Merge branch 'develop' into feature/multi_grid_no_community

.github/workflows/ci.yml

@@ -56,7 +56,7 @@ jobs:
              matrix.python-version == '3.10'
             )
           }}
-      uses: codecov/codecov-action@v4
+      uses: codecov/codecov-action@v5
       with:
         fail_ci_if_error: true
         token: ${{ secrets.CODECOV_TOKEN }}

docs/source/_toc.yaml

@@ -194,8 +194,8 @@ subtrees:
           - file: api/models/soil
             title: The soil model
             entries:
-              - file: api/models/soil/carbon
-                title: The carbon submodule
+              - file: api/models/soil/pools
+                title: The pools submodule
               - file: api/models/soil/constants
                 title: The constants submodule
               - file: api/models/soil/env_factors

docs/source/api/models/soil/carbon.md → docs/source/api/models/soil/pools.md

@@ -24,10 +24,10 @@ language_info:
   version: 3.11.9
 ---
 
-# API documentation for the {mod}`~virtual_ecosystem.models.soil.carbon` module
+# API documentation for the {mod}`~virtual_ecosystem.models.soil.pools` module
 
 ```{eval-rst}
-.. automodule:: virtual_ecosystem.models.soil.carbon
+.. automodule:: virtual_ecosystem.models.soil.pools
     :autosummary:
     :members:
 ```

pyproject.toml

@@ -52,7 +52,7 @@ types-tqdm = "^4.66.0.20240106"
 [tool.poetry.group.test.dependencies]
 hypothesis = "^6.54.2"
 pytest = ">=7.1.2,<9.0.0"
-pytest-cov = ">=3,<6"
+pytest-cov = ">=3,<7"
 pytest-datadir = "^1.4.1"
 pytest-mock = "^3.8.1"
 

tests/conftest.py

@@ -260,10 +260,13 @@ def dummy_carbon_data(fixture_core_components):
         "soil_c_pool_necromass": [0.058, 0.015, 0.093, 0.105],
         "soil_enzyme_pom": [0.022679, 0.009576, 0.050051, 0.003010],
         "soil_enzyme_maom": [0.0356, 0.0117, 0.02509, 0.00456],
+        "soil_n_pool_don": [0.000571428, 0.00142857, 0.00014285, 0.002857142],
+        "soil_n_pool_particulate": [0.00714285, 0.00071425, 0.00285714, 0.01428571],
         "pH": [3.0, 7.5, 9.0, 5.7],
         "bulk_density": [1350.0, 1800.0, 1000.0, 1500.0],
         "clay_fraction": [0.8, 0.3, 0.1, 0.9],
         "litter_C_mineralisation_rate": [0.00212106, 0.00106053, 0.00049000, 0.0055],
+        "litter_N_mineralisation_rate": [3.5351e-5, 7.0702e-5, 0.000183, 1.63333e-5],
         "vertical_flow": [0.1, 0.5, 2.5, 1.59],
     }
 

tests/core/test_data.py

@@ -974,6 +974,8 @@ def test_output_current_state(mocker, dummy_carbon_data, time_index):
             "soil_c_pool_necromass",
             "soil_enzyme_pom",
             "soil_enzyme_maom",
+            "soil_n_pool_don",
+            "soil_n_pool_particulate",
         ],
         time_index,
     )

tests/models/soil/conftest.py

@@ -75,3 +75,24 @@ def environmental_factors(dummy_carbon_data, fixture_core_components):
     return EnvironmentalEffectFactors(
         water=water_factors, pH=pH_factors, clay_saturation=clay_saturation_factors
     )
+
+
+@pytest.fixture
+def enzyme_mediated_rates(
+    dummy_carbon_data, fixture_core_components, environmental_factors
+):
+    """Enzyme mediated rates based on dummy carbon data."""
+    from virtual_ecosystem.models.soil.constants import SoilConsts
+    from virtual_ecosystem.models.soil.pools import calculate_enzyme_mediated_rates
+
+    return calculate_enzyme_mediated_rates(
+        soil_enzyme_pom=dummy_carbon_data["soil_enzyme_pom"],
+        soil_enzyme_maom=dummy_carbon_data["soil_enzyme_maom"],
+        soil_c_pool_pom=dummy_carbon_data["soil_c_pool_pom"],
+        soil_c_pool_maom=dummy_carbon_data["soil_c_pool_maom"],
+        soil_temp=dummy_carbon_data["soil_temperature"][
+            fixture_core_components.layer_structure.index_topsoil_scalar
+        ],
+        env_factors=environmental_factors,
+        constants=SoilConsts,
+    )

tests/models/soil/test_carbon.py → tests/models/soil/test_pools.py

@@ -1,4 +1,4 @@
-"""Test module for soil.carbon.py.
+"""Test module for soil.pools.py.
 
