Implementation of Arrhenius methods #389
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… circular imports; updating functions to remove calc_ftemp_arrh; updating imports
pyrealm/constants/pmodel_const.py
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| # Arrhenius values | ||
| arrhenius_vcmax: dict = field( | ||
| default_factory=lambda: dict( | ||
| simple=dict(ha=65330), | ||
| kattge_knorr=dict( | ||
| entropy_intercept=668.39, | ||
| entropy_slope=-1.07, | ||
| ha=71513, | ||
| hd=200000, | ||
| ), | ||
| ) | ||
| ) | ||
| """Coefficients of Arrhenius factor scaling for :math:`V_{cmax}`.""" | ||
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| arrhenius_jmax: dict = field( | ||
| default_factory=lambda: dict( | ||
| simple=dict(ha=43900), | ||
| kattge_knorr=dict( | ||
| entropy_intercept=659.70, | ||
| entropy_slope=-0.75, | ||
| ha=49884, | ||
| hd=200000, | ||
| ), | ||
| ) | ||
| ) | ||
| """Coefficients of Arrhenius factor scaling for :math:`J_{max}`.""" | ||
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I am sorry to be a bit stupid (Python is not my first language), but I am confused about this. Can you explain to me what the field in all those dicts and lambdas does?
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It's a peculiarity of the dataclass API. Default dataclass attributes get created from the class definition and so the value of mutable defaults ends up being shared and edited across all instances of the dataclass. So it forbids mutable defaults using the simple attr: type = val system and instead you have to wrap the default value in a lambda through the field constructor, which gives finer control over the attribute.
https://docs.python.org/3/library/dataclasses.html#mutable-default-values
From what I understand this looks sensible, and much cleaner. |
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## develop #389 +/- ##
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+ Coverage 96.27% 96.34% +0.06%
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Files 34 35 +1
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+ Hits 2560 2637 +77
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es mean_growth_temperature to be set
Description
This PR fixes #384, but also goes quite a bit further in trying to future proof the API of the
PModelandSubdailyPModela bit. The basic story is:The
PModelcurrently followsrpmodelin using a modified Arrhenius equation parameterised by Kattge and Knorr (2007). This is inconsistent withSubdailyPModel, is implemented a bit oddly (t_growthshould not be the same as the observed temperature) and there's no general agreement that using this form is better than the simple form at present.So, the simple equation (currently in
calc_ftemp_arrh) should be used but it is highly likely that we're going to want to be alter the Arrhenius scaling in the near future.So this PR:
calc_ftemp_arrh->calculate_simple_arrhenius_factorandcalc_modified_arrhenius_factor->calculate_kattge_knorr_arrhenius_factor) and tidies the function implementation up a bit.pyrealm.pmodel.arrheniusmodule that implements theArrheniusFactorABCandARRHENIUS_METHOD_REGISTRY. This ABC is really just a wrapper around the standalone functions that is tailored to run the calculations from within the context of aPModelorSubdailyPModelenvironment and the registry allows the implementations to be accessed via a short method name.methodattribute, which defines that short name. This name is used to:__init_subclass__,method_arrheniusargument to PModel, andtkandtkref) and then thecalculate_arrhenius_factormethod can be called with the coefficients for a given enzyme system. The base method checks the coefficients automatically and then calls the private_calculation_methodabstract method defined by the subclass.The PR then also:
I think the altered PModel API is sensible - even if the internals change a bit, the signatures should be stable.
Fixes #384
Type of change
Key checklist
pre-commitchecks:$ pre-commit run -a$ poetry run pytestFurther checks