Feature/separate hydrology

docs/source/api/abiotic_simple/simple_regression.md → docs/source/api/abiotic_simple/microclimate.md

@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-#  API for the {mod}`~virtual_rainforest.models.abiotic_simple.simple_regression` module
+#  API for the {mod}`~virtual_rainforest.models.abiotic_simple.microclimate` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.abiotic_simple.simple_regression
+.. automodule:: virtual_rainforest.models.abiotic_simple.microclimate
     :autosummary:
     :members:
     :special-members: __init__

docs/source/api/hydrology.md

@@ -0,0 +1,21 @@
+---
+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 reference for `hydrology` modules
+
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.hydrology
+```

docs/source/api/hydrology/hydrology_constants.md

@@ -0,0 +1,24 @@
+---
+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 for the {mod}`~virtual_rainforest.models.hydrology.hydrology_constants` module
+
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.hydrology.hydrology_constants
+    :autosummary:
+    :members:
+    :special-members: __init__
+```

docs/source/api/hydrology/hydrology_model.md

@@ -0,0 +1,25 @@
+---
+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
+---
+
+<!-- markdownlint-disable-next-line  MD013 -->
+# API documentation for the {mod}`~virtual_rainforest.models.hydrology.hydrology_model` module
+
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.hydrology.hydrology_model
+    :autosummary:
+    :members:
+    :exclude-members: model_name
+```

docs/source/index.md

@@ -95,7 +95,10 @@ team.
   Soil Constants <api/soil/constants.md>
   Abiotic Simple Overview <api/abiotic_simple.md>
   Abiotic Simple Model <api/abiotic_simple/abiotic_simple_model.md>
-  Abiotic Simple Regression <api/abiotic_simple/simple_regression.md>
+  Abiotic Simple Microclimate <api/abiotic_simple/microclimate.md>
+  Abiotic Hydrology Overview <api/hydrology.md>
+  Abiotic Hydrology Model <api/hydrology/hydrology_model.md>
+  Abiotic Hydrology Constants <api/hydrology/hydrology_constants.md>
   Abiotic Overview <api/abiotic.md>
   Abiotic Model <api/abiotic/abiotic_model.md>
   Abiotic Tools <api/abiotic/abiotic_tools.md>

docs/source/virtual_rainforest/module_overview.md

@@ -119,8 +119,8 @@ the Virtual Rainforest in high temporal resolution or for representative days pe
 ### Simple Abiotic Model
 
 The Simple Abiotic Model is a one-column model that operates on a grid cell basis and
-does not consider horizontal exchange of energy, water, and momentum. The model uses
-linear regressions from {cite}`hardwick_relationship_2015` and
+does not consider horizontal exchange of energy, atmospheric water, and momentum.
+The model uses linear regressions from {cite}`hardwick_relationship_2015` and
 {cite}`jucker_canopy_2018` to predict
 atmospheric temperature, relative humidity, and vapour pressure deficit
 at ground level (2m) given the above canopy conditions and leaf area index of
@@ -130,6 +130,15 @@ level prediction. Soil temperature is interpolated between the surface layer and
 temperature at 1 m depth which equals the mean annual temperature.
 The model also provides a constant vertical profile of atmospheric pressure and
 atmospheric $\ce{CO_{2}}$.
+
+### Simple Hydrology Model
+
+The simple version of the Hydrology Model is a one-column model that operates on a grid
+cell basis and does not consider horizontal exchange of water. We placed this
+functionality in a separate model in order to allow easy replacement with a different
+hydrology model, for example a process-based model that runs on a daily time step and
+returns monthly statistics to the data object for other modules to use.
+
 Soil moisture and surface runoff are calculated for each grid cell with a simple bucket
 model based on {cite}`davis_simple_2017`; vertical flow and horizontal flow (above and
 below ground) between grid cells are currently not implemented.

tests/models/abiotic_simple/test_abiotic_simple_model.py

@@ -1,7 +1,7 @@
 """Test module for abiotic_simple.abiotic_simple_model.py."""
 
 from contextlib import nullcontext as does_not_raise
-from logging import DEBUG, ERROR, INFO
+from logging import DEBUG, INFO
 
 import numpy as np
 import pint
@@ -10,17 +10,15 @@
 from xarray import DataArray
 
 from tests.conftest import log_check
-from virtual_rainforest.core.exceptions import InitialisationError
 from virtual_rainforest.models.abiotic_simple.abiotic_simple_model import (
     AbioticSimpleModel,
 )
 
