Update contents of book following pre-commit

book/content/_build/.doctrees/glue_cache.json

@@ -1 +1 @@
-{}
+{}

book/content/_build/html/_panels_static/panels-variables.06eb56fa6e07937060861dad626602ad.css

@@ -4,4 +4,4 @@
 --tabs-color-overline: rgb(207, 236, 238);
 --tabs-color-underline: rgb(207, 236, 238);
 --tabs-size-label: 1rem;
-}
+}

book/content/_build/html/_sources/base.rst

@@ -1,4 +1,4 @@
 Base class
 =============
-.. automodule:: DiverseSelector.base
-    :members:
+.. automodule:: selector.base
+    :members:

book/content/_build/html/_sources/dissimilarity.rst

@@ -1,4 +1,4 @@
 Dissimilarity based methods
 =============
-.. automodule:: DiverseSelector.dissimilarity
-    :members:
+.. automodule:: selector.dissimilarity
+    :members:

book/content/_build/html/_sources/installation.ipynb

@@ -16,7 +16,7 @@
     "We are preparing a 1.0 release. Until then, these instructions for installing a stable release will not work yet. If you enjoy living on the edge, try the development release as explained in the “Latest git revision” section below.\n",
     "</div>\n",
     "\n",
-    "The following dependencies are required to run DiverseSelector properly,\n",
+    "The following dependencies are required to run selector properly,\n",
     "\n",
     "* Python >= 3.6: http://www.python.org/ \n",
     "* NumPy >= 1.21.5: http://www.numpy.org/\n",
@@ -29,7 +29,7 @@
     "\n",
     "## Installation with Ana- or Miniconda:\n",
     "\n",
-    "1. To install DiverseSelector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:\n",
+    "1. To install selector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:\n",
     "\n",
     "```\n",
     "# Activate your main conda environment if it is not loaded in your .bashrc.\n",
@@ -96,20 +96,20 @@
     "\n",
     "## Latest git revision\n",
     "\n",
-    "This section shows how one can install the latest revision of DiverseSelector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.\n",
+    "This section shows how one can install the latest revision of selector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.\n",
     "\n",
     "There are two installation methods:\n",
     "\n",
     "1. **Quick and dirty.** Of this method, there are four variants, depending on the correctness of your `PATH` variable and the presence of a virtual or conda environment. These different scenarios are explained in more detail in the previous section.\n",
     "```\n",
     "# with env, correct PATH\n",
-    "pip install git+https://github.com/theochem/DiverseSelector.git\n",
+    "pip install git+https://github.com/theochem/Selector.git\n",
     "# with env, broken PATH\n",
-    "python -m pip install git+https://github.com/theochem/DiverseSelector.git\n",
+    "python -m pip install git+https://github.com/theochem/Selector.git\n",
     "# without env, correct PATH\n",
-    "pip install git+https://github.com/theochem/DiverseSelector.git --user\n",
+    "pip install git+https://github.com/theochem/Selector.git --user\n",
     "# without env, broken PATH\n",
-    "python -m pip install git+https://github.com/theochem/DiverseSelector.git --user\n",
+    "python -m pip install git+https://github.com/theochem/Selector.git --user\n",
     "```\n",
     "\n",
     "2. **Slow and Smart.** In addition to the four variations in the quick and dirty method, the slow and smart can be used with `pip` or just with `setup.py`. You also have the options to use SSH or HTTPS protocols to clone the git repository. Pick whichever works best for you.\n",
@@ -117,9 +117,9 @@
     "# A) Clone git repo with https OR ssh:\n",
     "# The second one only works if you have ssh set up for Github\n",
     "#  A1) https\n",
-    "git clone https://github.com/theochem/DiverseSelector.git\n",
+    "git clone https://github.com/theochem/Selector.git\n",
     "#  A2) ssh\n",
-    "git clone [email protected]:theochem/DiverseSelector.git\n",
+    "git clone [email protected]:theochem/Selector.git\n",
     "# B) Optionally write the version string\n",
     "pip install roberto  # or any of the three other ways of running pip, see above.\n",
     "rob write-version\n",
@@ -148,7 +148,7 @@
     "# Install pytest in your conda env.\n",
     "conda install pytest pytest-xdist\n",
     "# Then run the tests.\n",
-    "pytest --pyargs diverseselector -n auto\n",
+    "pytest --pyargs selector -n auto\n",
     "```\n",
     "\n",
     "With Pip:\n",
@@ -157,13 +157,13 @@
     "pip install pytest pytest-xdist\n",
     "# .. and refresh the virtual environment.\n",
     "# This is a venv quirk. Without it, pytest may not find IOData.\n",
-    "deactivate && source ~/diverseselector/activate\n",
+    "deactivate && source ~/selector/activate\n",
     "\n",
     "# Alternatively, install pytest in your home directory.\n",
     "pip install pytest pytest-xdist --user\n",
     "\n",
     "# Finally, run the tests.\n",
-    "pytest --pyargs diverseselector -n auto\n",
+    "pytest --pyargs selector -n auto\n",
     "```"
    ]
   }

book/content/_build/html/_sources/intro.md

@@ -1,11 +1,11 @@
 <!-- #region -->
 # Welcome to QC-Selector's Documentation!
 
