Merge pull request #69 from ImperialCollegeLondon/feature/splash_v1

Implementation of SPLASH 1.0 in pyrealm

README.md

@@ -18,6 +18,9 @@ The `pyrealm` package currently includes:
   and carbon isotope fractionation.
 * The T Model of the allocation of gross primary productivity to estimate net primary
   productivity and hence plant growth.
+* The SPLASH model for calculating soil moisture and actual evapotranspiration.
+* A suite of core physics functions and other utilities used to support the modules
+  above.
 
 For more details, see the package website:
 [https://pyrealm.readthedocs.io/](https://pyrealm.readthedocs.io/).

docs/source/_toc.yml

@@ -26,6 +26,7 @@ subtrees:
         - file: users/pmodel/c3c4model.md
         - file: users/pmodel/isotopic_discrimination.md
   - file: users/tmodel/tmodel.md
+  - file: users/splash.md
   - file: users/constants.md
   - file: users/hygro.md 
 

docs/source/api/core_api.md

@@ -21,10 +21,10 @@ kernelspec:
     :members:
 ```
 
-## The {mod}`~pyrealm.core.utilities` submodule
+## The {mod}`~pyrealm.core.calendar` submodule
 
 ```{eval-rst}
-.. automodule:: pyrealm.core.utilities
+.. automodule:: pyrealm.core.calendar
     :autosummary:
     :members:
 ```
@@ -45,6 +45,14 @@ kernelspec:
     :members:
 ```
 
+## The {mod}`~pyrealm.core.utilities` submodule
+
+```{eval-rst}
+.. automodule:: pyrealm.core.utilities
+    :autosummary:
+    :members:
+```
+
 ## The {mod}`~pyrealm.core.water` submodule
 
 ```{eval-rst}

docs/source/api/splash_api.md

@@ -0,0 +1,42 @@
+---
+jupytext:
+  formats: md:myst
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.13.8
+kernelspec:
+  display_name: Python 3
+  language: python
+  name: pyrealm_python3
+---
+
+
+# The {mod}`~pyrealm.splash` module
+
+```{eval-rst}
+.. automodule:: pyrealm.splash
+    :members:
+```
+
+## The DailySolarFluxes submodule
+
+```{eval-rst}
+.. automodule:: pyrealm.splash.solar
+    :members:
+```
+
+## The DailyEvapFluxes submodule
+
+```{eval-rst}
+.. automodule:: pyrealm.splash.evap
+    :members:
+```
+
+## The SplashModel submodule
+
+```{eval-rst}
+.. automodule:: pyrealm.splash.splash
+    :members:
+```

docs/source/conf.py

@@ -82,13 +82,62 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
 
 
 # Cross-reference checking
+# TODO - find some better solution than this to all of these bizarre cross reference
+#        problems.
 nitpicky = True
 nitpick_ignore = [
     ("py:class", "numpy._typing._array_like._ScalarType_co"),
     ("py:class", "numpy._typing._generic_alias.ScalarType"),
     ("py:class", "numpy.float32"),
     ("py:class", "numpy.timedelta64"),
+    ("py:class", "numpy.ndarray"),
+    ("py:class", "numpy.dtype"),
+    ("py:class", "numpy.dtype[+ScalarType]"),
+    ("py:class", "numpy.typing.NDArray"),
+    ("py:class", "dataclasses.InitVar"),
+    (
+        "py:class",
+        "dataclasses.InitVar[numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]]]",
+    ),
+    (
+        "py:class",
+        "dataclasses.InitVar[numpy.ndarray[typing.Any, numpy.dtype[+_ScalarType_co]]]",
+    ),
+    (
+        "py:class",
+        (
+            "tuple[numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]], "
+            "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]]]"
+        ),
+    ),
+    (
+        "py:obj",
+        (
+            "typing.Union[~numpy.ndarray[~typing.Any, "
+            "~numpy.dtype[~numpy._typing._generic_alias.ScalarType]], "
+            "tuple[numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]], "
+            "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]], "
+            "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]]]]"
+        ),
+    ),
+    (
+        "py:class",
+        (
+            "tuple[numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]], "
+            "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]], "
+            "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]]]"
+        ),
+    ),
+    (
+        "py:class",
+        (
+            "tuple[numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]], "
+            "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]], "
+            "numpy.ndarray[typing.Any, numpy.dtype[+ScalarType]]]"
+        ),
+    ),
 ]
+
 intersphinx_mapping = {
     "pytest": ("https://docs.pytest.org/en/stable/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),

docs/source/index.md

@@ -28,8 +28,8 @@ The `tmodel` module
   using the [T Model](users/tmodel/tmodel) {cite:p}`Li:2014bc`.
 
 The `core` module
-: Contains fundamental utilities and physics functionality which is shared across the
-code base. Contains the [hygro](users/hygro) and the utilities submodules.
+: Contains fundamental utilities and physics functionality shared across the
+  package, including the [hygro](users/hygro) and the utilities submodules.
 
 ## Indices and tables