Moving soil model to new configuration

docs/source/_toc.yaml

@@ -209,6 +209,8 @@ subtrees:
             entries:
               - file: api/models/soil/pools
                 title: The pools submodule
+              - file: api/models/soil/model_config
+                title: The model_config submodule
               - file: api/models/soil/constants
                 title: The constants submodule
               - file: api/models/soil/env_factors

docs/source/api/models/soil/model_config.md

@@ -0,0 +1,34 @@
+---
+jupytext:
+  cell_metadata_filter: -all
+  formats: md:myst
+  main_language: python
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.18.1
+kernelspec:
+  display_name: Python 3 (ipykernel)
+  language: python
+  name: python3
+language_info:
+  codemirror_mode:
+    name: ipython
+    version: 3
+  file_extension: .py
+  mimetype: text/x-python
+  name: python
+  nbconvert_exporter: python
+  pygments_lexer: ipython3
+  version: 3.11.9
+---
+
+# API documentation for the {mod}`~virtual_ecosystem.models.soil.model_config` module
+
+```{eval-rst}
+.. automodule:: virtual_ecosystem.models.soil.model_config
+    :autosummary:
+    :members:
+    :exclude-members: model_config
+```

docs/source/conf.py

@@ -194,6 +194,11 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ("py:class", "NegativeFloat"),
     ("py:class", "date"),
     ("py:class", "_PydanticGeneralMetadata"),
+    # Sphinx seems to insist that pydantic model types are classes, when they can be
+    # global Literals
+    ("py:class", "SUBSTRATES"),
+    ("py:class", "REQUIRED_MICROBIAL_GROUPS"),
+    ("py:class", "HIGHER_TAXONOMIC_GROUPS"),
     ("py:class", "dir"),
     # FOR PITY'S SAKE, SPHINX - why can you not find DIRPATH_PLACEHOLDER when you _can_
     # find FILEPATH_PLACEHOLDER, which is defined in the same way, in the same file and

docs/source/virtual_ecosystem/implementation/soil_implementation.md

@@ -81,10 +81,8 @@ function](virtual_ecosystem.models.soil.microbial_groups.make_full_set_of_microb
 Similarly, enzyme classes are distinguished by whether they were produced by fungi or
 bacteria and by what substrate they break down ({term}`MAOM` or {term}`POM`). So, there
 is a total of four enzyme classes in the model. The parameters associated with each
-class are stored in an [EnzymeConstants data
-class](virtual_ecosystem.models.soil.microbial_groups.EnzymeConstants), and the full set
-of them can be constructed using the [make_full_set_of_enzymes
-function](virtual_ecosystem.models.soil.microbial_groups.make_full_set_of_enzymes).
+class are stored in an [SoilEnzymeClass data
+class](virtual_ecosystem.models.soil.model_config.SoilEnzymeClass).
 
 ## Model variables
 

tests/models/animals/conftest.py

@@ -407,13 +407,11 @@ def functional_group_list_instance(shared_datadir, constants_instance):
 
 
 @pytest.fixture
-def microbial_c_n_p_ratios(fixture_config):
+def microbial_c_n_p_ratios(fixture_configuration):
     """Fixture containing the microbial C:N:P ratios for use in animal model testing."""
-    from virtual_ecosystem.models.soil.microbial_groups import (
-        find_microbial_stoichiometries,
-    )
+    from virtual_ecosystem.models.animal.cnp import find_microbial_stoichiometries
 
-    return find_microbial_stoichiometries(config=fixture_config)
+    return find_microbial_stoichiometries(config=fixture_configuration)
 
