ImperialCollegeLondon · davidorme · Feb 29, 2024 · Feb 21, 2024 · Feb 21, 2024 · Feb 21, 2024
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.10"
   jobs:
     post_create_environment:
       # Install poetry

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,6 +1,6 @@
-# Contributing to the Virtual Rainforest
+# Contributing to the Virtual Ecosystem
 
-We're really happy that you are thinking about contributing to the Virtual Rainforest
+We're really happy that you are thinking about contributing to the Virtual Ecosystem
 project. The whole point of the project is to generate a tool that can be used widely by
 the community and the best way for that to happen is for the community to build it.
 
@@ -9,7 +9,7 @@ To make contributing as seamless as possible, please note these developer guidel
 ## Development setup
 
 Further notes are available [here](source/docs/develop/developer_setup.md) but - once
-you have cloned the Virtual Rainforest repository to your own machine - you will need to
+you have cloned the Virtual Ecosystem repository to your own machine - you will need to
 set up our development toolchain on your machine to contribute to the project.
 
 * We use [`poetry`](https://https://python-poetry.org/) to manage the package
@@ -24,9 +24,9 @@ set up our development toolchain on your machine to contribute to the project.
 We expect all contributors to abide by our [Code of Conduct](CODE_OF_CONDUCT.md). The
 steps for contributing code are:
 
-* Code contributed to the Virtual Rainforest should usually address a documented issue
+* Code contributed to the Virtual Ecosystem should usually address a documented issue
   on the [issue
-  tracker](https://github.com/ImperialCollegeLondon/virtual_rainforest/issues). Very
+  tracker](https://github.com/ImperialCollegeLondon/virtual_ecosystem/issues). Very
   minor changes - typos or simple one-line fixes - may not need to have an issue.
 * If you are fixing an existing issue then that is great, but please do ask to be
   assigned to the issue to avoid duplicating effort!
@@ -39,13 +39,13 @@ steps for contributing code are:
   message body, to tie your pull request to the original issue.
 * Obviously, that code needs to pass the `pre-commit` checks!
 * Now submit a **pull request** to merge your branch into the `develop` branch of the
-  Virtual Rainforest project.
+  Virtual Ecosystem project.
 * We will then review the contributed code and merge it once any problems have been
   resolved.
 
 ## The `pytest` framework
 
 We use [`pytest`](https://docs.pytest.org/) to run continuous integration and other
-testing on the code in the Virtual Rainforest. If you are adding new functionality or
+testing on the code in the Virtual Ecosystem. If you are adding new functionality or
 fixing errors in existing implementations, please also add new tests or amend any
 existing tests.
diff --git a/README.md b/README.md
@@ -1,14 +1,14 @@
-# Welcome to the Virtual Rainforest
+# Welcome to the Virtual Ecosystem
 
 [![codecov](https://codecov.io/gh/ImperialCollegeLondon/virtual_rainforest/branch/develop/graph/badge.svg)](https://codecov.io/gh/ImperialCollegeLondon/virtual_rainforest)
 [![pre-commit.ci status](https://results.pre-commit.ci/badge/github/ImperialCollegeLondon/virtual_rainforest/develop.svg)](https://results.pre-commit.ci/latest/github/ImperialCollegeLondon/virtual_rainforest/develop)
 
-This repository is the home for the development of the Virtual Rainforest. The
-Virtual Rainforest is a project to develop a simulation of all of the major
-processes involved in a real rainforest including the:
+This repository is the home for the development of the Virtual Ecosystem. The
+Virtual Ecosystem is a project to develop a simulation of all of the major
+processes involved in a real ecosystem including the:
 
 * growth and demographic processes of the primary producers within the forest,
-* microclimatic processes within and around the rainforest,
+* microclimatic processes within and around the ecosystem,
 * hydrological processes within the canopy, soil and drainage networks,
 * biotic and abiotic processes within the soil, and the
 * growth and demography of heterotrophs.
@@ -46,5 +46,5 @@ team.
 
