Skip to content
Snippets Groups Projects
Commit 4296a4a8 authored by xo30xoqa's avatar xo30xoqa
Browse files

Merge branch 'development'

parents 1d7eedb4 872c08e2
Branches
No related tags found
No related merge requests found
Expand all Hide whitespace changes
Inline Side-by-side
Showing
with 3225 additions and 68 deletions
data/regions/auxiliary/persefone.qgz
+ 0
− 0
View file @ 4296a4a8
No preview for this file type
docs/build/.documenter-siteinfo.json 0 → 100644
+ 1
− 0
View file @ 4296a4a8
{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2025-03-18T14:39:16","documenter_version":"1.9.0"}}
\ No newline at end of file
docs/build/CHANGELOG.html 0 → 100644
+ 2
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/adapting.html 0 → 100644
+ 2
− 0
View file @ 4296a4a8
<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Adapting Persefone · Persefone.jl</title><meta name="title" content="Adapting Persefone · Persefone.jl"/><meta property="og:title" content="Adapting Persefone · Persefone.jl"/><meta property="twitter:title" content="Adapting Persefone · Persefone.jl"/><meta name="description" content="Documentation for Persefone.jl."/><meta property="og:description" content="Documentation for Persefone.jl."/><meta property="twitter:description" content="Documentation for Persefone.jl."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="Persefone.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">Persefone.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="index.html">Introduction</a></li><li><span class="tocitem">User guide</span><ul><li><a class="tocitem" href="using.html">The Persefone.jl Package</a></li><li><a class="tocitem" href="gui.html">Graphical User Interface</a></li><li><a class="tocitem" href="config.html">Configuration</a></li></ul></li><li><span class="tocitem">Scientific documentation</span><ul><li><a class="tocitem" href="management.html">Farm management</a></li><li><a class="tocitem" href="crop-models.html">Crop models</a></li><li><a class="tocitem" href="skylark.html">Skylark</a></li></ul></li><li><span class="tocitem">Developer guide</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li class="is-active"><a class="tocitem" href="adapting.html">Adapting Persefone</a></li><li><a class="tocitem" href="architecture.html">Source code architecture</a></li><li><a class="tocitem" href="gis.html">Maps and weather data</a></li><li><a class="tocitem" href="species-dsl.html">Defining new species</a></li><li><a class="tocitem" href="CHANGELOG.html">Changelog</a></li></ul></li><li><span class="tocitem">Software API</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input and Output</a></li><li><a class="tocitem" href="nature.html">Nature submodel</a></li><li><a class="tocitem" href="species.html">Species models</a></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Developer guide</a></li><li class="is-active"><a href="adapting.html">Adapting Persefone</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="adapting.html">Adapting Persefone</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model" title="View the repository"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">Repository</span></a><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model/-/tree/master/docs/src/adapting.md" title="Edit source"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Adapting-Persefone"><a class="docs-heading-anchor" href="#Adapting-Persefone">Adapting Persefone</a><a id="Adapting-Persefone-1"></a><a class="docs-heading-anchor-permalink" href="#Adapting-Persefone" title="Permalink"></a></h1><p>A key development goal of Persefone is to be <a href="https://doi.org/10.1515/itit-2019-0040">FAIR</a>: <em>findable, accessible, interoperable, and reusable</em>. We aim to build a model that is both easy to use and easy to adapt to new situations.</p><p>There are multiple ways to adapt Persefone for a new modelling study:</p><h3 id="Changing-the-parameters"><a class="docs-heading-anchor" href="#Changing-the-parameters">Changing the parameters</a><a id="Changing-the-parameters-1"></a><a class="docs-heading-anchor-permalink" href="#Changing-the-parameters" title="Permalink"></a></h3><p>The simplest way to adapt Persefone is simply by changing the parameters. Copy <code>src/parameters.toml</code> to a new location, adjust it to your needs, and run the model using <code>julia run.jl -c &lt;configfile&gt;</code>.