Move animals over to the new configuration system

docs/source/_toc.yaml

@@ -162,6 +162,8 @@ subtrees:
                 title: The animal_cohorts submodule
               - file: api/models/animal/animal_model
                 title: The animal_model submodule
+              - file: api/models/animal/model_config
+                title: The model_config submodule
               - file: api/models/animal/animal_traits
                 title: The animal_traits submodule
               - file: api/models/animal/constants

docs/source/api/models/animal/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.animal.model_config` module
+
+```{eval-rst}
+.. automodule:: virtual_ecosystem.models.animal.model_config
+    :autosummary:
+    :members:
+    :exclude-members: model_config
+```

docs/source/conf.py

@@ -205,6 +205,11 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     # when both do actually appear in the API docs? It's right there.
     ("py:class", "DIRPATH_PLACEHOLDER"),
     ("py:class", "PyrealmConst"),
+    # Typing on animal.model_config
+    ("py:class", "virtual_ecosystem.models.animal.animal_traits.Annotated"),
+    ("py:class", "virtual_ecosystem.models.animal.model_config.serialise_diet_type"),
+    ("py:class", "virtual_ecosystem.models.animal.model_config.deserialise_diet_type"),
+    ("py:class", "always"),
 ]
 
 intersphinx_mapping = {

docs/source/using_the_ve/virtual_ecosystem_in_static_mode.md

@@ -1,6 +1,4 @@
 ---
-execution:
-  timeout: 210
 jupytext:
   formats: md:myst
   main_language: python
@@ -13,16 +11,9 @@ 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: 3.11.14
+mystnb:
+  execution_timeout: 60
+  execution_mode: 'off'
 ---
 
 # Running the Virtual Ecosystem in Static Mode

tests/models/animals/conftest.py

@@ -388,9 +388,9 @@ def animal_data_for_cohorts_instance(fixture_core_components):
 @pytest.fixture
 def constants_instance():
     """Fixture for an instance of animal constants."""
-    from virtual_ecosystem.models.animal.constants import AnimalConsts
+    from virtual_ecosystem.models.animal.model_config import AnimalConstants
 
-    return AnimalConsts(density_scaling_method="madingley")
+    return AnimalConstants(density_scaling_method="madingley")
 
 
 @pytest.fixture
@@ -425,14 +425,15 @@ def animal_model_instance(
     from copy import deepcopy
 
     from virtual_ecosystem.models.animal.animal_model import AnimalModel
+    from virtual_ecosystem.models.animal.model_config import AnimalConstants
 
     # Make sure each call gets a fresh copy
     clean_data = deepcopy(dummy_animal_data)
 
     return AnimalModel(
         data=clean_data,
         core_components=fixture_core_components,
-        density_scaling_method="madingley",
+        model_constants=AnimalConstants(density_scaling_method="madingley"),
         functional_groups=functional_group_list_instance,
         microbial_c_n_p_ratios=microbial_c_n_p_ratios,
     )
@@ -449,14 +450,15 @@ def animal_model_damuth_instance(
     from copy import deepcopy
 
     from virtual_ecosystem.models.animal.animal_model import AnimalModel
+    from virtual_ecosystem.models.animal.model_config import AnimalConstants
 
     # Make sure each call gets a fresh copy
     clean_data = deepcopy(dummy_animal_data)
 
     return AnimalModel(
         data=clean_data,
         core_components=fixture_core_components,
-        density_scaling_method="damuth",
+        model_constants=AnimalConstants(density_scaling_method="damuth"),
         functional_groups=functional_group_list_instance,
         microbial_c_n_p_ratios=microbial_c_n_p_ratios,
     )

tests/models/animals/test_animal_cohorts.py

@@ -990,7 +990,7 @@ def test_calculate_alpha(
         """Testing for calculate alpha."""
         # Assuming necessary imports and setup based on previous examples
         from virtual_ecosystem.models.animal.animal_cohorts import AnimalCohort
-        from virtual_ecosystem.models.animal.constants import AnimalConsts
+        from virtual_ecosystem.models.animal.model_config import AnimalConstants
 
         # Mock the scaling function to control its return value
         mocker.patch(
@@ -999,7 +999,7 @@ def test_calculate_alpha(
         )
 
         # Setup constants and functional group mock
-        constants = AnimalConsts()
+        constants = AnimalConstants()
         functional_group_mock = herbivore_functional_group_instance
 
         # Initialize the AnimalCohort instance with test parameters

tests/models/animals/test_animal_constants.py

@@ -1,19 +1,20 @@
 """Test module for animal_traits.py."""
 
 import pytest
+from pydantic import ValidationError
 
 from virtual_ecosystem.models.animal.animal_traits import DietType, TaxaType
-from virtual_ecosystem.models.animal.constants import AnimalConsts
+from virtual_ecosystem.models.animal.model_config import AnimalConstants
 
 
-class TestAnimalConsts:
-    """Tests for the AnimalConsts dataclass methods."""
+class TestAnimalConstants:
+    """Tests for the AnimalConstants dataclass methods."""
 
     def test_get_population_density_terms_damuth(self):
         """Test Damuth method returns correct terms."""
 