 ## Model documentation
 
-The full documentation for the Virtual Rainforest model can be viewed
-[here](https://virtual-rainforest.readthedocs.io/en/latest/).
+The full documentation for the Virtual Ecosystem model can be viewed
+[here](https://virtual-ecosystem.readthedocs.io/en/latest/).
diff --git a/docs/source/api/abiotic_simple.md b/docs/source/api/abiotic_simple.md
@@ -17,5 +17,5 @@ kernelspec:
 # API reference for `abiotic_simple` modules
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.abiotic_simple
+.. automodule:: virtual_ecosystem.models.abiotic_simple
 ```
diff --git a/docs/source/api/abiotic_simple/abiotic_constants.md b/docs/source/api/abiotic_simple/abiotic_constants.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-#  API for the {mod}`~virtual_rainforest.models.abiotic_simple.constants` module
+#  API for the {mod}`~virtual_ecosystem.models.abiotic_simple.constants` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.abiotic_simple.constants
+.. automodule:: virtual_ecosystem.models.abiotic_simple.constants
     :autosummary:
     :members:
     :special-members: __init__

diff --git a/docs/source/api/abiotic_simple/abiotic_simple_model.md b/docs/source/api/abiotic_simple/abiotic_simple_model.md
@@ -15,17 +15,17 @@ kernelspec:
 ---
 
 <!-- markdownlint-disable-next-line  MD013 -->
-# API documentation for the {mod}`~virtual_rainforest.models.abiotic_simple.abiotic_simple_model` module
+# API documentation for the {mod}`~virtual_ecosystem.models.abiotic_simple.abiotic_simple_model` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.abiotic_simple.abiotic_simple_model
+.. automodule:: virtual_ecosystem.models.abiotic_simple.abiotic_simple_model
 ```
 
 <!-- markdownlint-disable-next-line  MD013 -->
-## The {mod}`~virtual_rainforest.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel` class
+## The {mod}`~virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel` class
 
 ```{eval-rst}
-.. autoclass:: virtual_rainforest.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel
+.. autoclass:: virtual_ecosystem.models.abiotic_simple.abiotic_simple_model.AbioticSimpleModel
     :autosummary:
     :members:
     :exclude-members: model_name

diff --git a/docs/source/api/abiotic_simple/microclimate.md b/docs/source/api/abiotic_simple/microclimate.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-#  API for the {mod}`~virtual_rainforest.models.abiotic_simple.microclimate` module
+#  API for the {mod}`~virtual_ecosystem.models.abiotic_simple.microclimate` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.abiotic_simple.microclimate
+.. automodule:: virtual_ecosystem.models.abiotic_simple.microclimate
     :autosummary:
     :members:
     :special-members: __init__

diff --git a/docs/source/api/animals.md b/docs/source/api/animals.md
@@ -17,5 +17,5 @@ kernelspec:
 # API reference for `animals` modules
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals
+.. automodule:: virtual_ecosystem.models.animals
 ```
diff --git a/docs/source/api/animals/animal_cohorts.md b/docs/source/api/animals/animal_cohorts.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.animal_cohorts` module
+# API for the {mod}`~virtual_ecosystem.models.animals.animal_cohorts` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.animal_cohorts
+.. automodule:: virtual_ecosystem.models.animals.animal_cohorts
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/animal_communities.md b/docs/source/api/animals/animal_communities.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.animal_communities` module
+# API for the {mod}`~virtual_ecosystem.models.animals.animal_communities` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.animal_communities
+.. automodule:: virtual_ecosystem.models.animals.animal_communities
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/animal_model.md b/docs/source/api/animals/animal_model.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.animal_model` module
+# API for the {mod}`~virtual_ecosystem.models.animals.animal_model` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.animal_model
+.. automodule:: virtual_ecosystem.models.animals.animal_model
     :autosummary:
     :members:
     :exclude-members: model_name