</p><h3 id="Changing-the-region"><a class="docs-heading-anchor" href="#Changing-the-region">Changing the region</a><a id="Changing-the-region-1"></a><a class="docs-heading-anchor-permalink" href="#Changing-the-region" title="Permalink"></a></h3><p>To apply Persefone to a new region, you need to create new input maps of land cover and farmplots. How to do so is described <a href="gis.html">here</a>.</p><p><em>You may also need to change aspects of the <code>farm</code> submodel. This is not yet implemented.</em></p><h3 id="Adding-new-animal-species"><a class="docs-heading-anchor" href="#Adding-new-animal-species">Adding new animal species</a><a id="Adding-new-animal-species-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-new-animal-species" title="Permalink"></a></h3><p>To implement a new species to the <code>nature</code> submodel, add a new file to the <code>src/nature/species</code> directory and <code>include</code> it in <code>src/Persefone.jl</code>, as well as adding the name of the species to the <code>nature.targetspecies</code> parameter. In the new file, implement the species using the <a href="nature.html#Persefone.@species-Tuple{Any, Any}"><code>@species</code></a> syntax as described <a href="species-dsl.html">here</a>.</p><h3 id="Adding-new-crop-species"><a class="docs-heading-anchor" href="#Adding-new-crop-species">Adding new crop species</a><a id="Adding-new-crop-species-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-new-crop-species" title="Permalink"></a></h3><p><em>Crop growth is not yet implemented.</em></p><h3 id="Adding-new-farmer-behaviour"><a class="docs-heading-anchor" href="#Adding-new-farmer-behaviour">Adding new farmer behaviour</a><a id="Adding-new-farmer-behaviour-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-new-farmer-behaviour" title="Permalink"></a></h3><p><em>Farmer behaviour is not yet implemented.</em></p><h3 id="Adding-a-new-submodel"><a class="docs-heading-anchor" href="#Adding-a-new-submodel">Adding a new submodel</a><a id="Adding-a-new-submodel-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-a-new-submodel" title="Permalink"></a></h3><p>To add a new submodel in addition to the existing ones (<code>nature</code>, <code>crop</code>, and <code>farm</code>), you need to familiarise yourself with the <a href="architecture.html">software architecture</a>. In particular, you need to understand how initialisation and scheduling works in <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/simulation.jl"><code>src/core/simulation.jl</code></a>, and what information is stored in the <code>model</code> object.</p><p>If you want to add a new agent type, create a subtype of <a href="simulation.html#Persefone.ModelAgent"><code>ModelAgent</code></a>, implement a <a href="@ref"><code>stepagent!</code></a> function for it and add it to <a href="simulation.html#Persefone.initmodel-Tuple{Dict{String, Any}}"><code>Persefone.initmodel</code></a>.</p><h3 id="Linking-to-another-model"><a class="docs-heading-anchor" href="#Linking-to-another-model">Linking to another model</a><a id="Linking-to-another-model-1"></a><a class="docs-heading-anchor-permalink" href="#Linking-to-another-model" title="Permalink"></a></h3><p>Persefone can also be used as a software library and be called from another application. For this purpose, it is set up as a <a href="https://pkgdocs.julialang.org/v1/">Julia package</a>, with a <a href="https://docs.julialang.org/en/v1/manual/modules/">module</a> exporting various model functions, types, and macros (see <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/Persephone.jl"><code>src/Persefone.jl</code></a>). Of particular interest are the functions <a href="simulation.html#Persefone.simulate-Tuple{}"><code>simulate</code></a> (set up and run a complete simulation based on a config file), <a href="simulation.html#Persefone.initialise-Tuple{}"><code>initialise</code></a> (create one or more <code>model</code> objects from a config file), <a href="simulation.html#Persefone.simulate!-Tuple{SimulationModel}"><code>simulate!