build based on 676c3db

dev/assets/Manifest.toml

@@ -1015,7 +1015,7 @@ version = "0.6.39"
 deps = ["ADTypes", "ArrayInterface", "ChainRulesCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FillArrays", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables", "TruncatedStacktraces", "ZygoteRules"]
 path = "/home/runner/work/SciMLBase.jl/SciMLBase.jl"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.0.5"
+version = "2.0.6"
 
     [deps.SciMLBase.extensions]
     ZygoteExt = "Zygote"

dev/interfaces/Differentiation/index.html

@@ -29,4 +29,4 @@
 
 function _concrete_solve_forward(args...; kwargs...)
   error("No sensitivity rules exist. Check that you added `using DiffEqSensitivity`")
-end</code></pre><p>The sensitivity mechanism is kept in a separate package because of the high dependency and load time cost introduced by the automatic differentiation libraries. Different choices of automatic differentiation are then selected by the <code>sensealg</code> keyword argument in <code>solve</code>, which is made into a positional argument in the <code>_solve_adjoint</code> and other functions in order to allow dispatch.</p><h2 id="SensitivityADPassThrough"><a class="docs-heading-anchor" href="#SensitivityADPassThrough">SensitivityADPassThrough</a><a id="SensitivityADPassThrough-1"></a><a class="docs-heading-anchor-permalink" href="#SensitivityADPassThrough" title="Permalink"></a></h2><p>The special sensitivity algorithm <code>SensitivityADPassThrough</code> is used to ignore the internal sensitivity dispatches and instead do automatic differentiation directly through the solver. Generally this <code>sensealg</code> is only used internally.</p><h2 id="Note-about-ForwardDiff"><a class="docs-heading-anchor" href="#Note-about-ForwardDiff">Note about ForwardDiff</a><a id="Note-about-ForwardDiff-1"></a><a class="docs-heading-anchor-permalink" href="#Note-about-ForwardDiff" title="Permalink"></a></h2><p>ForwardDiff does not use ChainRules.jl and thus it completely ignores the special handling.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Common_Keywords/">« Common Keyword Arguments</a><a class="docs-footer-nextpage" href="../PDE/">The PDE Definition Interface »</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="Friday 29 September 2023 08:22">Friday 29 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+end</code></pre><p>The sensitivity mechanism is kept in a separate package because of the high dependency and load time cost introduced by the automatic differentiation libraries. Different choices of automatic differentiation are then selected by the <code>sensealg</code> keyword argument in <code>solve</code>, which is made into a positional argument in the <code>_solve_adjoint</code> and other functions in order to allow dispatch.</p><h2 id="SensitivityADPassThrough"><a class="docs-heading-anchor" href="#SensitivityADPassThrough">SensitivityADPassThrough</a><a id="SensitivityADPassThrough-1"></a><a class="docs-heading-anchor-permalink" href="#SensitivityADPassThrough" title="Permalink"></a></h2><p>The special sensitivity algorithm <code>SensitivityADPassThrough</code> is used to ignore the internal sensitivity dispatches and instead do automatic differentiation directly through the solver. Generally this <code>sensealg</code> is only used internally.</p><h2 id="Note-about-ForwardDiff"><a class="docs-heading-anchor" href="#Note-about-ForwardDiff">Note about ForwardDiff</a><a id="Note-about-ForwardDiff-1"></a><a class="docs-heading-anchor-permalink" href="#Note-about-ForwardDiff" title="Permalink"></a></h2><p>ForwardDiff does not use ChainRules.jl and thus it completely ignores the special handling.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Common_Keywords/">« Common Keyword Arguments</a><a class="docs-footer-nextpage" href="../PDE/">The PDE Definition Interface »</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="Friday 29 September 2023 09:40">Friday 29 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/interfaces/Init_Solve/index.html

