Class reference type, forgot to add new animals conftest.py

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)

virtual_rainforest/models/animals/plant_resources.py

@@ -13,7 +13,7 @@ class PlantResources:
     """A class implementing the Resource protocol for plant data.
 
     This class acts as the interface between plant model data stored in the core data
-    object using the :class:`~virtual_rainforest.models.animals.protocols.Resources`
+    object using the :class:`~virtual_rainforest.models.animals.protocols.Resource`
     protocol.
 
     At present, it only exposes a single resource - the total leaf mass of the entire