</code></a> (do a simulation run with an existing <code>model</code> object), and <a href="simulation.html#Persefone.stepsimulation!-Tuple{SimulationModel}"><code>stepsimulation!</code></a> (update a <code>model</code> object by one time step).</p><p>To interface with Julia from another language, see the Julia docs <a href="https://docs.julialang.org/en/v1/manual/calling-c-and-fortran-code/">here</a> and <a href="https://docs.julialang.org/en/v1/manual/embedding/">here</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="developing.html">« Developing Persefone</a><a class="docs-footer-nextpage" href="architecture.html">Source code architecture »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
docs/build/architecture.html 0 → 100644
+ 2
− 0
View file @ 4296a4a8
<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Source code architecture · Persefone.jl</title><meta name="title" content="Source code architecture · Persefone.jl"/><meta property="og:title" content="Source code architecture · Persefone.jl"/><meta property="twitter:title" content="Source code architecture · Persefone.jl"/><meta name="description" content="Documentation for Persefone.jl."/><meta property="og:description" content="Documentation for Persefone.jl."/><meta property="twitter:description" content="Documentation for Persefone.jl."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="search_index.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="Persefone.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">Persefone.jl</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="index.html">Introduction</a></li><li><span class="tocitem">User guide</span><ul><li><a class="tocitem" href="using.html">The Persefone.jl Package</a></li><li><a class="tocitem" href="gui.html">Graphical User Interface</a></li><li><a class="tocitem" href="config.html">Configuration</a></li></ul></li><li><span class="tocitem">Scientific documentation</span><ul><li><a class="tocitem" href="management.html">Farm management</a></li><li><a class="tocitem" href="crop-models.html">Crop models</a></li><li><a class="tocitem" href="skylark.html">Skylark</a></li></ul></li><li><span class="tocitem">Developer guide</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li><a class="tocitem" href="adapting.html">Adapting Persefone</a></li><li class="is-active"><a class="tocitem" href="architecture.html">Source code architecture</a><ul class="internal"><li class="toplevel"><a class="tocitem" href="#Model-components"><span>Model components</span></a></li><li class="toplevel"><a class="tocitem" href="#Important-implementation-details"><span>Important implementation details</span></a></li></ul></li><li><a class="tocitem" href="gis.html">Maps and weather data</a></li><li><a class="tocitem" href="species-dsl.html">Defining new species</a></li><li><a class="tocitem" href="CHANGELOG.html">Changelog</a></li></ul></li><li><span class="tocitem">Software API</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input and Output</a></li><li><a class="tocitem" href="nature.html">Nature submodel</a></li><li><a class="tocitem" href="species.html">Species models</a></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Developer guide</a></li><li class="is-active"><a href="architecture.html">Source code architecture</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="architecture.html">Source code architecture</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model" title="View the repository"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">Repository</span></a><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model/-/tree/master/docs/src/architecture.md" title="Edit source"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Source-code-architecture"><a class="docs-heading-anchor" href="#Source-code-architecture">Source code architecture</a><a id="Source-code-architecture-1"></a><a class="docs-heading-anchor-permalink" href="#Source-code-architecture" title="Permalink"></a></h1><h1 id="Model-components"><a class="docs-heading-anchor" href="#Model-components">Model components</a><a id="Model-components-1"></a><a class="docs-heading-anchor-permalink" href="#Model-components" title="Permalink"></a></h1><p><img src="assets/architecture.png" alt="&quot;model architecture&quot;"/></p><p>Persefone is divided into four components, three of which are semi-independent submodels:</p><ol><li><p><code>core</code> and <code>world</code>: These two directories provide the foundation of the model software, which sets up and executes simulation runs. It also reads all input files (the configuration file, landscape maps, and weather data), and provides data output functionality.