API links updated to new model names

docs/source/api/abiotic.md

@@ -16,13 +16,6 @@ kernelspec:
 
 # API reference for `abiotic` modules
 
-The {mod}`~virtual_rainforest.models.abiotic` module is one of the component models of
-the Virtual Rainforest. It is comprised of several submodules that calculate the
-radiation balance, the energy balance, the water balance and the atmospheric CO2
-balance.
-
-Each of the abiotic sub-modules has its own API reference page:
-
-* The {mod}`~virtual_rainforest.models.abiotic.model` submodule instantiates the
-  AbioticModel class which consolidates the functionality of the abiotic module into a
-  single class, which the high level functions of the Virtual Rainforest can then use.
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.abiotic
+```

docs/source/api/abiotic/model.md → docs/source/api/abiotic/abiotic_model.md

@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.models.abiotic.model` module
+# API documentation for the {mod}`~virtual_rainforest.models.abiotic.abiotic_model` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.abiotic.model
+.. automodule:: virtual_rainforest.models.abiotic.abiotic_model
     :autosummary:
     :members:
     :special-members: __init_subclass__, __repr__, __str__

docs/source/api/core.md

@@ -16,27 +16,6 @@ kernelspec:
 
 # API reference for `core` modules
 
-The {mod}`~virtual_rainforest.core` module contains the key shared resources and
-building blocks used to develop the different component models of the Virtual Rainforest
-and then to configure them, populate them with data and provide logging.
-
-Each of the core sub-modules has its own API reference page:
-
-* The {mod}`~virtual_rainforest.core.config` submodule covers the
-  definition of formal configuration schema for components and the parsing and
-  validation of TOML configuration documents against those schema.
-* The {mod}`~virtual_rainforest.core.grid` submodule covers the
-  definition of the spatial layout to be used in a simulation and provides an interface
-  to the spatial relationships between cells.
-* The {mod}`~virtual_rainforest.core.data` submodule provides the
-  central data object used to store data required by the simulation and methods to
-  populate that data object for use in simulations.
-* The {mod}`~virtual_rainforest.core.axes` submodule provides validation for data to
-  ensure that it is congruent with the model configuration.
-* The {mod}`~virtual_rainforest.core.readers` submodule provides functionality to read
-  external data files into a standard internal format.
-* The {mod}`~virtual_rainforest.core.model` submodule provides an Abstract
-  Base Class describing the shared API to be used by science models within the Virtual
-  Rainforest.
-* The {mod}`~virtual_rainforest.core.logger` configures the {class}`~logging.LOGGER`
-  instance used throughout the package.
+```{eval-rst}
+.. automodule:: virtual_rainforest.core
+```

docs/source/api/core/model.md → docs/source/api/core/base_model.md

@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.model` module
+# API documentation for the {mod}`~virtual_rainforest.core.base_model` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.model
+.. automodule:: virtual_rainforest.core.base_model
     :autosummary:
     :members:
     :special-members: __init_subclass__, __repr__, __str__

docs/source/api/core/data.md

@@ -20,5 +20,5 @@ kernelspec:
 .. automodule:: virtual_rainforest.core.data
     :autosummary:
     :members:
-    :special-members: __repr__, __set_item__, __get_item__, __contains__
+    :special-members: __repr__, __setitem__, __getitem__, __contains__
 ```

docs/source/api/soil.md

@@ -16,13 +16,6 @@ kernelspec:
 
 # API reference for `soil` modules
 
-The {mod}`~virtual_rainforest.models.soil` module is one of the component models of the
-Virtual Rainforest. It is comprised of a number of submodules.
-
-Each of the soil sub-modules has its own API reference page:
-
-* The {mod}`~virtual_rainforest.models.soil.model` submodule instantiates the SoilModel
-  class which consolidates the functionality of the soil module into a single class,
-  which the high level functions of the Virtual Rainforest can then make use of.
-* The {mod}`~virtual_rainforest.models.soil.carbon` provides a model for the soil carbon
-  cycle.
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.soil
+```

docs/source/api/soil/carbon.md

@@ -14,7 +14,7 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.soil.carbon` module
+# API documentation for the {mod}`~virtual_rainforest.models.soil.carbon` module
 