-[DiverseSelector](https://github.com/theochem/DiverseSelector) is a free, open-source, and cross-platform Python library designed to help you effortlessly identify the most diverse subset of molecules from your dataset. Please use the following citation in any publication using DiverseSelector library:
+[selector](https://github.com/theochem/Selector) is a free, open-source, and cross-platform Python library designed to help you effortlessly identify the most diverse subset of molecules from your dataset. Please use the following citation in any publication using selector library:
 
 **"QC-Selector: A Generic Python Package for Subset Selection"**, Fanwang Meng, Alireza Tehrani, Valerii Chuiko, Abigail Broscius, Abdul, Hassan, Maximilian van Zyl, Marco Martínez González, Yang, Ramón Alain Miranda-Quintana, Paul W. Ayers, and Farnaz Heidar-Zadeh"
 
-The DiverseSelector source code is hosted on [GitHub](https://github.com/theochem/DiverseSelector) and is released under the [GNU General Public License v3.0](https://github.com/theochem/DiverseSelector/blob/main/LICENSE). We welcome any contributions to the DiverseSelector library in accordance with our Code of Conduct; please see our [Contributing Guidelines](https://qcdevs.org/guidelines/QCDevsCodeOfConduct/). Please report any issues you encounter while using DiverseSelector library on [GitHub Issues](https://github.com/theochem/DiverseSelector/issues). For further information and inquiries please contact us at [email protected].
+The selector source code is hosted on [GitHub](https://github.com/theochem/Selector) and is released under the [GNU General Public License v3.0](https://github.com/theochem/Selector/blob/main/LICENSE). We welcome any contributions to the selector library in accordance with our Code of Conduct; please see our [Contributing Guidelines](https://qcdevs.org/guidelines/QCDevsCodeOfConduct/). Please report any issues you encounter while using selector library on [GitHub Issues](https://github.com/theochem/Selector/issues). For further information and inquiries please contact us at [email protected].
 
 
 ## Why QC-Selector?

book/content/_build/html/_sources/partition.rst

@@ -1,5 +1,5 @@
 Partition based methods
 =============
 
-.. automodule:: DiverseSelector.partition
-    :members:
+.. automodule:: selector.partition
+    :members:

book/content/_build/html/_sources/starting.ipynb

@@ -32,8 +32,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# install the DiverseSelector module\n",
-    "!pip install git+https://github.com/theochem/DiverseSelector\n",
+    "# install the selector module\n",
+    "!pip install git+https://github.com/theochem/Selector\n",
     "!pip install rdkit"
    ]
   },
@@ -44,7 +44,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import DiverseSelector\n",
+    "import selector\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "from typing import Any, Tuple, Union\n",
@@ -215,8 +215,8 @@
    "outputs": [],
    "source": [
     "# MaxMin method\n",
-    "from DiverseSelector.methods.partition import *\n",
-    "from DiverseSelector.methods.dissimilarity import *\n",
+    "from selector.methods.partition import *\n",
+    "from selector.methods.dissimilarity import *\n",
     "\n",
     "# diverse subset selection from randomly generated data points\n",
     "selector = MaxMin()\n",

book/content/_build/html/_sources/utils.rst

@@ -1,4 +1,4 @@
 Utilities
 =============
-.. automodule:: DiverseSelector.utils
-    :members:
+.. automodule:: selector.utils
+    :members:

book/content/_build/html/_static/basic.css

@@ -901,4 +901,4 @@ div.math:hover a.headerlink {
     #top-link {
         display: none;
     }
-}
+}

book/content/_build/html/_static/clipboard.min.js

@@ -4,4 +4,4 @@
  *
  * Licensed MIT © Zeno Rocha
  */
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book/content/_build/html/_static/copybutton.js

@@ -194,4 +194,4 @@ var copyTargetText = (trigger) => {
   })
 }
 
-runWhenDOMLoaded(addCopyButtonToCodeCells)
+runWhenDOMLoaded(addCopyButtonToCodeCells)

book/content/_build/html/_static/css/blank.css

@@ -1,2 +1,2 @@
 /* This file is intentionally left blank to override the stylesheet of the
-parent theme via theme.conf. The parent style we import directly in theme.css */
+parent theme via theme.conf. The parent style we import directly in theme.css */

book/content/_build/html/_static/css/theme.css

@@ -41,7 +41,7 @@
 
   /*****************************************************************************
   * Color
-  * 
+  *
   * Colors are defined in rgb string way, "red, green, blue"
   **/
   --pst-color-primary: 19, 6, 84;

book/content/_build/html/_static/documentation_options.js

@@ -9,4 +9,4 @@ var DOCUMENTATION_OPTIONS = {
     HAS_SOURCE: true,
     SOURCELINK_SUFFIX: '',
     NAVIGATION_WITH_KEYS: true
-};
+};

book/content/_build/html/_static/language_data.js

@@ -293,5 +293,3 @@ function splitQuery(query) {
     }
     return result;
 }
-
-

book/content/_build/html/_static/panels-variables.06eb56fa6e07937060861dad626602ad.css

@@ -4,4 +4,4 @@
 --tabs-color-overline: rgb(207, 236, 238);
 --tabs-color-underline: rgb(207, 236, 238);
 --tabs-size-label: 1rem;
-}
+}

book/content/_build/html/_static/pygments.css

@@ -71,4 +71,4 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
 .highlight .vg { color: #bb60d5 } /* Name.Variable.Global */
 .highlight .vi { color: #bb60d5 } /* Name.Variable.Instance */
 .highlight .vm { color: #bb60d5 } /* Name.Variable.Magic */
-.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */
+.highlight .il { color: #208050 } /* Literal.Number.Integer.Long */

