Animal-Plant piping class draft

tests/models/animals/conftest.py

@@ -787,6 +787,39 @@ def herbivore_cohort_instance(
     )
 
 
+@pytest.fixture
+def fungivore_functional_group_instance(shared_datadir, constants_instance):
+    """Fixture for an animal functional group used in tests."""
+    from virtual_ecosystem.models.animal.functional_group import (
+        import_functional_groups,
+    )
+
+    file = shared_datadir / "example_functional_group_import.csv"
+    fg_list = import_functional_groups(file, constants_instance)
+
+    return fg_list[16]
+
+
+@pytest.fixture
+def fungivore_cohort_instance(
+    fungivore_functional_group_instance,
+    animal_data_for_cohorts_instance,
+    constants_instance,
+):
+    """Fixture for an animal cohort used in tests."""
+    from virtual_ecosystem.models.animal.animal_cohorts import AnimalCohort
+
+    return AnimalCohort(
+        fungivore_functional_group_instance,
+        10000.0,
+        1,
+        10,
+        1,  # centroid
+        animal_data_for_cohorts_instance.grid,  # grid
+        constants_instance,
+    )
+
+
 @pytest.fixture
 def predator_functional_group_instance(shared_datadir, constants_instance):
     """Fixture for an animal functional group used in tests."""
@@ -1108,3 +1141,36 @@ def herbivory_waste_pool_instance():
     )
 
     return herbivory_waste
+
+
+@pytest.fixture
+def mushroom_instance(litter_soil_data_instance):
+    """Fixture for a single FungalFruitPool object."""
+    from virtual_ecosystem.models.animal.decay import (
+        FungalFruitPool,
+    )  # Adjust as needed
+
+    return FungalFruitPool(
+        cell_id=0,
+        data=litter_soil_data_instance,
+        cell_area=100.0,  # m²
+        c_n_ratio=25.0,
+        c_p_ratio=100.0,
+    )
+
+
+@pytest.fixture
+def mushroom_list_instance(litter_soil_data_instance):
+    """Fixture for multiple FungalFruitPool objects across grid cells."""
+    from virtual_ecosystem.models.animal.decay import FungalFruitPool
+
+    return [
+        FungalFruitPool(
+            cell_id=cell_id,
+            data=litter_soil_data_instance,
+            cell_area=100.0,
+            c_n_ratio=25.0,
+            c_p_ratio=100.0,
+        )
+        for cell_id in litter_soil_data_instance.grid.cell_id
+    ]

tests/models/animals/data/example_functional_group_import.csv

@@ -15,3 +15,4 @@ earthworm,invertebrate,detritus,ectothermic,terrestrial,iteroparous,direct,adult
 dung_beetle,invertebrate,waste,ectothermic,terrestrial,iteroparous,direct,adult,dung_beetle,uricotelic,none,soil_ground,0.0003,0.003, 0.005
 scavenging_mammal,mammal,carcasses,endothermic,terrestrial,iteroparous,direct,adult,scavenging_mammal,ureotelic,none,ground,2.0,20.0, 0.005
 detritivorous_insect,invertebrate,detritus,ectothermic,terrestrial,iteroparous,direct,adult,detritivorous_insect,uricotelic,none,soil_ground,0.0004,0.004, 0.005
+fungivorous_mammal,mammal,fungus,endothermic,terrestrial,iteroparous,direct,adult,fungivorous_mammal,ureotelic,none,soil_ground,1.0,10.0, 0.005

tests/models/animals/test_animal_cohorts.py

@@ -1864,14 +1864,15 @@ def test_delta_mass_excrement_scavenging_calls_forage_resource_list(
         assert result == {"carbon": 4.0, "nitrogen": 1.0, "phosphorus": 0.5}
 