 This module tests the functionality of the soil carbon module
 """
@@ -9,51 +9,52 @@
 from virtual_ecosystem.models.soil.constants import SoilConsts
 
 
-def test_calculate_soil_carbon_updates(dummy_carbon_data, fixture_core_components):
+def test_calculate_all_pool_updates(dummy_carbon_data, fixture_core_components):
     """Test that the two pool update functions work correctly."""
-    from virtual_ecosystem.core.constants import CoreConsts
-    from virtual_ecosystem.models.soil.carbon import calculate_soil_carbon_updates
+    from virtual_ecosystem.models.soil.pools import SoilPools
+    from virtual_ecosystem.models.soil.soil_model import SoilModel, make_slices
+
+    # Find and store order of pools (this requires loads of steps because it needs to
+    # work with the integrator)
+    y0 = np.concatenate(
+        [
+            dummy_carbon_data[name].to_numpy()
+            for name in map(str, dummy_carbon_data.data.keys())
+            if name in SoilModel.vars_updated
+        ]
+    )
+    delta_pools_ordered = {
+        name: np.array([])
+        for name in map(str, dummy_carbon_data.data.keys())
+        if name in SoilModel.vars_updated
+    }
+    no_cells = 4
+    slices = make_slices(no_cells, len(delta_pools_ordered))
+    pools = {
+        str(pool): y0[slc] for slc, pool in zip(slices, delta_pools_ordered.keys())
+    }
+    soil_pools = SoilPools(data=dummy_carbon_data, pools=pools, constants=SoilConsts)
 
     change_in_pools = {
-        "soil_c_pool_lmwc": [0.0022585928, 0.0060483065, -0.019175058, 0.024247214],
+        "soil_c_pool_lmwc": [0.00226177439, 0.006049897295, -0.019174323, 0.024255464],
         "soil_c_pool_maom": [0.038767651, 0.00829848, 0.05982197, 0.07277182],
         "soil_c_pool_microbe": [-0.04978105, -0.02020101, -0.10280967, -0.00719517],
-        "soil_c_pool_pom": [0.00178122, -0.00785937, -0.01201551, 0.00545857],
+        "soil_c_pool_pom": [0.00177803841, -0.007860960795, -0.012016245, 0.00545032],
         "soil_c_pool_necromass": [0.001137474, 0.009172067, 0.033573266, -0.08978050],
         "soil_enzyme_pom": [1.18e-8, 1.67e-8, 1.8e-9, -1.12e-8],
         "soil_enzyme_maom": [-0.00031009, -5.09593e-5, 0.0005990658, -3.72112e-5],
+        "soil_n_pool_don": [2.4081961e-5, 2.84920682e-6, 4.84845086e-5, -5.83499913e-5],
+        "soil_n_pool_particulate": [1.102338e-5, 6.422491e-5, 0.000131687, 1.461799e-5],
     }
 
     # Make order of pools object
     pool_order = {}
     for pool in change_in_pools.keys():
         pool_order[pool] = np.array([])
 
-    delta_pools = calculate_soil_carbon_updates(
-        soil_c_pool_lmwc=dummy_carbon_data["soil_c_pool_lmwc"].to_numpy(),
-        soil_c_pool_maom=dummy_carbon_data["soil_c_pool_maom"].to_numpy(),
-        soil_c_pool_microbe=dummy_carbon_data["soil_c_pool_microbe"].to_numpy(),
-        soil_c_pool_pom=dummy_carbon_data["soil_c_pool_pom"].to_numpy(),
-        soil_c_pool_necromass=dummy_carbon_data["soil_c_pool_necromass"].to_numpy(),
-        soil_enzyme_pom=dummy_carbon_data["soil_enzyme_pom"].to_numpy(),
-        soil_enzyme_maom=dummy_carbon_data["soil_enzyme_maom"].to_numpy(),
-        pH=dummy_carbon_data["pH"],
-        bulk_density=dummy_carbon_data["bulk_density"],
-        soil_moisture=dummy_carbon_data["soil_moisture"][
-            fixture_core_components.layer_structure.index_topsoil_scalar
-        ].to_numpy(),
-        soil_water_potential=dummy_carbon_data["matric_potential"][
-            fixture_core_components.layer_structure.index_topsoil_scalar
-        ].to_numpy(),
-        vertical_flow_rate=dummy_carbon_data["vertical_flow"],
-        soil_temp=dummy_carbon_data["soil_temperature"][
-            fixture_core_components.layer_structure.index_topsoil_scalar
-        ],
-        clay_fraction=dummy_carbon_data["clay_fraction"],
-        mineralisation_rate=dummy_carbon_data["litter_C_mineralisation_rate"],
+    delta_pools = soil_pools.calculate_all_pool_updates(
         delta_pools_ordered=pool_order,
-        model_constants=SoilConsts,
-        core_constants=CoreConsts,
+        top_soil_layer_index=fixture_core_components.layer_structure.index_topsoil_scalar,
     )
 
