix (non-breaking change which fixes an issue)

Key checklist

• [x] Make sure you've run the pre-commit checks: $ pre-commit run -a
• [x] All tests pass: $ poetry run pytest

Further checks

• [x] Code is commented, particularly in hard-to-understand areas
• [x] Tests added that prove fix is effective or that feature works

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 99.80769% with 1 lines in your changes are missing coverage. Please review.

Project coverage is 94.11%. Comparing base (25e9edf) to head (bd073d7).

Files	Patch %	Lines
...le_data/generation_scripts/climate_example_data.py	0.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## develop #406 +/- ## =========================================== + Coverage 93.20% 94.11% +0.91% =========================================== Files 60 68 +8 Lines 2959 3434 +475 =========================================== + Hits 2758 3232 +474 - Misses 201 202 +1 ```

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[vgro]

Thank you again for your feedback on the overall structure. I tried to implement the changes you suggested. Still outstanding/to discuss:

• The mixing of DataArray and np.array is not great but this comes from using functions in different parts of the VE where they have different requirements. It has to be some sort of compromise I guess
• All the info we want in the LayerStructure, the topsoil layer index and the number of canopy layers which updates every time step. I tentatively put it in setup and update which is obviously not great, but I would prefer to tackle this in a separate PR.