link to dev simulation

docs/_modules/index.html

@@ -108,6 +108,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../developer.html#todo-list">Todo list</a></li>
 </ul>
 

docs/_modules/mushi/histories.html

@@ -108,6 +108,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html#todo-list">Todo list</a></li>
 </ul>
 

docs/_modules/mushi/ksfs.html

@@ -108,6 +108,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html#todo-list">Todo list</a></li>
 </ul>
 

docs/_modules/mushi/optimization.html

@@ -108,6 +108,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html#todo-list">Todo list</a></li>
 </ul>
 

docs/_modules/mushi/utils.html

@@ -108,6 +108,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../developer.html#todo-list">Todo list</a></li>
 </ul>
 

docs/_sources/developer.rst.txt

@@ -1,7 +1,7 @@
 Update documentation
 ====================
 
-Inspired  by: https://www.docslikecode.com/articles/github-pages-python-sphinx/
+Inspired by: https://www.docslikecode.com/articles/github-pages-python-sphinx/
 
 Go to the ``docsrc`` directory::
 
@@ -45,6 +45,12 @@ From the ``docsrc`` dir::
 You can then see the generated documentation in
 ``docs/index.html``.
 
+Test notebook
+=============
+
+A test notebook that simulates under the linkage-free forward model (where the PRF composite likelihood is not approximate): `<notebooks/simulation_simple.html>`_
+
+
 Todo list
 =========
 

docs/developer.html

@@ -114,6 +114,7 @@
 <li class="toctree-l2"><a class="reference internal" href="#github-pages-build">Github Pages build</a></li>
 </ul>
 </li>
+<li class="toctree-l1"><a class="reference internal" href="#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="#todo-list">Todo list</a></li>
 </ul>
 
@@ -205,7 +206,7 @@
 </style>
 <div class="section" id="update-documentation">
 <h1>Update documentation<a class="headerlink" href="#update-documentation" title="Permalink to this headline">¶</a></h1>
-<p>Inspired  by: <a class="reference external" href="https://www.docslikecode.com/articles/github-pages-python-sphinx/">https://www.docslikecode.com/articles/github-pages-python-sphinx/</a></p>
+<p>Inspired by: <a class="reference external" href="https://www.docslikecode.com/articles/github-pages-python-sphinx/">https://www.docslikecode.com/articles/github-pages-python-sphinx/</a></p>
 <p>Go to the <code class="docutils literal notranslate"><span class="pre">docsrc</span></code> directory:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">docsrc</span>
 </pre></div>
@@ -246,6 +247,10 @@ <h2>Github Pages build<a class="headerlink" href="#github-pages-build" title="Pe
 <code class="docutils literal notranslate"><span class="pre">docs/index.html</span></code>.</p>
 </div>
 </div>
+<div class="section" id="test-notebook">
+<h1>Test notebook<a class="headerlink" href="#test-notebook" title="Permalink to this headline">¶</a></h1>
+<p>A test notebook that simulates under the linkage-free forward model (where the PRF composite likelihood is not approximate): <a class="reference external" href="notebooks/simulation_simple.html">notebooks/simulation_simple.html</a></p>
+</div>
 <div class="section" id="todo-list">
 <h1>Todo list<a class="headerlink" href="#todo-list" title="Permalink to this headline">¶</a></h1>
 <div class="admonition-todo admonition">
@@ -255,24 +260,24 @@ <h1>Todo list<a class="headerlink" href="#todo-list" title="Permalink to this he
 <p class="todo-source">(The <a class="reference internal" href="cite.html#id1"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/cite.rst, line 4.)</p>
 <div class="admonition-todo admonition">
 <p class="admonition-title">Todo</p>
-<p>set up Google collab for notebooks</p>
+<p>setup Conda install</p>
 </div>
-<p class="todo-source">(The <a class="reference internal" href="index.html#id1"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/index.rst, line 26.)</p>
+<p class="todo-source">(The <a class="reference internal" href="install.html#id1"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/install.rst, line 9.)</p>
 <div class="admonition-todo admonition">
 <p class="admonition-title">Todo</p>
-<p>document CLI</p>
+<p>cut version and create PyPy wheels</p>
 </div>
-<p class="todo-source">(The <a class="reference internal" href="index.html#id2"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/index.rst, line 47.)</p>
+<p class="todo-source">(The <a class="reference internal" href="install.html#id2"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/install.rst, line 23.)</p>
 <div class="admonition-todo admonition">
 <p class="admonition-title">Todo</p>
-<p>setup Conda install</p>
+<p>set up Google collab for notebooks</p>
 </div>
-<p class="todo-source">(The <a class="reference internal" href="install.html#id1"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/install.rst, line 9.)</p>
+<p class="todo-source">(The <a class="reference internal" href="index.html#id1"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/index.rst, line 26.)</p>
 <div class="admonition-todo admonition">
 <p class="admonition-title">Todo</p>
-<p>cut version and create PyPy wheels</p>
+<p>document CLI</p>
 </div>
-<p class="todo-source">(The <a class="reference internal" href="install.html#id2"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/install.rst, line 23.)</p>
+<p class="todo-source">(The <a class="reference internal" href="index.html#id2"><em>original entry</em></a> is located in /Users/williamdewitt/Desktop/repos.nosync/mushi/docsrc/index.rst, line 47.)</p>
 </div>
 
 

docs/genindex.html

@@ -109,6 +109,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="developer.html#todo-list">Todo list</a></li>
 </ul>
 

docs/index.html

@@ -109,6 +109,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="developer.html#todo-list">Todo list</a></li>
 </ul>
 
@@ -251,6 +252,7 @@ <h1>Mutation Spectrum History Inference<a class="headerlink" href="#mutation-spe
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="developer.html#todo-list">Todo list</a></li>
 </ul>
 </div>

docs/py-modindex.html

@@ -111,6 +111,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="developer.html#todo-list">Todo list</a></li>
 </ul>
 

docs/search.html

@@ -109,6 +109,7 @@
 <p class="caption"><span class="caption-text">Developer Documentation</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="developer.html">Update documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="developer.html#test-notebook">Test notebook</a></li>
 <li class="toctree-l1"><a class="reference internal" href="developer.html#todo-list">Todo list</a></li>
 </ul>
 

docsrc/developer.rst

@@ -1,7 +1,7 @@
 Update documentation
 ====================
 
-Inspired  by: https://www.docslikecode.com/articles/github-pages-python-sphinx/
+Inspired by: https://www.docslikecode.com/articles/github-pages-python-sphinx/
 
 Go to the ``docsrc`` directory::
 
@@ -45,6 +45,12 @@ From the ``docsrc`` dir::
 You can then see the generated documentation in
 ``docs/index.html``.
 
+Test notebook
+=============
+
+A test notebook that simulates under the linkage-free forward model (where the PRF composite likelihood is not approximate): `<notebooks/simulation_simple.html>`_
+
+
 Todo list
 =========