     # Check that the updates are correctly calculated. Using a loop here implicitly
@@ -67,7 +68,7 @@ def test_calculate_microbial_changes(
 ):
     """Check that calculation of microbe related changes works correctly."""
 
-    from virtual_ecosystem.models.soil.carbon import calculate_microbial_changes
+    from virtual_ecosystem.models.soil.pools import calculate_microbial_changes
 
     expected_lmwc_uptake = [1.29159055e-2, 8.43352433e-3, 5.77096991e-2, 5.77363558e-5]
     expected_microbe = [-0.04978105, -0.02020101, -0.10280967, -0.00719517]
@@ -100,7 +101,7 @@ def test_calculate_enzyme_mediated_rates(
 ):
     """Check that calculation of enzyme mediated rates works as expected."""
 
-    from virtual_ecosystem.models.soil.carbon import calculate_enzyme_mediated_rates
+    from virtual_ecosystem.models.soil.pools import calculate_enzyme_mediated_rates
 
     expected_pom_to_lmwc = [3.39844565e-4, 8.91990315e-3, 1.25055119e-2, 4.14247999e-5]
     expected_maom_to_lmwc = [1.45988485e-3, 2.10172756e-3, 4.69571604e-3, 8.62951373e-6]
@@ -124,7 +125,7 @@ def test_calculate_enzyme_mediated_rates(
 def test_calculate_enzyme_changes(dummy_carbon_data):
     """Check that the determination of enzyme pool changes works correctly."""
 
-    from virtual_ecosystem.models.soil.carbon import calculate_enzyme_changes
+    from virtual_ecosystem.models.soil.pools import calculate_enzyme_changes
 
     biomass_loss = np.array([0.05443078, 0.02298407, 0.12012258, 0.00722288])
 
@@ -148,7 +149,7 @@ def test_calculate_maintenance_biomass_synthesis(
     dummy_carbon_data, fixture_core_components
 ):
     """Check maintenance respiration cost calculates correctly."""
-    from virtual_ecosystem.models.soil.carbon import (
+    from virtual_ecosystem.models.soil.pools import (
         calculate_maintenance_biomass_synthesis,
     )
 
@@ -167,7 +168,7 @@ def test_calculate_maintenance_biomass_synthesis(
 
 def test_calculate_carbon_use_efficiency(dummy_carbon_data, fixture_core_components):
     """Check carbon use efficiency calculates correctly."""
-    from virtual_ecosystem.models.soil.carbon import calculate_carbon_use_efficiency
+    from virtual_ecosystem.models.soil.pools import calculate_carbon_use_efficiency
 
     expected_cues = [0.36, 0.33, 0.3, 0.48]
 
@@ -202,7 +203,7 @@ def test_calculate_carbon_use_efficiency(dummy_carbon_data, fixture_core_compone
 )
 def test_calculate_enzyme_turnover(dummy_carbon_data, turnover, expected_decay):
     """Check that enzyme turnover rates are calculated correctly."""
-    from virtual_ecosystem.models.soil.carbon import calculate_enzyme_turnover
+    from virtual_ecosystem.models.soil.pools import calculate_enzyme_turnover
 
     actual_decay = calculate_enzyme_turnover(
         enzyme_pool=dummy_carbon_data["soil_enzyme_pom"], turnover_rate=turnover
@@ -215,7 +216,9 @@ def test_calculate_microbial_carbon_uptake(
     dummy_carbon_data, fixture_core_components, environmental_factors
 ):
     """Check microbial carbon uptake calculates correctly."""
-    from virtual_ecosystem.models.soil.carbon import calculate_microbial_carbon_uptake
+    from virtual_ecosystem.models.soil.pools import (
+        calculate_microbial_carbon_uptake,
+    )
 
