Merge pull request #322 from ImperialCollegeLondon/feature/plants_model

Feature/plants model

docs/source/api/animals/dummy_plants.md → docs/source/api/animals/plant_resources.md

@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.dummy_plants` module
+# API for the {mod}`~virtual_rainforest.models.animals.plant_resources` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.dummy_plants
+.. automodule:: virtual_rainforest.models.animals.plant_resources
     :autosummary:
     :members:
     :exclude-members: model_name

docs/source/data_recipes/plant_dummy.md

@@ -26,15 +26,18 @@ section provides a recipe to create such an input conform with the dummy data fo
 import numpy as np
 from xarray import DataArray, Dataset
 
-# set layer roles
-layer_roles = ["above"] + 10 * ["canopy"] + ["subcanopy"] + ["surface"] + 2 * ["soil"]
+from virtual_rainforest.core.utils import set_layer_roles
 
-plant_dummy = {}
+layer_roles = set_layer_roles(10, [-0.5, -1.0])
+
+# Compile a dataset
+
+plant_dummy_dataset = Dataset()
 layer_heights = np.repeat(
         a=[32.0, 30.0, 20.0, 10.0, np.nan, 1.5, 0.1, -0.1, -1.0],
         repeats=[1, 1, 1, 1, 7, 1, 1, 1, 1],
     )
-plant_dummy["layer_heights"] = DataArray(
+plant_dummy_dataset["layer_heights"] = DataArray(
         np.broadcast_to(layer_heights, (81, 15)).T,
         dims=["layers", "cell_id"],
         coords={
@@ -46,7 +49,7 @@ plant_dummy["layer_heights"] = DataArray(
     )
 
 leaf_area_index = np.repeat(a=[np.nan, 1.0, np.nan], repeats=[1, 3, 11])
-plant_dummy["leaf_area_index"] = DataArray(
+plant_dummy_dataset["leaf_area_index"] = DataArray(
         np.broadcast_to(leaf_area_index, (81, 15)).T,
         dims=["layers", "cell_id"],
         coords={
@@ -57,8 +60,21 @@ plant_dummy["leaf_area_index"] = DataArray(
         name="leaf_area_index",
 )
 
+layer_leaf_mass = np.repeat(a=[np.nan, 10000.0, np.nan], repeats=[1, 3, 11])
+plant_dummy_dataset["layer_leaf_mass"] = DataArray(
+        np.broadcast_to(leaf_area_index, (81, 15)).T,
+        dims=["layers", "cell_id"],
+        coords={
+            "layers": np.arange(15),
+            "layer_roles": ("layers", layer_roles),
+            "cell_id": np.arange(0,81),
+        },
+        name="layer_leaf_mass",
+)
+
+
 evapotranspiration = np.repeat(a=[np.nan, 20.0, np.nan], repeats=[1, 3, 11])
-plant_dummy["evapotranspiration"] = DataArray(
+plant_dummy_dataset["evapotranspiration"] = DataArray(
         np.broadcast_to(evapotranspiration, (81, 15)).T,
         dims=["layers", "cell_id"],
         coords={
@@ -68,8 +84,6 @@ plant_dummy["evapotranspiration"] = DataArray(
         },
         name="evapotranspiration",
 )
-# Make dictionary of DataArrays into a Dataset
-plant_dummy_dataset = Dataset(plant_dummy)
 
