New PModelEnvironment implementation

[davidorme]

Description

This PR updates the definition of PModelEnvironment to the proposed structure in the version 2.0.0 sketch in #394

• The fAPAR and PPFD forcing variables are now included in the list of arguments,
• All of the other directly defined arguments for optional variables are removed (theta, rootzonestress, mean_growth_temperature, aridity_index) and instead __init__ treats all kwargs variables as potential additional variables.
• The class uses the new BoundsChecker to validate inputs.
• The changes add tk as an internal attribute.

It also updates all of the test and doc usages of PModelEnvironment. It does not remove usage of fAPAR and PPFD outside of PModelEnvironment - these will become redundant when #401 is merged, addressing #386 and #385, so I'll tidy up on that branch.

Tip

There are a lot of files changed because of all the test and docstring usage of this core class, but the main thing to review is the new pmodel_environment.py file.

Important

Having had to update mutiple test and doc files to set fapar=1, ppfd=1, I think it makes sense to have these two variables default to one.

90% of the time, users will want to set them, but some use cases don't need fapar and ppfd and it is annoying to have to do so. Can you see any downsides to this tweak?

Fixes #390

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

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 80.00000% with 7 lines in your changes missing coverage. Please review.

Please upload report for BASE (383-meta-release-200@c642de6). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
pyrealm/pmodel/pmodel_environment.py	74.07%	7 Missing ⚠️

Additional details and impacted files

@@                   Coverage Diff                   @@
##             383-meta-release-200     #412   +/-   ##
=======================================================
  Coverage                        ?   96.42%           
=======================================================
  Files                           ?       36           
  Lines                           ?     2744           
  Branches                        ?        0           
=======================================================
  Hits                            ?     2646           
  Misses                          ?       98           
  Partials                        ?        0           

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

[MarionBWeinzierl]

Two small suggestions