@@ -4,4 +4,4 @@
   gtag('js', new Date());
   gtag('config', 'UA-90474609-3', {'page_path': location.pathname + location.search + location.hash});
 </script><script data-outdated-warner src="../../assets/warner.js"></script><link rel="canonical" href="https://docs.sciml.ai/SciMLBase/stable/interfaces/Init_Solve/"/><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/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/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="../../siteinfo.js"></script><script src="../../../versions.js"></script><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><link href="../../assets/favicon.ico" rel="icon" type="image/x-icon"/></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="../../"><img src="../../assets/logo.png" alt="SciMLBase.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="../../">SciMLBase.jl</a></span></div><form class="docs-search" action="../../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../../">Home</a></li><li><span class="tocitem">Interfaces</span><ul><li><a class="tocitem" href="../Problems/">SciMLProblems</a></li><li><a class="tocitem" href="../SciMLFunctions/">SciMLFunctions (Jacobians, Sparsity, Etc.)</a></li><li><a class="tocitem" href="../Algorithms/">SciMLAlgorithms</a></li><li><a class="tocitem" href="../Solutions/">SciMLSolutions</a></li><li class="is-active"><a class="tocitem" href>The SciML init and solve Functions</a><ul class="internal"><li><a class="tocitem" href="#init-and-the-Iterator-Interface"><span><code>init</code> and the Iterator Interface</span></a></li><li><a class="tocitem" href="#__solve-and-High-Level-Handling"><span>__solve and High-Level Handling</span></a></li></ul></li><li><a class="tocitem" href="../Common_Keywords/">Common Keyword Arguments</a></li><li><a class="tocitem" href="../Differentiation/">Automatic Differentiation and Sensitivity Algorithms (Adjoints)</a></li><li><a class="tocitem" href="../PDE/">The PDE Definition Interface</a></li></ul></li><li><span class="tocitem">Fundamentals</span><ul><li><a class="tocitem" href="../../fundamentals/FAQ/">Frequently Asked Questions</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"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Interfaces</a></li><li class="is-active"><a href>The SciML init and solve Functions</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>The SciML init and solve Functions</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/SciML/SciMLBase.jl/blob/master/docs/src/interfaces/Init_Solve.md" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="The-SciML-init-and-solve-Functions"><a class="docs-heading-anchor" href="#The-SciML-init-and-solve-Functions">The SciML init and solve Functions</a><a id="The-SciML-init-and-solve-Functions-1"></a><a class="docs-heading-anchor-permalink" href="#The-SciML-init-and-solve-Functions" title="Permalink"></a></h1><p><code>solve</code> function has the default definition</p><pre><code class="language-julia hljs">solve(args...; kwargs...) = solve!(init(args...; kwargs...))</code></pre><p>The interface for the three functions is as follows:</p><pre><code class="language-julia hljs">init(::ProblemType, args...; kwargs...) :: IteratorType
-solve!(::IteratorType) :: SolutionType</code></pre><p>where <code>ProblemType</code>, <code>IteratorType</code>, and <code>SolutionType</code> are the types defined in your package.</p><p>To avoid method ambiguity, the first argument of <code>solve</code>, <code>solve!</code>, and <code>init</code> <em>must</em> be dispatched on the type defined in your package.  For example, do <em>not</em> define a method such as</p><pre><code class="language-julia hljs">init(::AbstractVector, ::AlgorithmType)</code></pre><h2 id="init-and-the-Iterator-Interface"><a class="docs-heading-anchor" href="#init-and-the-Iterator-Interface"><code>init</code> and the Iterator Interface</a><a id="init-and-the-Iterator-Interface-1"></a><a class="docs-heading-anchor-permalink" href="#init-and-the-Iterator-Interface" title="Permalink"></a></h2><p><code>init</code>&#39;s return gives an <code>IteratorType</code> which is designed to allow the user to have more direct handling over the internal solving process. Because of this internal nature, the <code>IteratorType</code> has a less unified interface across problem types than other portions like <code>ProblemType</code> and <code>SolutionType</code>. For example, for differential equations this is the  <a href="https://docs.sciml.ai/DiffEqDocs/stable/basics/integrator/">Integrator Interface</a> designed for mutating solutions in a manner for callback implementation, which is distinctly different from the  <a href="https://docs.sciml.ai/LinearSolve/stable/tutorials/caching_interface">LinearSolve init interface</a> which is designed for caching efficiency with reusing factorizations.