 
 @pytest.fixture

tests/models/animals/test_animal_model.py

@@ -75,7 +75,6 @@ def test_animal_model_initialization(
                 does_not_raise(),
                 (
                     (INFO, "Initialised animal.AnimalConsts from config"),
-                    (INFO, "Initialised core.CoreConsts from config"),
                     (
                         INFO,
                         "Information required to initialise the animal model"

tests/models/animals/test_cnp.py

@@ -144,3 +144,19 @@ def test_get_proportions_zero_handling(self):
         assert proportions["carbon"] == 0.0
         assert proportions["nitrogen"] == 0.0
         assert proportions["phosphorus"] == 0.0
+
+
+def test_find_microbial_stoichiometries(fixture_configuration):
+    """Check that extraction of stoichiometries from microbial groups works."""
+    from virtual_ecosystem.models.animal.cnp import find_microbial_stoichiometries
+
+    expected_ratios = {
+        "bacteria": {"nitrogen": 5.2, "phosphorus": 16.0},
+        "saprotrophic_fungi": {"nitrogen": 6.5, "phosphorus": 40.0},
+        "arbuscular_mycorrhiza": {"nitrogen": 18.0, "phosphorus": 120.0},
+        "ectomycorrhiza": {"nitrogen": 18.0, "phosphorus": 120.0},
+    }
+
+    actual_ratios = find_microbial_stoichiometries(config=fixture_configuration)
+
+    assert expected_ratios == actual_ratios

tests/models/soil/conftest.py

@@ -143,6 +143,27 @@ def fixture_soil_configuration(microbial_groups_cfg):
     return generate_configuration(config_data.data)
 
 
+@pytest.fixture
+def fixture_core_constants(fixture_soil_configuration):
+    """Get the core constants instance from the config."""
+
+    return fixture_soil_configuration.core.constants
+
+
+@pytest.fixture
+def fixture_soil_constants(fixture_soil_configuration):
+    """Get the soil constants instance from the config."""
+
+    return fixture_soil_configuration.soil.constants
+
+
+@pytest.fixture
+def fixture_hydrology_constants(fixture_soil_configuration):
+    """Get the hydrology constants instance from the config."""
+
+    return fixture_soil_configuration.hydrology.constants
+
+
 @pytest.fixture
 def fixture_soil_core_components(fixture_soil_configuration):
     """Create a core components from the fixture_soil_config."""
@@ -180,12 +201,13 @@ def fixture_soil_model(
 
 
 @pytest.fixture
-def environmental_factors(dummy_carbon_data, fixture_core_components):
+def environmental_factors(
+    dummy_carbon_data, fixture_soil_constants, fixture_core_components
+):
     """Environmental factors based on dummy carbon data."""
     from virtual_ecosystem.models.litter.env_factors import (
         average_water_potential_over_microbially_active_layers,
     )
-    from virtual_ecosystem.models.soil.constants import SoilConsts
     from virtual_ecosystem.models.soil.env_factors import (
         calculate_environmental_effect_factors,
     )
@@ -197,24 +219,24 @@ def environmental_factors(dummy_carbon_data, fixture_core_components):
         ),
         pH=dummy_carbon_data["pH"].to_numpy(),
         clay_fraction=dummy_carbon_data["clay_fraction"].to_numpy(),
-        constants=SoilConsts,
+        constants=fixture_soil_constants,
     )
 
 
 @pytest.fixture
-def carbon_supply_from_plants(dummy_carbon_data):
+def carbon_supply_from_plants(
+    dummy_carbon_data, fixture_core_constants, fixture_soil_constants
+):
     """Carbon supply from plants split between the different symbiotic groups."""
-    from virtual_ecosystem.core.constants import CoreConsts
-    from virtual_ecosystem.models.soil.constants import SoilConsts
     from virtual_ecosystem.models.soil.microbial_groups import (
         calculate_symbiotic_carbon_supply,
     )
 
     return calculate_symbiotic_carbon_supply(
         total_plant_supply=dummy_carbon_data["plant_symbiote_carbon_supply"]
-        / CoreConsts.max_depth_of_microbial_activity,
-        nitrogen_fixer_fraction=SoilConsts.nitrogen_fixer_supply_fraction,
-        ectomycorrhiza_fraction=SoilConsts.ectomycorrhiza_supply_fraction,
+        / fixture_core_constants.max_depth_of_microbial_activity,
+        nitrogen_fixer_fraction=fixture_soil_constants.nitrogen_fixer_supply_fraction,
+        ectomycorrhiza_fraction=fixture_soil_constants.ectomycorrhiza_supply_fraction,
     )
 
