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matt-graham · Jul 8, 2020 · cf7003a · cf7003a
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diff --git a/README.md b/README.md
@@ -12,6 +12,7 @@
     <img src="https://zenodo.org/badge/52494384.svg" alt="DOI"/>
   </a>
   <img src="images/coverage.svg" alt="Coverage"/>
+  <img src="https://github.com/matt-graham/mici/workflows/Tests/badge.svg" alt="Test status" />
 </p>
 
 **Mici** is a Python package providing implementations of *Markov chain Monte

diff --git a/docs/docs/adapters.html b/docs/docs/adapters.html
diff --git a/docs/docs/autodiff.html b/docs/docs/autodiff.html
@@ -47,7 +47,7 @@ <h1 class="title">Module <code>mici.autodiff</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autodiff.py#L0-L58" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autodiff.py#L30-L59" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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.

diff --git a/docs/docs/autograd_wrapper.html b/docs/docs/autograd_wrapper.html
@@ -51,7 +51,7 @@ <h1 class="title">Module <code>mici.autograd_wrapper</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L0-L124" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L24-L33" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L36-L53" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L56-L78" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L81-L99" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/autograd_wrapper.py#L102-L125" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/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):

diff --git a/docs/docs/errors.html b/docs/docs/errors.html
@@ -70,7 +70,7 @@ <h1 class="title">Module <code>mici.errors</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L0-L32" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L0-L32" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">&#34;&#34;&#34;Exception types.&#34;&#34;&#34;
 
@@ -125,7 +125,7 @@ <h2 class="section-title" id="header-classes">Classes</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L4-L5" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L4-L5" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class Error(RuntimeError):
     &#34;&#34;&#34;Base class for errors.&#34;&#34;&#34;</code></pre>
@@ -153,7 +153,7 @@ <h3>Subclasses</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L8-L9" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L8-L9" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class IntegratorError(Error):
     &#34;&#34;&#34;Error raised when integrator step fails.&#34;&#34;&#34;</code></pre>
@@ -181,7 +181,7 @@ <h3>Subclasses</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L12-L13" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L12-L13" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class NonReversibleStepError(IntegratorError):
     &#34;&#34;&#34;Error raised when integrator step fails reversibility check.&#34;&#34;&#34;</code></pre>
@@ -204,7 +204,7 @@ <h3>Ancestors</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L16-L17" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L16-L17" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class ConvergenceError(IntegratorError):
     &#34;&#34;&#34;Error raised when solver fails to converge within allowed iterations.&#34;&#34;&#34;</code></pre>
@@ -227,7 +227,7 @@ <h3>Ancestors</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L20-L21" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L20-L21" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class LinAlgError(Error):
     &#34;&#34;&#34;Error raised when a matrix operation raises a linear algebra error.&#34;&#34;&#34;</code></pre>
@@ -249,7 +249,7 @@ <h3>Ancestors</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L24-L25" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L24-L25" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class HamiltonianDivergenceError(IntegratorError):
     &#34;&#34;&#34;Error raised when integration of Hamiltonian dynamics diverges.&#34;&#34;&#34;</code></pre>
@@ -272,7 +272,7 @@ <h3>Ancestors</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L28-L29" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L28-L29" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class AdaptationError(Error):
     &#34;&#34;&#34;Error raised when adaptation of transition parameters fails.&#34;&#34;&#34;</code></pre>
@@ -294,7 +294,7 @@ <h3>Ancestors</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/errors.py#L32-L33" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/errors.py#L32-L33" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class ReadOnlyStateError(Error):
     &#34;&#34;&#34;Error raised when writing to attributes of read-only chain state.&#34;&#34;&#34;</code></pre>

diff --git a/docs/docs/index.html b/docs/docs/index.html
@@ -37,6 +37,7 @@
 <li><code><a title="mici.progressbars" href="progressbars.html">mici.progressbars</a></code></li>
 <li><code><a title="mici.samplers" href="samplers.html">mici.samplers</a></code></li>
 <li><code><a title="mici.solvers" href="solvers.html">mici.solvers</a></code></li>
+<li><code><a title="mici.stagers" href="stagers.html">mici.stagers</a></code></li>
 <li><code><a title="mici.states" href="states.html">mici.states</a></code></li>
 <li><code><a title="mici.systems" href="systems.html">mici.systems</a></code></li>
 <li><code><a title="mici.transitions" href="transitions.html">mici.transitions</a></code></li>
@@ -54,7 +55,7 @@ <h1 class="title">Package <code>mici</code></h1>
 <details class="source">
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-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/__init__.py#L0-L15" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/__init__.py#L0-L15" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python"># -*- coding: utf-8 -*-
 &#34;&#34;&#34; MCMC samplers based on simulating Hamiltonian dynamics on a manifold. &#34;&#34;&#34;
@@ -68,10 +69,10 @@ <h1 class="title">Package <code>mici</code></h1>
 import mici.matrices
 import mici.samplers
 import mici.solvers
+import mici.stagers
 import mici.states
 import mici.systems
-import mici.transitions
-import mici.utils</code></pre>
+import mici.transitions</code></pre>
 </details>
 </section>
 <section>
@@ -113,9 +114,13 @@ <h2 class="section-title" id="header-submodules">Modules</h2>
 <dd>
 <section class="desc"><p>Solvers for non-linear systems of equations for implicit integrators.</p></section>
 </dd>
+<dt><code class="name"><a title="mici.stagers" href="stagers.html">mici.stagers</a></code></dt>
+<dd>
+<section class="desc"><p>Classes for controlling sampling of Markov chains split into stages.</p></section>
+</dd>
 <dt><code class="name"><a title="mici.states" href="states.html">mici.states</a></code></dt>
 <dd>
-<section class="desc"><p>Objects for recording state of a Markov chain.</p></section>
+<section class="desc"><p>Objects for recording state of a Markov chain and caching computations.</p></section>
 </dd>
 <dt><code class="name"><a title="mici.systems" href="systems.html">mici.systems</a></code></dt>
 <dd>

diff --git a/docs/docs/integrators.html b/docs/docs/integrators.html
@@ -70,7 +70,7 @@ <h1 class="title">Module <code>mici.integrators</code></h1>
 <details class="source">
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-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/integrators.py#L0-L355" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/integrators.py#L0-L354" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">&#34;&#34;&#34;Symplectic integrators for simulation of Hamiltonian dynamics.&#34;&#34;&#34;
 
@@ -126,7 +126,6 @@ <h1 class="title">Module <code>mici.integrators</code></h1>
         &#34;&#34;&#34;
 
 
-
 class LeapfrogIntegrator(Integrator):
     r&#34;&#34;&#34;
     Leapfrog integrator for Hamiltonian systems with tractable component flows.
@@ -458,7 +457,7 @@ <h2 id="args">Args</h2>
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-<a href="https://github.com/matt-graham/mici/blob/39019d0bfc441dc54a297e7623bac13534f7c2c1/mici/integrators.py#L9-L52" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/integrators.py#L9-L52" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class Integrator(ABC):
     &#34;&#34;&#34;Base class for integrators.&#34;&#34;&#34;
@@ -537,7 +536,7 @@ <h2 id="returns">Returns</h2>
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+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/integrators.py#L24-L42" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">def step(self, state):
     &#34;&#34;&#34;Perform a single integrator step from a supplied state.
@@ -589,7 +588,7 @@ <h2 id="args">Args</h2>
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+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/integrators.py#L55-L83" class="git-link">Browse git</a>
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 <pre><code class="python">class LeapfrogIntegrator(Integrator):
     r&#34;&#34;&#34;
@@ -705,7 +704,7 @@ <h2 id="args">Args</h2>
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+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/integrators.py#L86-L196" class="git-link">Browse git</a>
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 <pre><code class="python">class ImplicitLeapfrogIntegrator(Integrator):
     r&#34;&#34;&#34;
@@ -948,7 +947,7 @@ <h2 id="args">Args</h2>
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+<a href="https://github.com/matt-graham/mici/blob/056095624298b0e017652794677e9ba43f7f5ed8/mici/integrators.py#L199-L355" class="git-link">Browse git</a>
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 <pre><code class="python">class ConstrainedLeapfrogIntegrator(Integrator):
     r&#34;&#34;&#34;