 plant_dummy_dataset
 ```

docs/source/index.md

@@ -115,7 +115,7 @@ team.
   Animal Scaling Functions <api/animals/scaling_functions.md> 
   Animal Constants <api/animals/constants.md> 
   Animal Decay <api/animals/decay.md> 
-  Animal Dummy Plants and Soils <api/animals/dummy_plants.md> 
+  Animal Plant Resources <api/animals/plant_resources.md> 
   Litter Overview <api/litter.md>
   Litter Model <api/litter/litter_model.md>
   Litter Pools <api/litter/litter_pools.md>

tests/conftest.py

@@ -401,76 +401,3 @@ def dummy_climate_data(layer_roles_fixture):
     )
 
     return data
-
-
-@pytest.fixture
-def functional_group_list_instance(shared_datadir):
-    """Fixture for an animal functional group used in tests."""
-    from virtual_rainforest.models.animals.functional_group import (
-        import_functional_groups,
-    )
-
-    file = shared_datadir / "example_functional_group_import.csv"
-    fg_list = import_functional_groups(file)
-
-    return fg_list
-
-
-@pytest.fixture
-def animal_model_instance(data_instance, functional_group_list_instance):
-    """Fixture for an animal model object used in tests."""
-    from pint import Quantity
-
-    from virtual_rainforest.models.animals.animal_model import AnimalModel
-
-    return AnimalModel(data_instance, Quantity("1 day"), functional_group_list_instance)
-
-
-@pytest.fixture
-def animal_community_instance(functional_group_list_instance, animal_model_instance):
-    """Fixture for an animal community used in tests."""
-    from virtual_rainforest.models.animals.animal_communities import AnimalCommunity
-
-    return AnimalCommunity(
-        functional_group_list_instance,
-        0,
-        [0, 1, 3],
-        animal_model_instance.get_community_by_key,
-    )
-
-
-@pytest.fixture
-def herbivore_functional_group_instance(shared_datadir):
-    """Fixture for an animal functional group used in tests."""
-    from virtual_rainforest.models.animals.functional_group import (
-        import_functional_groups,
-    )
-
-    file = shared_datadir / "example_functional_group_import.csv"
-    fg_list = import_functional_groups(file)
-
-    return fg_list[3]
-
-
-@pytest.fixture
-def herbivore_cohort_instance(herbivore_functional_group_instance):
-    """Fixture for an animal cohort used in tests."""
-    from virtual_rainforest.models.animals.animal_cohorts import AnimalCohort
-
-    return AnimalCohort(herbivore_functional_group_instance, 10000.0, 1)
-
-
-@pytest.fixture
-def excrement_instance():
-    """Fixture for a soil pool used in tests."""
-    from virtual_rainforest.models.animals.decay import ExcrementPool
-
-    return ExcrementPool(100000.0, 0.0)
-
-
-@pytest.fixture
-def plant_instance():
-    """Fixture for a plant community used in tests."""
-    from virtual_rainforest.models.animals.dummy_plants import PlantCommunity
-
-    return PlantCommunity(10000.0)

tests/models/animals/conftest.py

@@ -0,0 +1,98 @@
+"""Collection of fixtures to assist the animal model testing scripts."""
+
+import numpy as np
+import pytest
+import xarray
+
+
+@pytest.fixture
+def plant_data_instance():
+    """Fixture returning a simple data instance containing plant resource data."""
+    from virtual_rainforest.core.data import Data
+    from virtual_rainforest.core.grid import Grid
+
+    # Populate data with a layers x cell id layer_leaf_mass array
+    data = Data(grid=Grid(cell_nx=3, cell_ny=3))
+    leaf_mass = np.full((15, 9), fill_value=np.nan)
+    leaf_mass[1:4, :] = 10000
+    data["layer_leaf_mass"] = xarray.DataArray(
+        data=leaf_mass, dims=["layers", "cell_id"]
+    )
+
+    return data
+
+
+@pytest.fixture
+def functional_group_list_instance(shared_datadir):
+    """Fixture for an animal functional group used in tests."""
+    from virtual_rainforest.models.animals.functional_group import (
+        import_functional_groups,
+    )
+
+    file = shared_datadir / "example_functional_group_import.csv"
+    fg_list = import_functional_groups(file)
+
+    return fg_list
+
+
+@pytest.fixture
+def animal_model_instance(data_instance, functional_group_list_instance):
+    """Fixture for an animal model object used in tests."""
+    from pint import Quantity
+
+    from virtual_rainforest.models.animals.animal_model import AnimalModel
+
+    return AnimalModel(data_instance, Quantity("1 day"), functional_group_list_instance)
+
+
+@pytest.fixture
+def animal_community_instance(
+    functional_group_list_instance, animal_model_instance, plant_data_instance
+):
+    """Fixture for an animal community used in tests."""
+    from virtual_rainforest.models.animals.animal_communities import AnimalCommunity
+
+    return AnimalCommunity(
+        functional_groups=functional_group_list_instance,
+        data=plant_data_instance,
+        community_key=4,
+        neighbouring_keys=[1, 3, 5, 7],
+        get_destination=animal_model_instance.get_community_by_key,
+    )
+
+
+@pytest.fixture
+def herbivore_functional_group_instance(shared_datadir):
+    """Fixture for an animal functional group used in tests."""