book/content/_build/html/_static/togglebutton.css

@@ -87,4 +87,4 @@ button.toggle-button {
 
 .toggle-button-hidden .vertical {
     transform: rotate(-90deg);
-}
+}

book/content/_build/html/_static/underscore.js

@@ -3,4 +3,4 @@
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ur(n,r,!1)},without:Kr,uniq:Jr,unique:Jr,union:Gr,intersection:function(n){for(var r=[],t=arguments.length,e=0,u=Y(n);e<u;e++){var o=n[e];if(!Er(r,o)){var i;for(i=1;i<t&&Er(arguments[i],o);i++);i===t&&r.push(o)}}return r},difference:Cr,unzip:Hr,transpose:Hr,zip:Qr,object:function(n,r){for(var t={},e=0,u=Y(n);e<u;e++)r?t[n[e]]=r[e]:t[n[e][0]]=n[e][1];return t},range:function(n,r,t){null==r&&(r=n||0,n=0),t||(t=r<n?-1:1);for(var e=Math.max(Math.ceil((r-n)/t),0),u=Array(e),o=0;o<e;o++,n+=t)u[o]=n;return u},chunk:function(n,r){if(null==r||r<1)return[];for(var t=[],e=0,u=n.length;e<u;)t.push(i.call(n,e,e+=r));return t},mixin:Yr,default:tn});return Zr._=Zr,Zr}));

book/content/_build/html/_static/webpack-macros.html

@@ -22,4 +22,4 @@
 
 {% macro body_post() %}
   <script src="{{ pathto('_static/js/index.be7d3bbb2ef33a8344ce.js', 1) }}"></script>
-{% endmacro %}
+{% endmacro %}

book/content/_build/html/base.html

@@ -7,11 +7,11 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Base class &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
   <link rel="stylesheet"
     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -19,10 +19,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
-    
+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
@@ -31,7 +31,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
+
   <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -57,34 +57,34 @@
     <link rel="prev" title="Getting started" href="starting.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
-    
+
 
     <!-- Google Analytics -->
-    
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
 <div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -153,17 +153,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -172,15 +172,15 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
 <div class="dropdown-buttons-trigger">
     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
             class="fas fa-download"></i></button>
 
     <div class="dropdown-buttons">
         <!-- ipynb file if we had a myst markdown file -->
-        
+
         <!-- Download raw file -->
         <a class="dropdown-buttons" href="_sources/base.rst"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
@@ -198,14 +198,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Fbase.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Fbase.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -222,25 +222,25 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
         </div>
     </div>
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
-  <section id="module-DiverseSelector.base">
-<span id="base-class"></span><h1>Base class<a class="headerlink" href="#module-DiverseSelector.base" title="Permalink to this headline">¶</a></h1>
+
+  <section id="module-selector.base">
+<span id="base-class"></span><h1>Base class<a class="headerlink" href="#module-selector.base" title="Permalink to this headline">¶</a></h1>
 <p>Base class for diversity based subset selection.</p>
 <dl class="py class">
-<dt class="sig sig-object py" id="DiverseSelector.base.SelectionBase">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">DiverseSelector.base.</span></span><span class="sig-name descname"><span class="pre">SelectionBase</span></span><a class="headerlink" href="#DiverseSelector.base.SelectionBase" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.base.SelectionBase">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">selector.base.</span></span><span class="sig-name descname"><span class="pre">SelectionBase</span></span><a class="headerlink" href="#selector.base.SelectionBase" title="Permalink to this definition">¶</a></dt>
 <dd><p>Base class for selecting subset of sample points.</p>
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.base.SelectionBase.select">
-<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">numpy.ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">numpy.ndarray</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">numpy.ndarray</span></span></span><a class="headerlink" href="#DiverseSelector.base.SelectionBase.select" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.base.SelectionBase.select">
+<span class="sig-name descname"><span class="pre">select</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">numpy.ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">numpy.ndarray</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">numpy.ndarray</span></span></span><a class="headerlink" href="#selector.base.SelectionBase.select" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return indices representing subset of sample points.</p>
 <dl class="simple">
 <dt>X: ndarray of shape (n_samples, n_features) or (n_samples, n_samples)</dt><dd><p>Feature matrix of <cite>n_samples</cite> samples in <cite>n_features</cite> dimensional feature space.
@@ -260,8 +260,8 @@ If labels are provided, selection is made from each cluster.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.base.SelectionBase.select_from_cluster">
-<em class="property"><span class="pre">abstract</span> </em><span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">numpy.ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">numpy.ndarray</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">numpy.ndarray</span></span></span><a class="headerlink" href="#DiverseSelector.base.SelectionBase.select_from_cluster" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.base.SelectionBase.select_from_cluster">
+<em class="property"><span class="pre">abstract</span> </em><span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">numpy.ndarray</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">int</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="p"><span class="pre">:</span></span> <span class="n"><span class="pre">Optional</span><span class="p"><span class="pre">[</span></span><span class="pre">numpy.ndarray</span><span class="p"><span class="pre">]</span></span></span> <span class="o"><span class="pre">=</span></span> <span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">numpy.ndarray</span></span></span><a class="headerlink" href="#selector.base.SelectionBase.select_from_cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return indices representing subset of sample points from one cluster.</p>
 <dl class="simple">
 <dt>X: ndarray of shape (n_samples, n_features) or (n_samples, n_samples)</dt><dd><p>Feature matrix of <cite>n_samples</cite> samples in <cite>n_features</cite> dimensional feature space.
@@ -288,7 +288,7 @@ If labels are provided, selection is made from each cluster.</p>
     {
         requestKernel: true,
         binderOptions: {
-            repo: "theochem/DiverseSelector",
+            repo: "theochem/Selector",
             ref: "main",
         },
         codeMirrorConfig: {
@@ -305,10 +305,10 @@ If labels are provided, selection is made from each cluster.</p>
     <script>kernelName = 'python3'</script>
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
+<div class='prev-next-area'>
     <a class='left-prev' id="prev-link" href="starting.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
@@ -324,15 +324,15 @@ If labels are provided, selection is made from each cluster.</p>
     <i class="fas fa-angle-right"></i>
     </a>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -342,8 +342,8 @@ If labels are provided, selection is made from each cluster.</p>
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/html/dissimilarity.html