</p></li><li><p><code>nature</code>: This is an individual-based model of species in agricultural landscapes. It defines the <a href="nature.html#Persefone.Animal"><code>Animal</code></a> agent type, and a set of macros that can be used to rapidly create new species. It also includes ecological process functions that are useful for all species.</p></li><li><p><code>farm</code>: This is an agent-based model of farmer decision making. It is not yet implemented, but will provide the <a href="farm.html#Persefone.Farmer"><code>Farmer</code></a> agent type.</p></li><li><p><code>crop</code>: This is a mathematical growth model for various crops. It is not yet implemented, but already provides the agent type <a href="crops.html#Persefone.FarmPlot"><code>FarmPlot</code></a>, representing one field and its associated extent and crop type.</p></li></ol><p>Conceptually, <code>core</code> provides functionality that is needed by all of the submodels. Decisions made by <code>Farmer</code>s affect the <code>FarmPlot</code>s they own, and (directly or indirectly) the <code>Animal</code>s in the model landscape.</p><h1 id="Important-implementation-details"><a class="docs-heading-anchor" href="#Important-implementation-details">Important implementation details</a><a id="Important-implementation-details-1"></a><a class="docs-heading-anchor-permalink" href="#Important-implementation-details" title="Permalink"></a></h1><p><img src="assets/model_object.png" alt="&quot;the model object&quot;"/></p><h3 id="The-model-object"><a class="docs-heading-anchor" href="#The-model-object">The <code>model</code> object</a><a id="The-model-object-1"></a><a class="docs-heading-anchor-permalink" href="#The-model-object" title="Permalink"></a></h3><p>A cursory reading of the source code will quickly show that most functions take an <code>SimulationModel</code> object as one of their arguments. The concrete type for this is <a href="simulation.html#Persefone.AgricultureModel"><code>AgricultureModel</code></a>, a struct that holds all state that is in any way relevant to a simulation run. (Persefone has a strict &quot;no global state&quot; policy to avoid state-dependent bugs and allow parallelisation.) The model object gives access to all agent instances. It also stores the configuration (<code>model.settings</code>), the landscape (<code>model.landscape</code>, a matrix of <a href="simulation.html#Persefone.Pixel"><code>Pixel</code></a> objects that store the local land cover, amongst other things), and the current simulation date (<code>model.date</code>). (See <a href="simulation.html#Persefone.initmodel-Tuple{Dict{String, Any}}"><code>Persefone.initmodel</code></a> for details.)</p><h3 id="Model-configuration/the-@param-macro"><a class="docs-heading-anchor" href="#Model-configuration/the-@param-macro">Model configuration/the <code>@param</code> macro</a><a id="Model-configuration/the-@param-macro-1"></a><a class="docs-heading-anchor-permalink" href="#Model-configuration/the-@param-macro" title="Permalink"></a></h3><p>The model is configured via a <a href="https://toml.io/en/">TOML</a> file, the default version of which is at <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/parameters.toml"><code>src/parameters.toml</code></a>. An individual run can be configured using a user-defined configuration file, commandline arguments, or function calls (when Persefone is used as a package rather than an application). During a model run, the <a href="io.html#Persefone.@param-Tuple{Any}"><code>@param</code></a> macro can be used to access parameter values. Note that parameter names are prepended with the name of the component they are associated with. For example, the <code>outdir</code> parameter belongs to the <code>[core]</code> section of the TOML file, and must therefore be referenced as <code>@param(core.outdir)</code>. (See <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/input.jl"><code>src/core/input.jl</code></a> for details.)