Publish docs @ 93b9868

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@@ -307,10 +307,10 @@
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- <span class="menu-text">v0.39</span>
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.40" role="link" data-bs-toggle="dropdown" aria-expanded="false">
+ <span class="menu-text">v0.40</span>
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@@ -1162,7 +1162,7 @@ <h5>Supported by leading researchers</h5>
 
     </div>
     <div class="footer-bottom">
-      <p>Turing is created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
+      <p>Turing.jl was created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
       <a href="https://github.com/TuringLang/docs/" target="_blank" rel="noopener" class="footer-source-link"><i class="bi bi-github"></i> Website Source</a>
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changelog.html

@@ -344,10 +344,10 @@
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- <span class="menu-text">v0.39</span>
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.40" role="link" data-bs-toggle="dropdown" aria-expanded="false">
+ <span class="menu-text">v0.40</span>
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@@ -1456,7 +1456,7 @@ <h5>Supported by leading researchers</h5>
 
     </div>
     <div class="footer-bottom">
-      <p>Turing is created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
+      <p>Turing.jl was created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
       <a href="https://github.com/TuringLang/docs/" target="_blank" rel="noopener" class="footer-source-link"><i class="bi bi-github"></i> Website Source</a>
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core-functionality/index.html

@@ -373,10 +373,10 @@
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-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.39" role="link" data-bs-toggle="dropdown" aria-expanded="false">
- <span class="menu-text">v0.39</span>
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.40" role="link" data-bs-toggle="dropdown" aria-expanded="false">
+ <span class="menu-text">v0.40</span>
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+    <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="nav-menu-v0.40">    
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@@ -1034,15 +1034,15 @@ <h1>Consider a probabilistic model defined by</h1>
 <span id="cb14-10"><a href="#cb14-10" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb14-11"><a href="#cb14-11" aria-hidden="true" tabindex="-1"></a><span class="fu">sample</span>(<span class="fu">turing_m</span>(<span class="fl">3.0</span>), <span class="fu">MH</span>(<span class="fu">ScalMat</span>(<span class="fl">2</span>, <span class="fl">1.0</span>)), <span class="fl">1_000_000</span>, progress<span class="op">=</span><span class="cn">false</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
 <div class="cell-output cell-output-display" data-execution_count="1">
-<pre><code>Chains MCMC chain (1000000×3×1 Array{Float64, 3}):
+<pre><code>Chains MCMC chain (1000000×5×1 Array{Float64, 3}):
 
 Iterations        = 1:1:1000000
 Number of chains  = 1
 Samples per chain = 1000000
-Wall duration     = 21.09 seconds
-Compute duration  = 21.09 seconds
+Wall duration     = 22.59 seconds
+Compute duration  = 22.59 seconds
 parameters        = a, b
-internals         = lp
+internals         = lp, logprior, loglikelihood
 
 Use `describe(chains)` for summary statistics and quantiles.</code></pre>
 </div>
@@ -1519,7 +1519,7 @@ <h5>Supported by leading researchers</h5>
 
     </div>
     <div class="footer-bottom">
-      <p>Turing is created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
+      <p>Turing.jl was created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
       <a href="https://github.com/TuringLang/docs/" target="_blank" rel="noopener" class="footer-source-link"><i class="bi bi-github"></i> Website Source</a>
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developers/compiler/design-overview/index.html

@@ -344,10 +344,10 @@
 </ul>
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-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.39" role="link" data-bs-toggle="dropdown" aria-expanded="false">
- <span class="menu-text">v0.39</span>
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.40" role="link" data-bs-toggle="dropdown" aria-expanded="false">
+ <span class="menu-text">v0.40</span>
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@@ -748,6 +748,19 @@ <h1 class="title">A Mini Turing Implementation II: Contexts</h1>
 