@@ -7,11 +7,11 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Dissimilarity based methods &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
   <link rel="stylesheet"
     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -19,10 +19,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
-    
+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
@@ -31,7 +31,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
+
   <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -57,34 +57,34 @@
     <link rel="prev" title="Base class" href="base.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
-    
+
 
     <!-- Google Analytics -->
-    
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
 <div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -153,17 +153,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -172,15 +172,15 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
 <div class="dropdown-buttons-trigger">
     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
             class="fas fa-download"></i></button>
 
     <div class="dropdown-buttons">
         <!-- ipynb file if we had a myst markdown file -->
-        
+
         <!-- Download raw file -->
         <a class="dropdown-buttons" href="_sources/dissimilarity.rst"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
@@ -198,14 +198,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Fdissimilarity.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Fdissimilarity.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -222,21 +222,21 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
         </div>
     </div>
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
+
   <section id="dissimilarity-based-methods">
 <h1>Dissimilarity based methods<a class="headerlink" href="#dissimilarity-based-methods" title="Permalink to this headline">¶</a></h1>
-<span class="target" id="module-DiverseSelector.dissimilarity"></span><p>Module for Dissimilarity-Based Selection Methods.</p>
+<span class="target" id="module-selector.dissimilarity"></span><p>Module for Dissimilarity-Based Selection Methods.</p>
 <dl class="py class">
-<dt class="sig sig-object py" id="DiverseSelector.dissimilarity.MaxMin">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">DiverseSelector.dissimilarity.</span></span><span class="sig-name descname"><span class="pre">MaxMin</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.dissimilarity.MaxMin" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.dissimilarity.MaxMin">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">selector.dissimilarity.</span></span><span class="sig-name descname"><span class="pre">MaxMin</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.dissimilarity.MaxMin" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selecting samples using MaxMin algorithm.</p>
 <p>MaxMin is possibly the most widely used method for dissimilarity-based
 compound selection. When presented with a dataset of samples, the
@@ -253,8 +253,8 @@ in the previous step.</p></li>
 property‐based and fragment‐based molecular descriptions, Quantitative
 Structure‐Activity Relationships 21.6 (2002): 598-604.</p>
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.dissimilarity.MaxMin.select_from_cluster">
-<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.dissimilarity.MaxMin.select_from_cluster" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.dissimilarity.MaxMin.select_from_cluster">
+<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.dissimilarity.MaxMin.select_from_cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return selected samples from a cluster based on MaxMin algorithm.</p>
 <dl class="simple">
 <dt>X: ndarray of shape (n_samples, n_features) or (n_samples, n_samples)</dt><dd><p>Feature matrix of <cite>n_samples</cite> samples in <cite>n_features</cite> dimensional feature space.
@@ -274,8 +274,8 @@ If fun_distance is <cite>None</cite>, this X is treated as a square pairwise dis
 </dd></dl>
 
 <dl class="py class">
-<dt class="sig sig-object py" id="DiverseSelector.dissimilarity.MaxSum">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">DiverseSelector.dissimilarity.</span></span><span class="sig-name descname"><span class="pre">MaxSum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.dissimilarity.MaxSum" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.dissimilarity.MaxSum">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">selector.dissimilarity.</span></span><span class="sig-name descname"><span class="pre">MaxSum</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">func_distance</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.dissimilarity.MaxSum" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selecting samples using MaxSum algorithm.</p>
 <p>Whereas the goal of the MaxMin algorithm is to maximize the minimum distance
 between any pair of distinct elements in the selected subset of a dataset,
@@ -294,8 +294,8 @@ in the previous step.</p></li>
 submodular functions and dynamic updates, Proceedings of the 31st ACM SIGMOD-SIGACT-SIGAI
 symposium on Principles of Database Systems. 2012.</p>
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.dissimilarity.MaxSum.select_from_cluster">
-<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.dissimilarity.MaxSum.select_from_cluster" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.dissimilarity.MaxSum.select_from_cluster">
+<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.dissimilarity.MaxSum.select_from_cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return selected samples from a cluster based on MaxSum algorithm.</p>
 <dl class="simple">
 <dt>X: ndarray of shape (n_samples, n_features) or (n_samples, n_samples)</dt><dd><p>Feature matrix of <cite>n_samples</cite> samples in <cite>n_features</cite> dimensional feature space.
@@ -315,8 +315,8 @@ If fun_distance is <cite>None</cite>, this X is treated as a square pairwise dis
 </dd></dl>
 
