Adding two leaf irradience model

[j-emberton]

Description

Adding irradience calculation class, supporting functions and constants dataclass for the two leaf canopy model implementation.

Fixes #236 and #244

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

[davidorme]

This looks great - structure is very compliant with the existing package and popping out the constants class is good. I've added some comments but there isn't any refactoring or major stuff to worry about.

[davidorme]

The reference for this is page 554 of this:
https://onlinelibrary.wiley.com/doi/epdf/10.1111/j.1365-3040.1997.00094.x

I think beta_angle here is (or should be) solar elevation angle - which might make it part of the solar functionality rather than an irradiance specific thing. If we move to using one of the existing solar packages, we might get a more accurate model.

[j-emberton]

I've added pysolar alternatives in the latest commit which calculate solar elevation directly from latitude, longitude and date time. However, they don't take array inputs natively so you need to use and enumerate operation, so there will be a speed accuracy trade.

The best pysolar solar elevation implementation includes atmospheric distortion, but they also have a faster/simpler version which is the same as the first version I wrote. Because the first version uses numpy vectorisation it may well be faster but I've included the pysolar fast version anyway.

[j-emberton]

I will move these calcs into the core solar library in a sec

[davidorme]

I've adopted Keith's short variable names in my rough and ready translation to Python, but we should shift to longer names (latitude, declination, hour_angle)?

[davidorme]

Although these variable names are acronyms, I think we should stick to lower case variable names: ppfd, lai, patm (and arguably longer - leaf_area_index, although I know I'm guilty of using patm and tc elsewhere.

We could do with a sweep to standardise /check variable names, really!

[vgro]

Looks very good to me, I agree with David's comments. One minor point, I would suggest to start docstrings with capital letters for consistency (and potentially to avoid some warning messages).

[j-emberton]

@davidorme Could you help me with a query.

I have been implementing the irradience model into a Pyrealm irradience class, and along the way separating out the individual functions. It appears that a variable defined in the .md is surplus to requirements as it is never used. I have checked dePury& Farquhar(1997) and this appears to be the case. The extraneous variable is Ibs calculated at line 155 in the .md. Could you confirm?

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 30.61224% with 136 lines in your changes missing coverage. Please review.

Project coverage is 88.57%. Comparing base (a800662) to head (b683b51).
Report is 23 commits behind head on develop.

Files	Patch %	Lines
pyrealm/pmodel/two_leaf_irradience.py	24.02%	136 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #245      +/-   ##
===========================================
- Coverage    95.24%   88.57%   -6.68%     
===========================================
  Files           28       30       +2     
  Lines         1703     1899     +196     
===========================================
+ Hits          1622     1682      +60     
- Misses          81      217     +136     

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