Merge branch 'main' into SplitP-rewrite

.github/workflows/python-publish.yml

@@ -22,7 +22,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v2
       with:
-        python-version: '3.6'
+        python-version: '3.9'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

CITATION.cff

@@ -0,0 +1,10 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+- family-names: "Stevenson"
+  given-names: "Joshua"
+  orcid: "https://orcid.org/0000-0002-1037-9996"
+title: "SplitP"
+doi: 10.5281/zenodo.6366718
+date-released: 2022-03-20
+url: "https://github.com/js51/SplitP"

README.md

@@ -2,6 +2,7 @@
 
 [![](https://img.shields.io/pypi/v/SplitP.svg)](https://pypi.org/project/SplitP/)  ![](https://github.com/js51/SplitP/workflows/build/badge.svg)
 [![Coverage Status](https://coveralls.io/repos/github/js51/SplitP/badge.svg?branch=main&service=github)](https://coveralls.io/github/js51/SplitP?branch=main)
+[![DOI](https://zenodo.org/badge/216925092.svg)](https://zenodo.org/badge/latestdoi/216925092)
 
 Python package which implements split- and rank-based tools for inferring phylogenies, such as _flattenings_ and _subflattenings_.
 

docs/.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: d0e20330c9cf4425ec05b07231d0346a
+config: 888323e8186e56c9bfb5c00dd0b3a66e
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/genindex.html

@@ -36,10 +36,12 @@ <h1 id="index">Index</h1>
 <div class="genindex-jumpbox">
  <a href="#A"><strong>A</strong></a>
  | <a href="#B"><strong>B</strong></a>
+ | <a href="#C"><strong>C</strong></a>
  | <a href="#D"><strong>D</strong></a>
  | <a href="#E"><strong>E</strong></a>
  | <a href="#F"><strong>F</strong></a>
  | <a href="#G"><strong>G</strong></a>
+ | <a href="#H"><strong>H</strong></a>
  | <a href="#I"><strong>I</strong></a>
  | <a href="#J"><strong>J</strong></a>
  | <a href="#M"><strong>M</strong></a>
@@ -62,14 +64,32 @@ <h2 id="A">A</h2>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.all_singular_values">all_singular_values() (splitp.nx_tree.NXTree method)</a>
 </li>
       <li><a href="splitp.html#splitp.tree_helper_functions.all_splits">all_splits() (in module splitp.tree_helper_functions)</a>
+
+      <ul>
+        <li><a href="splitp.html#splitp.nx_tree.NXTree.all_splits">(splitp.nx_tree.NXTree method)</a>
 </li>
+      </ul></li>
   </ul></td>
 </tr></table>
 
 <h2 id="B">B</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="splitp.html#splitp.tree_helper_functions.balanced_newick_tree">balanced_newick_tree() (in module splitp.tree_helper_functions)</a>
+</li>
+  </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.build_JC_matrix">build_JC_matrix() (splitp.nx_tree.NXTree method)</a>
+</li>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.build_K2ST_matrix">build_K2ST_matrix() (splitp.nx_tree.NXTree method)</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="splitp.html#splitp.tree_helper_functions.check_splits_representatives">check_splits_representatives() (in module splitp.tree_helper_functions)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -86,17 +106,27 @@ <h2 id="E">E</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="splitp.html#splitp.squangles.SquangleEvaluator.evaluate_polynomial">evaluate_polynomial() (splitp.squangles.SquangleEvaluator method)</a>
+</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.evolve_pattern">evolve_pattern() (splitp.nx_tree.NXTree method)</a>
 </li>
   </ul></td>
 </tr></table>
 