 
@@ -272,74 +294,71 @@ def enzyme_mediated_rates(
 
 
 @pytest.fixture
-def necromass_breakdown(dummy_carbon_data):
+def necromass_breakdown(dummy_carbon_data, fixture_soil_constants):
     """Necromass breakdown rate based on dummy carbon data."""
-    from virtual_ecosystem.models.soil.constants import SoilConsts
     from virtual_ecosystem.models.soil.pools import calculate_necromass_breakdown
 
     return calculate_necromass_breakdown(
         soil_c_pool_necromass=dummy_carbon_data["soil_c_pool_necromass"],
-        necromass_decay_rate=SoilConsts.necromass_decay_rate,
+        necromass_decay_rate=fixture_soil_constants.necromass_decay_rate,
     )
 
 
 @pytest.fixture
-def necromass_sorption(dummy_carbon_data):
+def necromass_sorption(dummy_carbon_data, fixture_soil_constants):
     """Necromass sorption rate based on dummy carbon data."""
-    from virtual_ecosystem.models.soil.constants import SoilConsts
     from virtual_ecosystem.models.soil.pools import calculate_sorption_to_maom
 
     return calculate_sorption_to_maom(
         soil_c_pool=dummy_carbon_data["soil_c_pool_necromass"],
-        sorption_rate_constant=SoilConsts.necromass_sorption_rate,
+        sorption_rate_constant=fixture_soil_constants.necromass_sorption_rate,
     )
 
 
 @pytest.fixture
-def lmwc_sorption(dummy_carbon_data):
+def lmwc_sorption(dummy_carbon_data, fixture_soil_constants):
     """Low molecular weight carbon sorption rate based on dummy carbon data."""
-    from virtual_ecosystem.models.soil.constants import SoilConsts
     from virtual_ecosystem.models.soil.pools import calculate_sorption_to_maom
 
     return calculate_sorption_to_maom(
         soil_c_pool=dummy_carbon_data["soil_c_pool_lmwc"],
-        sorption_rate_constant=SoilConsts.lmwc_sorption_rate,
+        sorption_rate_constant=fixture_soil_constants.lmwc_sorption_rate,
     )
 
 
 @pytest.fixture
-def maom_desorption(dummy_carbon_data):
+def maom_desorption(dummy_carbon_data, fixture_soil_constants):
     """MAOM desorption rate based on dummy carbon data."""
-    from virtual_ecosystem.models.soil.constants import SoilConsts
     from virtual_ecosystem.models.soil.pools import calculate_maom_desorption
 
     return calculate_maom_desorption(
         soil_c_pool_maom=dummy_carbon_data["soil_c_pool_maom"],
-        desorption_rate_constant=SoilConsts.maom_desorption_rate,
+        desorption_rate_constant=fixture_soil_constants.maom_desorption_rate,
     )
 
 
 @pytest.fixture
-def functional_groups(fixture_config, enzyme_classes):
+def functional_groups(fixture_configuration, enzyme_classes, fixture_core_constants):
     """Set of functional groups based on the soil model constants."""
-    from virtual_ecosystem.core.constants import CoreConsts
     from virtual_ecosystem.models.soil.microbial_groups import (
         make_full_set_of_microbial_groups,
     )
 
     return make_full_set_of_microbial_groups(
-        config=fixture_config, enzyme_classes=enzyme_classes, core_constants=CoreConsts
+        config=fixture_configuration.soil,
+        enzyme_classes=enzyme_classes,
+        core_constants=fixture_core_constants,
     )
 