 
 <p>In the <a href="../../../developers/compiler/minituring-compiler">Mini Turing</a> tutorial we developed a miniature version of the Turing language, to illustrate its core design. A passing mention was made of contexts. In this tutorial we develop that aspect of our mini Turing language further to demonstrate how and why contexts are an important part of Turing’s design.</p>
+<div class="callout callout-style-default callout-important callout-titled">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Important
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>Note: The way Turing actually uses contexts changed somewhat in releases 0.39 and 0.40. The content of this page remains relevant, the principles of how contexts operate remain the same, and concepts like leaf and parent contexts still exist. However, we’ve moved away from using contexts for quite as many things as we used to. Most importantly, whether to accumulate the log joint, log prior, or log likelihood is no longer done using different contexts. Please keep this in mind as you read this page: The principles remain, but the details have changed. We will update this page once the refactoring of internals that is happening around releases like 0.39 and 0.40 is done.</p>
+</div>
+</div>
 <section id="mini-turing-expanded-now-with-more-contexts" class="level1">
 <h1>Mini Turing expanded, now with more contexts</h1>
 <p>If you haven’t read <a href="../../../developers/compiler/minituring-compiler">Mini Turing</a> yet, you should do that first. We start by repeating verbatim much of the code from there. Define the type for holding values for variables:</p>
@@ -1510,7 +1523,7 @@ <h5>Supported by leading researchers</h5>
 
     </div>
     <div class="footer-bottom">
-      <p>Turing is created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
+      <p>Turing.jl was created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
       <a href="https://github.com/TuringLang/docs/" target="_blank" rel="noopener" class="footer-source-link"><i class="bi bi-github"></i> Website Source</a>
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developers/compiler/minituring-compiler/index.html

@@ -344,10 +344,10 @@
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   <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.39" role="link" data-bs-toggle="dropdown" aria-expanded="false">
- <span class="menu-text">v0.39</span>
+    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-v0.40" role="link" data-bs-toggle="dropdown" aria-expanded="false">
+ <span class="menu-text">v0.40</span>
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-    <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="nav-menu-v0.39">    
+    <ul class="dropdown-menu dropdown-menu-end" aria-labelledby="nav-menu-v0.40">    
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@@ -764,21 +764,21 @@ <h1 class="title">Manually Defining a Model</h1>
 <div class="code-copy-outer-scaffold"><div class="sourceCode cell-code" id="cb3"><pre class="sourceCode julia code-with-copy"><code class="sourceCode julia"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="im">using</span> <span class="bu">DynamicPPL</span></span>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="co"># Create the model function.</span></span>
-<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="kw">function</span> <span class="fu">gdemo2</span>(model, varinfo, context, x)</span>
+<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a><span class="kw">function</span> <span class="fu">gdemo2</span>(model, varinfo, x)</span>
 <span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a>    <span class="co"># Assume s² has an InverseGamma distribution.</span></span>
 <span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a>    s², varinfo <span class="op">=</span> DynamicPPL.<span class="fu">tilde_assume!!</span>(</span>
-<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a>        context, <span class="fu">InverseGamma</span>(<span class="fl">2</span>, <span class="fl">3</span>), <span class="pp">@varname</span>(s²), varinfo</span>
+<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a>        model.context, <span class="fu">InverseGamma</span>(<span class="fl">2</span>, <span class="fl">3</span>), <span class="pp">@varname</span>(s²), varinfo</span>
 <span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>    )</span>
 <span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a>    <span class="co"># Assume m has a Normal distribution.</span></span>
 <span id="cb3-11"><a href="#cb3-11" aria-hidden="true" tabindex="-1"></a>    m, varinfo <span class="op">=</span> DynamicPPL.<span class="fu">tilde_assume!!</span>(</span>
-<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a>        context, <span class="fu">Normal</span>(<span class="fl">0</span>, <span class="fu">sqrt</span>(s²)), <span class="pp">@varname</span>(m), varinfo</span>
+<span id="cb3-12"><a href="#cb3-12" aria-hidden="true" tabindex="-1"></a>        model.context, <span class="fu">Normal</span>(<span class="fl">0</span>, <span class="fu">sqrt</span>(s²)), <span class="pp">@varname</span>(m), varinfo</span>
 <span id="cb3-13"><a href="#cb3-13" aria-hidden="true" tabindex="-1"></a>    )</span>
 <span id="cb3-14"><a href="#cb3-14" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-15"><a href="#cb3-15" aria-hidden="true" tabindex="-1"></a>    <span class="co"># Observe each value of x[i] according to a Normal distribution.</span></span>
 <span id="cb3-16"><a href="#cb3-16" aria-hidden="true" tabindex="-1"></a>    <span class="cf">for</span> i <span class="kw">in</span> <span class="fu">eachindex</span>(x)</span>
 <span id="cb3-17"><a href="#cb3-17" aria-hidden="true" tabindex="-1"></a>        _retval, varinfo <span class="op">=</span> DynamicPPL.<span class="fu">tilde_observe!!</span>(</span>
-<span id="cb3-18"><a href="#cb3-18" aria-hidden="true" tabindex="-1"></a>            context, <span class="fu">Normal</span>(m, <span class="fu">sqrt</span>(s²)), x[i], <span class="pp">@varname</span>(x[i]), varinfo</span>
+<span id="cb3-18"><a href="#cb3-18" aria-hidden="true" tabindex="-1"></a>            model.context, <span class="fu">Normal</span>(m, <span class="fu">sqrt</span>(s²)), x[i], <span class="pp">@varname</span>(x[i]), varinfo</span>
 <span id="cb3-19"><a href="#cb3-19" aria-hidden="true" tabindex="-1"></a>        )</span>
 <span id="cb3-20"><a href="#cb3-20" aria-hidden="true" tabindex="-1"></a>    <span class="cf">end</span></span>
 <span id="cb3-21"><a href="#cb3-21" aria-hidden="true" tabindex="-1"></a></span>
@@ -800,20 +800,20 @@ <h1 class="title">Manually Defining a Model</h1>
 <div class="cell-output cell-output-stdout">
 <div class="ansi-escaped-output">
 <pre><span class="ansi-cyan-fg ansi-bold">┌ </span><span class="ansi-cyan-fg ansi-bold">Info: </span>Found initial step size
-<span class="ansi-cyan-fg ansi-bold">└ </span>  ϵ = 0.8500000000000001
+<span class="ansi-cyan-fg ansi-bold">└ </span>  ϵ = 0.8
 </pre>
 </div>
 </div>
 <div class="cell-output cell-output-display" data-execution_count="1">
-<pre><code>Chains MCMC chain (1000×14×1 Array{Float64, 3}):
+<pre><code>Chains MCMC chain (1000×16×1 Array{Float64, 3}):
 