 <h2 id="F">F</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="splitp.html#splitp.nx_tree.NXTree.flattening">flattening() (splitp.nx_tree.NXTree method)</a>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.false_splits">false_splits() (splitp.nx_tree.NXTree method)</a>
+</li>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.fast_signed_sum_subflattening">fast_signed_sum_subflattening() (splitp.nx_tree.NXTree method)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.fast_sparse_flattening">fast_sparse_flattening() (splitp.nx_tree.NXTree method)</a>
+</li>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.flattening">flattening() (splitp.nx_tree.NXTree method)</a>
+</li>
       <li><a href="splitp.html#splitp.tree_helper_functions.frob_norm">frob_norm() (in module splitp.tree_helper_functions)</a>
 </li>
   </ul></td>
@@ -105,6 +135,8 @@ <h2 id="F">F</h2>
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.generate_alignment">generate_alignment() (splitp.nx_tree.NXTree method)</a>
+</li>
       <li><a href="splitp.html#splitp.tree_helper_functions.get_balance">get_balance() (in module splitp.tree_helper_functions)</a>
 </li>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.get_descendants">get_descendants() (splitp.nx_tree.NXTree method)</a>
@@ -128,6 +160,14 @@ <h2 id="G">G</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="H">H</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.hartigan_algorithm">hartigan_algorithm() (splitp.nx_tree.NXTree method)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="I">I</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -184,11 +224,13 @@ <h2 id="N">N</h2>
 </li>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.node_name">node_name() (splitp.nx_tree.NXTree method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.nodes">nodes() (splitp.nx_tree.NXTree method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.nodes_list">nodes_list() (splitp.nx_tree.NXTree method)</a>
+</li>
+      <li><a href="splitp.html#splitp.tree_helper_functions.normalised">normalised() (in module splitp.tree_helper_functions)</a>
 </li>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.num_nodes">num_nodes() (splitp.nx_tree.NXTree method)</a>
 </li>
@@ -214,6 +256,8 @@ <h2 id="P">P</h2>
 <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.rate_matrix">rate_matrix() (splitp.nx_tree.NXTree method)</a>
+</li>
       <li><a href="splitp.html#splitp.tree_helper_functions.read_alignment_from_file">read_alignment_from_file() (in module splitp.tree_helper_functions)</a>
 </li>
   </ul></td>
@@ -228,6 +272,8 @@ <h2 id="R">R</h2>
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.scale_TR_rate_matrix">scale_TR_rate_matrix() (splitp.nx_tree.NXTree method)</a>
+</li>
       <li><a href="splitp.html#splitp.tree_helper_functions.scaled_h_matrix">scaled_h_matrix() (in module splitp.tree_helper_functions)</a>
 </li>
       <li><a href="splitp.html#splitp.tree_helper_functions.scores_to_weights">scores_to_weights() (in module splitp.tree_helper_functions)</a>
@@ -237,6 +283,8 @@ <h2 id="S">S</h2>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.sparse_flattening">sparse_flattening() (splitp.nx_tree.NXTree method)</a>
 </li>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.sparse_subflattening">sparse_subflattening() (splitp.nx_tree.NXTree method)</a>
+</li>
+      <li><a href="splitp.html#splitp.tree_helper_functions.split_equivalence_classes">split_equivalence_classes() (in module splitp.tree_helper_functions)</a>
 </li>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.split_score">split_score() (splitp.nx_tree.NXTree method)</a>
 </li>
@@ -295,11 +343,15 @@ <h2 id="T">T</h2>
 </li>
       <li><a href="splitp.html#splitp.squangles.SquangleEvaluator.to_int">to_int() (splitp.squangles.SquangleEvaluator method)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="splitp.html#splitp.squangles.SquangleEvaluator.to_pattern">to_pattern() (splitp.squangles.SquangleEvaluator method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="splitp.html#splitp.nx_tree.NXTree.transformed_flattening">transformed_flattening() (splitp.nx_tree.NXTree method)</a>
+</li>
+      <li><a href="splitp.html#splitp.squangles.SquangleEvaluator.transformed_prob_dist">transformed_prob_dist() (splitp.squangles.SquangleEvaluator method)</a>
+</li>
+      <li><a href="splitp.html#splitp.nx_tree.NXTree.true_splits">true_splits() (splitp.nx_tree.NXTree method)</a>
 </li>
   </ul></td>
 </tr></table>