</p><div class="admonition is-info"><header class="admonition-header">@param and other macros</header><div class="admonition-body"><p>As <code>@param(parameter)</code> expands to <code>model.settings[&quot;parameter&quot;]</code>, it can obviously only be used in a context where the <code>model</code> object is actually available. (This is the case for most functions in Persefone, but not for all.) Similarly, many of the <code>nature</code> macros depend on specific variables being available where they are called, and can therefore only be used in specific contexts (this is indicated in their documentation).</p></div></div><h3 id="Output-data"><a class="docs-heading-anchor" href="#Output-data">Output data</a><a id="Output-data-1"></a><a class="docs-heading-anchor-permalink" href="#Output-data" title="Permalink"></a></h3><p>Persefone can output model data into text files with a specified frequency (daily, monthly, yearly, or at the simulation end). Submodels can use <a href="io.html#Persefone.newdataoutput!"><code>Persefone.newdataoutput!</code></a> to plug into this system. For an example of how to use this, see <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/nature/ecologicaldata.jl"><code>src/nature/ecologicaldata.jl</code></a>. (See <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/output.jl"><code>src/core/output.jl</code></a> for details.)</p><h3 id="Farm-events"><a class="docs-heading-anchor" href="#Farm-events">Farm events</a><a id="Farm-events-1"></a><a class="docs-heading-anchor-permalink" href="#Farm-events" title="Permalink"></a></h3><p>The <a href="simulation.html#Persefone.FarmEvent"><code>FarmEvent</code></a> struct is used to communicate farming-related events between submodels. An event can be triggered with <a href="simulation.html#Persefone.createevent!"><code>createevent!</code></a> and affects all pixels within a <a href="crops.html#Persefone.FarmPlot"><code>FarmPlot</code></a>. (See <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/landscape.jl"><code>src/core/landscape.jl</code></a> for details.)</p><h3 id="Random-numbers-and-logging"><a class="docs-heading-anchor" href="#Random-numbers-and-logging">Random numbers and logging</a><a id="Random-numbers-and-logging-1"></a><a class="docs-heading-anchor-permalink" href="#Random-numbers-and-logging" title="Permalink"></a></h3><p>By default in Julia, the <a href="https://docs.julialang.org/en/v1/stdlib/Random/">random number generator</a> (RNG) and the <a href="https://docs.julialang.org/en/v1/stdlib/Logging/#Logging.global_logger">system logger</a> are two globally accessible variables. As Persefone needs to avoid all global data (since this would interfere with reproducibility in parallel runs), the <code>model</code> object stores a local logger and a local RNG. The local logger generally does not change the way the model uses <a href="https://docs.julialang.org/en/v1/stdlib/Logging/">log statements</a>, it is only relevant for some functions in <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/simulation.jl"><code>src/core/simulation.jl</code></a>.</p><div class="admonition is-info"><header class="admonition-header">Using the model RNG</header><div class="admonition-body"><p>Whenever you need to use a <a href="https://docs.julialang.org/en/v1/stdlib/Random/#Base.rand">random number</a>, you must use the <code>model.rng</code>. The easiest way to do this is with the <a href="simulation.html#Persefone.@rand-Tuple"><code>@rand</code></a> and <a href="simulation.html#Persefone.@shuffle!-Tuple{Any}"><code>@shuffle!</code></a> macros. (Note that these, too, require access to the <code>model</code> object.)</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="adapting.html">« Adapting Persefone</a><a class="docs-footer-nextpage" href="gis.html">Maps and weather data »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
docs/build/assets/architecture.png
+ 0
− 0
View replaced file @ 1d7eedb4 View file @ 4296a4a8
docs/build/assets/architecture.png