     @pytest.mark.parametrize(
-        "cohort_instance, diet_type, plant_list, animal_list, expected_nutrient_gain,"
-        "delta_mass_mock",
+        "cohort_instance, diet_type, plant_list, animal_list, mushroom_list,"
+        " expected_nutrient_gain, delta_mass_mock",
         [
             (
                 "herbivore_cohort_instance",
                 "HERBIVORE",
                 "plant_list_instance",
                 [],
+                [],
                 {"carbon": 60.0, "nitrogen": 30.0, "phosphorus": 10.0},
                 "delta_mass_herbivory",
             ),
@@ -1880,10 +1881,21 @@ def test_delta_mass_excrement_scavenging_calls_forage_resource_list(
                 "CARNIVORE",
                 [],
                 "animal_list_instance",
+                [],
                 {"carbon": 120.0, "nitrogen": 60.0, "phosphorus": 20.0},
                 "delta_mass_predation",
             ),
+            (
+                "fungivore_cohort_instance",
+                "FUNGUS",
+                [],
+                [],
+                "mushroom_list_instance",
+                {"carbon": 25.0, "nitrogen": 5.0, "phosphorus": 2.5},
+                "delta_mass_fruiting_fungivory",
+            ),
         ],
+        ids=["herbivore", "carnivore", "fungivore"],
     )
     def test_forage_cohort(
         self,
@@ -1893,10 +1905,12 @@ def test_forage_cohort(
         diet_type,
         plant_list,
         animal_list,
+        mushroom_list,
         expected_nutrient_gain,
         delta_mass_mock,
         plant_list_instance,
         animal_list_instance,
+        mushroom_list_instance,
         excrement_pool_instance,
         carcass_pools_by_cell_instance,
         herbivory_waste_pool_instance,
@@ -1913,6 +1927,8 @@ def test_forage_cohort(
             plant_list = request.getfixturevalue(plant_list)
         if isinstance(animal_list, str):
             animal_list = request.getfixturevalue(animal_list)
+        if isinstance(mushroom_list, str):
+            mushroom_list = request.getfixturevalue(mushroom_list)
 
         # Construct herbivory waste pools if herbivore
         herbivory_waste_pools = {
@@ -1924,7 +1940,6 @@ def test_forage_cohort(
         mock_delta_mass = mocker.patch.object(
             cohort, delta_mass_mock, return_value=expected_nutrient_gain
         )
-        mock_eat = mocker.patch.object(cohort, "eat")
 
         # Dummy values for untested inputs
         empty_list = []
@@ -1933,8 +1948,9 @@ def test_forage_cohort(
         cohort.forage_cohort(
             plant_list=plant_list,
             animal_list=animal_list,
+            mushroom_list=mushroom_list,
             litter_pools=empty_list,
-            excrement_pools=excrement_pool_instance,
+            excrement_pools=[excrement_pool_instance],
             carcass_pool_map=carcass_pools_by_cell_instance,
             scavenge_carcass_pools=empty_list,
             scavenge_excrement_pools=empty_list,
@@ -1953,15 +1969,17 @@ def test_forage_cohort(
             assert kwargs["herbivory_waste_pools"] == herbivory_waste_pools
             assert isinstance(kwargs["adjusted_dt"], int | float)
 
-        else:
+        elif diet_type == "CARNIVORE":
             assert kwargs["animal_list"] == animal_list_instance
             assert kwargs["carcass_pools"] == carcass_pools_by_cell_instance
             assert isinstance(kwargs["adjusted_dt"], int | float)
 
-        # Validate assimilation call
-        mock_eat.assert_called_once_with(
-            expected_nutrient_gain, excrement_pool_instance
-        )
+        elif diet_type == "FUNGUS":
+            assert kwargs["mushroom_list"] == mushroom_list_instance
+            assert isinstance(kwargs["adjusted_dt"], int | float)
+
+        else:
+            assert False, f"Unhandled diet_type: {diet_type}"
 
     def test_forage_cohort_skips_when_no_individuals(
         self, mocker, herbivore_cohort_instance
@@ -1981,6 +1999,7 @@ def test_forage_cohort_skips_when_no_individuals(
         cohort.forage_cohort(
             plant_list=[],
             animal_list=[],
+            mushroom_list=[],
             litter_pools=[],
             excrement_pools=[],
             carcass_pool_map={},
@@ -2011,6 +2030,7 @@ def test_forage_cohort_skips_when_no_mass(self, mocker, herbivore_cohort_instanc
         cohort.forage_cohort(
             plant_list=[],
             animal_list=[],
+            mushroom_list=[],
             litter_pools=[],
             excrement_pools=[],
             carcass_pool_map={},

tests/models/animals/test_animal_model.py

@@ -2087,6 +2087,28 @@ def test_forage_community(
             "predator": predator_cohort_instance,
         }
 
+        # Show where AnimalModel comes from (guards against stray imports)
+        import inspect
+
+        from virtual_ecosystem.models.animal.animal_model import AnimalModel
+
+        # Comment: make failures descriptive and short to read in pytest output.
+        assert hasattr(animal_model_instance, "plant_resources"), (
+            "plant_resources missing. "
+            f"_setup defined at: {inspect.getsourcefile(AnimalModel._setup)}:"
+            f"{inspect.getsourcelines(AnimalModel._setup)[1]} | "
+            f"attrs={sorted(vars(animal_model_instance))}"
+        )
+
+        # Optional: verify other _setup outputs exist; helps pinpoint where it failed.
+        for name in (
+            "excrement_pools",
+            "carcass_pools",
+            "leaf_waste_pools",
+            "litter_pools",
+        ):
+            assert hasattr(animal_model_instance, name), f"Missing {name}"
+
         # Run the forage_community method
         animal_model_instance.forage_community(dt=30)
 

tests/models/animals/test_scaling_functions.py

@@ -160,6 +160,7 @@ def test_herbivore_prey_group_selection(functional_group_list_instance):
     expected = {
         "plants": (0.0, 0.0),
         "litter": (0.0, 0.0),
+        "fungal_fruiting_bodies": (0.0, 0.0),
     }
     assert result == expected
 
@@ -191,12 +192,29 @@ def test_carnivore_prey_group_selection(functional_group_list_instance):
         "detritivorous_insect": (0.0001, 1000.0),
         "dung_beetle": (0.0001, 1000.0),
         "scavenging_mammal": (0.0001, 1000.0),
+        "fungivorous_mammal": (0.0001, 1000.0),
         "carcasses": (0.0, 0.0),
         "excrement": (0.0, 0.0),
     }
     assert result == expected_output
 
 
+def test_fungivore_prey_group_selection(functional_group_list_instance):
+    """Test for fungivore diet type selection."""
+    from virtual_ecosystem.models.animal.scaling_functions import (
+        DietType,
+        prey_group_selection,
+    )
+
+    result = prey_group_selection(
+        DietType.FUNGUS, 10.0, (0.1, 1000.0), functional_group_list_instance
+    )
+    expected = {
+        "fungal_fruiting_bodies": (0.0, 0.0),
+    }
+    assert result == expected
+
+
 @pytest.mark.parametrize(
     "diet_flag, expected",
     [
@@ -211,12 +229,22 @@ def test_carnivore_prey_group_selection(functional_group_list_instance):
         # Herbivory + scavenging
         (
             DietType.HERBIVORE | DietType.CARCASSES,
-            {"plants": (0.0, 0.0), "litter": (0.0, 0.0), "carcasses": (0.0, 0.0)},
+            {
+                "plants": (0.0, 0.0),
+                "litter": (0.0, 0.0),
+                "carcasses": (0.0, 0.0),
+                "fungal_fruiting_bodies": (0.0, 0.0),
+            },
         ),
         # Herbivory + waste
         (
             DietType.HERBIVORE | DietType.WASTE,
-            {"plants": (0.0, 0.0), "litter": (0.0, 0.0), "excrement": (0.0, 0.0)},
+            {
+                "plants": (0.0, 0.0),
+                "litter": (0.0, 0.0),
+                "excrement": (0.0, 0.0),
+                "fungal_fruiting_bodies": (0.0, 0.0),
+            },
         ),
         # Detritivory only
         (