 ```{eval-rst}
 .. automodule:: virtual_rainforest.models.soil.carbon

docs/source/api/soil/model.md → docs/source/api/soil/constants.md

@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.soil.model` module
+# API documentation for the {mod}`~virtual_rainforest.models.soil.constants` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.soil.model
+.. automodule:: virtual_rainforest.models.soil.constants
     :autosummary:
     :members:
 ```

docs/source/api/soil/soil_model.md

@@ -0,0 +1,23 @@
+---
+jupytext:
+  cell_metadata_filter: -all
+  formats: md:myst
+  main_language: python
+  text_representation:
+    extension: .md
+    format_name: myst
+    format_version: 0.13
+    jupytext_version: 1.13.8
+kernelspec:
+  display_name: vr_python3
+  language: python
+  name: vr_python3
+---
+
+# API documentation for the {mod}`~virtual_rainforest.models.soil.soil_model` module
+
+```{eval-rst}
+.. automodule:: virtual_rainforest.models.soil.soil_model
+    :autosummary:
+    :members:
+```

docs/source/conf.py

@@ -58,6 +58,7 @@
     "sphinx.ext.autodoc",
     "autodocsumm",
     "sphinx.ext.napoleon",
+    "sphinx.ext.intersphinx",
     "sphinx.ext.mathjax",
     "sphinx.ext.autosummary",
     # "sphinx.ext.autosectionlabel",  # Generates hard to trace exception
@@ -69,6 +70,22 @@
 autodoc_default_flags = ["members"]
 autosummary_generate = True
 
+# Reference checking
+nitpicky = True
+nitpick_ignore = [
+    ("py:class", "jsonschema.validators.Draft202012Validator"),
+    ("py:class", "numpy.float32"),
+    ("py:class", "numpy.int64"),
+]
+intersphinx_mapping = {
+    "numpy": ("https://numpy.org/doc/stable/", None),
+    "python": ("https://docs.python.org/3/", None),
+    "xarray": ("https://docs.xarray.dev/en/stable/", None),
+    "shapely": ("https://shapely.readthedocs.io/en/stable/", None),
+    "jsonschema": ("https://python-jsonschema.readthedocs.io/en/stable/", None),
+}
+
+
 # Set auto labelling to section level
 autosectionlabel_prefix_document = True
 autosectionlabel_maxdepth = 2

docs/source/development/defining_new_models.md

@@ -47,7 +47,7 @@ from virtual_rainforest.core.logger import LOGGER
 # New model class will inherit from BaseModel.
 # InitialisationError is a custom exception, for case where a `Model` class cannot be
 # properly initialised based on the data contained in the configuration
-from virtual_rainforest.core.model import BaseModel, InitialisationError
+from virtual_rainforest.core.base_model import BaseModel, InitialisationError
 ```
 
 The new model class is created using a class method, which means that the model is

docs/source/index.md

@@ -85,12 +85,13 @@ team.
   Data <api/core/data.md>
   File readers <api/core/readers.md>
   Core axes <api/core/axes.md>
-  Base Model <api/core/model.md>
+  Base Model <api/core/base_model.md>
   Soil Overview <api/soil.md>
-  Soil Model <api/soil/model.md>
+  Soil Model <api/soil/soil_model.md>
   Soil Carbon <api/soil/carbon.md>
+  Soil Constants <api/soil/constants.md>
   Abiotic Overview <api/abiotic.md>
-  Abiotic Model <api/abiotic/model.md>
+  Abiotic Model <api/abiotic/abiotic_model.md>
 ```
 
