Deploying to docs from @ ea3a068 🚀

.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 4f1d90bc4cf00a8afcb9806470b6325e
+config: 8ca26009d44a97cede737e18079e125b
 tags: 645f666f9bcd5a90fca523b33c5a78b7

_modules/historydag/compact_genome.html

@@ -32,6 +32,7 @@
 
           <a href="../../index.html">
 
+              <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
@@ -78,7 +79,14 @@
            <div itemprop="articleBody">
 
   <h1>Source code for historydag.compact_genome</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">frozendict</span> <span class="kn">import</span> <span class="n">frozendict</span>
+<span></span><span class="sd">&quot;&quot;&quot;This module provides a CompactGenome class, intended as a convenient and compact representation of</span>
+<span class="sd">a nucleotide sequence as a collection of mutations relative to a reference sequence. This object also</span>
+<span class="sd">provides methods to conveniently mutate CompactGenome objects according to a list of mutations, produce</span>
+<span class="sd">mutations defining the difference between two CompactGenome objects, and efficiently access the base</span>
+<span class="sd">at a site (or the entire sequence, as a string) implied by a CompactGenome.</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<span class="kn">from</span> <span class="nn">frozendict</span> <span class="kn">import</span> <span class="n">frozendict</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">Sequence</span>
 <span class="kn">from</span> <span class="nn">warnings</span> <span class="kn">import</span> <span class="n">warn</span>
 <span class="kn">from</span> <span class="nn">historydag.parsimony_utils</span> <span class="kn">import</span> <span class="p">(</span>

_modules/historydag/counterops.html

@@ -32,6 +32,7 @@
 
           <a href="../../index.html">
 
+              <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

_modules/historydag/dag.html

@@ -32,6 +32,7 @@
 
           <a href="../../index.html">
 
+              <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

_modules/historydag/mutation_annotated_dag.html

@@ -32,6 +32,7 @@
 
           <a href="../../index.html">
 
+              <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

_modules/historydag/parsimony.html

@@ -32,6 +32,7 @@
 
           <a href="../../index.html">
 
+              <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

_modules/historydag/sequence_dag.html

@@ -32,6 +32,7 @@
 
           <a href="../../index.html">
 
+              <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

_modules/historydag/utils.html

@@ -32,6 +32,7 @@
 
           <a href="../../index.html">
 
+              <img src="../../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">

_modules/index.html

@@ -32,6 +32,7 @@
 
           <a href="../index.html">
 
+              <img src="../_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -83,6 +84,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="historydag/dag_node.html">historydag.dag_node</a></li>
 <li><a href="historydag/mutation_annotated_dag.html">historydag.mutation_annotated_dag</a></li>
 <li><a href="historydag/parsimony.html">historydag.parsimony</a></li>
+<li><a href="historydag/parsimony_utils.html">historydag.parsimony_utils</a></li>
 <li><a href="historydag/sequence_dag.html">historydag.sequence_dag</a></li>
 <li><a href="historydag/utils.html">historydag.utils</a></li>
 </ul>

_sources/api.rst.txt

@@ -54,5 +54,8 @@ Modules
     mutation_annotated_dag
     utils
     parsimony
+    parsimony_utils
     compact_genome
+    dag_node
     counterops
+    beast_loader

_sources/stubs/historydag.dag_node.rst.txt

@@ -0,0 +1,37 @@
+historydag.dag\_node
+====================
+
+.. automodule:: historydag.dag_node
+
+
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      empty_node
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      EdgeSet
+      HistoryDagNode
+      UANode
+
+
+
+
+
+
+
+
+

_sources/stubs/historydag.parsimony_utils.rst.txt

@@ -0,0 +1,59 @@
+historydag.parsimony\_utils
+===========================
+
+.. automodule:: historydag.parsimony_utils
+
+
+
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+
+      standard_nt_ambiguity_map
+      standard_nt_ambiguity_map_gap_as_char
+      default_nt_transitions
+      default_nt_gaps_transitions
+      hamming_edge_weight
+      hamming_edge_weight_ambiguous_leaves
+      hamming_cg_edge_weight
+      hamming_cg_edge_weight_ambiguous_leaves
+      hamming_distance_countfuncs
+      leaf_ambiguous_hamming_distance_countfuncs
+      compact_genome_hamming_distance_countfuncs
+      leaf_ambiguous_compact_genome_hamming_distance_countfuncs
+
+
+
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      hamming_cg_edge_weight
+      hamming_cg_edge_weight_ambiguous_leaves
+      hamming_edge_weight
+      hamming_edge_weight_ambiguous_leaves
+
+
+
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      AmbiguityMap
+      ReversedAmbiguityMap
+      SitewiseTransitionModel
+      TransitionModel
+      UnitTransitionModel
+
+
+
+
+
+
+
+
+

api.html

@@ -35,6 +35,7 @@
 
           <a href="index.html">
 
+              <img src="_static/logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="search.html" method="get">
@@ -71,7 +72,9 @@
 <li class="toctree-l2"><a class="reference internal" href="stubs/historydag.mutation_annotated_dag.html">historydag.mutation_annotated_dag</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stubs/historydag.utils.html">historydag.utils</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stubs/historydag.parsimony.html">historydag.parsimony</a></li>
+<li class="toctree-l2"><a class="reference internal" href="stubs/historydag.parsimony_utils.html">historydag.parsimony_utils</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stubs/historydag.compact_genome.html">historydag.compact_genome</a></li>
+<li class="toctree-l2"><a class="reference internal" href="stubs/historydag.dag_node.html">historydag.dag_node</a></li>
 <li class="toctree-l2"><a class="reference internal" href="stubs/historydag.counterops.html">historydag.counterops</a></li>
 </ul>
 </li>
@@ -175,7 +178,13 @@ <h1>Modules<a class="headerlink" href="#modules" title="Link to this heading">
 <tr class="row-odd"><td><p><a class="reference internal" href="stubs/historydag.parsimony.html#module-historydag.parsimony" title="historydag.parsimony"><code class="xref py py-obj docutils literal notranslate"><span class="pre">parsimony</span></code></a></p></td>
 <td><p>A module implementing Sankoff Algorithm.</p></td>
 </tr>
-<tr class="row-even"><td><p><a class="reference internal" href="stubs/historydag.compact_genome.html#module-historydag.compact_genome" title="historydag.compact_genome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compact_genome</span></code></a></p></td>
+<tr class="row-even"><td><p><a class="reference internal" href="stubs/historydag.parsimony_utils.html#module-historydag.parsimony_utils" title="historydag.parsimony_utils"><code class="xref py py-obj docutils literal notranslate"><span class="pre">parsimony_utils</span></code></a></p></td>
+<td><p>This module provides tools for describing and computing parsimony and weighted parsimony, and for describing allowed characters and ambiguity codes.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="stubs/historydag.compact_genome.html#module-historydag.compact_genome" title="historydag.compact_genome"><code class="xref py py-obj docutils literal notranslate"><span class="pre">compact_genome</span></code></a></p></td>
+<td><p>This module provides a CompactGenome class, intended as a convenient and compact representation of a nucleotide sequence as a collection of mutations relative to a reference sequence.</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="stubs/historydag.dag_node.html#module-historydag.dag_node" title="historydag.dag_node"><code class="xref py py-obj docutils literal notranslate"><span class="pre">dag_node</span></code></a></p></td>
 <td><p></p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="stubs/historydag.counterops.html#module-historydag.counterops" title="historydag.counterops"><code class="xref py py-obj docutils literal notranslate"><span class="pre">counterops</span></code></a></p></td>