Added separate bacteria and fungi pools

docs/source/_toc.yaml

@@ -202,6 +202,8 @@ subtrees:
                 title: The constants submodule
               - file: api/models/soil/env_factors
                 title: The env_factors submodule
+              - file: api/models/soil/microbial_groups
+                title: The microbial_groups submodule
               - file: api/models/soil/soil_model
                 title: The soil_model submodule
           - file: api/models/plants

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

@@ -0,0 +1,33 @@
+---
+jupytext:
+  cell_metadata_filter: -all
+  formats: md:myst
+  main_language: python
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.16.7
+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.microbial_groups` module
+
+```{eval-rst}
+.. automodule:: virtual_ecosystem.models.soil.microbial_groups
+    :autosummary:
+    :members:
+```

tests/conftest.py

@@ -83,7 +83,47 @@ def reset_module_registry():
 
 
 @pytest.fixture
-def fixture_config():
+def microbial_groups_cfg():
+    """Configuration string containing full set of required microbial groups."""
+    return """
+        [[soil.microbial_group_definition]]
+        name = "bacteria"
+        max_uptake_rate_labile_C = 0.04
+        activation_energy_uptake_rate = 47000
+        half_sat_labile_C_uptake = 0.364
+        activation_energy_uptake_saturation = 30000
+        max_uptake_rate_ammonium = 5e-3
+        half_sat_ammonium_uptake = 0.02275
+        max_uptake_rate_nitrate = 5e-4
+        half_sat_nitrate_uptake = 0.02275
+        max_uptake_rate_labile_p = 0.0025
+        half_sat_labile_p_uptake = 0.02275
+        turnover_rate = 0.005
+        activation_energy_turnover = 20000
+        c_n_ratio = 5.2
+        c_p_ratio = 16
+
+        [[soil.microbial_group_definition]]
+        name = "fungi"
+        max_uptake_rate_labile_C = 0.04
+        activation_energy_uptake_rate = 47000
+        half_sat_labile_C_uptake = 0.364
+        activation_energy_uptake_saturation = 30000
+        max_uptake_rate_ammonium = 5e-3
+        half_sat_ammonium_uptake = 0.02275
+        max_uptake_rate_nitrate = 5e-4
+        half_sat_nitrate_uptake = 0.02275
+        max_uptake_rate_labile_p = 0.0025
+        half_sat_labile_p_uptake = 0.02275
+        turnover_rate = 0.005
+        activation_energy_turnover = 20000
+        c_n_ratio = 6.5
+        c_p_ratio = 40.0
+        """
+
+
+@pytest.fixture
+def fixture_config(microbial_groups_cfg):
     """Simple configuration fixture for use in tests."""
 
     from virtual_ecosystem.core.config import Config
@@ -250,7 +290,7 @@ def fixture_config():
         [hydrology]
     """
 
-    return Config(cfg_strings=cfg_string)
+    return Config(cfg_strings=[cfg_string, microbial_groups_cfg])
 
 
 @pytest.fixture
@@ -288,7 +328,8 @@ def dummy_carbon_data(fixture_core_components):
     data_values = {
         "soil_c_pool_lmwc": [0.05, 0.02, 0.1, 0.005],
         "soil_c_pool_maom": [2.5, 1.7, 4.5, 0.5],
-        "soil_c_pool_microbe": [5.8, 2.3, 11.3, 1.0],
+        "soil_c_pool_bacteria": [5.8, 2.3, 11.3, 1.0],
+        "soil_c_pool_fungi": [0.89, 8.55, 2.21, 4.54],
         "soil_c_pool_pom": [0.1, 1.0, 0.7, 0.35],
         "soil_c_pool_necromass": [0.058, 0.015, 0.093, 0.105],
         "soil_enzyme_pom": [0.022679, 0.009576, 0.050051, 0.003010],

tests/core/test_data.py

@@ -968,7 +968,8 @@ def test_output_current_state(mocker, dummy_carbon_data, time_index):
         [
             "soil_c_pool_maom",
             "soil_c_pool_lmwc",
-            "soil_c_pool_microbe",
+            "soil_c_pool_bacteria",
+            "soil_c_pool_fungi",
             "soil_c_pool_pom",
             "soil_c_pool_necromass",
             "soil_enzyme_pom",

tests/models/soil/conftest.py

@@ -6,13 +6,15 @@
 
 
 @pytest.fixture
-def fixture_soil_config():
+def fixture_soil_config(microbial_groups_cfg):
     """Create a soil config with faster update interval."""
     from virtual_ecosystem.core.config import Config
 
     return Config(
-        cfg_strings="[core]\n[core.timing]\nupdate_interval = '12 hours'\n[soil]\n"
-        "[hydrology]\n"
+        cfg_strings=[
+            "[core]\n[core.timing]\nupdate_interval = '12 hours'",
+            microbial_groups_cfg,
+        ]
     )
 
