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Converted virtual_ecosystem_in_static_mode.md to a juypter notebook #1269

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Merged
jacobcook1995 merged 4 commits into from
Jan 22, 2026
Merged

Converted virtual_ecosystem_in_static_mode.md to a juypter notebook #1269

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72ed3fe
Converted virtual_ecosystem_in_static_mode.md to be a juypter noteboo…
jacobcook1995 Jan 21, 2026
6dd8f1d
Merge branch 'develop' into 1268-store-virtual_ecosystem_in_static_mo…
jacobcook1995 Jan 21, 2026
021df4c
Added script to update all notebook + fixed issues in ve_in_use notebook
jacobcook1995 Jan 22, 2026
93b05e2
Added pandas.DataFrame to the nickpick ignore
jacobcook1995 Jan 22, 2026
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3 changes: 3 additions & 0 deletions docs/source/conf.py
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Expand Up @@ -215,6 +215,9 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
("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"),
# This broke when pandas upgraded to 3.0. We should review this once we've upgraded
# to that major version
("py:class", "pandas.core.frame.DataFrame"),
]

intersphinx_mapping = {
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25 changes: 25 additions & 0 deletions docs/source/update_notebooks.sh
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@@ -0,0 +1,25 @@
#!/usr/bin/env bash
# Bash script to update all notebooks used in the documentation.
# To reduce build times the notebooks included in the documentation don't update
# automatically when the documentation runs and instead just show their saved output.
# However, if major changes are made to model we would want to update all of the relevant
# notebooks, so this script exists to simplify the process.

# This should be kept upto date manually as we may want to add notebooks that never get
# updated, in which case we wouldn't want to use autodiscovery
NOTEBOOKS=(
"./using_the_ve/virtual_ecosystem_in_static_mode.ipynb"
"./using_the_ve/virtual_ecosystem_in_use.ipynb"
)

# Loop over notebooks, loading, executing and saving each one in turn
for notebook in "${NOTEBOOKS[@]}"; do

jupyter nbconvert \
--to notebook \
--execute \
--inplace \
--ExecutePreprocessor.timeout=600 \
--ExecutePreprocessor.kernel_name=python3 \
"${notebook}"
done
1 change: 1 addition & 0 deletions docs/source/using_the_ve/.gitignore
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@@ -1 +1,2 @@
!virtual_ecosystem_in_use.ipynb
!virtual_ecosystem_in_static_mode.ipynb
2 changes: 1 addition & 1 deletion docs/source/using_the_ve/configuration/config.md
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Expand Up @@ -222,7 +222,7 @@ useful to set some models to keep their data in a static state. For example:
To implement this, all models (except `core`) accept a boolean configuration option,
`static`, that indicates if such the model data should held static. Changing the default
configuration `static=false` to `static=true` puts a model into static mode. For an
example of this in use, see [this tutorial](../virtual_ecosystem_in_static_mode.md).
example of this in use, see [this tutorial](../virtual_ecosystem_in_static_mode.ipynb).

However, even when the model is run in static mode the model constants and variables
need to be populated, for use by any models that are not in static mode. Because of
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2 changes: 1 addition & 1 deletion docs/source/using_the_ve/example_data.md
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Expand Up @@ -402,4 +402,4 @@ The example model data directory also contains:
[data inputs](./model_data_inputs.md) using data for your ecosystem.

* The `static_config` directory is empty and is used as part of the advanced usage of
[static models](./virtual_ecosystem_in_static_mode.md) in the Virtual Ecosystem.
[static models](./virtual_ecosystem_in_static_mode.ipynb) in the Virtual Ecosystem.
7 changes: 4 additions & 3 deletions docs/source/using_the_ve/overview.md
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Expand Up @@ -67,6 +67,7 @@ Once you have your own model running, you can run experiments on the system.
sensitivity of your simulation to changes in the parameterisation.

