build based on 28c9d6b

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-24T21:38:20","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-26T18:27:18","documenter_version":"1.5.0"}}

dev/assets/Manifest.toml

@@ -305,9 +305,9 @@ version = "5.9.0"
     ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c"
 
 [[deps.BufferedStreams]]
-git-tree-sha1 = "4ae47f9a4b1dc19897d3743ff13685925c5202ec"
+git-tree-sha1 = "6863c5b7fc997eadcabdbaf6c5f201dc30032643"
 uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
-version = "1.2.1"
+version = "1.2.2"
 
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -2036,9 +2036,9 @@ version = "9.26.0"
 
 [[deps.ModelingToolkitStandardLibrary]]
 deps = ["ChainRulesCore", "DiffEqBase", "IfElse", "LinearAlgebra", "ModelingToolkit", "Symbolics"]
-git-tree-sha1 = "862e6f77409c3ee33ade20b0242b10225fcc5e5a"
+git-tree-sha1 = "53c2eb67a861a4c2bb5d37b3526659e033dc5c31"
 uuid = "16a59e39-deab-5bd0-87e4-056b12336739"
-version = "2.9.0"
+version = "2.10.0"
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
@@ -2313,9 +2313,9 @@ version = "1.6.3"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "IfElse", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "0c5d89483f9538efedb3f1c1b72e14d5f65830b0"
+git-tree-sha1 = "a8b2d333cd90562b58b977b4033739360b37fb1f"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.86.0"
+version = "6.87.0"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -2721,9 +2721,9 @@ version = "0.1.0"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
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 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.45.1"
+version = "2.46.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -3024,9 +3024,9 @@ version = "2.2.0"
 
 [[deps.StochasticDiffEq]]
 deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
-git-tree-sha1 = "5237f2ebdf3b6b7ad2ec635440b59a390988feeb"
+git-tree-sha1 = "b47f8ccc5bd06d5f7a643bf6671365ab9d6595d9"
 uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.66.0"
+version = "6.67.0"
 
 [[deps.StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"]
@@ -3232,9 +3232,9 @@ uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf"
 version = "0.2.1"
 
 [[deps.Tricks]]
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 uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775"
-version = "0.1.8"
+version = "0.1.9"
 
 [[deps.TruncatedStacktraces]]
 deps = ["InteractiveUtils", "MacroTools", "Preferences"]

dev/getting_started/index.html

@@ -22,7 +22,7 @@
 \end{align}
  \]</p><p>To solve the system, we first create an ODEProblem and then solve it over the tspan of (0,100) using a stiff solver.  The solution is saved every 0.1ms. The unit of time in Neuroblox is 1ms.</p><pre><code class="language-julia hljs">prob = ODEProblem(sys, [], (0.0, 100), [])
 sol = solve(prob, Rodas4(), saveat=0.1)
-plot(sol)</code></pre><img src="28da62dd.svg" alt="Example block output"/><h2 id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models"><a class="docs-heading-anchor" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models">Example 2 : Building a Brain Circuit from literature using Neural Mass Models</a><a id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models-1"></a><a class="docs-heading-anchor-permalink" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models" title="Permalink"></a></h2><p>In this example, we will construct a Parkinsons model from eight Jansen-Rit Neural Mass Models as described in Liu et al. (2020). DOI: 10.1016/j.neunet.2019.12.021. The Jansen-Rit Neural Mass model is defined by the following differential equations:</p><p class="math-container">\[\frac{dx}{dt} = y-\frac{2}{\tau}x
+plot(sol)</code></pre><img src="91fd99fd.svg" alt="Example block output"/><h2 id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models"><a class="docs-heading-anchor" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models">Example 2 : Building a Brain Circuit from literature using Neural Mass Models</a><a id="Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models-1"></a><a class="docs-heading-anchor-permalink" href="#Example-2-:-Building-a-Brain-Circuit-from-literature-using-Neural-Mass-Models" title="Permalink"></a></h2><p>In this example, we will construct a Parkinsons model from eight Jansen-Rit Neural Mass Models as described in Liu et al. (2020). DOI: 10.1016/j.neunet.2019.12.021. The Jansen-Rit Neural Mass model is defined by the following differential equations:</p><p class="math-container">\[\frac{dx}{dt} = y-\frac{2}{\tau}x
 \frac{dy}{dt} = -\frac{x}{\tau^2} + \frac{H}{\tau} [\frac{2\lambda}{1+\text{exp}(-r*\sum{jcn})} - \lambda]\]</p><pre><code class="language-julia hljs">using Neuroblox
 using DifferentialEquations
 using Graphs
@@ -121,4 +121,4 @@
  1.0
  1.0</code></pre><p>We select an algorithm and solve the system</p><pre><code class="language-julia hljs">alg = Tsit5()
 sol_dde_no_delays = solve(prob, alg, saveat=1)
-plot(sol_dde_no_delays)</code></pre><img src="8e049f77.svg" alt="Example block output"/><p>In a later tutorial, we will show how to introduce edge delays.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Neuroblox</a><a class="docs-footer-nextpage" href="../tutorials/resting_state_wb/">Tutorial on resting state simulation using neural mass models »</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 24 July 2024 21:38">Wednesday 24 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot(sol_dde_no_delays)</code></pre><img src="682067d5.svg" alt="Example block output"/><p>In a later tutorial, we will show how to introduce edge delays.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Neuroblox</a><a class="docs-footer-nextpage" href="../tutorials/resting_state_wb/">Tutorial on resting state simulation using neural mass models »</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="Friday 26 July 2024 18:27">Friday 26 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -4,4 +4,4 @@
 using PkgAuthentication
 PkgAuthentication.install("juliahub.com")
 Pkg.Registry.add()
-Pkg.add(&quot;Neuroblox&quot;)</code></pre><h2 id="Licensing"><a class="docs-heading-anchor" href="#Licensing">Licensing</a><a id="Licensing-1"></a><a class="docs-heading-anchor-permalink" href="#Licensing" title="Permalink"></a></h2><p>Neuroblox is free for non-commerical and academic use. For full details of the license, please see  <a href="https://github.com/Neuroblox/NeurobloxEULA">the Neuroblox EULA</a>. For commercial use, get in contact with [email protected].</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="getting_started/">Getting Started »</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 24 July 2024 21:38">Wednesday 24 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Pkg.add(&quot;Neuroblox&quot;)</code></pre><h2 id="Licensing"><a class="docs-heading-anchor" href="#Licensing">Licensing</a><a id="Licensing-1"></a><a class="docs-heading-anchor-permalink" href="#Licensing" title="Permalink"></a></h2><p>Neuroblox is free for non-commerical and academic use. For full details of the license, please see  <a href="https://github.com/Neuroblox/NeurobloxEULA">the Neuroblox EULA</a>. For commercial use, get in contact with [email protected].</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="getting_started/">Getting Started »</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="Friday 26 July 2024 18:27">Friday 26 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>