 <dl class="py class">
-<dt class="sig sig-object py" id="DiverseSelector.dissimilarity.OptiSim">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">DiverseSelector.dissimilarity.</span></span><span class="sig-name descname"><span class="pre">OptiSim</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r0</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random_seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_iter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.dissimilarity.OptiSim" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.dissimilarity.OptiSim">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">selector.dissimilarity.</span></span><span class="sig-name descname"><span class="pre">OptiSim</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r0</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">k</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.01</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">start_id</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random_seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_iter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.dissimilarity.OptiSim" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selecting samples using OptiSim algorithm.</p>
 <p>The OptiSim algorithm selects samples from a dataset by first choosing the medoid center as the
 initial point. Next, points are randomly chosen and added to a subsample if they exist
@@ -326,8 +326,8 @@ to the previously selected points is chosen. Then, the subsample is cleared and
 repeated.</p>
 <p>[1] J. Chem. Inf. Comput. Sci. 1997, 37, 6, 1181–1188. <a class="reference external" href="https://doi.org/10.1021/ci970282v">https://doi.org/10.1021/ci970282v</a></p>
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.dissimilarity.OptiSim.algorithm">
-<span class="sig-name descname"><span class="pre">algorithm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_size</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="headerlink" href="#DiverseSelector.dissimilarity.OptiSim.algorithm" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.dissimilarity.OptiSim.algorithm">
+<span class="sig-name descname"><span class="pre">algorithm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_size</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">list</span></span></span><a class="headerlink" href="#selector.dissimilarity.OptiSim.algorithm" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return selected samples based on OptiSim algorithm.</p>
 <dl class="simple">
 <dt>X<span class="classifier">np.ndarray</span></dt><dd><p>Coordinate array of samples.</p>
@@ -342,8 +342,8 @@ repeated.</p>
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.dissimilarity.OptiSim.select_from_cluster">
-<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.dissimilarity.OptiSim.select_from_cluster" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.dissimilarity.OptiSim.select_from_cluster">
+<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">labels</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.dissimilarity.OptiSim.select_from_cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return selected samples from a cluster based on OptiSim algorithm.</p>
 <dl class="simple">
 <dt>X<span class="classifier">np.ndarray</span></dt><dd><p>Coordinate array of samples.</p>
@@ -367,7 +367,7 @@ repeated.</p>
     {
         requestKernel: true,
         binderOptions: {
-            repo: "theochem/DiverseSelector",
+            repo: "theochem/Selector",
             ref: "main",
         },
         codeMirrorConfig: {
@@ -384,10 +384,10 @@ repeated.</p>
     <script>kernelName = 'python3'</script>
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
+<div class='prev-next-area'>
     <a class='left-prev' id="prev-link" href="base.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
@@ -403,15 +403,15 @@ repeated.</p>
     <i class="fas fa-angle-right"></i>
     </a>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -421,8 +421,8 @@ repeated.</p>
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/html/genindex.html

@@ -6,11 +6,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Index &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
   <link rel="stylesheet"
     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -18,10 +18,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
-    
+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
@@ -30,7 +30,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
+
   <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -47,34 +47,34 @@
     <link rel="search" title="Search" href="search.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
-    
+
 
     <!-- Google Analytics -->
-    
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
 <div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -143,17 +143,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -162,8 +162,8 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
             <!-- Source interaction buttons -->
 
 <div class="dropdown-buttons-trigger">
@@ -171,14 +171,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Fgenindex.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Fgenindex.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -195,15 +195,15 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
         </div>
     </div>
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
+
 
 <h1 id="index">Index</h1>
 
@@ -214,15 +214,15 @@
  | <a href="#M"><strong>M</strong></a>
  | <a href="#O"><strong>O</strong></a>
  | <a href="#S"><strong>S</strong></a>
- 
+
 </div>
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="dissimilarity.html#DiverseSelector.dissimilarity.OptiSim.algorithm">algorithm() (DiverseSelector.dissimilarity.OptiSim method)</a>
+      <li><a href="dissimilarity.html#selector.dissimilarity.OptiSim.algorithm">algorithm() (selector.dissimilarity.OptiSim method)</a>
 
       <ul>
-        <li><a href="partition.html#DiverseSelector.partition.DirectedSphereExclusion.algorithm">(DiverseSelector.partition.DirectedSphereExclusion method)</a>
+        <li><a href="partition.html#selector.partition.DirectedSphereExclusion.algorithm">(selector.partition.DirectedSphereExclusion method)</a>
 </li>
       </ul></li>
   </ul></td>
@@ -231,36 +231,36 @@
 <h2 id="D">D</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="partition.html#DiverseSelector.partition.DirectedSphereExclusion">DirectedSphereExclusion (class in DiverseSelector.partition)</a>
+      <li><a href="partition.html#selector.partition.DirectedSphereExclusion">DirectedSphereExclusion (class in selector.partition)</a>
 </li>
       <li>
-    DiverseSelector.base
+    selector.base
 
       <ul>
-        <li><a href="base.html#module-DiverseSelector.base">module</a>
+        <li><a href="base.html#module-selector.base">module</a>
 </li>
       </ul></li>
       <li>
-    DiverseSelector.dissimilarity
+    selector.dissimilarity
 
       <ul>
-        <li><a href="dissimilarity.html#module-DiverseSelector.dissimilarity">module</a>
+        <li><a href="dissimilarity.html#module-selector.dissimilarity">module</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li>
-    DiverseSelector.partition
+    selector.partition
 
       <ul>
-        <li><a href="partition.html#module-DiverseSelector.partition">module</a>
+        <li><a href="partition.html#module-selector.partition">module</a>
 </li>
       </ul></li>
       <li>
-    DiverseSelector.utils
+    selector.utils
 
