Incrementing version number and updating autogenerated docs

matt-graham · Jan 8, 2020 · 946eeda · 946eeda
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diff --git a/docs/docs/autodiff.html b/docs/docs/autodiff.html
@@ -27,7 +27,7 @@ <h1 class="title">Package <code>mici.autodiff</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autodiff.py#L0-L62" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/autodiff.py#L0-L62" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">&#34;&#34;&#34;Automatic differentation fallback for constructing derivative functions.
 
@@ -132,7 +132,7 @@ <h2 id="returns">Returns</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autodiff.py#L34-L63" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/autodiff.py#L34-L63" 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
@@ -25,7 +25,7 @@ <h1 class="title">Package <code>mici.autograd_wrapper</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autograd_wrapper.py#L0-L124" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/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;
 
@@ -169,7 +169,7 @@ <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/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autograd_wrapper.py#L24-L33" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/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):
@@ -194,7 +194,7 @@ <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/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autograd_wrapper.py#L36-L53" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/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):
@@ -236,7 +236,7 @@ <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/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autograd_wrapper.py#L56-L78" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/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):
@@ -274,7 +274,7 @@ <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/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autograd_wrapper.py#L81-L99" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/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):
@@ -316,7 +316,7 @@ <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/2a3d6cae71fd207485990a9650546f423185f9d9/mici/autograd_wrapper.py#L102-L125" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/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
@@ -25,7 +25,7 @@ <h1 class="title">Package <code>mici.errors</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/errors.py#L0-L12" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/errors.py#L0-L12" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">&#34;&#34;&#34;Exception types.&#34;&#34;&#34;
 
@@ -60,7 +60,7 @@ <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/2a3d6cae71fd207485990a9650546f423185f9d9/mici/errors.py#L4-L5" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/errors.py#L4-L5" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class IntegratorError(RuntimeError):
     &#34;&#34;&#34;Error raised when integrator step fails.&#34;&#34;&#34;</code></pre>
@@ -86,7 +86,7 @@ <h3>Subclasses</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/errors.py#L8-L9" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/errors.py#L8-L9" 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>
@@ -108,7 +108,7 @@ <h3>Ancestors</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/errors.py#L12-L13" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/errors.py#L12-L13" 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>

diff --git a/docs/docs/index.html b/docs/docs/index.html
@@ -25,7 +25,7 @@ <h1 class="title">Package <code>mici</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/__init__.py#L0-L14" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/__init__.py#L0-L14" 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;

diff --git a/docs/docs/integrators.html b/docs/docs/integrators.html
@@ -25,7 +25,7 @@ <h1 class="title">Package <code>mici.integrators</code></h1>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L0-L348" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L0-L350" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">&#34;&#34;&#34;Symplectic integrators for simulation of Hamiltonian dynamics.&#34;&#34;&#34;
 
@@ -160,6 +160,8 @@ <h1 class="title">Package <code>mici.integrators</code></h1>
         self.reverse_check_tol = reverse_check_tol
         self.reverse_check_norm = maximum_norm
         self.fixed_point_solver = fixed_point_solver
+        if fixed_point_solver_kwargs is None:
+            fixed_point_solver_kwargs = {}
         self.fixed_point_solver_kwargs = fixed_point_solver_kwargs
 
     def _solve_fixed_point(self, fixed_point_func, x_init):
@@ -180,7 +182,7 @@ <h1 class="title">Package <code>mici.integrators</code></h1>
         mom_init = state.mom.copy()
         state.mom -= dt * self.system.dh2_dpos(state)
         state_back = state.copy()
-        self.step_b_fwd(state_back, -dt)
+        self._step_b_fwd(state_back, -dt)
         rev_diff = self.reverse_check_norm(state_back.mom - mom_init)
         if rev_diff &gt; self.reverse_check_tol:
             raise NonReversibleStepError(
@@ -191,7 +193,7 @@ <h1 class="title">Package <code>mici.integrators</code></h1>
         pos_init = state.pos.copy()
         state.pos += dt * self.system.dh2_dmom(state)
         state_back = state.copy()
-        self.step_c_adj(state_back, -dt)
+        self._step_c_adj(state_back, -dt)
         rev_diff = self.reverse_check_norm(state_back.pos - pos_init)
         if rev_diff &gt; self.reverse_check_tol:
             raise NonReversibleStepError(
@@ -404,7 +406,7 @@ <h2 id="args">Args</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L11-L35" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L11-L35" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class Integrator(ABC):
     &#34;&#34;&#34;Base class for integrators.&#34;&#34;&#34;
@@ -464,7 +466,7 @@ <h2 id="returns">Returns</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L24-L35" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L24-L35" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">@abstractmethod
 def step(self, state):
@@ -508,7 +510,7 @@ <h2 id="args">Args</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L38-L71" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L38-L71" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class ExplicitLeapfrogIntegrator(Integrator):
     r&#34;&#34;&#34;
@@ -572,7 +574,7 @@ <h2 id="returns">Returns</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L65-L71" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L65-L71" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">def step(self, state):
     dt = state.dir * self.step_size
@@ -640,7 +642,7 @@ <h2 id="args">Args</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L78-L188" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L78-L190" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class ImplicitLeapfrogIntegrator(Integrator):
     r&#34;&#34;&#34;
@@ -698,6 +700,8 @@ <h2 id="args">Args</h2>
         self.reverse_check_tol = reverse_check_tol
         self.reverse_check_norm = maximum_norm
         self.fixed_point_solver = fixed_point_solver
+        if fixed_point_solver_kwargs is None:
+            fixed_point_solver_kwargs = {}
         self.fixed_point_solver_kwargs = fixed_point_solver_kwargs
 
     def _solve_fixed_point(self, fixed_point_func, x_init):
@@ -718,7 +722,7 @@ <h2 id="args">Args</h2>
         mom_init = state.mom.copy()
         state.mom -= dt * self.system.dh2_dpos(state)
         state_back = state.copy()
-        self.step_b_fwd(state_back, -dt)
+        self._step_b_fwd(state_back, -dt)
         rev_diff = self.reverse_check_norm(state_back.mom - mom_init)
         if rev_diff &gt; self.reverse_check_tol:
             raise NonReversibleStepError(
@@ -729,7 +733,7 @@ <h2 id="args">Args</h2>
         pos_init = state.pos.copy()
         state.pos += dt * self.system.dh2_dmom(state)
         state_back = state.copy()
-        self.step_c_adj(state_back, -dt)
+        self._step_c_adj(state_back, -dt)
         rev_diff = self.reverse_check_norm(state_back.pos - pos_init)
         if rev_diff &gt; self.reverse_check_tol:
             raise NonReversibleStepError(
@@ -773,7 +777,7 @@ <h3>Methods</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L179-L188" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L181-L190" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">def step(self, state):
     dt = 0.5 * state.dir * self.step_size
@@ -889,7 +893,7 @@ <h2 id="args">Args</h2>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L191-L349" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L193-L351" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">class ConstrainedLeapfrogIntegrator(Integrator):
     r&#34;&#34;&#34;
@@ -1070,7 +1074,7 @@ <h3>Methods</h3>
 <details class="source">
 <summary>
 <span>Expand source code</span>
-<a href="https://github.com/matt-graham/mici/blob/2a3d6cae71fd207485990a9650546f423185f9d9/mici/integrators.py#L343-L349" class="git-link">Browse git</a>
+<a href="https://github.com/matt-graham/mici/blob/6382e9888f02d9a2cdd4968652247c5bf837184f/mici/integrators.py#L345-L351" class="git-link">Browse git</a>
 </summary>
 <pre><code class="python">def step(self, state):
     dt = state.dir * self.step_size