Build updated sphinx docs

biotaphy · Nov 22, 2019 · 969a929 · 969a929
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diff --git a/docs/sphinx/.doctrees/environment.pickle b/docs/sphinx/.doctrees/environment.pickle
diff --git a/docs/sphinx/.doctrees/source/analyses.ancestral_state.doctree b/docs/sphinx/.doctrees/source/analyses.ancestral_state.doctree
diff --git a/docs/sphinx/.doctrees/source/analyses.doctree b/docs/sphinx/.doctrees/source/analyses.doctree
diff --git a/docs/sphinx/.doctrees/source/analyses.phylo_beta_diversity.doctree b/docs/sphinx/.doctrees/source/analyses.phylo_beta_diversity.doctree
diff --git a/docs/sphinx/.doctrees/source/analyses.tools.doctree b/docs/sphinx/.doctrees/source/analyses.tools.doctree
diff --git a/docs/sphinx/genindex.html b/docs/sphinx/genindex.html
@@ -45,7 +45,6 @@ <h1 id="index">Index</h1>
  | <a href="#G"><strong>G</strong></a>
  | <a href="#L"><strong>L</strong></a>
  | <a href="#N"><strong>N</strong></a>
- | <a href="#P"><strong>P</strong></a>
  | <a href="#Q"><strong>Q</strong></a>
  | <a href="#R"><strong>R</strong></a>
  | <a href="#S"><strong>S</strong></a>
@@ -54,50 +53,26 @@ <h1 id="index">Index</h1>
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="source/analyses.tools.html#analyses.tools.annotators.add_all_annotations">add_all_annotations() (in module analyses.tools.annotators)</a>
-</li>
       <li><a href="source/analyses.helpers.html#analyses.helpers.data_readers.AlignmentIOError">AlignmentIOError</a>
-</li>
-      <li><a href="source/analyses.html#module-analyses">analyses (module)</a>
-</li>
-      <li><a href="source/analyses.ancestral_state.html#module-analyses.ancestral_state">analyses.ancestral_state (module)</a>
 </li>
       <li><a href="source/analyses.helpers.html#module-analyses.helpers">analyses.helpers (module)</a>
-</li>
-      <li><a href="source/analyses.helpers.html#module-analyses.helpers.data_readers">analyses.helpers.data_readers (module)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="source/analyses.helpers.html#module-analyses.helpers.sequence">analyses.helpers.sequence (module)</a>
-</li>
-      <li><a href="source/analyses.phylo_beta_diversity.html#module-analyses.phylo_beta_diversity">analyses.phylo_beta_diversity (module)</a>
-</li>
-      <li><a href="source/analyses.phylo_beta_diversity.html#module-analyses.phylo_beta_diversity.phylo_beta_diversity">analyses.phylo_beta_diversity.phylo_beta_diversity (module)</a>
-</li>
-      <li><a href="source/analyses.tools.html#module-analyses.tools">analyses.tools (module)</a>
-</li>
-      <li><a href="source/analyses.tools.html#module-analyses.tools.annotators">analyses.tools.annotators (module)</a>
+      <li><a href="source/analyses.helpers.html#module-analyses.helpers.data_readers">analyses.helpers.data_readers (module)</a>
 </li>
-      <li><a href="source/analyses.tools.html#analyses.tools.annotators.annotate_tree_with_label">annotate_tree_with_label() (in module analyses.tools.annotators)</a>
+      <li><a href="source/analyses.helpers.html#module-analyses.helpers.sequence">analyses.helpers.sequence (module)</a>
 </li>
   </ul></td>
 </tr></table>
 
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="source/analyses.phylo_beta_diversity.html#analyses.phylo_beta_diversity.phylo_beta_diversity.calculate_phylo_beta_diversity_jaccard">calculate_phylo_beta_diversity_jaccard() (in module analyses.phylo_beta_diversity.phylo_beta_diversity)</a>
-</li>
-      <li><a href="source/analyses.phylo_beta_diversity.html#analyses.phylo_beta_diversity.phylo_beta_diversity.calculate_phylo_beta_diversity_sorensen">calculate_phylo_beta_diversity_sorensen() (in module analyses.phylo_beta_diversity.phylo_beta_diversity)</a>
-</li>
       <li><a href="source/analyses.helpers.html#analyses.helpers.sequence.Sequence.cont_values">cont_values (analyses.helpers.sequence.Sequence attribute)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="source/analyses.phylo_beta_diversity.html#analyses.phylo_beta_diversity.phylo_beta_diversity.core_Beta_calc">core_Beta_calc() (in module analyses.phylo_beta_diversity.phylo_beta_diversity)</a>
-</li>
-      <li><a href="source/analyses.phylo_beta_diversity.html#analyses.phylo_beta_diversity.phylo_beta_diversity.core_PD_calc">core_PD_calc() (in module analyses.phylo_beta_diversity.phylo_beta_diversity)</a>
-</li>
       <li><a href="source/analyses.helpers.html#analyses.helpers.data_readers.create_sequence_list_from_dict">create_sequence_list_from_dict() (in module analyses.helpers.data_readers)</a>
 </li>
   </ul></td>
@@ -107,14 +82,12 @@ <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="source/analyses.helpers.html#analyses.helpers.data_readers.get_character_matrix_from_sequences_list">get_character_matrix_from_sequences_list() (in module analyses.helpers.data_readers)</a>
-</li>
-      <li><a href="source/analyses.helpers.html#analyses.helpers.sequence.Sequence.get_fasta">get_fasta() (analyses.helpers.sequence.Sequence method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="source/analyses.helpers.html#analyses.helpers.sequence.Sequence.get_fastq">get_fastq() (analyses.helpers.sequence.Sequence method)</a>
+      <li><a href="source/analyses.helpers.html#analyses.helpers.sequence.Sequence.get_fasta">get_fasta() (analyses.helpers.sequence.Sequence method)</a>
 </li>
-      <li><a href="source/analyses.phylo_beta_diversity.html#analyses.phylo_beta_diversity.phylo_beta_diversity.get_species_index_lookup">get_species_index_lookup() (in module analyses.phylo_beta_diversity.phylo_beta_diversity)</a>
+      <li><a href="source/analyses.helpers.html#analyses.helpers.sequence.Sequence.get_fastq">get_fastq() (analyses.helpers.sequence.Sequence method)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -135,14 +108,6 @@ <h2 id="N">N</h2>
   </ul></td>
 </tr></table>
 