105 KiB | W: | H:

docs/build/assets/architecture.png

105 KiB | W: | H:

docs/build/assets/architecture.png
docs/build/assets/architecture.png
docs/build/assets/architecture.png
docs/build/assets/architecture.png
  • 2-up
  • Swipe
  • Onion skin
docs/build/assets/architecture.svg
+ 76
− 68
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/documenter.js 0 → 100644
+ 1187
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/modellstruktur_vereinfacht.pdf 0 → 100644
+ 0
− 0
View file @ 4296a4a8
File added
docs/build/assets/modellstruktur_vereinfacht.png 0 → 100644
+ 0
− 0
View file @ 4296a4a8
docs/build/assets/modellstruktur_vereinfacht.png

881 KiB

docs/build/assets/modellstruktur_vereinfacht.svg 0 → 100644
+ 1851
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/persefone_qr.png 0 → 100644
+ 0
− 0
View file @ 4296a4a8
docs/build/assets/persefone_qr.png

8.21 KiB

docs/build/assets/soil_types_english.png 0 → 100644
+ 0
− 0
View file @ 4296a4a8
docs/build/assets/soil_types_english.png

923 KiB

docs/build/assets/themes/catppuccin-frappe.css 0 → 100644
+ 1
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/themes/catppuccin-latte.css 0 → 100644
+ 1
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/themes/catppuccin-macchiato.css 0 → 100644
+ 1
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/themes/catppuccin-mocha.css 0 → 100644
+ 1
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/themes/documenter-dark.css 0 → 100644
+ 7
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/themes/documenter-light.css 0 → 100644
+ 9
− 0
View file @ 4296a4a8
This diff is collapsed.
docs/build/assets/themeswap.js 0 → 100644
+ 84
− 0
View file @ 4296a4a8
// Small function to quickly swap out themes. Gets put into the <head> tag..
function set_theme_from_local_storage() {
// Initialize the theme to null, which means default
var theme = null;
// If the browser supports the localstorage and is not disabled then try to get the
// documenter theme
if (window.localStorage != null) {
// Get the user-picked theme from localStorage. May be `null`, which means the default
// theme.
theme = window.localStorage.getItem("documenter-theme");
}
// Check if the users preference is for dark color scheme
var darkPreference =
window.matchMedia("(prefers-color-scheme: dark)").matches === true;
// Initialize a few variables for the loop:
//
// - active: will contain the index of the theme that should be active. Note that there
// is no guarantee that localStorage contains sane values. If `active` stays `null`
// we either could not find the theme or it is the default (primary) theme anyway.
// Either way, we then need to stick to the primary theme.
//
// - disabled: style sheets that should be disabled (i.e. all the theme style sheets
// that are not the currently active theme)
var active = null;
var disabled = [];
var primaryLightTheme = null;
var primaryDarkTheme = null;
for (var i = 0; i < document.styleSheets.length; i++) {
var ss = document.styleSheets[i];
// The <link> tag of each style sheet is expected to have a data-theme-name attribute
// which must contain the name of the theme. The names in localStorage much match this.
var themename = ss.ownerNode.getAttribute("data-theme-name");
// attribute not set => non-theme stylesheet => ignore
if (themename === null) continue;
// To distinguish the default (primary) theme, it needs to have the data-theme-primary
// attribute set.
if (ss.ownerNode.getAttribute("data-theme-primary") !== null) {
primaryLightTheme = themename;
}
// Check if the theme is primary dark theme so that we could store its name in darkTheme
if (ss.ownerNode.getAttribute("data-theme-primary-dark") !== null) {
primaryDarkTheme = themename;
}
// If we find a matching theme (and it's not the default), we'll set active to non-null
if (themename === theme) active = i;
// Store the style sheets of inactive themes so that we could disable them
if (themename !== theme) disabled.push(ss);
}
var activeTheme = null;
if (active !== null) {
// If we did find an active theme, we'll (1) add the theme--$(theme) class to <html>
document.getElementsByTagName("html")[0].className = "theme--" + theme;
activeTheme = theme;
} else {
// If we did _not_ find an active theme, then we need to fall back to the primary theme
// which can either be dark or light, depending on the user's OS preference.
var activeTheme = darkPreference ? primaryDarkTheme : primaryLightTheme;
// In case it somehow happens that the relevant primary theme was not found in the
// preceding loop, we abort without doing anything.
if (activeTheme === null) {
console.error("Unable to determine primary theme.");
return;
}
// When switching to the primary light theme, then we must not have a class name
// for the <html> tag. That's only for non-primary or the primary dark theme.
if (darkPreference) {
document.getElementsByTagName("html")[0].className =
"theme--" + activeTheme;
} else {
document.getElementsByTagName("html")[0].className = "";
}
}
for (var i = 0; i < document.styleSheets.length; i++) {
var ss = document.styleSheets[i];
// The <link> tag of each style sheet is expected to have a data-theme-name attribute
// which must contain the name of the theme. The names in localStorage much match this.
var themename = ss.ownerNode.getAttribute("data-theme-name");
// attribute not set => non-theme stylesheet => ignore
if (themename === null) continue;
// we'll disable all the stylesheets, except for the active one
ss.disabled = !(themename == activeTheme);
}
}
set_theme_from_local_storage();
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment