Annual fAPAR_max and LAI_max

docs/source/api/phenology_api.md

@@ -0,0 +1,36 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
+---
+
+# The {mod}`~pyrealm.phenology` module
+
+```{eval-rst}
+.. automodule:: pyrealm.phenology
+    :members:
+```
+
+## The FAPAR limitation module
+
+```{eval-rst}
+.. automodule:: pyrealm.phenology.fapar_limitation
+    :members:
+```

docs/source/conf.py

@@ -21,10 +21,7 @@
 
 from pyrealm import __version__ as pyrealm_version
 
-# +
 sys.path.insert(0, os.path.abspath("../"))
-# -
-
 
 # -- Project information -----------------------------------------------------
 
@@ -52,6 +49,7 @@
     "sphinx.ext.mathjax",
     "sphinx.ext.autosummary",
     "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
     "sphinxcontrib.bibtex",
     "myst_nb",
     "sphinx_rtd_theme",
@@ -62,11 +60,11 @@
 external_toc_path = "_toc.yml"  # optional, default: _toc.yml
 external_toc_exclude_missing = False  # optional, default: False
 
-# + [markdown]
-# Citation styling
-# -
+# Include TODOs
+todo_include_todos = True
 
 
+# Citation styling
 def bracket_style() -> BracketStyle:
     """Custom citation parenthesis style."""
     return BracketStyle(
@@ -156,7 +154,6 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ("py:class", "pandas.core.frame.DataFrame"),
 ]
 
-# +
 intersphinx_mapping = {
     "pytest": ("https://docs.pytest.org/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
@@ -166,7 +163,6 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
     "marshmallow": ("https://marshmallow.readthedocs.io/en/stable/", None),
 }
-# -
 
 
 autodoc_default_flags = ["members"]
@@ -213,7 +209,6 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 # html_theme = 'sphinx_material'
 html_theme = "sphinx_rtd_theme"
 
-# +
 html_theme_options = {
     "logo_only": True,
     "version_selector": True,
@@ -227,7 +222,6 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     "includehidden": True,
     "titles_only": False,
 }
-# -
 
 
 # Add any paths that contain custom static files (such as style sheets) here,

pyrealm/constants/__init__.py

@@ -7,12 +7,14 @@
 * :class:`~pyrealm.constants.isotope_const.IsotopesConst`
 * :class:`~pyrealm.constants.pmodel_const.PModelConst`
 * :class:`~pyrealm.constants.tmodel_const.TModelTraits`
+* :class:`~pyrealm.constants.phenology_const.PhenologyConst`
 """  # noqa: D205, D415
 
 from pyrealm.constants.base import ConstantsClass
 from pyrealm.constants.competition_const import C3C4Const
 from pyrealm.constants.core_const import CoreConst
 from pyrealm.constants.isotope_const import IsotopesConst
+from pyrealm.constants.phenology_const import PhenologyConst
 from pyrealm.constants.pmodel_const import PModelConst
 from pyrealm.constants.tmodel_const import TModelTraits
 
@@ -22,5 +24,6 @@
     "CoreConst",
     "IsotopesConst",
     "PModelConst",
+    "PhenologyConst",
     "TModelTraits",
 ]

pyrealm/constants/phenology_const.py

@@ -0,0 +1,26 @@
+"""The phenology_const module TODO."""
+
+from dataclasses import dataclass
+
+from pyrealm.constants import ConstantsClass
+
+
+@dataclass(frozen=True)
+class PhenologyConst(ConstantsClass):
+    r"""Model constants for the phenology module class.
+
+    This data class holds constants needed for the FaparLimitation and other classes
+    in the phenology module.
+    """
+
+    z: float = 12.227
+    """z accounts for the costs of building and maintaining leaves and the total
+       below-ground allocation required to support the nutrient demand of those
+       leaves. [mol m^{-2} year^{-1}]."""
+
+    k: float = 0.5
+    """Light extinction coefficient."""
+
+    f0_coefficients = (0.65, 0.604169, 1.9)
+    """Coefficients to calculate f_0, the ratio of annual total transpiration of annual 
+    total precipitation."""

pyrealm/phenology/__init__.py

@@ -0,0 +1 @@
+"""The phenology module."""