 Iterations        = 501:1:1500
 Number of chains  = 1
 Samples per chain = 1000
-Wall duration     = 7.78 seconds
-Compute duration  = 7.78 seconds
+Wall duration     = 8.3 seconds
+Compute duration  = 8.3 seconds
 parameters        = s², m
-internals         = lp, n_steps, is_accept, acceptance_rate, log_density, hamiltonian_energy, hamiltonian_energy_error, max_hamiltonian_energy_error, tree_depth, numerical_error, step_size, nom_step_size
+internals         = n_steps, is_accept, acceptance_rate, log_density, hamiltonian_energy, hamiltonian_energy_error, max_hamiltonian_energy_error, tree_depth, numerical_error, step_size, nom_step_size, lp, logprior, loglikelihood
 
 Use `describe(chains)` for summary statistics and quantiles.</code></pre>
 </div>
@@ -1289,7 +1289,7 @@ <h5>Supported by leading researchers</h5>
 
     </div>
     <div class="footer-bottom">
-      <p>Turing is created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
+      <p>Turing.jl was created by <a href="https://mlg.eng.cam.ac.uk/hong/" target="_blank" rel="noopener">Hong Ge</a>, and maintained by the core <a href="https://turinglang.org/team/" target="_blank" rel="noopener">team</a> of developers and <a href="https://github.com/TuringLang/Turing.jl/graphs/contributors" target="_blank" rel="noopener">contributors</a>.<br>© 2025 The Turing Project Contributors. <a href="https://github.com/TuringLang/Turing.jl/blob/master/LICENCE" target="_blank" rel="noopener">MIT License</a>.</p>
       <a href="https://github.com/TuringLang/docs/" target="_blank" rel="noopener" class="footer-source-link"><i class="bi bi-github"></i> Website Source</a>
     </div>
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