       <ul>
-        <li><a href="utils.html#module-DiverseSelector.utils">module</a>
+        <li><a href="utils.html#module-selector.utils">module</a>
 </li>
       </ul></li>
   </ul></td>
@@ -269,7 +269,7 @@
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="partition.html#DiverseSelector.partition.GridPartitioning">GridPartitioning (class in DiverseSelector.partition)</a>
+      <li><a href="partition.html#selector.partition.GridPartitioning">GridPartitioning (class in selector.partition)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -277,23 +277,23 @@
 <h2 id="M">M</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="dissimilarity.html#DiverseSelector.dissimilarity.MaxMin">MaxMin (class in DiverseSelector.dissimilarity)</a>
+      <li><a href="dissimilarity.html#selector.dissimilarity.MaxMin">MaxMin (class in selector.dissimilarity)</a>
 </li>
-      <li><a href="dissimilarity.html#DiverseSelector.dissimilarity.MaxSum">MaxSum (class in DiverseSelector.dissimilarity)</a>
+      <li><a href="dissimilarity.html#selector.dissimilarity.MaxSum">MaxSum (class in selector.dissimilarity)</a>
 </li>
-      <li><a href="partition.html#DiverseSelector.partition.Medoid">Medoid (class in DiverseSelector.partition)</a>
+      <li><a href="partition.html#selector.partition.Medoid">Medoid (class in selector.partition)</a>
 </li>
       <li>
     module
 
       <ul>
-        <li><a href="base.html#module-DiverseSelector.base">DiverseSelector.base</a>
+        <li><a href="base.html#module-selector.base">selector.base</a>
 </li>
-        <li><a href="dissimilarity.html#module-DiverseSelector.dissimilarity">DiverseSelector.dissimilarity</a>
+        <li><a href="dissimilarity.html#module-selector.dissimilarity">selector.dissimilarity</a>
 </li>
-        <li><a href="partition.html#module-DiverseSelector.partition">DiverseSelector.partition</a>
+        <li><a href="partition.html#module-selector.partition">selector.partition</a>
 </li>
-        <li><a href="utils.html#module-DiverseSelector.utils">DiverseSelector.utils</a>
+        <li><a href="utils.html#module-selector.utils">selector.utils</a>
 </li>
       </ul></li>
   </ul></td>
@@ -302,11 +302,11 @@
 <h2 id="O">O</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="utils.html#DiverseSelector.utils.optimize_radius">optimize_radius() (in module DiverseSelector.utils)</a>
+      <li><a href="utils.html#selector.utils.optimize_radius">optimize_radius() (in module selector.utils)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="dissimilarity.html#DiverseSelector.dissimilarity.OptiSim">OptiSim (class in DiverseSelector.dissimilarity)</a>
+      <li><a href="dissimilarity.html#selector.dissimilarity.OptiSim">OptiSim (class in selector.dissimilarity)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -314,27 +314,27 @@
 <h2 id="S">S</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="base.html#DiverseSelector.base.SelectionBase.select">select() (DiverseSelector.base.SelectionBase method)</a>
+      <li><a href="base.html#selector.base.SelectionBase.select">select() (selector.base.SelectionBase method)</a>
 </li>
-      <li><a href="base.html#DiverseSelector.base.SelectionBase.select_from_cluster">select_from_cluster() (DiverseSelector.base.SelectionBase method)</a>
+      <li><a href="base.html#selector.base.SelectionBase.select_from_cluster">select_from_cluster() (selector.base.SelectionBase method)</a>
 
       <ul>
-        <li><a href="dissimilarity.html#DiverseSelector.dissimilarity.MaxMin.select_from_cluster">(DiverseSelector.dissimilarity.MaxMin method)</a>
+        <li><a href="dissimilarity.html#selector.dissimilarity.MaxMin.select_from_cluster">(selector.dissimilarity.MaxMin method)</a>
 </li>
-        <li><a href="dissimilarity.html#DiverseSelector.dissimilarity.MaxSum.select_from_cluster">(DiverseSelector.dissimilarity.MaxSum method)</a>
+        <li><a href="dissimilarity.html#selector.dissimilarity.MaxSum.select_from_cluster">(selector.dissimilarity.MaxSum method)</a>
 </li>
-        <li><a href="dissimilarity.html#DiverseSelector.dissimilarity.OptiSim.select_from_cluster">(DiverseSelector.dissimilarity.OptiSim method)</a>
+        <li><a href="dissimilarity.html#selector.dissimilarity.OptiSim.select_from_cluster">(selector.dissimilarity.OptiSim method)</a>
 </li>
-        <li><a href="partition.html#DiverseSelector.partition.DirectedSphereExclusion.select_from_cluster">(DiverseSelector.partition.DirectedSphereExclusion method)</a>
+        <li><a href="partition.html#selector.partition.DirectedSphereExclusion.select_from_cluster">(selector.partition.DirectedSphereExclusion method)</a>
 </li>
-        <li><a href="partition.html#DiverseSelector.partition.GridPartitioning.select_from_cluster">(DiverseSelector.partition.GridPartitioning method)</a>
+        <li><a href="partition.html#selector.partition.GridPartitioning.select_from_cluster">(selector.partition.GridPartitioning method)</a>
 </li>
-        <li><a href="partition.html#DiverseSelector.partition.Medoid.select_from_cluster">(DiverseSelector.partition.Medoid method)</a>
+        <li><a href="partition.html#selector.partition.Medoid.select_from_cluster">(selector.partition.Medoid method)</a>
 </li>
       </ul></li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="base.html#DiverseSelector.base.SelectionBase">SelectionBase (class in DiverseSelector.base)</a>
+      <li><a href="base.html#selector.base.SelectionBase">SelectionBase (class in selector.base)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -342,20 +342,20 @@
 
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
 <div class='prev-next-area'>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -365,8 +365,8 @@
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/html/installation.html

@@ -7,11 +7,11 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Installation &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
   <link rel="stylesheet"
     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -19,10 +19,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
-    
+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
@@ -31,7 +31,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
+
   <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -57,34 +57,34 @@
     <link rel="prev" title="Welcome to QC-Selector’s Documentation!" href="intro.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
-    
+
 
