Pyrealm

Lavergne et al 2020 soil theta estimation of beta, c4 with negigible
photorespiration.
- Addition of optional soil theta to PModelEnvironment, underpinning
the lavergne2020 CalcOptimalChi method.
- Alteration of PModel arguments. Since there are now different options
for simulating C3/C4, the c4 argument is replaced with method_optchi,
which sets C3/C4 status internally from the method selected.
- Refactor and integration of Alienor's CalcCarbonIsotopes and
C3C4Competition models, from:
https://github.com/Alielav/pyrealm/tree/alienorlavergne
- Refactor of utilities TemporalInterpolator and DailyRepresentativeValues
to handle multiple dimensions and ragged arrays of indices.
- Extended pytest framework to include TemporalInterpolator,
DailyRepresentativeValues, CalcCarbonIsotopes and
C3C4Competition.

object directly, not named args for kmm etc.
- PModel testing update: new set of input test values of 100 values across
envt space, not just 4 arbitrary values. Updated R outputs.
- Restructure of test_pmodel - much cleaner use of parameterisations args.
- Addition of units to utilities.summarize_attr and extensive addition
of units throughout docs.
- Flexibility in the units of PPFD - previous versions were agnostic about
However, that leads to nonsensical values of Jmax and Vcmax, which must
the units of PPFD - so that the scaling of GPP could be set by the user.
be in µmol m-2 s-1. So, PPFD now must also be in µmol m-2 s-1.
- Bug in Jmax calculation - not carrying ftemp_kphio correctly into calculation -
corrected by baking ftemp_kphio correction to kphio early.
- Breaking change to calculation of Jmax and Vcmax. Previous versions
followed rpmodel in using a more complex calculation for Jmax and Vcmax
that allowed Stocker's empirical soil moisture effects (beta(theta)) to
be worked back into Vcmax then Jmax, rd and gs. pyrealm no longer does
this: the soil moisture correction is applied _only_ to LUE and the
getter function for vcmax, jmax, gs and rd issue a warning that they are
uncorrected when soil moisture effects are applied.
- Internal changes - the CalcLUEVcmax class has been retired. This structuring
was integral to the soil moisture correction approach, but with that
change, a simple JmaxLimitation class replaces it.
- Updated value of param_classes.PModelParam.soilmstress_b to published
default

- Added estimate_productivity.md in docs to show behaviour of those
variables for C3 and C4 - revealed some issues!
0.5.6 - Bugs in calculation of Jmax and g_s fixed.
- Fixed issue with utilities.summarize_attr with masked arrays containing
all NaN values

plants, not just 1.0. Updated documentation and examples to illustrate.

and 'masking' using np.nan. See notes in pyrealm/bounds_checker.py. This
was revisited even before release to remove built in masking completely
and just provide some warnings on sane ranges. A hard limit for temps
< 25°C is imposed due to the behaviour of calc_density_h2o.

to consider this - and the constraint approach which generates masked
inputs.