         # Create instance with damuth method
-        animal_consts = AnimalConsts(density_scaling_method="damuth")
+        animal_consts = AnimalConstants(density_scaling_method="damuth")
 
         # Get terms for Mammal Herbivore
         result = animal_consts.get_population_density_terms(
@@ -30,7 +31,7 @@ def test_get_population_density_terms_madingley(self):
         """Test Madingley method returns correct terms."""
 
         # Create instance with madingley method
-        animal_consts = AnimalConsts(density_scaling_method="madingley")
+        animal_consts = AnimalConstants(density_scaling_method="madingley")
 
         # Get terms (taxa/diet ignored in madingley)
         result = animal_consts.get_population_density_terms(
@@ -43,11 +44,6 @@ def test_get_population_density_terms_madingley(self):
     def test_get_population_density_terms_invalid_method(self):
         """Test invalid scaling method raises ValueError."""
 
-        # Create instance with invalid method
-        animal_consts = AnimalConsts(density_scaling_method="invalid_method")
-
-        # Ensure ValueError is raised
-        with pytest.raises(ValueError):
-            animal_consts.get_population_density_terms(
-                TaxaType.MAMMAL, DietType.HERBIVORE
-            )
+        # Ensure ValidationError is raised
+        with pytest.raises(ValidationError):
+            AnimalConstants(density_scaling_method="invalid_method")

tests/models/animals/test_animal_model.py

@@ -49,13 +49,14 @@ def test_animal_model_initialization(
         """Test `AnimalModel` initialization with both scaling methods."""
         from virtual_ecosystem.core.base_model import BaseModel
         from virtual_ecosystem.models.animal.animal_model import AnimalModel
+        from virtual_ecosystem.models.animal.model_config import AnimalConstants
 
         # Initialize the model
         model = AnimalModel(
             data=dummy_animal_data,
             core_components=fixture_core_components,
             functional_groups=functional_group_list_instance,
-            density_scaling_method=scaling_method,
+            model_constants=AnimalConstants(density_scaling_method=scaling_method),
             microbial_c_n_p_ratios=microbial_c_n_p_ratios,
         )
 
@@ -74,7 +75,6 @@ def test_animal_model_initialization(
             pytest.param(
                 does_not_raise(),
                 (
-                    (INFO, "Initialised animal.AnimalConsts from config"),
                     (
                         INFO,
                         "Information required to initialise the animal model"
@@ -207,25 +207,24 @@ def test_from_config(
         self,
         scaling_method,
         dummy_animal_data,
-        animal_fixture_config,
         animal_fixture_configuration,
         fixture_core_components,
     ):
         """Test that AnimalModel.from_config correctly sets density_scaling_method."""
         from virtual_ecosystem.models.animal.animal_model import AnimalModel
 
-        # Update the config to include the scaling method
-        animal_fixture_config["animal"]["density_scaling_method"] = scaling_method
-
+        # Update the constants to set the scaling method
         # Configuration classes are frozen so update via the __dict__ entries
-        animal_fixture_configuration.animal.__dict__["density_scaling_method"]
+        animal_fixture_configuration.animal.constants.__dict__[
+            "density_scaling_method"
+        ] = scaling_method
 
         # Create the model using from_config
         model = AnimalModel.from_config(
             data=dummy_animal_data,
             configuration=animal_fixture_configuration,
             core_components=fixture_core_components,
-            config=animal_fixture_config,
+            config=dict(),
         )
 
         # Check that the model has the correct scaling method set
@@ -638,6 +637,7 @@ def test_calculate_total_soil_consumption(
         self,
         litter_soil_data_instance,
         fixture_core_components,
+        fixture_core_constants,
         functional_group_list_instance,
         constants_instance,
         microbial_c_n_p_ratios,
@@ -647,7 +647,6 @@ def test_calculate_total_soil_consumption(
 
         import numpy as np
 
-        from virtual_ecosystem.core.constants import CoreConsts
         from virtual_ecosystem.models.animal.animal_model import AnimalModel
         from virtual_ecosystem.models.animal.decay import SoilPool
 
@@ -724,7 +723,7 @@ def test_calculate_total_soil_consumption(
                     cell_id=cid,
                     data=new_data,
                     cell_area=cell_area,
-                    max_depth_microbial_activity=CoreConsts.max_depth_of_microbial_activity,
+                    max_depth_microbial_activity=fixture_core_constants.max_depth_of_microbial_activity,
                     c_n_p_ratios=microbial_c_n_p_ratios,
                 )
                 for pool_name in pool_names
@@ -982,8 +981,8 @@ def test_estimate_total_individuals(
 
         from math import ceil
 
-        from virtual_ecosystem.models.animal.constants import AnimalConsts
         from virtual_ecosystem.models.animal.functional_group import FunctionalGroup
+        from virtual_ecosystem.models.animal.model_config import AnimalConstants
 
         # Always patch damuths_law to return predictable 42.0
         mock_damuth = mocker.patch(
@@ -1016,7 +1015,7 @@ def test_estimate_total_individuals(
             vertical_occupancy="ground",
             birth_mass=0.1,
             adult_mass=10.0,
-            constants=AnimalConsts(density_scaling_method=scaling_method),
+            constants=AnimalConstants(density_scaling_method=scaling_method),
             density_individuals_m2=density,
         )