     expected_uptake = [1.29159055e-2, 8.43352433e-3, 5.77096991e-2, 5.77363558e-5]
     expected_assimilation = [4.64972597e-3, 2.78306303e-3, 1.73129097e-2, 2.77134508e-5]
@@ -239,7 +242,7 @@ def test_calculate_enzyme_mediated_decomposition(
     dummy_carbon_data, fixture_core_components, environmental_factors
 ):
     """Check that particulate organic matter decomposition is calculated correctly."""
-    from virtual_ecosystem.models.soil.carbon import (
+    from virtual_ecosystem.models.soil.pools import (
         calculate_enzyme_mediated_decomposition,
     )
 
@@ -265,7 +268,7 @@ def test_calculate_enzyme_mediated_decomposition(
 def test_calculate_maom_desorption(dummy_carbon_data):
     """Check that mineral associated matter desorption is calculated correctly."""
 
-    from virtual_ecosystem.models.soil.carbon import calculate_maom_desorption
+    from virtual_ecosystem.models.soil.pools import calculate_maom_desorption
 
     expected_desorption = [2.5e-5, 1.7e-5, 4.5e-5, 5.0e-6]
 
@@ -297,7 +300,7 @@ def test_calculate_sorption_to_maom(
 ):
     """Check that sorption to mineral associated matter is calculated correctly."""
 
-    from virtual_ecosystem.models.soil.carbon import calculate_sorption_to_maom
+    from virtual_ecosystem.models.soil.pools import calculate_sorption_to_maom
 
     actual_sorption = calculate_sorption_to_maom(
         soil_c_pool=dummy_carbon_data[pool_name],
@@ -310,7 +313,7 @@ def test_calculate_sorption_to_maom(
 def test_calculate_necromass_breakdown(dummy_carbon_data):
     """Check that necromass breakdown to lmwc is calculated correctly."""
 
-    from virtual_ecosystem.models.soil.carbon import calculate_necromass_breakdown
+    from virtual_ecosystem.models.soil.pools import calculate_necromass_breakdown
 
     expected_breakdown = [0.0134008455, 0.0034657359, 0.0214875626, 0.0242601513]
 
@@ -320,3 +323,44 @@ def test_calculate_necromass_breakdown(dummy_carbon_data):
     )
 
     assert np.allclose(actual_breakdown, expected_breakdown)
+
+
+def test_calculate_litter_mineralisation_split(dummy_carbon_data):
+    """Test that the calculation of the mineralisation split works as expected."""
+    from virtual_ecosystem.models.soil.pools import (
+        calculate_litter_mineralisation_split,
+    )
+
+    expected_split = {
+        "dissolved": [3.18159e-6, 1.590795e-6, 7.35e-7, 8.25e-6],
+        "particulate": [0.00211787841, 0.001058939205, 0.000489265, 0.00549175],
+    }
+
+    actual_split = calculate_litter_mineralisation_split(
+        mineralisation_rate=dummy_carbon_data["litter_C_mineralisation_rate"],
+        litter_leaching_coefficient=SoilConsts.litter_leaching_fraction_carbon,
+    )
+
+    assert set(expected_split.keys()) == set(actual_split.keys())
+
+    for key in actual_split.keys():
+        assert np.allclose(actual_split[key], expected_split[key])
+
+
+def test_calculate_soil_nutrient_mineralisation(
+    dummy_carbon_data, enzyme_mediated_rates
+):
+    """Test that function to calculate soil nutrient mineralisation works properly."""
+    from virtual_ecosystem.models.soil.pools import (
+        calculate_soil_nutrient_mineralisation,
+    )
+
+    expected_rate = [2.42745875e-5, 6.371041e-6, 5.104285e-5, 1.690808e-6]
+
+    actual_rate = calculate_soil_nutrient_mineralisation(
+        pool_carbon=dummy_carbon_data["soil_c_pool_pom"],
+        pool_nutrient=dummy_carbon_data["soil_n_pool_particulate"],
+        breakdown_rate=enzyme_mediated_rates.pom_to_lmwc,
+    )
+
+    assert np.allclose(actual_rate, expected_rate)