</p><h2 id="__solve-and-High-Level-Handling"><a class="docs-heading-anchor" href="#__solve-and-High-Level-Handling">__solve and High-Level Handling</a><a id="__solve-and-High-Level-Handling-1"></a><a class="docs-heading-anchor-permalink" href="#__solve-and-High-Level-Handling" title="Permalink"></a></h2><p>While <code>init</code> and <code>solve</code> are the common entry point for users, solver packages will mostly define dispatches on <code>SciMLBase.__init</code> and <code>SciMLBase.__solve</code>. The reason is because this allows for <code>SciMLBase.init</code> and <code>SciMLBase.solve</code> to have common implementations across all solvers for doing things such as checking for common errors and throwing high level messages. Solvers can opt-out of the high level error handling by directly defining <code>SciMLBase.init</code> and <code>SciMLBase.solve</code> instead, though this is not recommended in order to allow for uniformity of the error messages.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Solutions/">« SciMLSolutions</a><a class="docs-footer-nextpage" href="../Common_Keywords/">Common Keyword Arguments »</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="Friday 29 September 2023 08:22">Friday 29 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+solve!(::IteratorType) :: SolutionType</code></pre><p>where <code>ProblemType</code>, <code>IteratorType</code>, and <code>SolutionType</code> are the types defined in your package.</p><p>To avoid method ambiguity, the first argument of <code>solve</code>, <code>solve!</code>, and <code>init</code> <em>must</em> be dispatched on the type defined in your package.  For example, do <em>not</em> define a method such as</p><pre><code class="language-julia hljs">init(::AbstractVector, ::AlgorithmType)</code></pre><h2 id="init-and-the-Iterator-Interface"><a class="docs-heading-anchor" href="#init-and-the-Iterator-Interface"><code>init</code> and the Iterator Interface</a><a id="init-and-the-Iterator-Interface-1"></a><a class="docs-heading-anchor-permalink" href="#init-and-the-Iterator-Interface" title="Permalink"></a></h2><p><code>init</code>&#39;s return gives an <code>IteratorType</code> which is designed to allow the user to have more direct handling over the internal solving process. Because of this internal nature, the <code>IteratorType</code> has a less unified interface across problem types than other portions like <code>ProblemType</code> and <code>SolutionType</code>. For example, for differential equations this is the  <a href="https://docs.sciml.ai/DiffEqDocs/stable/basics/integrator/">Integrator Interface</a> designed for mutating solutions in a manner for callback implementation, which is distinctly different from the  <a href="https://docs.sciml.ai/LinearSolve/stable/tutorials/caching_interface">LinearSolve init interface</a> which is designed for caching efficiency with reusing factorizations.</p><h2 id="__solve-and-High-Level-Handling"><a class="docs-heading-anchor" href="#__solve-and-High-Level-Handling">__solve and High-Level Handling</a><a id="__solve-and-High-Level-Handling-1"></a><a class="docs-heading-anchor-permalink" href="#__solve-and-High-Level-Handling" title="Permalink"></a></h2><p>While <code>init</code> and <code>solve</code> are the common entry point for users, solver packages will mostly define dispatches on <code>SciMLBase.__init</code> and <code>SciMLBase.__solve</code>. The reason is because this allows for <code>SciMLBase.init</code> and <code>SciMLBase.solve</code> to have common implementations across all solvers for doing things such as checking for common errors and throwing high level messages. Solvers can opt-out of the high level error handling by directly defining <code>SciMLBase.init</code> and <code>SciMLBase.solve</code> instead, though this is not recommended in order to allow for uniformity of the error messages.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../Solutions/">« SciMLSolutions</a><a class="docs-footer-nextpage" href="../Common_Keywords/">Common Keyword Arguments »</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="Friday 29 September 2023 09:40">Friday 29 September 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>