build based on 0d1c6f9

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-10T16:54:59","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-10T21:25:11","documenter_version":"1.5.0"}}

dev/developer/checklist/index.html

@@ -20,4 +20,4 @@
 
    Either of those should automatically publish a new version to the Julia registry.
  - Once registered, the `TagBot.yml` workflow should create a tag, and rebuild the documentation for this tag.
- - These steps can take quite a bit of time (1 hour or more), so don&#39;t be surprised if the new documentation takes a while to appear.</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../contributing/">« Contributing</a><a class="docs-footer-nextpage" href="../../release-notes/">Release notes »</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 1.5.0 on <span class="colophon-date" title="Wednesday 10 July 2024 16:54">Wednesday 10 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ - These steps can take quite a bit of time (1 hour or more), so don&#39;t be surprised if the new documentation takes a while to appear.</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../contributing/">« Contributing</a><a class="docs-footer-nextpage" href="../../release-notes/">Release notes »</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 1.5.0 on <span class="colophon-date" title="Wednesday 10 July 2024 21:25">Wednesday 10 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/getting-started/explainers/intro/index.html

@@ -60,4 +60,4 @@
 
 E-->|sample...NUTS...| G
 G-->H
-H--&gt;I</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../julia/">« Working with Julia</a><a class="docs-footer-nextpage" href="../modelling-infections/">Modelling infections »</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 1.5.0 on <span class="colophon-date" title="Wednesday 10 July 2024 16:54">Wednesday 10 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+H--&gt;I</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../julia/">« Working with Julia</a><a class="docs-footer-nextpage" href="../modelling-infections/">Modelling infections »</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 1.5.0 on <span class="colophon-date" title="Wednesday 10 July 2024 21:25">Wednesday 10 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/getting-started/explainers/julia/index.html

@@ -36,4 +36,4 @@
     },
     "julia.liveTestFile": "path/to/runtests.jl",
     "julia.environmentPath": "path/to/project/directory",
-}</code></pre><p>These settings set basic code formatting and whitespace settings for Julia files, as well as setting the path to the test file for the project and the path to the project directory for the environment.</p><p>The <code>VS-Code</code> command <code>Julia: Start REPL</code> will start a REPL in <code>TERMINAL</code> tab in the editor with the environment set to the project directory and the <code>Testing</code> tab will detect the defined tests for the project.</p><h2 id="Literate-programming-with-Julia-in-EpiAware"><a class="docs-heading-anchor" href="#Literate-programming-with-Julia-in-EpiAware">Literate programming with Julia in EpiAware</a><a id="Literate-programming-with-Julia-in-EpiAware-1"></a><a class="docs-heading-anchor-permalink" href="#Literate-programming-with-Julia-in-EpiAware" title="Permalink"></a></h2><p>Its common to develop technical computing projects using a literate programming style, where code and documentation are interwoven. Julia supports this style of programming through a number of packages. In <code>EpiAware</code> we recommend the following:</p><ul><li><code>Pluto</code>: A native Julia notebook for interactive development. <code>Pluto</code> notebooks are reactive, meaning that the output of all cells are updated as input changes. Installation instructions are available <a href="https://github.com/fonsp/Pluto.jl">here</a>. Pluto notebook files have the extension <code>.jl</code> and can be run as scripts.</li><li><code>Quarto</code>: A literate programming tool that allows you to write documents in markdown with embedded Julia code. Installation instructions are available <a href="https://quarto.org/">here</a>. Quarto files have the extension <code>.qmd</code>.</li></ul><p>We use <code>Pluto</code> for interactive development and <code>Quarto</code> for generating reports and academic articles. Both tools are useful for developing reproducible workflows.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../intro/">Introduction to EpiAware »</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 1.5.0 on <span class="colophon-date" title="Wednesday 10 July 2024 16:54">Wednesday 10 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+}</code></pre><p>These settings set basic code formatting and whitespace settings for Julia files, as well as setting the path to the test file for the project and the path to the project directory for the environment.</p><p>The <code>VS-Code</code> command <code>Julia: Start REPL</code> will start a REPL in <code>TERMINAL</code> tab in the editor with the environment set to the project directory and the <code>Testing</code> tab will detect the defined tests for the project.</p><h2 id="Literate-programming-with-Julia-in-EpiAware"><a class="docs-heading-anchor" href="#Literate-programming-with-Julia-in-EpiAware">Literate programming with Julia in EpiAware</a><a id="Literate-programming-with-Julia-in-EpiAware-1"></a><a class="docs-heading-anchor-permalink" href="#Literate-programming-with-Julia-in-EpiAware" title="Permalink"></a></h2><p>Its common to develop technical computing projects using a literate programming style, where code and documentation are interwoven. Julia supports this style of programming through a number of packages. In <code>EpiAware</code> we recommend the following:</p><ul><li><code>Pluto</code>: A native Julia notebook for interactive development. <code>Pluto</code> notebooks are reactive, meaning that the output of all cells are updated as input changes. Installation instructions are available <a href="https://github.com/fonsp/Pluto.jl">here</a>. Pluto notebook files have the extension <code>.jl</code> and can be run as scripts.</li><li><code>Quarto</code>: A literate programming tool that allows you to write documents in markdown with embedded Julia code. Installation instructions are available <a href="https://quarto.org/">here</a>. Quarto files have the extension <code>.qmd</code>.</li></ul><p>We use <code>Pluto</code> for interactive development and <code>Quarto</code> for generating reports and academic articles. Both tools are useful for developing reproducible workflows.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Overview</a><a class="docs-footer-nextpage" href="../intro/">Introduction to EpiAware »</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 1.5.0 on <span class="colophon-date" title="Wednesday 10 July 2024 21:25">Wednesday 10 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>