Delete unused variables from soil/litter testing

tests/conftest.py

@@ -455,7 +455,6 @@ def dummy_litter_data(fixture_core_components):
         "root_lignin": [0.2, 0.35, 0.27, 0.4],
         "plant_reproductive_tissue_turnover_c_n_ratio": [12.5, 23.8, 15.7, 18.2],
         "plant_reproductive_tissue_turnover_c_p_ratio": [125.5, 105.0, 145.0, 189.2],
-        "root_turnover_c_p_ratio": [656.7, 450.6, 437.3, 371.9],
         "litter_consumption_above_metabolic": [0.019785, 0.011631, 0.016129, 0.023456],
         "litter_consumption_above_structural": [0.02097, 0.01609, 0.01019, 0.00988],
         "litter_consumption_woody": [0.4773833, 0.385701, 0.373456, 0.162192],

tests/models/plants/test_plants_model.py

@@ -406,32 +406,6 @@ def test_PlantsModel_calculate_turnover(fxt_plants_model):
         consts.plant_reproductive_tissue_lignin,
     )
     assert np.allclose(fxt_plants_model.data["root_lignin"], consts.root_lignin)
-    assert np.allclose(fxt_plants_model.data["leaf_lignin"], consts.leaf_lignin)
-
-
-def test_PlantsModel_calculate_turnover_constant_override(
-    plants_data, fixture_configuration, fixture_core_components
-):
-    """Test that the turnover constants can be overridden by values in config.
-
-    TODO - not sure what this actually tests?
-    """
-
-    from virtual_ecosystem.models.plants.plants_model import PlantsModel
-
-    # Force setting of new value on frozen pydantic configuration class.
-    fixture_configuration.plants.constants.__dict__["leaf_lignin"] = 100.0
-
-    plants_model = PlantsModel.from_config(
-        data=plants_data,
-        configuration=fixture_configuration,
-        core_components=fixture_core_components,
-    )
-
-    plants_model.reset_update_vars()
-    plants_model.calculate_turnover()
-
-    assert np.allclose(plants_model.data["leaf_lignin"], 100.0)
 
 
 def test_PlantsModel_calculate_nutrient_uptake(fxt_plants_model):

tests/models/soil/conftest.py

@@ -66,11 +66,6 @@ def dummy_carbon_data(fixture_core_components):
         "animal_ectomycorrhiza_consumption": [9.52e-4, 3.84e-4, 3.77e-4, 9.43e-4],
         "animal_arbuscular_mycorrhiza_consumption": [3.43e-4, 4.29e-4, 6.0e-4, 2.30e-4],
         "decay_of_fungal_fruiting_bodies": [2.2499e-4, 5.8168e-4, 3.2185e-4, 2.5871e-3],
-        "new_fungal_fruiting_body_production": [0.0, 0.0, 0.0, 0.0],
-        "new_amf_n_supply": [0.0, 0.0, 0.0, 0.0],
-        "new_amf_p_supply": [0.0, 0.0, 0.0, 0.0],
-        "new_emf_n_supply": [0.0, 0.0, 0.0, 0.0],
-        "new_emf_p_supply": [0.0, 0.0, 0.0, 0.0],
     }
 
     for var_name, var_values in data_values.items():
@@ -239,18 +234,26 @@ def soil_pool_data(dummy_carbon_data):
     from virtual_ecosystem.models.soil.pools import PoolData
     from virtual_ecosystem.models.soil.soil_model import SoilModel
 
+    # As well as the values stored in the data object, the temporary arrays should be
+    # added to the pool data
+    refreshed_variables = [
+        "new_fungal_fruiting_body_production",
+        "new_amf_n_supply",
+        "new_amf_p_supply",
+        "new_emf_n_supply",
+        "new_emf_p_supply",
+    ]
+
     pools = {
-        var: pool
-        for var, pool in dummy_carbon_data.data.items()
-        if var in SoilModel.vars_updated
-        or var
-        in [
-            "new_fungal_fruiting_body_production",
-            "new_amf_n_supply",
-            "new_amf_p_supply",
-            "new_emf_n_supply",
-            "new_emf_p_supply",
-        ]
+        **{
+            var: pool
+            for var, pool in dummy_carbon_data.data.items()
+            if var in SoilModel.vars_updated
+        },
+        **{
+            name: np.zeros_like(dummy_carbon_data["soil_c_pool_lmwc"])
+            for name in refreshed_variables
+        },
     }
 
     return PoolData(**pools)

tests/models/soil/test_soil_model.py

@@ -302,7 +302,7 @@ def test_update(mocker, fixture_soil_model, dummy_carbon_data):
     # Set of pools to be returned to test that update does use (mocked) integrator
     end_lmwc = [0.04980117, 0.01999411, 0.09992829, 0.00499986]
     end_maom = [2.50019883, 1.70000589, 4.50007171, 0.50000014]
-    end_microbe = [5.8, 2.3, 11.3, 1.0]
+    end_bacteria = [5.8, 2.3, 11.3, 1.0]
     end_pom = [0.25, 2.34, 0.746, 0.3467]
     end_necromass = [0.058, 0.015, 0.093, 0.105]
 