+    from virtual_rainforest.models.animals.functional_group import (
+        import_functional_groups,
+    )
+
+    file = shared_datadir / "example_functional_group_import.csv"
+    fg_list = import_functional_groups(file)
+
+    return fg_list[3]
+
+
+@pytest.fixture
+def herbivore_cohort_instance(herbivore_functional_group_instance):
+    """Fixture for an animal cohort used in tests."""
+    from virtual_rainforest.models.animals.animal_cohorts import AnimalCohort
+
+    return AnimalCohort(herbivore_functional_group_instance, 10000.0, 1)
+
+
+@pytest.fixture
+def excrement_instance():
+    """Fixture for a soil pool used in tests."""
+    from virtual_rainforest.models.animals.decay import ExcrementPool
+
+    return ExcrementPool(100000.0, 0.0)
+
+
+@pytest.fixture
+def plant_instance(plant_data_instance):
+    """Fixture for a plant community used in tests."""
+    from virtual_rainforest.models.animals.plant_resources import PlantResources
+
+    return PlantResources(data=plant_data_instance, cell_id=4)

tests/models/animals/test_animal_cohorts.py

@@ -213,13 +213,13 @@ def test_forage_cohort(
         from virtual_rainforest.models.animals.animal_cohorts import AnimalCohort
         from virtual_rainforest.models.animals.animal_traits import DietType
         from virtual_rainforest.models.animals.decay import CarcassPool, ExcrementPool
-        from virtual_rainforest.models.animals.dummy_plants import PlantCommunity
+        from virtual_rainforest.models.animals.plant_resources import PlantResources
 
         # Mocking the eat method of AnimalCohort
         mock_eat = mocker.patch.object(AnimalCohort, "eat")
 
         # Instances
-        plant_list_instance = [mocker.MagicMock(spec=PlantCommunity)]
+        plant_list_instance = [mocker.MagicMock(spec=PlantResources)]
         animal_list_instance = [
             mocker.MagicMock(spec=AnimalCohort) for _ in range(3)
         ]  # Assuming 3 animal cohorts

tests/models/animals/test_animal_communities.py

@@ -5,16 +5,17 @@
 
 @pytest.fixture
 def animal_community_destination_instance(
-    functional_group_list_instance, animal_model_instance
+    functional_group_list_instance, animal_model_instance, plant_data_instance
 ):
     """Fixture for an animal community used in tests."""
     from virtual_rainforest.models.animals.animal_communities import AnimalCommunity
 
     return AnimalCommunity(
-        functional_group_list_instance,
-        1,
-        [0, 1, 2, 4],
-        animal_model_instance.get_community_by_key,
+        functional_groups=functional_group_list_instance,
+        data=plant_data_instance,
+        community_key=4,
+        neighbouring_keys=[1, 3, 5, 7],
+        get_destination=animal_model_instance.get_community_by_key,
     )
 
 

tests/models/animals/test_animal_model.py

@@ -102,7 +102,7 @@ def test_animal_model_initialization(
 )
 def test_generate_animal_model(
     caplog,
-    data_instance,
+    plant_data_instance,
     config,
     time_interval,
     raises,
@@ -114,7 +114,7 @@ def test_generate_animal_model(
     # Check whether model is initialised (or not) as expected
     with raises:
         model = AnimalModel.from_config(
-            data_instance,
+            plant_data_instance,
             config,
             pint.Quantity(config["core"]["timing"]["update_interval"]),
         )
@@ -198,13 +198,13 @@ def test_update_method_sequence(data_instance, functional_group_list_instance):
 
 
 def test_update_method_time_index_argument(
-    data_instance, functional_group_list_instance
+    plant_data_instance, functional_group_list_instance
 ):
     """Test update to ensure the time index argument does not create an error."""
     from virtual_rainforest.models.animals.animal_model import AnimalModel
 
     model = AnimalModel(
-        data_instance, pint.Quantity("1 week"), functional_group_list_instance
+        plant_data_instance, pint.Quantity("1 week"), functional_group_list_instance
     )
 
     time_index = 5

tests/models/animals/test_dummy_plants.py → tests/models/animals/test_plant_resources.py

@@ -1,27 +1,9 @@
-"""Test module for dummy_plants.py."""
+"""Test module for plant_resources.py."""
 
-import pytest
 
-
-class TestPlantCommunity:
+class TestPlantResources:
     """Test Plant class."""
 
-    @pytest.mark.parametrize(
-        "initial, final",
-        [(182000000000.0, 182000000000.0), (10000.0, 19999.999450), (0.0, 0.0)],
-    )
-    def test_grow(self, plant_instance, initial, final):
-        """Testing grow at 100%, 50%, and 0% maximum energy."""
-        plant_instance.stored_energy = initial
-        plant_instance.grow()
-        assert plant_instance.stored_energy == pytest.approx(final, rel=1e-6)
-
-    def test_die(self, plant_instance):
-        """Testing die."""
-        assert plant_instance.is_alive
-        plant_instance.die()
-        assert not plant_instance.is_alive
-
     def test_get_eaten(
         self, plant_instance, herbivore_cohort_instance, excrement_instance
     ):