     <!-- Google Analytics -->
-    
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
 <div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -153,17 +153,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -172,15 +172,15 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
 <div class="dropdown-buttons-trigger">
     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
             class="fas fa-download"></i></button>
 
     <div class="dropdown-buttons">
         <!-- ipynb file if we had a myst markdown file -->
-        
+
         <!-- Download raw file -->
         <a class="dropdown-buttons" href="_sources/installation.ipynb"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
@@ -198,14 +198,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Finstallation.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Finstallation.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -222,24 +222,24 @@
     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
         aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
     <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/theochem/DiverseSelector/main?urlpath=tree/book/content/installation.ipynb"><button type="button"
+
+        <a class="binder-button" href="https://mybinder.org/v2/gh/theochem/Selector/main?urlpath=tree/book/content/installation.ipynb"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
                 data-placement="left"><img class="binder-button-logo"
                     src="_static/images/logo_binder.svg"
                     alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/theochem/DiverseSelector/blob/main/book/content/installation.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
+
+
+
+        <a class="colab-button" href="https://colab.research.google.com/github/theochem/Selector/blob/main/book/content/installation.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
                 title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
                     src="_static/images/logo_colab.png"
                     alt="Interact on Colab">Colab</button></a>
-        
+
         <button type="button" class="btn btn-secondary topbarbtn"
             onclick="initThebeSBT()" title="Launch Thebe" data-toggle="tooltip" data-placement="left"><i
                 class="fas fa-play"></i><span style="margin-left: .4em;">Live Code</span></button>
-        
+
     </div>
 </div>
 
@@ -247,7 +247,7 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
             <div class="tocsection onthispage pt-5 pb-3">
                 <i class="fas fa-list"></i> Contents
             </div>
@@ -286,9 +286,9 @@
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
+
   <section class="tex2jax_ignore mathjax_ignore" id="installation">
 <h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
 <section id="stable-releases">
@@ -298,7 +298,7 @@
 </b>
 <p>We are preparing a 1.0 release. Until then, these instructions for installing a stable release will not work yet. If you enjoy living on the edge, try the development release as explained in the “Latest git revision” section below.</p>
 </div>
-<p>The following dependencies are required to run DiverseSelector properly,</p>
+<p>The following dependencies are required to run selector properly,</p>
 <ul class="simple">
 <li><p>Python &gt;= 3.6: <a class="reference external" href="http://www.python.org/">http://www.python.org/</a></p></li>
 <li><p>NumPy &gt;= 1.21.5: <a class="reference external" href="http://www.numpy.org/">http://www.numpy.org/</a></p></li>
@@ -311,7 +311,7 @@
 <section id="installation-with-ana-or-miniconda">
 <h2>Installation with Ana- or Miniconda:<a class="headerlink" href="#installation-with-ana-or-miniconda" title="Permalink to this headline">¶</a></h2>
 <ol class="simple">
-<li><p>To install DiverseSelector using the conda package management system, install <a class="reference external" href="https://conda.io/miniconda.html">miniconda</a> or <a class="reference external" href="https://www.anaconda.com/download">anaconda</a> first, and then:</p></li>
+<li><p>To install selector using the conda package management system, install <a class="reference external" href="https://conda.io/miniconda.html">miniconda</a> or <a class="reference external" href="https://www.anaconda.com/download">anaconda</a> first, and then:</p></li>
 </ol>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Activate your main conda environment if it is not loaded in your .bashrc.</span>
 <span class="c1"># E.g. run the following if you have miniconda installed in e.g. ~/miniconda3</span>
@@ -375,19 +375,19 @@ Python modules.</p>
 </section>
 <section id="latest-git-revision">
 <h2>Latest git revision<a class="headerlink" href="#latest-git-revision" title="Permalink to this headline">¶</a></h2>
-<p>This section shows how one can install the latest revision of DiverseSelector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.</p>
+<p>This section shows how one can install the latest revision of selector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.</p>
 <p>There are two installation methods:</p>
 <ol class="simple">
 <li><p><strong>Quick and dirty.</strong> Of this method, there are four variants, depending on the correctness of your <code class="docutils literal notranslate"><span class="pre">PATH</span></code> variable and the presence of a virtual or conda environment. These different scenarios are explained in more detail in the previous section.</p></li>
 </ol>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># with env, correct PATH</span>
-<span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">DiverseSelector</span><span class="o">.</span><span class="n">git</span>
+<span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">selector</span><span class="o">.</span><span class="n">git</span>
 <span class="c1"># with env, broken PATH</span>
-<span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">DiverseSelector</span><span class="o">.</span><span class="n">git</span>
+<span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">selector</span><span class="o">.</span><span class="n">git</span>
 <span class="c1"># without env, correct PATH</span>
-<span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">DiverseSelector</span><span class="o">.</span><span class="n">git</span> <span class="o">--</span><span class="n">user</span>
+<span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">selector</span><span class="o">.</span><span class="n">git</span> <span class="o">--</span><span class="n">user</span>
 <span class="c1"># without env, broken PATH</span>
-<span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">DiverseSelector</span><span class="o">.</span><span class="n">git</span> <span class="o">--</span><span class="n">user</span>
+<span class="n">python</span> <span class="o">-</span><span class="n">m</span> <span class="n">pip</span> <span class="n">install</span> <span class="n">git</span><span class="o">+</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">selector</span><span class="o">.</span><span class="n">git</span> <span class="o">--</span><span class="n">user</span>
 </pre></div>
 </div>
 <ol class="simple">
@@ -396,9 +396,9 @@ Python modules.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># A) Clone git repo with https OR ssh:</span>
 <span class="c1"># The second one only works if you have ssh set up for Github</span>
 <span class="c1">#  A1) https</span>
-<span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">DiverseSelector</span><span class="o">.</span><span class="n">git</span>
+<span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">theochem</span><span class="o">/</span><span class="n">selector</span><span class="o">.</span><span class="n">git</span>
 <span class="c1">#  A2) ssh</span>
-<span class="n">git</span> <span class="n">clone</span> <span class="n">git</span><span class="nd">@github</span><span class="o">.</span><span class="n">com</span><span class="p">:</span><span class="n">theochem</span><span class="o">/</span><span class="n">DiverseSelector</span><span class="o">.</span><span class="n">git</span>
+<span class="n">git</span> <span class="n">clone</span> <span class="n">git</span><span class="nd">@github</span><span class="o">.</span><span class="n">com</span><span class="p">:</span><span class="n">theochem</span><span class="o">/</span><span class="n">selector</span><span class="o">.</span><span class="n">git</span>
 <span class="c1"># B) Optionally write the version string</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="n">roberto</span>  <span class="c1"># or any of the three other ways of running pip, see above.</span>
 <span class="n">rob</span> <span class="n">write</span><span class="o">-</span><span class="n">version</span>
@@ -425,7 +425,7 @@ Python modules.</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1"># Install pytest in your conda env.</span>
 <span class="n">conda</span> <span class="n">install</span> <span class="n">pytest</span> <span class="n">pytest</span><span class="o">-</span><span class="n">xdist</span>
 <span class="c1"># Then run the tests.</span>
-<span class="n">pytest</span> <span class="o">--</span><span class="n">pyargs</span> <span class="n">diverseselector</span> <span class="o">-</span><span class="n">n</span> <span class="n">auto</span>
+<span class="n">pytest</span> <span class="o">--</span><span class="n">pyargs</span> <span class="n">selector</span> <span class="o">-</span><span class="n">n</span> <span class="n">auto</span>
 </pre></div>
 </div>
 <p>With Pip:</p>
@@ -433,13 +433,13 @@ Python modules.</p>
 <span class="n">pip</span> <span class="n">install</span> <span class="n">pytest</span> <span class="n">pytest</span><span class="o">-</span><span class="n">xdist</span>
 <span class="c1"># .. and refresh the virtual environment.</span>
 <span class="c1"># This is a venv quirk. Without it, pytest may not find IOData.</span>
-<span class="n">deactivate</span> <span class="o">&amp;&amp;</span> <span class="n">source</span> <span class="o">~/</span><span class="n">diverseselector</span><span class="o">/</span><span class="n">activate</span>
+<span class="n">deactivate</span> <span class="o">&amp;&amp;</span> <span class="n">source</span> <span class="o">~/</span><span class="n">selector</span><span class="o">/</span><span class="n">activate</span>
 