 
 @pytest.fixture
-def enzyme_classes(fixture_config):
+def enzyme_classes(fixture_configuration):
     """Set of functional groups based on the soil model constants."""
-    from virtual_ecosystem.models.soil.microbial_groups import (
-        make_full_set_of_enzymes,
-    )
 
-    return make_full_set_of_enzymes(config=fixture_config)
+    return {
+        f"{e.source}_{e.substrate}": e
+        for e in fixture_configuration.soil.enzyme_class_definition
+    }
 
 
 @pytest.fixture
@@ -373,14 +392,15 @@ def biomass_losses(soil_pool_data, functional_groups, averaged_soil_temp):
 @pytest.fixture
 def growth_rates(
     dummy_carbon_data,
+    fixture_soil_constants,
     environmental_factors,
     functional_groups,
     soil_pool_data,
     averaged_soil_temp,
     carbon_supply_from_plants,
 ):
     """Fixture to store growth rates of all the microbial groups."""
-    from virtual_ecosystem.models.soil.constants import SoilConsts
+
     from virtual_ecosystem.models.soil.pools import calculate_nutrient_uptake_rates
 
     bacterial_growth, _ = calculate_nutrient_uptake_rates(
@@ -397,7 +417,7 @@ def growth_rates(
         water_factor=environmental_factors.water,
         pH_factor=environmental_factors.pH,
         soil_temp=averaged_soil_temp,
-        constants=SoilConsts,
+        constants=fixture_soil_constants,
         functional_group=functional_groups["bacteria"],
     )
     saprotrophic_fungal_growth, _ = calculate_nutrient_uptake_rates(
@@ -414,7 +434,7 @@ def growth_rates(
         water_factor=environmental_factors.water,
         pH_factor=environmental_factors.pH,
         soil_temp=averaged_soil_temp,
-        constants=SoilConsts,
+        constants=fixture_soil_constants,
         functional_group=functional_groups["saprotrophic_fungi"],
     )
     arbuscular_mycorrhizal_growth, _ = calculate_nutrient_uptake_rates(
@@ -431,7 +451,7 @@ def growth_rates(
         water_factor=environmental_factors.water,
         pH_factor=environmental_factors.pH,
         soil_temp=averaged_soil_temp,
-        constants=SoilConsts,
+        constants=fixture_soil_constants,
         functional_group=functional_groups["arbuscular_mycorrhiza"],
     )
     ectomycorrhizal_growth, _ = calculate_nutrient_uptake_rates(
@@ -448,7 +468,7 @@ def growth_rates(
         water_factor=environmental_factors.water,
         pH_factor=environmental_factors.pH,
         soil_temp=averaged_soil_temp,
-        constants=SoilConsts,
+        constants=fixture_soil_constants,
         functional_group=functional_groups["ectomycorrhiza"],
     )
 
@@ -472,18 +492,17 @@ def enzyme_production(functional_groups, growth_rates):
 
 
 @pytest.fixture
-def carbon_use_efficiency(averaged_soil_temp):
+def carbon_use_efficiency(averaged_soil_temp, fixture_soil_constants):
     """Fixture to store the carbon use efficiency."""
-    from virtual_ecosystem.models.soil.constants import SoilConsts
     from virtual_ecosystem.models.soil.env_factors import (
         calculate_carbon_use_efficiency,
     )
 
     return calculate_carbon_use_efficiency(
         soil_temp=averaged_soil_temp,
-        reference_cue_logit=SoilConsts.reference_cue_logit,
-        cue_reference_temp=SoilConsts.cue_reference_temp,
-        logit_cue_with_temp=SoilConsts.logit_cue_with_temperature,
+        reference_cue_logit=fixture_soil_constants.reference_cue_logit,
+        cue_reference_temp=fixture_soil_constants.cue_reference_temp,
+        logit_cue_with_temp=fixture_soil_constants.logit_cue_with_temperature,
     )