Merge pull request #370 from ImperialCollegeLondon/368-remove-outdate…

…d-t-model-module

Remove outdated T Model module

docs/source/_toc.yml

@@ -36,8 +36,6 @@ subtrees:
         - file: users/demography/crown.md
         - file: users/demography/community.md
         - file: users/demography/canopy.md
-  - file: users/tmodel/tmodel.md
-  - file: users/tmodel/canopy.md
   - file: users/splash.md
   - file: users/constants.md
   - file: users/hygro.md 

docs/source/api/demography_api.md

@@ -46,10 +46,10 @@ language_info:
     :members:
 ```
 
-## The {mod}`~pyrealm.demography.t_model_functions` module
+## The {mod}`~pyrealm.demography.tmodel` module
 
 ```{eval-rst}
-.. automodule:: pyrealm.demography.t_model_functions
+.. automodule:: pyrealm.demography.tmodel
     :autosummary:
     :members:
 ```

docs/source/index.md

@@ -30,18 +30,27 @@ following modules:
 
 ## Module overview
 
+The `core` module
+: Contains fundamental utilities and physics functionality shared across the
+  package, including the [hygro](users/hygro) and the utilities submodules.
+
 The `pmodel` module
 : Fitting the [P Model](users/pmodel/module_overview), which is an ecophysiological
   model of optimal carbon dioxide uptake by plants {cite:p}`Prentice:2014bc,
   Wang:2017go,Stocker:2020dh`, along with various extensions.
 
-The `tmodel` module
-: Estimating plant allocation of gross primary productivity to growth and respiration,
-  using the [T Model](users/tmodel/tmodel) {cite:p}`Li:2014bc`.
-
-The `core` module
-: Contains fundamental utilities and physics functionality shared across the
-  package, including the [hygro](users/hygro) and the utilities submodules.
+The `splash` module
+: Fits the [SPLASH v1 model](users/splash.md), which can be used to
+  estimate soil moisture, actual evapotranspiration and soil runoff from daily
+  temperature, precipitation and sunshine data {cite:p}`davis:2017a`.
+
+The `demography` module
+: Provides functionality for [modelling plant allocation and growth and
+  demography](users/demography/module_overview.md), including classes to represent plant
+  functional types, cohorts and communities. This module includes an implementation of
+  the T Model for estimating plant allocation of gross primary productivity to growth
+  and respiration {cite:p}`Li:2014bc`. This module is still in active development but a
+  lot of initial functionality is present.
 
 ## Indices and tables
 

docs/source/users/demography/canopy.md

@@ -43,7 +43,7 @@ from pyrealm.demography.flora import PlantFunctionalType, Flora
 from pyrealm.demography.community import Cohorts, Community
 from pyrealm.demography.crown import CrownProfile, get_crown_xy
 from pyrealm.demography.canopy import Canopy
-from pyrealm.demography.t_model_functions import StemAllometry
+from pyrealm.demography.tmodel import StemAllometry
 ```
 
 The `canopy` module in `pyrealm` is used to calculate a model of the light environment

docs/source/users/demography/crown.md

@@ -45,7 +45,7 @@ from pyrealm.demography.flora import (
     Flora,
 )
 
-from pyrealm.demography.t_model_functions import (
+from pyrealm.demography.tmodel import (
     calculate_dbh_from_height,
     StemAllometry,
 )
@@ -198,7 +198,7 @@ profiles for PFTs. It requires:
 
 * a {class}`~pyrealm.demography.flora.Flora` instance providing a set of PFTs to be
   compared,
-* a {class}`~pyrealm.demography.t_model_functions.StemAllometry` instance setting the
+* a {class}`~pyrealm.demography.tmodel.StemAllometry` instance setting the
   specific stem sizes for the profile, and
 * a set of heights at which to estimate the profile variables
 