 
 @pytest.mark.parametrize(
-    "ini_soil_moisture,raises,expected_log_entries",
+    "raises,expected_log_entries",
     [
         (
-            0.5,
             does_not_raise(),
             (
                 (
@@ -37,10 +35,6 @@
                     "abiotic_simple model: required var 'atmospheric_pressure_ref' "
                     "checked",
                 ),
-                (
-                    DEBUG,
-                    "abiotic_simple model: required var 'precipitation' checked",
-                ),
                 (
                     DEBUG,
                     "abiotic_simple model: required var 'atmospheric_co2_ref' checked",
@@ -60,32 +54,11 @@
                 ),
             ),
         ),
-        (
-            -0.5,
-            pytest.raises(InitialisationError),
-            (
-                (
-                    ERROR,
-                    "The initial soil moisture has to be between 0 and 1!",
-                ),
-            ),
-        ),
-        (
-            DataArray([50, 30, 20]),
-            pytest.raises(InitialisationError),
-            (
-                (
-                    ERROR,
-                    "The initial soil moisture must be a float!",
-                ),
-            ),
-        ),
     ],
 )
 def test_abiotic_simple_model_initialization(
     caplog,
     dummy_climate_data,
-    ini_soil_moisture,
     raises,
     expected_log_entries,
     layer_roles_fixture,
@@ -101,7 +74,6 @@ def test_abiotic_simple_model_initialization(
             pint.Quantity("1 week"),
             soil_layers,
             canopy_layers,
-            ini_soil_moisture,
         )
 
         # In cases where it passes then checks that the object has the right properties
@@ -116,7 +88,6 @@ def test_abiotic_simple_model_initialization(
         assert model.model_name == "abiotic_simple"
         assert repr(model) == "AbioticSimpleModel(update_interval = 1 week)"
         assert model.layer_roles == layer_roles_fixture
-        assert model.initial_soil_moisture == ini_soil_moisture
 
     # Final check that expected logging entries are produced
     log_check(caplog, expected_log_entries)
@@ -143,9 +114,6 @@ def test_abiotic_simple_model_initialization(
                         "canopy_layers": 10,
                     },
                 },
-                "abiotic_simple": {
-                    "initial_soil_moisture": 0.5,
-                },
             },
             pint.Quantity("1 week"),
             does_not_raise(),
@@ -169,10 +137,6 @@ def test_abiotic_simple_model_initialization(
                     "abiotic_simple model: required var 'atmospheric_pressure_ref' "
                     "checked",
                 ),
-                (
-                    DEBUG,
-                    "abiotic_simple model: required var 'precipitation' checked",
-                ),
                 (
                     DEBUG,
                     "abiotic_simple model: required var 'atmospheric_co2_ref' checked",
@@ -234,9 +198,6 @@ def test_generate_abiotic_simple_model(
                         "canopy_layers": 10,
                     },
                 },
-                "abiotic_simple": {
-                    "initial_soil_moisture": 0.5,
-                },
             },
             pint.Quantity("1 week"),
         )
@@ -261,24 +222,23 @@ def test_setup(
 
     model.setup()
 
-    soil_moisture_values = np.repeat(a=[np.nan, 0.5], repeats=[13, 2])
-
     xr.testing.assert_allclose(
-        dummy_climate_data["soil_moisture"],
+        model.data["soil_temperature"],
         DataArray(
-            np.broadcast_to(soil_moisture_values, (3, 15)).T,
+            np.full((15, 3), np.nan),
             dims=["layers", "cell_id"],
             coords={
-                "layers": np.arange(15),
-                "layer_roles": ("layers", layer_roles_fixture),
+                "layers": np.arange(0, 15),
+                "layer_roles": (
+                    "layers",
+                    model.layer_roles,
+                ),
                 "cell_id": [0, 1, 2],
             },
-            name="soil_moisture",
         ),
     )
-
     xr.testing.assert_allclose(
-        dummy_climate_data["vapour_pressure_deficit_ref"],
+        model.data["vapour_pressure_deficit_ref"],
         DataArray(
             np.full((3, 3), 0.141727),
             dims=["cell_id", "time_index"],