build based on c0b16a2

dev/assets/Manifest.toml

@@ -576,9 +576,9 @@ version = "0.21.4"
 
 [[deps.JuliaFormatter]]
 deps = ["CSTParser", "CommonMark", "DataStructures", "Glob", "Pkg", "PrecompileTools", "Tokenize"]
-git-tree-sha1 = "c0ac2f93058fd148267154c42dd7dc79869f7923"
+git-tree-sha1 = "d6bb89d51ec10f6b0110c2aa27721a0cf3d58c7d"
 uuid = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
-version = "1.0.37"
+version = "1.0.38"
 
 [[deps.JumpProcesses]]
 deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"]
@@ -883,9 +883,9 @@ version = "6.57.0"
 
 [[deps.PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "b7c4f29f93b548caa58f703580f4d79ab753c8ac"
+git-tree-sha1 = "35882aa39079c44ea6c1f07827f98dc78bf1ce91"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.21"
+version = "0.11.22"
 
 [[deps.PackageExtensionCompat]]
 git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518"

dev/index.html

@@ -24,10 +24,10 @@
   Official https://julialang.org/ release
 Platform Info:
   OS: Linux (x86_64-linux-gnu)
-  CPU: 2 × Intel(R) Xeon(R) Platinum 8370C CPU @ 2.80GHz
+  CPU: 2 × Intel(R) Xeon(R) Platinum 8272CL CPU @ 2.60GHz
   WORD_SIZE: 64
   LIBM: libopenlibm
-  LLVM: libLLVM-14.0.6 (ORCJIT, icelake-server)
+  LLVM: libLLVM-14.0.6 (ORCJIT, skylake-avx512)
   Threads: 1 on 2 virtual cores</code></pre></details><details><summary>A more complete overview of all dependencies and their versions is also provided.</summary><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Status `~/work/StructuralIdentifiability.jl/StructuralIdentifiability.jl/docs/Manifest.toml`
   [47edcb42] ADTypes v0.2.4
   [a4c015fc] ANSIColoredPrinters v0.0.1
@@ -101,7 +101,7 @@
   [82899510] IteratorInterfaceExtensions v1.0.0
   [692b3bcd] JLLWrappers v1.5.0
   [682c06a0] JSON v0.21.4
-  [98e50ef6] JuliaFormatter v1.0.37
+  [98e50ef6] JuliaFormatter v1.0.38
   [ccbc3e58] JumpProcesses v9.8.0
   [ef3ab10e] KLU v0.4.1
   [ba0b0d4f] Krylov v0.9.4
@@ -131,7 +131,7 @@
   [6fe1bfb0] OffsetArrays v1.12.10
   [bac558e1] OrderedCollections v1.6.2
   [1dea7af3] OrdinaryDiffEq v6.57.0
-  [90014a1f] PDMats v0.11.21
+  [90014a1f] PDMats v0.11.22
   [65ce6f38] PackageExtensionCompat v1.0.2
   [3e851597] ParamPunPam v0.1.0
   [d96e819e] Parameters v0.12.3
@@ -254,4 +254,4 @@
   [3f19e933] p7zip_jll v17.4.0+0
 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`</code></pre></details>You can also download the 
 <a href="https://github.com/SciML/StructuralIdentifiability.jl/tree/gh-pages/v0.4.10/assets/Manifest.toml">manifest</a> file and the
-<a href="https://github.com/SciML/StructuralIdentifiability.jl/tree/gh-pages/v0.4.10/assets/Project.toml">project</a> file.</article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorials/creating_ode/">Creating ODE System »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Tuesday 3 October 2023 07:16">Tuesday 3 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<a href="https://github.com/SciML/StructuralIdentifiability.jl/tree/gh-pages/v0.4.10/assets/Project.toml">project</a> file.</article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorials/creating_ode/">Creating ODE System »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 4 October 2023 10:30">Wednesday 4 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/input/input/index.html

