Minor tweaks to HTML docs templates and rebuilding for docstring updates

matt-graham · Jun 30, 2020 · ac7265a · ac7265a
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diff --git a/README.md b/README.md
@@ -211,7 +211,7 @@ def neg_log_dens(q):
 system = systems.DenseConstrainedEuclideanMetricSystem(neg_log_dens, constr)
 
 # System is constrained therefore use constrained leapfrog integrator
-integrator = integrators.ConstrainedLeapfrogIntegrator(system, step_size=0.2)
+integrator = integrators.ConstrainedLeapfrogIntegrator(system)
 
 # Seed a random number generator
 rng = np.random.default_rng(seed=1234)
@@ -233,9 +233,11 @@ def trace_func(state):
     x, y, z = state.pos
     return {'x': x, 'y': y, 'z': z}
 
-# Sample four chains of 2500 samples in parallel
-final_states, traces, stats = sampler.sample_chains(
-    n_sample=2500, init_states=q_init, n_process=4, trace_funcs=[trace_func])
+# Sample 4 chains in parallel with 500 adaptive warm up iterations in which the
+# integrator step size is tuned, followed by 2000 non-adaptive iterations
+final_states, traces, stats = sampler.sample_chains_with_adaptive_warm_up(
+    n_warm_up_iter=500, n_main_iter=2000, init_states=q_init, n_process=4, 
+    trace_funcs=[trace_func])
 
 # Print average accept probability and number of integrator steps per chain
 for c in range(n_chain):

diff --git a/docs/docs/adapters.html b/docs/docs/adapters.html
diff --git a/docs/docs/autodiff.html b/docs/docs/autodiff.html
@@ -3,14 +3,14 @@
 <head>
 <meta charset="utf-8">
 <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1" />
-<meta name="generator" content="pdoc 0.7.2.dev0+g1b644f6.d20200507" />
+<meta name="generator" content="pdoc 0.7.2.dev0+g1b644f6.d20200630" />
 <title>mici.autodiff API documentation</title>
 <meta name="description" content="Automatic differentation fallback for constructing derivative functions." />
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+<style media="screen and (min-width: 700px)">@media screen and (min-width:1000px){#sidebar{width:540px;position:fixed;z-index:1;top:0;bottom:0;overflow-x:hidden;overflow-y:auto}#content{margin-left:540px;max-width:100ch;padding:3em 4em;border-left:1px solid #ddd}#footer{margin-left:540px}pre code{font-size:1em}.item .name{font-size:1em}main{display:flex;flex-direction:row-reverse;justify-content:flex-end}.toc ul ul,#index ul{padding-left:1.5em}.toc > ul > li{margin-top:.5em}}</style>
 <style media="print">@media print{#sidebar h1{page-break-before:always}.source{display:none}}@media print{*{background:transparent !important;color:#000 !important;box-shadow:none !important;text-shadow:none !important}a[href]:after{content:" (" attr(href) ")";font-size:90%}a[href][title]:after{content:none}abbr[title]:after{content:" (" attr(title) ")"}.ir a:after,a[href^="javascript:"]:after,a[href^="#"]:after{content:""}pre,blockquote{border:1px solid #999;page-break-inside:avoid}thead{display:table-header-group}tr,img{page-break-inside:avoid}img{max-width:100% !important}@page{margin:0.5cm}p,h2,h3{orphans:3;widows:3}h1,h2,h3,h4,h5,h6{page-break-after:avoid}}</style>
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 </head>
@@ -40,14 +40,14 @@
 </nav>
 <article id="content">
 <header>
-<h1 class="title">Package <code>mici.autodiff</code></h1>
+<h1 class="title">Module <code>mici.autodiff</code></h1>
 </header>
 <section id="section-intro">
 <p>Automatic differentation fallback for constructing derivative functions.</p>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autodiff.py#L0-L58" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autodiff.py#L0-L58" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">&#34;&#34;&#34;Automatic differentation fallback for constructing derivative functions.&#34;&#34;&#34;
 
@@ -148,7 +148,7 @@ <h2 id="returns">Returns</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autodiff.py#L30-L59" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autodiff.py#L30-L59" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">def autodiff_fallback(diff_func, func, diff_op_name, name):
     &#34;&#34;&#34;Generate derivative function automatically if not provided.
@@ -190,7 +190,7 @@ <h2 id="returns">Returns</h2>
 </main>
 <footer id="footer">
 Copyright © 2019 Matt Graham
-<p>Generated by <a href="https://pdoc3.github.io/pdoc"><cite>pdoc</cite> 0.7.2.dev0+g1b644f6.d20200507</a>.</p>
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diff --git a/docs/docs/autograd_wrapper.html b/docs/docs/autograd_wrapper.html
@@ -3,14 +3,14 @@
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 <meta charset="utf-8">
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-<meta name="generator" content="pdoc 0.7.2.dev0+g1b644f6.d20200507" />
+<meta name="generator" content="pdoc 0.7.2.dev0+g1b644f6.d20200630" />
 <title>mici.autograd_wrapper API documentation</title>
 <meta name="description" content="Additional autograd differential operators." />
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+<style media="screen and (min-width: 700px)">@media screen and (min-width:1000px){#sidebar{width:540px;position:fixed;z-index:1;top:0;bottom:0;overflow-x:hidden;overflow-y:auto}#content{margin-left:540px;max-width:100ch;padding:3em 4em;border-left:1px solid #ddd}#footer{margin-left:540px}pre code{font-size:1em}.item .name{font-size:1em}main{display:flex;flex-direction:row-reverse;justify-content:flex-end}.toc ul ul,#index ul{padding-left:1.5em}.toc > ul > li{margin-top:.5em}}</style>
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 <script async src='https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS_CHTML'></script>
 </head>
@@ -44,14 +44,14 @@
 </nav>
 <article id="content">
 <header>
-<h1 class="title">Package <code>mici.autograd_wrapper</code></h1>
+<h1 class="title">Module <code>mici.autograd_wrapper</code></h1>
 </header>
 <section id="section-intro">
 <p>Additional autograd differential operators.</p>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autograd_wrapper.py#L0-L124" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L0-L124" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">&#34;&#34;&#34;Additional autograd differential operators.&#34;&#34;&#34;
 
@@ -195,7 +195,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autograd_wrapper.py#L24-L33" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L24-L33" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">@_wrapped_unary_to_nary
 def grad_and_value(fun, x):
@@ -220,7 +220,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autograd_wrapper.py#L36-L53" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L36-L53" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">@_wrapped_unary_to_nary
 def jacobian_and_value(fun, x):
@@ -262,7 +262,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autograd_wrapper.py#L56-L78" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L56-L78" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">@_wrapped_unary_to_nary
 def mhp_jacobian_and_value(fun, x):
@@ -300,7 +300,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autograd_wrapper.py#L81-L99" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L81-L99" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">@_wrapped_unary_to_nary
 def hessian_grad_and_value(fun, x):
@@ -342,7 +342,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/be3c4cd91f60faf5182ee5704e8e9e61e5dc5b23/mici/autograd_wrapper.py#L102-L125" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L102-L125" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">@_wrapped_unary_to_nary
 def mtp_hessian_grad_and_value(fun, x):
@@ -378,7 +378,7 @@ <h2 class="section-title" id="header-functions">Functions</h2>
 </main>
 <footer id="footer">
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