@@ -226,7 +226,7 @@ flora.to_pandas()[["name", "h_max", "ca_ratio", "m", "n", "f_g", "q_m", "z_max_p
 
 The next section of code generates the `StemAllometry` to use for the profiles.
 The T Model requires DBH to define stem size - here the
-{meth}`~pyrealm.demography.t_model_functions.calculate_dbh_from_height` function
+{meth}`~pyrealm.demography.tmodel.calculate_dbh_from_height` function
 is used to back-calculate the required DBH values to give three stems with similar
 heights that are near the maximum height for each PFT.
 

docs/source/users/demography/t_model.md

@@ -36,7 +36,7 @@ import numpy as np
 import pandas as pd
 
 from pyrealm.demography.flora import PlantFunctionalType, Flora
-from pyrealm.demography.t_model_functions import StemAllocation, StemAllometry
+from pyrealm.demography.tmodel import StemAllocation, StemAllometry
 ```
 
 To generate predictions under the T Model, we need a Flora object providing the
@@ -55,7 +55,7 @@ flora = Flora([short_pft, medium_pft, tall_pft])
 ## Stem allometry
 
 We can visualise how the stem size, canopy size and various masses of PFTs change with
-stem diameter by using the {class}`~pyrealm.demography.t_model_functions.StemAllometry`
+stem diameter by using the {class}`~pyrealm.demography.tmodel.StemAllometry`
 class. Creating a `StemAllometry` instance needs an existing `Flora` instance and an
 array of values for diameter at breast height (DBH, metres). The returned class contains
 the predictions of the T Model for:
@@ -77,7 +77,7 @@ for each PFT. This then calculates a single estimate at the given size for each
 single_allometry = StemAllometry(stem_traits=flora, at_dbh=np.array([0.1, 0.1, 0.1]))
 ```
 
-The {meth}`~pyrealm.demography.t_model_functions.StemAllometry` class provides the
+The {meth}`~pyrealm.demography.tmodel.StemAllometry` class provides the
 {meth}`~pyrealm.demography.core.PandasExporter.to_pandas()` method to export the stem
 data for data exploration.
 
@@ -124,7 +124,7 @@ for ax, (var, ylab) in zip(axes.flatten(), plot_details):
 ```
 
 The {meth}`~pyrealm.demography.core.PandasExporter.to_pandas()` method of the
-{meth}`~pyrealm.demography.t_model_functions.StemAllometry` class can still be used, but
+{meth}`~pyrealm.demography.tmodel.StemAllometry` class can still be used, but
 the values are stacked into columns along with a index showing the different cohorts.
 
 ```{code-cell} ipython3
@@ -135,7 +135,7 @@ allometries.to_pandas()
 
 The T Model also predicts how potential GPP will be allocated to respiration, turnover
 and growth for stems with a given PFT and allometry using the
-{meth}`~pyrealm.demography.t_model_functions.StemAllometry` class. Again, a single
+{meth}`~pyrealm.demography.tmodel.StemAllometry` class. Again, a single
 value can be provided to get a single estimate of the allocation model for each stem:
 
 ```{code-cell} ipython3
@@ -146,7 +146,7 @@ single_allocation
 ```
 
 The {meth}`~pyrealm.demography.core.PandasExporter.to_pandas()` method of the
-{meth}`~pyrealm.demography.t_model_functions.StemAllocation` class can be used to
+{meth}`~pyrealm.demography.tmodel.StemAllocation` class can be used to
 export data for exploration.
 
 ```{code-cell} ipython3
@@ -229,7 +229,7 @@ fig.delaxes(axes[-1])
 ```
 
 As before, the {meth}`~pyrealm.demography.core.PandasExporter.to_pandas()` method of the
-{meth}`~pyrealm.demography.t_model_functions.StemAllometry` classs can be used to export
+{meth}`~pyrealm.demography.tmodel.StemAllometry` classs can be used to export
 the data for each stem:
 
 ```{code-cell} ipython3