diff --git a/docs/source/api/animals/animal_traits.md b/docs/source/api/animals/animal_traits.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.animal_traits` module
+# API for the {mod}`~virtual_ecosystem.models.animals.animal_traits` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.animal_traits
+.. automodule:: virtual_ecosystem.models.animals.animal_traits
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/constants.md b/docs/source/api/animals/constants.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.constants` module
+# API for the {mod}`~virtual_ecosystem.models.animals.constants` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.constants
+.. automodule:: virtual_ecosystem.models.animals.constants
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/decay.md b/docs/source/api/animals/decay.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.decay` module
+# API for the {mod}`~virtual_ecosystem.models.animals.decay` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.decay
+.. automodule:: virtual_ecosystem.models.animals.decay
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/functional_group.md b/docs/source/api/animals/functional_group.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.functional_group` module
+# API for the {mod}`~virtual_ecosystem.models.animals.functional_group` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.functional_group
+.. automodule:: virtual_ecosystem.models.animals.functional_group
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/plant_resources.md b/docs/source/api/animals/plant_resources.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.plant_resources` module
+# API for the {mod}`~virtual_ecosystem.models.animals.plant_resources` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.plant_resources
+.. automodule:: virtual_ecosystem.models.animals.plant_resources
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/protocols.md b/docs/source/api/animals/protocols.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.protocols` module
+# API for the {mod}`~virtual_ecosystem.models.animals.protocols` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.protocols
+.. automodule:: virtual_ecosystem.models.animals.protocols
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/animals/scaling_functions.md b/docs/source/api/animals/scaling_functions.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API for the {mod}`~virtual_rainforest.models.animals.scaling_functions` module
+# API for the {mod}`~virtual_ecosystem.models.animals.scaling_functions` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.models.animals.scaling_functions
+.. automodule:: virtual_ecosystem.models.animals.scaling_functions
     :autosummary:
     :members:
     :exclude-members: model_name
diff --git a/docs/source/api/core.md b/docs/source/api/core.md
@@ -17,5 +17,5 @@ kernelspec:
 # API reference for `core` modules
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core
+.. automodule:: virtual_ecosystem.core
 ```
diff --git a/docs/source/api/core/axes.md b/docs/source/api/core/axes.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.axes` module
+# API documentation for the {mod}`~virtual_ecosystem.core.axes` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.axes
+.. automodule:: virtual_ecosystem.core.axes
     :autosummary:
     :members:
     :special-members: __init_subclass__

diff --git a/docs/source/api/core/base_model.md b/docs/source/api/core/base_model.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.base_model` module
+# API documentation for the {mod}`~virtual_ecosystem.core.base_model` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.base_model
+.. automodule:: virtual_ecosystem.core.base_model
     :autosummary:
     :members:
     :special-members: __init_subclass__, __repr__, __str__, __init__

diff --git a/docs/source/api/core/config.md b/docs/source/api/core/config.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.config` module
+# API documentation for the {mod}`~virtual_ecosystem.core.config` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.config
+.. automodule:: virtual_ecosystem.core.config
     :autosummary:
     :members:
 ```
diff --git a/docs/source/api/core/constants.md b/docs/source/api/core/constants.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.constants` module
+# API documentation for the {mod}`~virtual_ecosystem.core.constants` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.constants
+.. automodule:: virtual_ecosystem.core.constants
     :autosummary:
     :members:
 ```
diff --git a/docs/source/api/core/constants_class.md b/docs/source/api/core/constants_class.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.constants_class` module
+# API documentation for the {mod}`~virtual_ecosystem.core.constants_class` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.constants_class
+.. automodule:: virtual_ecosystem.core.constants_class
     :autosummary:
     :members:
 ```
diff --git a/docs/source/api/core/constants_loader.md b/docs/source/api/core/constants_loader.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.constants_loader` module
+# API documentation for the {mod}`~virtual_ecosystem.core.constants_loader` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.constants_loader
+.. automodule:: virtual_ecosystem.core.constants_loader
     :autosummary:
     :members:
 ```
diff --git a/docs/source/api/core/core_components.md b/docs/source/api/core/core_components.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.core_components` module
+# API documentation for the {mod}`~virtual_ecosystem.core.core_components` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.core_components
+.. automodule:: virtual_ecosystem.core.core_components
     :autosummary:
     :members: 
     :special-members: __post_init__

diff --git a/docs/source/api/core/data.md b/docs/source/api/core/data.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.data` module
+# API documentation for the {mod}`~virtual_ecosystem.core.data` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.data
+.. automodule:: virtual_ecosystem.core.data
     :autosummary:
     :members:
     :special-members: __repr__, __setitem__, __getitem__, __contains__

diff --git a/docs/source/api/core/exceptions.md b/docs/source/api/core/exceptions.md
@@ -14,10 +14,10 @@ kernelspec:
   name: vr_python3
 ---
 
-# API documentation for the {mod}`~virtual_rainforest.core.exceptions` module
+# API documentation for the {mod}`~virtual_ecosystem.core.exceptions` module
 
 ```{eval-rst}
-.. automodule:: virtual_rainforest.core.exceptions
+.. automodule:: virtual_ecosystem.core.exceptions
     :autosummary:
     :members:
 ```