 
@@ -120,7 +122,7 @@ def microbial_changes(
         soil_n_pool_nitrate=dummy_carbon_data["soil_n_pool_nitrate"],
         soil_p_pool_dop=dummy_carbon_data["soil_p_pool_dop"],
         soil_p_pool_labile=dummy_carbon_data["soil_p_pool_labile"],
-        soil_c_pool_microbe=dummy_carbon_data["soil_c_pool_microbe"],
+        soil_c_pool_bacteria=dummy_carbon_data["soil_c_pool_bacteria"],
         soil_enzyme_pom=dummy_carbon_data["soil_enzyme_pom"],
         soil_enzyme_maom=dummy_carbon_data["soil_enzyme_maom"],
         soil_temp=dummy_carbon_data["soil_temperature"][
@@ -177,3 +179,13 @@ def maom_desorption(dummy_carbon_data):
         soil_c_pool_maom=dummy_carbon_data["soil_c_pool_maom"],
         desorption_rate_constant=SoilConsts.maom_desorption_rate,
     )
+
+
+@pytest.fixture
+def functional_groups(fixture_config):
+    """Set of functional groups based on the soil model constants."""
+    from virtual_ecosystem.models.soil.microbial_groups import (
+        make_full_set_of_microbial_groups,
+    )
+
+    return make_full_set_of_microbial_groups(config=fixture_config)

