Minimal carbon pool model

docs/source/api/soil.md

@@ -16,13 +16,13 @@ kernelspec:
 
 # API reference for `soil` modules
 
-This page contains the detailed documentation of the functions and classes in the
-`virtual_rainforest.soil` modules.
+The {mod}`~virtual_rainforest.models.soil` module is one of the component models of the
+Virtual Rainforest. It is comprised of a number of submodules.
 
-## The {mod}`~virtual_rainforest.soil.model` module
+Each of the soil sub-modules has its own API reference page:
 
-```{eval-rst}
-.. automodule:: virtual_rainforest.soil.model
-    :autosummary:
-    :members:
-```
+* The {mod}`~virtual_rainforest.models.soil.model` submodule instantiates the SoilModel
+  class which consolidates the functionality of the soil module into a single class,
+  which the high level functions of the Virtual Rainforest can then make use of.
+* The {mod}`~virtual_rainforest.models.soil.carbon` provides a model for the soil carbon
+  cycle.

docs/source/api/soil/carbon.md

@@ -0,0 +1,23 @@
+---
+jupytext:
+  cell_metadata_filter: -all
+  formats: md:myst
+  main_language: python
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.13.8
+kernelspec:
+  display_name: vr_python3
+  language: python
+  name: vr_python3
+---
+
+# API documentation for the {mod}`~virtual_rainforest.soil.carbon` module
+
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.soil.carbon
+    :autosummary:
+    :members:
+```

docs/source/api/soil/model.md

@@ -0,0 +1,23 @@
+---
+jupytext:
+  cell_metadata_filter: -all
+  formats: md:myst
+  main_language: python
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.13.8
+kernelspec:
+  display_name: vr_python3
+  language: python
+  name: vr_python3
+---
+
+# API documentation for the {mod}`~virtual_rainforest.soil.model` module
+
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.soil.model
+    :autosummary:
+    :members:
+```

docs/source/index.md

@@ -86,8 +86,9 @@ team.
   File readers <api/core/readers.md>
   Core axes <api/core/axes.md>
   Base Model <api/core/model.md>
-  Soil Model <api/soil.md>
-
+  Soil Overview <api/soil.md>
+  Soil Model <api/soil/model.md>
+  Soil Carbon <api/soil/carbon.md>
 ```
 
 ```{eval-rst}
@@ -110,6 +111,7 @@ team.
   Docstring Style <development/documentation/docstring_style.md>
   API Generation <development/documentation/api_generation.md>
   Core Design <development/design/core.md>
+  Adding New Models <development/defining_new_models.md>
 ```
 
 ```{eval-rst}

docs/source/refs.bib

@@ -183,47 +183,26 @@ @article{Metcalfe2015
 }
 
 @article{cheng_wei_2021,
-  author       = {Cheng, Wei and
-                  Dan, Li and
-                  Deng, Xiangzheng and
-                  Feng, Jinming and
-                  Wang, Yongli and
-                  Peng, Jing and
-                  Tian, Jing and
-                  Qi, Wei and
-                  Liu, Zhu and
-                  Zheng, Xinqi and
-                  Zhou, Demin and
-                  Jiang, Sijian and
-                  Zhao, Haipeng and
-                  Wang, Xiaoyu},
-  title        = {{Global monthly distributions of atmospheric CO2 
-                   concentrations under the historical and future
-                   scenarios}},
-  month        = jun,
-  year         = 2021,
-  note         = {{The data records include 1 file Network Common 
-                   Data Form (NetCDF) format for CO2 distributions in
-                   historical period named
-                   CO2\_1deg\_month\_1850-2013.nc, and 8 files NetCDF
-                   format with the naming convention
-                   CO2\_SSP{XYY}\_2015\_2150.nc, where X and YY are the
-                   shared socioeconomic pathway and radiative forcing
-                   level at 2100, respectively, for CO2 distributions
-                   in the future scenarios. Each NetCDF file includes
-                   3 dimensions: time (month of the year expressed as
-                   days since the first day of 1850, n = 1968 and
-                   1632 for the historical and the future,
-                   respectively); latitude (Degrees North of the
-                   equator [cell centres], n = 180); longitude
-                   (Degrees East of the Prime Meridian [cell
-                   centres], n = 360). Each NetCDF file contains a
-                   monthly variable representing mole fraction of
-                   carbon dioxide in air (variable name: value in the
-                   historical file and CO2 in the future scenario
-                   files) with the unit ppm and the 1º × 1º
-                   resolution.}},
-  publisher    = {Zenodo},
-  doi          = {10.5281/zenodo.5021361},
-  url          = {https://doi.org/10.5281/zenodo.5021361}
+  author  = {Cheng, Wei and
+             Dan, Li and
+             Deng, Xiangzheng and
+             Feng, Jinming and
+             Wang, Yongli and
+             Peng, Jing and
+             Tian, Jing and
+             Qi, Wei and
+             Liu, Zhu and
+             Zheng, Xinqi and
+             Zhou, Demin and
+             Jiang, Sijian and
+             Zhao, Haipeng and
+             Wang, Xiaoyu},
+  title   = {{Global monthly distributions of atmospheric CO2 
+             concentrations under the historical and future
+             scenarios [Data set]}},
+  journal = {Zenodo},
+  month   = jun,
+  year    = 2021,
+  doi     = {10.5281/zenodo.5021361},
+  url     = {https://doi.org/10.5281/zenodo.5021361}
 }

tests/test_main.py

@@ -19,7 +19,7 @@
     select_models,
     vr_run,
 )
-from virtual_rainforest.soil.model import SoilModel
+from virtual_rainforest.models.soil.model import SoilModel
 
 from .conftest import log_check
 

tests/test_models.py

@@ -11,7 +11,7 @@
 from numpy import datetime64, timedelta64
 
 from virtual_rainforest.core.model import BaseModel, InitialisationError
-from virtual_rainforest.soil.model import SoilModel
+from virtual_rainforest.models.soil.model import SoilModel
 
 from .conftest import log_check