Merge branch 'develop' into 687_fix_static

docs/source/api/models/abiotic/abiotic_model.md

@@ -38,4 +38,5 @@ language_info:
     :autosummary:
     :members:
     :exclude-members: model_name
+    :inherited-members:
 ```

docs/source/api/models/abiotic_simple/abiotic_simple_model.md

@@ -39,4 +39,5 @@ language_info:
     :autosummary:
     :members:
     :exclude-members: model_name
+    :inherited-members:
 ```

docs/source/api/models/animal/animal_model.md

@@ -31,4 +31,5 @@ language_info:
     :autosummary:
     :members:
     :exclude-members: model_name, random
+    :inherited-members:
 ```

docs/source/api/models/hydrology/hydrology_model.md

@@ -32,4 +32,5 @@ language_info:
     :autosummary:
     :members:
     :exclude-members: model_name
+    :inherited-members:
 ```

docs/source/api/models/litter/litter_model.md

@@ -31,4 +31,5 @@ language_info:
     :autosummary:
     :members:
     :exclude-members: model_name
+    :inherited-members:
 ```

docs/source/api/models/plants/plants_model.md

@@ -33,6 +33,7 @@ language_info:
     :autosummary:
     :members:
     :exclude-members: model_name
+    :inherited-members:
 ```
 