tests/models/soil/test_microbial_groups.py

@@ -0,0 +1,197 @@
+"""Test module for soil.microbial_groups.py.
+
+This module tests the functions which generate microbial functional groups.
+"""
+
+from logging import CRITICAL
+
+import pytest
+
+from tests.conftest import log_check
+from virtual_ecosystem.core.config import Config, ConfigurationError
+
+
+def test_make_full_set_of_microbial_groups(fixture_config):
+    """Test that the function to make all the microbial group works."""
+    from virtual_ecosystem.models.soil.microbial_groups import (
+        MicrobialGroupConstants,
+        make_full_set_of_microbial_groups,
+    )
+
+    expected_groups = ["bacteria", "fungi"]
+
+    functional_groups = make_full_set_of_microbial_groups(fixture_config)
+
+    assert set(expected_groups) == set(functional_groups.keys())
+
+    for group in expected_groups:
+        assert type(functional_groups[group]) is MicrobialGroupConstants
+
+    # Only testing one value, as testing them all seems like overkill/hard to maintain
+    assert functional_groups["bacteria"].c_n_ratio == 5.2
+    assert functional_groups["fungi"].c_n_ratio == 6.5
+
+
+@pytest.mark.parametrize(
+    argnames=["cfg_strings", "exp_log"],
+    argvalues=[
+        pytest.param(
+            """[core]""",
+            [
+                (CRITICAL, "Model configuration for soil model not found."),
+            ],
+            id="no_soil_config",
+        ),
+        pytest.param(
+            """
+            [[soil.microbial_group_definition]]
+            name = "bacteria"
+            max_uptake_rate_labile_C = 0.04
+            activation_energy_uptake_rate = 47000
+            half_sat_labile_C_uptake = 0.364
+            activation_energy_uptake_saturation = 30000
+            max_uptake_rate_ammonium = 5e-3
+            half_sat_ammonium_uptake = 0.02275
+            max_uptake_rate_nitrate = 5e-4
+            half_sat_nitrate_uptake = 0.02275
+            max_uptake_rate_labile_p = 0.0025
+            half_sat_labile_p_uptake = 0.02275
+            turnover_rate = 0.005
+            activation_energy_turnover = 20000
+            c_n_ratio = 5.2
+            c_p_ratio = 16
+            """,
+            [
+                (
+                    CRITICAL,
+                    "The following expected soil microbial groups are not defined: "
+                    "fungi",
+                )
+            ],
+            id="missing_fungi",
+        ),
+        pytest.param(  # archaea included but they shouldn't be
+            """
+            [[soil.microbial_group_definition]]
+            name = "bacteria"
+            max_uptake_rate_labile_C = 0.04
+            activation_energy_uptake_rate = 47000
+            half_sat_labile_C_uptake = 0.364
+            activation_energy_uptake_saturation = 30000
+            max_uptake_rate_ammonium = 5e-3
+            half_sat_ammonium_uptake = 0.02275
+            max_uptake_rate_nitrate = 5e-4
+            half_sat_nitrate_uptake = 0.02275
+            max_uptake_rate_labile_p = 0.0025
+            half_sat_labile_p_uptake = 0.02275
+            turnover_rate = 0.005
+            activation_energy_turnover = 20000
+            c_n_ratio = 5.2
+            c_p_ratio = 16
+
+            [[soil.microbial_group_definition]]
+            name = "fungi"
+            max_uptake_rate_labile_C = 0.04
+            activation_energy_uptake_rate = 47000
+            half_sat_labile_C_uptake = 0.364
+            activation_energy_uptake_saturation = 30000
+            max_uptake_rate_ammonium = 5e-3
+            half_sat_ammonium_uptake = 0.02275
+            max_uptake_rate_nitrate = 5e-4
+            half_sat_nitrate_uptake = 0.02275
+            max_uptake_rate_labile_p = 0.0025
+            half_sat_labile_p_uptake = 0.02275
+            turnover_rate = 0.005
+            activation_energy_turnover = 20000
+            c_n_ratio = 5.2
+            c_p_ratio = 16
+
+            [[soil.microbial_group_definition]]
+            name = "archaea"
+            max_uptake_rate_labile_C = 0.04
+            activation_energy_uptake_rate = 47000
+            half_sat_labile_C_uptake = 0.364
+            activation_energy_uptake_saturation = 30000
+            max_uptake_rate_ammonium = 5e-3
+            half_sat_ammonium_uptake = 0.02275
+            max_uptake_rate_nitrate = 5e-4
+            half_sat_nitrate_uptake = 0.02275
+            max_uptake_rate_labile_p = 0.0025
+            half_sat_labile_p_uptake = 0.02275
+            turnover_rate = 0.005
+            activation_energy_turnover = 20000
+            c_n_ratio = 5.2
+            c_p_ratio = 16
+            """,
+            [
+                (
+                    CRITICAL,
+                    "The following microbial groups are not valid: archaea",
+                ),
+            ],
+            id="unexpected_archaea",
+        ),
+        pytest.param(
+            """
+            [[soil.microbial_group_definition]]
+            name = "bacteria"
+            max_uptake_rate_labile_C = 0.04
+            activation_energy_uptake_rate = 47000
+            half_sat_labile_C_uptake = 0.364
+            activation_energy_uptake_saturation = 30000
+            max_uptake_rate_ammonium = 5e-3
+            half_sat_ammonium_uptake = 0.02275
+            max_uptake_rate_nitrate = 5e-4
+            half_sat_nitrate_uptake = 0.02275
+            max_uptake_rate_labile_p = 0.0025
+            half_sat_labile_p_uptake = 0.02275
+            turnover_rate = 0.005
+            activation_energy_turnover = 20000
+            c_n_ratio = 5.2
+            c_p_ratio = 16
+
+            [[soil.microbial_group_definition]]
+            name = "archaea"
+            max_uptake_rate_labile_C = 0.04
+            activation_energy_uptake_rate = 47000
+            half_sat_labile_C_uptake = 0.364
+            activation_energy_uptake_saturation = 30000
+            max_uptake_rate_ammonium = 5e-3
+            half_sat_ammonium_uptake = 0.02275
+            max_uptake_rate_nitrate = 5e-4
+            half_sat_nitrate_uptake = 0.02275
+            max_uptake_rate_labile_p = 0.0025
+            half_sat_labile_p_uptake = 0.02275
+            turnover_rate = 0.005
+            activation_energy_turnover = 20000
+            c_n_ratio = 5.2
+            c_p_ratio = 16
+            """,
+            [
+                (
+                    CRITICAL,
+                    "The following expected soil microbial groups are not defined: "
+                    "fungi",
+                ),
+                (
+                    CRITICAL,
+                    "The following microbial groups are not valid: archaea",
+                ),
+            ],
+            id="missing_fungi_and_unexpected_archaea",
+        ),
+    ],
+)
+def test_make_full_set_of_microbial_groups_errors(caplog, cfg_strings, exp_log):
+    """Check that bad configs generate errors during microbial group generation."""
+    from virtual_ecosystem.models.soil.microbial_groups import (
+        make_full_set_of_microbial_groups,
+    )
+
+    config = Config(cfg_strings=cfg_strings)
+    caplog.clear()
+
+    with pytest.raises(ConfigurationError):
+        _ = make_full_set_of_microbial_groups(config)
+
+    log_check(caplog, exp_log)