 ```{eval-rst}

docs/source/virtual_rainforest/core/data.md

@@ -103,7 +103,7 @@ two methods:
 data['var_name'] = load_to_dataarray('path/to/file.nc', var='temperature')
 ```
 
-1. The  {meth}`~virtual_rainforest.core.data.Data.load_from_config` method takes a
+1. The  {meth}`~virtual_rainforest.core.data.Data.load_data_config` method takes a
    loaded Data configuration - which is a set of named variables and source files - and
    then just uses {func}`~virtual_rainforest.core.readers.load_to_dataarray` to try and
    load each one.

tests/core/test_model.py → tests/core/test_base_model.py

@@ -1,7 +1,7 @@
-"""Test module for model.py.
+"""Test module for base_model.py.
 
-This module tests the functionality of model.py, which defines the basic model API that
-specific models (e.g. `soil_model.py`) utilise.
+This module tests the functionality of base_model.py, which defines the basic model API
+that specific models (e.g. `soil_model.py`) utilise.
 """
 
 from contextlib import nullcontext as does_not_raise
@@ -11,7 +11,7 @@
 from numpy import datetime64, timedelta64
 
 from tests.conftest import log_check
-from virtual_rainforest.core.model import BaseModel
+from virtual_rainforest.core.base_model import BaseModel
 
 
 def test_base_model_initialization(caplog, mocker):

tests/models/abiotic/test_abiotic_model.py

@@ -7,7 +7,7 @@
 from numpy import datetime64, timedelta64
 
 from tests.conftest import log_check
-from virtual_rainforest.core.model import InitialisationError
+from virtual_rainforest.core.base_model import InitialisationError
 from virtual_rainforest.models.abiotic.abiotic_model import AbioticModel
 
 

tests/models/soil/test_carbon.py

@@ -10,7 +10,7 @@
 import pytest
 
 from tests.conftest import log_check
-from virtual_rainforest.core.model import InitialisationError
+from virtual_rainforest.core.base_model import InitialisationError
 from virtual_rainforest.models.soil.carbon import SoilCarbonPools
 
 

tests/models/soil/test_soil_model.py

@@ -7,7 +7,7 @@
 from numpy import datetime64, timedelta64
 
 from tests.conftest import log_check
-from virtual_rainforest.core.model import InitialisationError
+from virtual_rainforest.core.base_model import InitialisationError
 from virtual_rainforest.models.soil.soil_model import SoilModel
 
 

tests/test_main.py

@@ -11,7 +11,7 @@
 import pytest
 from numpy import datetime64, timedelta64
 
-from virtual_rainforest.core.model import BaseModel, InitialisationError
+from virtual_rainforest.core.base_model import BaseModel, InitialisationError
 from virtual_rainforest.main import (
     check_for_fast_models,
     configure_models,

virtual_rainforest/core/__init__.py

@@ -1,3 +1,32 @@
+"""The :mod:`~virtual_rainforest.core` module contains the key shared resources and
+building blocks used to develop the different component models of the Virtual Rainforest
+and then to configure them, populate them with data and provide logging.
+
+Each of the core sub-modules has its own API reference page:
+
+* The :mod:`~virtual_rainforest.core.config` submodule covers the
+  definition of formal configuration schema for components and the parsing and
+  validation of TOML configuration documents against those schema.
+* The :mod:`~virtual_rainforest.core.grid` submodule covers the
+  definition of the spatial layout to be used in a simulation and provides an interface
+  to the spatial relationships between cells.
+* The :mod:`~virtual_rainforest.core.data` submodule provides the
+  central data object used to store data required by the simulation and methods to
+  populate that data object for use in simulations.
+* The :mod:`~virtual_rainforest.core.axes` submodule provides validation for data to
+  ensure that it is congruent with the model configuration.
+* The :mod:`~virtual_rainforest.core.readers` submodule provides functionality to read
+  external data files into a standard internal format.
+* The :mod:`~virtual_rainforest.core.base_model` submodule provides an Abstract
+  Base Class describing the shared API to be used by science models within the Virtual
+  Rainforest.
+* The :mod:`~virtual_rainforest.core.logger` configures the :class:`~logging.Logger`
+  instance used throughout the package.
+
+The :mod:`~virtual_rainforest.core` module itself is only responsible for loading the
+configuration schema for the core submodules.
+"""  # noqa: D205, D415
+
 import json
 from pathlib import Path
 

virtual_rainforest/core/axes.py

@@ -1,7 +1,7 @@
-"""The :mod:`core.axes` module handles the validation of data being loaded into the core
-data storage of the virtual rainforest simulation. The main functionality in this module
-is ensuring that any loaded data is congruent with the core axes of the simulation and
-the configuration of a given simulation.
+"""The :mod:`~virtual_rainforest.core.axes` module handles the validation of data being
+loaded into the core data storage of the virtual rainforest simulation. The main
+functionality in this module is ensuring that any loaded data is congruent with the core
+axes of the simulation and the configuration of a given simulation.
 
 The AxisValidator class
 =======================
@@ -16,21 +16,21 @@
 
 When new :class:`~virtual_rainforest.core.axes.AxisValidator` subclasses are defined,
 they are automatically added to the
-:attr:`~virtual_rainforest.core.axes.AXIS_VALIDATORS` registry. This maintains a list
-of the validators defined for each core axis.
+:attr:`~virtual_rainforest.core.axes.AXIS_VALIDATORS` registry. This maintains a list of
+the validators defined for each core axis.
 
 Note that the set of validators defined for a specific core axis should be mutually
 exclusive: only one should be applicable to any given dataset being tested on that axis.
 
 DataArray validation
 ====================
 
-The :func:`~virtual_rainforest.core.axes.validate_datarray` function takes an input Data
-Array and applies validation where applicable across all the core axes. The function
-returns the validated input (possibly altered to align with the core axes) along with a
-dictionary using the set of core axes as names: the value associated with each axis name
-is the name of the AxisValidator applied or None if the input did not match a validator
-on that axis.
+The :func:`~virtual_rainforest.core.axes.validate_dataarray` function takes an input
+Data Array and applies validation where applicable across all the core axes. The
+function returns the validated input (possibly altered to align with the core axes)
+along with a dictionary using the set of core axes as names: the value associated with
+each axis name is the name of the AxisValidator applied or None if the input did not
+match a validator on that axis.
 
 Core axes
 =========
@@ -90,11 +90,11 @@ def __init_subclass__(cls) -> None:
         :attr:`~virtual_rainforest.core.axes.AXIS_VALIDATORS` registry. AxisValidators
         are arranged in the registry dictionary as lists keyed under core axis names,
         and the core axis name for a given subclass is set in the  subclass
-        :attr:`~virtual_rainforest.core.axes.AxisValidator.AxisValidator.core_axis`
+        :attr:`~virtual_rainforest.core.axes.AxisValidator.core_axis`
         class attribute.
 
         Raises:
-            Value Error: if the subclass attributes are invalid.
+            ValueError: if the subclass attributes are invalid.
         """
 
         if not hasattr(cls, "core_axis"):