@@ -9,4 +9,4 @@
     x1'(t) = a * x1(t) + u(t),
     x2'(t) = b * x2(t) + c*x1(t)*x2(t),
     y(t) = x1(t)
-)</code></pre><p>Here,</p><ul><li><code>x1</code>, <code>x2</code> are state variables</li><li><code>y</code> is an output variable</li><li><code>u</code> is an input variable</li><li><code>a</code>, <code>b</code>, <code>c</code> are time-indepdendent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/53d1b5dc968c982c0d94d4a6411bf61f0159d9bc/src/ODE.jl#L339-L365">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="StructuralIdentifiability.ODE" href="#StructuralIdentifiability.ODE"><code>StructuralIdentifiability.ODE</code></a> — <span class="docstring-category">Type</span></header><section><div><p>The main structure that represents input ODE system.</p><p>Stores information about states (<code>x_vars</code>), outputs (<code>y_vars</code>), inputs (<code>u_vars</code>), parameters (<code>parameters</code>) and the equations.</p><p>This structure is constructed via <code>@ODEmodel</code> macro.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/53d1b5dc968c982c0d94d4a6411bf61f0159d9bc/src/ODE.jl#L2-L8">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="StructuralIdentifiability.set_parameter_values" href="#StructuralIdentifiability.set_parameter_values"><code>StructuralIdentifiability.set_parameter_values</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">set_parameter_values(ode, param_values)</code></pre><p>Input:</p><ul><li><code>ode</code> - an ODE as above</li><li><code>param_values</code> - values for (possibly, some of) the parameters as dictionary <code>parameter</code> =&gt; <code>value</code></li></ul><p>Output:</p><ul><li>new ode with the parameters in param_values plugged with the given numbers</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/53d1b5dc968c982c0d94d4a6411bf61f0159d9bc/src/ODE.jl#L85-L94">source</a></section></article><h2 id="Create-Compartmental-Model"><a class="docs-heading-anchor" href="#Create-Compartmental-Model">Create Compartmental Model</a><a id="Create-Compartmental-Model-1"></a><a class="docs-heading-anchor-permalink" href="#Create-Compartmental-Model" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="StructuralIdentifiability.linear_compartment_model" href="#StructuralIdentifiability.linear_compartment_model"><code>StructuralIdentifiability.linear_compartment_model</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">linear_compartment_model(graph, inputs, outputs, leaks)</code></pre><p>Input: defines a linear compartment model with nodes numbered from 1 to <code>n</code> by</p><ul><li><code>graph</code> - and array of integer arrays representing the adjacency lists of the graph</li><li><code>inputs</code> - array of input nodes</li><li><code>outputs</code> - array of output nodes</li><li><code>leaks</code> - array of sink nodes</li></ul><p>Output:</p><ul><li>the corresponding ODE system in the notation of https://doi.org/10.1007/s11538-015-0098-0</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/53d1b5dc968c982c0d94d4a6411bf61f0159d9bc/src/lincomp.jl#L16-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/identifiable_functions/">« Globally Identifiable Functions</a><a class="docs-footer-nextpage" href="../../identifiability/identifiability/">ָFunctions to Assess Identifiability »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Tuesday 3 October 2023 07:16">Tuesday 3 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+)</code></pre><p>Here,</p><ul><li><code>x1</code>, <code>x2</code> are state variables</li><li><code>y</code> is an output variable</li><li><code>u</code> is an input variable</li><li><code>a</code>, <code>b</code>, <code>c</code> are time-indepdendent parameters</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/c0b16a264989070fd1439b674b13e2d9673e73da/src/ODE.jl#L339-L365">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="StructuralIdentifiability.ODE" href="#StructuralIdentifiability.ODE"><code>StructuralIdentifiability.ODE</code></a> — <span class="docstring-category">Type</span></header><section><div><p>The main structure that represents input ODE system.</p><p>Stores information about states (<code>x_vars</code>), outputs (<code>y_vars</code>), inputs (<code>u_vars</code>), parameters (<code>parameters</code>) and the equations.</p><p>This structure is constructed via <code>@ODEmodel</code> macro.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/c0b16a264989070fd1439b674b13e2d9673e73da/src/ODE.jl#L2-L8">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="StructuralIdentifiability.set_parameter_values" href="#StructuralIdentifiability.set_parameter_values"><code>StructuralIdentifiability.set_parameter_values</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">set_parameter_values(ode, param_values)</code></pre><p>Input:</p><ul><li><code>ode</code> - an ODE as above</li><li><code>param_values</code> - values for (possibly, some of) the parameters as dictionary <code>parameter</code> =&gt; <code>value</code></li></ul><p>Output:</p><ul><li>new ode with the parameters in param_values plugged with the given numbers</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/c0b16a264989070fd1439b674b13e2d9673e73da/src/ODE.jl#L85-L94">source</a></section></article><h2 id="Create-Compartmental-Model"><a class="docs-heading-anchor" href="#Create-Compartmental-Model">Create Compartmental Model</a><a id="Create-Compartmental-Model-1"></a><a class="docs-heading-anchor-permalink" href="#Create-Compartmental-Model" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="StructuralIdentifiability.linear_compartment_model" href="#StructuralIdentifiability.linear_compartment_model"><code>StructuralIdentifiability.linear_compartment_model</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">linear_compartment_model(graph, inputs, outputs, leaks)</code></pre><p>Input: defines a linear compartment model with nodes numbered from 1 to <code>n</code> by</p><ul><li><code>graph</code> - and array of integer arrays representing the adjacency lists of the graph</li><li><code>inputs</code> - array of input nodes</li><li><code>outputs</code> - array of output nodes</li><li><code>leaks</code> - array of sink nodes</li></ul><p>Output:</p><ul><li>the corresponding ODE system in the notation of https://doi.org/10.1007/s11538-015-0098-0</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/SciML/StructuralIdentifiability.jl/blob/c0b16a264989070fd1439b674b13e2d9673e73da/src/lincomp.jl#L16-L27">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/identifiable_functions/">« Globally Identifiable Functions</a><a class="docs-footer-nextpage" href="../../identifiability/identifiability/">ָFunctions to Assess Identifiability »</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Wednesday 4 October 2023 10:30">Wednesday 4 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>