@@ -334,7 +334,7 @@ def test_update(mocker, fixture_soil_model, dummy_carbon_data):
         data_vars=dict(
             soil_c_pool_lmwc=DataArray(end_lmwc, dims="cell_id"),
             soil_c_pool_maom=DataArray(end_maom, dims="cell_id"),
-            soil_c_pool_microbe=DataArray(end_microbe, dims="cell_id"),
+            soil_c_pool_bacteria=DataArray(end_bacteria, dims="cell_id"),
             soil_c_pool_pom=DataArray(end_pom, dims="cell_id"),
             soil_c_pool_necromass=DataArray(end_necromass, dims="cell_id"),
             soil_n_pool_nitrate=DataArray(end_nitrate, dims="cell_id"),
@@ -358,7 +358,7 @@ def test_update(mocker, fixture_soil_model, dummy_carbon_data):
     # Check that data fixture has been updated correctly
     assert np.allclose(dummy_carbon_data["soil_c_pool_lmwc"], end_lmwc)
     assert np.allclose(dummy_carbon_data["soil_c_pool_maom"], end_maom)
-    assert np.allclose(dummy_carbon_data["soil_c_pool_microbe"], end_microbe)
+    assert np.allclose(dummy_carbon_data["soil_c_pool_bacteria"], end_bacteria)
     assert np.allclose(dummy_carbon_data["soil_c_pool_pom"], end_pom)
     assert np.allclose(dummy_carbon_data["soil_c_pool_necromass"], end_necromass)
 

virtual_ecosystem/data_variables.toml

@@ -1408,69 +1408,6 @@ name = "canopy_non_propagule_c_mass"
 unit = "NEEDS UNIT"
 variable_type = "float"
 
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "leaf_lignin"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "nitrogen_fixation_carbon_supply"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "new_fungal_fruiting_body_production"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "new_amf_n_supply"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "new_amf_p_supply"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "new_emf_n_supply"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "new_emf_p_supply"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "soil_c_pool_microbe"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
-[[variable]]
-axis = ["spatial"]
-description = "NEEDS DESCRIPTION"
-name = "root_turnover_c_p_ratio"
-unit = "NEEDS UNIT"
-variable_type = "float"
-
 [[variable]]
 axis = ["spatial"]
 description = "NEEDS DESCRIPTION"

virtual_ecosystem/models/plants/model_config.py

@@ -39,9 +39,6 @@ class PlantsConstants(Configuration):
     senesced_leaf_lignin: float = 0.05
     """Fraction of senesced leaf biomass that is lignin."""
 
-    leaf_lignin: float = 0.10
-    """Fraction of leaf biomass that is lignin."""
-
     plant_reproductive_tissue_lignin: float = 0.01
     """Fraction of plant reproductive tissue biomass that is lignin."""
 

virtual_ecosystem/models/plants/plants_model.py

@@ -140,9 +140,7 @@ class PlantsModel(
         "foliage_turnover_cnp",
         "root_turnover_cnp",
         "fallen_n_propagules",
-        "nitrogen_fixation_carbon_supply",
         "canopy_n_propagules",
-        "leaf_lignin",
         "canopy_non_propagule_c_mass",
         "fallen_non_propagule_c_mass",
         "plant_ammonium_uptake",
@@ -1324,19 +1322,13 @@ def calculate_turnover(self) -> None:
         self.data["senesced_leaf_lignin"] = xr.full_like(
             self.data["elevation"], self.model_constants.senesced_leaf_lignin
         )
-        self.data["leaf_lignin"] = xr.full_like(
-            self.data["elevation"], self.model_constants.leaf_lignin
-        )
         self.data["plant_reproductive_tissue_lignin"] = xr.full_like(
             self.data["elevation"],
             self.model_constants.plant_reproductive_tissue_lignin,
         )
         self.data["root_lignin"] = xr.full_like(
             self.data["elevation"], self.model_constants.root_lignin
         )
-        self.data["nitrogen_fixation_carbon_supply"] = xr.full_like(
-            self.data["elevation"], 0.01
-        )
 
     def calculate_nutrient_uptake(self) -> None:
         """Calculate uptake of soil nutrients by the plant community.