-<h2 id="P">P</h2>
-<table style="width: 100%" class="indextable genindextable"><tr>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="source/analyses.phylo_beta_diversity.html#analyses.phylo_beta_diversity.phylo_beta_diversity.pdnew">pdnew() (in module analyses.phylo_beta_diversity.phylo_beta_diversity)</a>
-</li>
-  </ul></td>
-</tr></table>
-
 <h2 id="Q">Q</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>

diff --git a/docs/sphinx/objects.inv b/docs/sphinx/objects.inv
diff --git a/docs/sphinx/py-modindex.html b/docs/sphinx/py-modindex.html
@@ -53,12 +53,7 @@ <h1>Python Module Index</h1>
        <td><img src="_static/minus.png" class="toggler"
               id="toggle-1" style="display: none" alt="-" /></td>
        <td>
-       <a href="source/analyses.html#module-analyses"><code class="xref">analyses</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="source/analyses.ancestral_state.html#module-analyses.ancestral_state"><code class="xref">analyses.ancestral_state</code></a></td><td>
+       <code class="xref">analyses</code></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
@@ -75,26 +70,6 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="source/analyses.helpers.html#module-analyses.helpers.sequence"><code class="xref">analyses.helpers.sequence</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="source/analyses.phylo_beta_diversity.html#module-analyses.phylo_beta_diversity"><code class="xref">analyses.phylo_beta_diversity</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="source/analyses.phylo_beta_diversity.html#module-analyses.phylo_beta_diversity.phylo_beta_diversity"><code class="xref">analyses.phylo_beta_diversity.phylo_beta_diversity</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="source/analyses.tools.html#module-analyses.tools"><code class="xref">analyses.tools</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="source/analyses.tools.html#module-analyses.tools.annotators"><code class="xref">analyses.tools.annotators</code></a></td><td>
-       <em></em></td></tr>
    </table>
 
 

diff --git a/docs/sphinx/searchindex.js b/docs/sphinx/searchindex.js
diff --git a/docs/sphinx/source/analyses.ancestral_state.html b/docs/sphinx/source/analyses.ancestral_state.html
@@ -43,8 +43,8 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <div class="section" id="analyses-ancestral-state-anc-dp-module">
 <h2>analyses.ancestral_state.anc_dp module<a class="headerlink" href="#analyses-ancestral-state-anc-dp-module" title="Permalink to this headline">¶</a></h2>
 </div>
-<div class="section" id="module-analyses.ancestral_state">
-<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-analyses.ancestral_state" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="module-contents">
+<h2>Module contents<a class="headerlink" href="#module-contents" title="Permalink to this headline">¶</a></h2>
 </div>
 </div>
 

diff --git a/docs/sphinx/source/analyses.html b/docs/sphinx/source/analyses.html
@@ -44,7 +44,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <li class="toctree-l1"><a class="reference internal" href="analyses.ancestral_state.html">analyses.ancestral_state package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="analyses.ancestral_state.html#submodules">Submodules</a></li>
 <li class="toctree-l2"><a class="reference internal" href="analyses.ancestral_state.html#analyses-ancestral-state-anc-dp-module">analyses.ancestral_state.anc_dp module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="analyses.ancestral_state.html#module-analyses.ancestral_state">Module contents</a></li>
+<li class="toctree-l2"><a class="reference internal" href="analyses.ancestral_state.html#module-contents">Module contents</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="analyses.helpers.html">analyses.helpers package</a><ul>
@@ -56,16 +56,16 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 </li>
 <li class="toctree-l1"><a class="reference internal" href="analyses.tools.html">analyses.tools package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="analyses.tools.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="analyses.tools.html#module-analyses.tools.annotators">analyses.tools.annotators module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="analyses.tools.html#analyses-tools-annotators-module">analyses.tools.annotators module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="analyses.tools.html#analyses-tools-plots-module">analyses.tools.plots module</a></li>
-<li class="toctree-l2"><a class="reference internal" href="analyses.tools.html#module-analyses.tools">Module contents</a></li>
+<li class="toctree-l2"><a class="reference internal" href="analyses.tools.html#module-contents">Module contents</a></li>
 </ul>
 </li>
 </ul>
 </div>
 </div>
-<div class="section" id="module-analyses">
-<span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-analyses" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="module-contents">
+<h2>Module contents<a class="headerlink" href="#module-contents" title="Permalink to this headline">¶</a></h2>
 </div>
 </div>