 ## The plants {mod}`~virtual_ecosystem.models.plants.constants` module

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

@@ -31,4 +31,5 @@ language_info:
     :autosummary:
     :members:
     :exclude-members: model_name
+    :inherited-members:
 ```

docs/source/conf.py

@@ -154,7 +154,9 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ("py:class", "numpy.bool_"),
     ("py:class", "np.float32"),
     ("py:class", "np.datetime64"),
+    ("py:class", "np.ndarray"),
     ("py:class", "np.timedelta64"),
+    ("py:class", "timedelta64"),
     ("py:class", "InitVar"),
     ("py:class", "dataclasses.InitVar"),
     ("py:class", "Quantity"),

virtual_ecosystem/core/base_model.py

@@ -9,6 +9,8 @@
 
 * Creating a model instance (:class:`~virtual_ecosystem.core.base_model.BaseModel`).
 * Setup a model instance (:meth:`~virtual_ecosystem.core.base_model.BaseModel._setup`).
+  This method should include any initialization logic including validating and
+  populating class attributes.
 * Perform any spinup required to get a model state to equilibrate
   (:meth:`~virtual_ecosystem.core.base_model.BaseModel.spinup`).
 * Update the model from one time step to the next
@@ -56,8 +58,10 @@
 The ``BaseModel.__init__`` method
 ----------------------------------
 
-Each model subclass will include an ``__init__`` method that validates and populates
-model specific attributes. That ``__init__`` method **must** call the
+Each model subclass should include an ``__init__`` method that defines all
+model specific attributes. The ``__init__`` should not contain any further
+initialization logic, which should happen in the subclass ``_setup`` method instead.
+The ``__init__`` method **must** call the
 :meth:`BaseModel.__init__() <virtual_ecosystem.core.base_model.BaseModel.__init__>`
 method, as this populates core shared model attrributes - see the linked method
 description for details.
@@ -605,8 +609,6 @@ class ExampleModel(
                 defined
             TypeError: If model_name is not a string
         """
-        if cls.__init__ != BaseModel.__init__:
-            raise NotImplementedError("Model subclasses cannot override __init__.")
 
         if cls.update != BaseModel.update:
             raise NotImplementedError(

virtual_ecosystem/models/abiotic/abiotic_model.py

@@ -147,6 +147,26 @@ class AbioticModel(
         model_constants: Set of constants for the abiotic model.
     """
 
+    def __init__(
+        self,
+        data: Data,
+        core_components: CoreComponents,
+        static: bool = False,
+        **kwargs: Any,
+    ):
+        """Abiotic init function.
+
+        The init function is used only to define class attributes. Any logic should be
+        handeled in :fun:`~virtual_ecosystem.abiotic.abiotic_model._setup`.
+        """
+
+        super().__init__(data, core_components, static, **kwargs)
+
+        self.model_constants: AbioticConsts
+        """Set of constants for the abiotic model."""
+        self.simple_constants: AbioticSimpleConsts
+        """Set of constants for simple abiotic model."""
+
     @classmethod
     def from_config(
         cls, data: Data, core_components: CoreComponents, config: Config
@@ -193,10 +213,8 @@ def _setup(
             **kwargs: Further arguments to the setup method.
         """
 
-        self.model_constants: AbioticConsts = model_constants
-        """Set of constants for the abiotic model."""
-        self.simple_constants: AbioticSimpleConsts = AbioticSimpleConsts()
-        """Set of constants for simple abiotic model."""
+        self.model_constants = model_constants
+        self.simple_constants = AbioticSimpleConsts()
 
         # create soil temperature array
         self.data["soil_temperature"] = self.layer_structure.from_template()

virtual_ecosystem/models/abiotic_simple/abiotic_simple_model.py

@@ -73,10 +73,26 @@ class AbioticSimpleModel(
         model_constants: Set of constants for the abiotic_simple model.
     """
 
-    model_constants: AbioticSimpleConsts
-    """Set of constants for the abiotic simple model"""
-    bounds: AbioticSimpleBounds
-    """Upper and lower bounds for abiotic variables."""
+    def __init__(
+        self,
+        data: Data,
+        core_components: CoreComponents,
+        static: bool = False,
+        **kwargs: Any,
+    ):
+        """Abiotic simple init.
+
+        The init function is used only to define class attributes. Any logic should be
+        handeled in
+        :fun:`~virtual_ecosystem.abiotic_simple.abiotic_simple_model._setup`.
+        """
+
+        super().__init__(data, core_components, static, **kwargs)
+
+        self.model_constants: AbioticSimpleConsts
+        """Set of constants for the abiotic simple model"""
+        self.bounds: AbioticSimpleBounds
+        """Upper and lower bounds for abiotic variables."""
 
     @classmethod
     def from_config(

virtual_ecosystem/models/animal/animal_model.py

@@ -121,11 +121,39 @@ class AnimalModel(
         model_constants: Set of constants for the animal model.
     """
 
-    communities: dict[int, list[AnimalCohort]]
-    """Animal communities with grid cell IDs and lists of AnimalCohorts."""
+    def __init__(
+        self,
+        data: Data,
+        core_components: CoreComponents,
+        static: bool = False,
+        **kwargs: Any,
+    ):
+        """Animal init function.
+
+        The init function is used only to define class attributes. Any logic should be
+        handeled in :fun:`~virtual_ecosystem.animal.animal_model._setup`.
+        """
 
-    cohorts: dict[uuid.UUID, AnimalCohort]
-    """A dictionary of all animal cohorts and their unique ids."""
+        super().__init__(data, core_components, static, **kwargs)
+
+        self.communities: dict[int, list[AnimalCohort]]
+        """Animal communities with grid cell IDs and lists of AnimalCohorts."""
+        self.cohorts: dict[uuid.UUID, AnimalCohort]
+        """A dictionary of all animal cohorts and their unique ids."""
+        self.update_interval_timedelta: timedelta64
+        """Convert pint update_interval to timedelta64 once during initialization."""
+        self.functional_groups: list[FunctionalGroup]
+        """List of functional groups in the model."""
+        self.model_constants: AnimalConsts
+        """Animal constants."""
+        self.plant_resources: dict[int, list[Resource]]
+        """The plant resource pools in the model with associated grid cell ids."""
+        self.excrement_pools: dict[int, list[ExcrementPool]]
+        """The excrement pools in the model with associated grid cell ids."""
+        self.carcass_pools: dict[int, list[CarcassPool]]
+        """The carcass pools in the model with associated grid cell ids."""
+        self.leaf_waste_pools: dict[int, HerbivoryWaste]
+        """A pool for leaves removed by herbivory but not actually consumed."""
 
     def _setup_grid_neighbours(self) -> None:
         """Set up grid neighbours for the model.
@@ -231,22 +259,19 @@ def _setup(
         self._setup_grid_neighbours()
         """Determine grid square adjacency."""
         self.functional_groups = functional_groups
-        """List of functional groups in the model."""
         self.model_constants = model_constants
-        """Animal constants."""
-        self.plant_resources: dict[int, list[Resource]] = {
+        self.plant_resources = {
             cell_id: [
                 PlantResources(
                     data=self.data, cell_id=cell_id, constants=self.model_constants
                 )
             ]
             for cell_id in self.data.grid.cell_id
         }
-        """The plant resource pools in the model with associated grid cell ids."""
         # TODO - In future, need to take in data on average size of excrement and
         # carcasses pools and their stoichiometries for the initial scavengeable pool
         # parameterisations
-        self.excrement_pools: dict[int, list[ExcrementPool]] = {
+        self.excrement_pools = {
             cell_id: [
                 ExcrementPool(
                     scavengeable_carbon=1e-3,
@@ -259,8 +284,7 @@ def _setup(
             ]
             for cell_id in self.data.grid.cell_id
         }
-        """The excrement pools in the model with associated grid cell ids."""
-        self.carcass_pools: dict[int, list[CarcassPool]] = {
+        self.carcass_pools = {
             cell_id: [
                 CarcassPool(
                     scavengeable_carbon=1e-3,
@@ -273,17 +297,13 @@ def _setup(
             ]
             for cell_id in self.data.grid.cell_id
         }
-        """The carcass pools in the model with associated grid cell ids."""
-        self.leaf_waste_pools: dict[int, HerbivoryWaste] = {
+
+        self.leaf_waste_pools = {
             cell_id: HerbivoryWaste(plant_matter_type="leaf")
             for cell_id in self.data.grid.cell_id
         }
-        """A pool for leaves removed by herbivory but not actually consumed."""
-        self.cohorts: dict[uuid.UUID, AnimalCohort] = {}
-        """A dictionary of all animal cohorts and their unique ids."""
-        self.communities: dict[int, list[AnimalCohort]] = {
-            cell_id: list() for cell_id in self.data.grid.cell_id
-        }
+        self.cohorts = {}
+        self.communities = {cell_id: list() for cell_id in self.data.grid.cell_id}
 
         self._initialize_communities(functional_groups)
         """Create the dictionary of animal communities and populate each community with