* Isolate a single component of the model to see how it responds to constant inputs
through time using the [static model system](./virtual_ecosystem_in_static_mode.md).
Although this is primarily intended as a model development tool, it can be useful to
understand the details of how different components of your model are behaving.
through time using the [static model
system](./virtual_ecosystem_in_static_mode.ipynb). Although this is primarily intended
as a model development tool, it can be useful to understand the details of how
different components of your model are behaving.
81 changes: 40 additions & 41 deletions docs/source/using_the_ve/truncated_logfile.log
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@@ -1,42 +1,41 @@
[INFO] - config - collect_config_paths(329) - Config paths resolve to 5 files
[INFO] - config - load_config_toml(358) - Config TOML loaded from ve_example/config/soil_microbial_groups.toml
[INFO] - config - load_config_toml(358) - Config TOML loaded from ve_example/config/ve_run.toml
[INFO] - config - load_config_toml(358) - Config TOML loaded from ve_example/config/plant_config.toml
[INFO] - config - load_config_toml(358) - Config TOML loaded from ve_example/config/data_config.toml
[INFO] - config - load_config_toml(358) - Config TOML loaded from ve_example/config/animal_functional_groups.toml
[INFO] - config - build_config(463) - Config built from 5 file(s)
[INFO] - config - build_config(465) - Config input file: ve_example/config
[INFO] - registry - register_module(109) - Registering module: virtual_ecosystem.core
[INFO] - registry - register_module(159) - Schema registered for virtual_ecosystem.core: /Users/dorme/Research/Virtual_Rainforest/virtual_ecosystem/virtual_ecosystem/core/module_schema.json
[INFO] - registry - register_module(181) - Constants class registered for virtual_ecosystem.core: CoreConsts
[INFO] - registry - register_module(109) - Registering module: virtual_ecosystem.models.soil
[INFO] - registry - register_module(143) - Registering model class for virtual_ecosystem.models.soil: SoilModel
[INFO] - registry - register_module(159) - Schema registered for virtual_ecosystem.models.soil: /Users/dorme/Research/Virtual_Rainforest/virtual_ecosystem/virtual_ecosystem/models/soil/module_schema.json
[INFO] - registry - register_module(181) - Constants class registered for virtual_ecosystem.models.soil: SoilConsts
[INFO] - registry - register_module(109) - Registering module: virtual_ecosystem.models.hydrology
[INFO] - registry - register_module(143) - Registering model class for virtual_ecosystem.models.hydrology: HydrologyModel
[INFO] - registry - register_module(159) - Schema registered for virtual_ecosystem.models.hydrology: /Users/dorme/Research/Virtual_Rainforest/virtual_ecosystem/virtual_ecosystem/models/hydrology/module_schema.json
[INFO] - registry - register_module(181) - Constants class registered for virtual_ecosystem.models.hydrology: HydroConsts
# Does that need changing manually?
[INFO] - registry - register_module(109) - Registering module: virtual_ecosystem.models.abiotic_simple
[INFO] - config_builder - _collect_config_paths(416) - Config paths resolve to 5 files
[INFO] - config_builder - _load_config_toml(439) - Config TOML loaded from ve_example/config/soil_microbial_groups.toml
[INFO] - config_builder - _load_config_toml(439) - Config TOML loaded from ve_example/config/ve_run.toml
[INFO] - config_builder - _load_config_toml(439) - Config TOML loaded from ve_example/config/plant_config.toml
[INFO] - config_builder - _load_config_toml(439) - Config TOML loaded from ve_example/config/data_config.toml
[INFO] - config_builder - _load_config_toml(439) - Config TOML loaded from ve_example/config/animal_config.toml
[INFO] - config_builder - _compile_data(363) - Configuration data compiled.
[INFO] - registry - register_module(91) - Registering module: virtual_ecosystem.models.soil
[INFO] - registry - get_model(161) - Registering model class for virtual_ecosystem.models.soil: SoilModel
[INFO] - registry - register_module(104) - Configuration class registered for virtual_ecosystem.models.soil
[INFO] - registry - register_module(91) - Registering module: virtual_ecosystem.core
[INFO] - registry - register_module(104) - Configuration class registered for virtual_ecosystem.core
[INFO] - registry - register_module(91) - Registering module: virtual_ecosystem.models.hydrology
[INFO] - registry - get_model(161) - Registering model class for virtual_ecosystem.models.hydrology: HydrologyModel
[INFO] - registry - register_module(104) - Configuration class registered for virtual_ecosystem.models.hydrology
[INFO] - registry - register_module(91) - Registering module: virtual_ecosystem.models.abiotic
[INFO] - registry - get_model(161) - Registering model class for virtual_ecosystem.models.abiotic: AbioticModel
[INFO] - registry - register_module(104) - Configuration class registered for virtual_ecosystem.models.abiotic
[INFO] - registry - register_module(91) - Registering module: virtual_ecosystem.models.animal
[INFO] - registry - get_model(161) - Registering model class for virtual_ecosystem.models.animal: AnimalModel
--- many lines omitted ---
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_n_pool_necromass'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_n_pool_maom'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_n_pool_ammonium'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_n_pool_nitrate'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_p_pool_dop'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_p_pool_particulate'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_p_pool_necromass'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_p_pool_maom'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_p_pool_primary'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_p_pool_secondary'
[INFO] - data - __setitem__(226) - Replacing data array for 'soil_p_pool_labile'
[INFO] - data - __setitem__(226) - Replacing data array for 'production_of_fungal_fruiting_bodies'
[INFO] - data - __setitem__(226) - Replacing data array for 'dissolved_nitrate'
[INFO] - data - __setitem__(226) - Replacing data array for 'dissolved_ammonium'
[INFO] - data - __setitem__(226) - Replacing data array for 'dissolved_phosphorus'
[INFO] - data - __setitem__(226) - Replacing data array for 'ecto_supply_limit_n'
[INFO] - data - __setitem__(226) - Replacing data array for 'ecto_supply_limit_p'
[INFO] - data - __setitem__(226) - Replacing data array for 'arbuscular_supply_limit_n'
[INFO] - data - __setitem__(226) - Replacing data array for 'arbuscular_supply_limit_p'
[INFO] - main - ve_run(251) - Virtual Ecosystem model run completed!
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_n_pool_necromass'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_n_pool_maom'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_n_pool_ammonium'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_n_pool_nitrate'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_p_pool_dop'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_p_pool_particulate'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_p_pool_necromass'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_p_pool_maom'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_p_pool_primary'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_p_pool_secondary'
[INFO] - data - __setitem__(233) - Replacing data array for 'soil_p_pool_labile'
[INFO] - data - __setitem__(233) - Replacing data array for 'production_of_fungal_fruiting_bodies'
[INFO] - data - __setitem__(233) - Replacing data array for 'dissolved_nitrate'
[INFO] - data - __setitem__(233) - Replacing data array for 'dissolved_ammonium'
[INFO] - data - __setitem__(233) - Replacing data array for 'dissolved_phosphorus'
[INFO] - data - __setitem__(233) - Replacing data array for 'ecto_supply_limit_n'
[INFO] - data - __setitem__(233) - Replacing data array for 'ecto_supply_limit_p'
[INFO] - data - __setitem__(233) - Replacing data array for 'arbuscular_supply_limit_n'
[INFO] - data - __setitem__(233) - Replacing data array for 'arbuscular_supply_limit_p'
[INFO] - main - ve_run(308) - Virtual Ecosystem model run completed!
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