Implementation of Community object init and factory methods.

docs/source/api/demography_api.md

@@ -26,3 +26,19 @@ kernelspec:
  :autosummary:
  :members:
 ```
+
+## The {mod}`~pyrealm.demography.community` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography.community
+ :autosummary:
+ :members:
+```
+
+## The {mod}`~pyrealm.demography.t_model_functions` module
+
+```{eval-rst}
+.. automodule:: pyrealm.demography.t_model_functions
+ :autosummary:
+ :members:
+```

docs/source/conf.py

@@ -96,6 +96,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
  ("py:class", "numpy._typing._array_like._ScalarType_co"),
  ("py:class", "numpy._typing._generic_alias.ScalarType"),
  ("py:class", "numpy.float32"),
+ ("py:class", "numpy.int64"),
  ("py:class", "numpy.timedelta64"),
  ("py:class", "numpy.bool_"),
  ("py:class", "numpy.ndarray"),
@@ -144,6 +145,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
  "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]]]"
  ),
  ),
+ ("py:class", "pandas.core.frame.DataFrame"),
 ]
 
 # +
@@ -152,7 +154,9 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
  "numpy": ("https://numpy.org/doc/stable/", None),
  "python": ("https://docs.python.org/3/", None),
  "xarray": ("https://docs.xarray.dev/en/stable/", None),
+ "pandas": ("http://pandas.pydata.org/pandas-docs/dev/", None),
  "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
+ "marshmallow": ("https://marshmallow.readthedocs.io/en/stable/", None),
 }
 # -
 

pyproject.toml

@@ -40,6 +40,7 @@ tabulate = "^0.8.10"
 marshmallow = "^3.22.0"
 pandas = "^2.2.2"
 marshmallow-dataclass = "^8.7.0"
+pandas-stubs = "^2.2.2.240909"
 [tool.poetry.group.types.dependencies]
 pandas-stubs = "^2.2.0.240218"
 types-tabulate = "^0.9.0.0"

pyrealm/constants/tmodel_const.py

@@ -35,7 +35,7 @@ class TModelTraits(ConstantsClass):
  """Fine-root turnover time (:math:`\tau_r`, 1.04, years)"""
  par_ext: float = 0.5 # k, PAR extinction coefficient (-)
  """PAR extinction coefficient (:math:`k`, 0.5, -)"""
- yld: float = 0.17 # y, Yield_factor (-)
+ yld: float = 0.6 # y, Yield_factor (-)
  """Yield_factor (:math:`y`, 0.17, -)"""
  zeta: float = 0.17 # zeta, Ratio of fine-root mass to foliage area (kgCm-2)
  r"""Ratio of fine-root mass to foliage area (:math:`\zeta`, 0.17, kg C m-2)"""