 <span class="c1"># Alternatively, install pytest in your home directory.</span>
 <span class="n">pip</span> <span class="n">install</span> <span class="n">pytest</span> <span class="n">pytest</span><span class="o">-</span><span class="n">xdist</span> <span class="o">--</span><span class="n">user</span>
 
 <span class="c1"># Finally, run the tests.</span>
-<span class="n">pytest</span> <span class="o">--</span><span class="n">pyargs</span> <span class="n">diverseselector</span> <span class="o">-</span><span class="n">n</span> <span class="n">auto</span>
+<span class="n">pytest</span> <span class="o">--</span><span class="n">pyargs</span> <span class="n">selector</span> <span class="o">-</span><span class="n">n</span> <span class="n">auto</span>
 </pre></div>
 </div>
 </section>
@@ -449,7 +449,7 @@ Python modules.</p>
     {
         requestKernel: true,
         binderOptions: {
-            repo: "theochem/DiverseSelector",
+            repo: "theochem/Selector",
             ref: "main",
         },
         codeMirrorConfig: {
@@ -466,10 +466,10 @@ Python modules.</p>
     <script>kernelName = 'python3'</script>
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
+<div class='prev-next-area'>
     <a class='left-prev' id="prev-link" href="intro.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
@@ -485,15 +485,15 @@ Python modules.</p>
     <i class="fas fa-angle-right"></i>
     </a>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -503,8 +503,8 @@ Python modules.</p>
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/html/intro.html

@@ -7,11 +7,11 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Welcome to QC-Selector’s Documentation! &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
   <link rel="stylesheet"
     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -19,10 +19,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
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+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
@@ -31,7 +31,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
+
   <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -56,34 +56,34 @@
     <link rel="next" title="Installation" href="installation.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
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-    
+
 
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+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
 <div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -152,17 +152,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -171,15 +171,15 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
 <div class="dropdown-buttons-trigger">
     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
             class="fas fa-download"></i></button>
 
     <div class="dropdown-buttons">
         <!-- ipynb file if we had a myst markdown file -->
-        
+
         <!-- Download raw file -->
         <a class="dropdown-buttons" href="_sources/intro.md"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
@@ -197,14 +197,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Fintro.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Fintro.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -221,7 +221,7 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
             <div class="tocsection onthispage pt-5 pb-3">
                 <i class="fas fa-list"></i> Contents
             </div>
@@ -245,15 +245,15 @@
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
+
   <!-- #region -->
 <section class="tex2jax_ignore mathjax_ignore" id="welcome-to-qc-selector-s-documentation">
 <h1>Welcome to QC-Selector’s Documentation!<a class="headerlink" href="#welcome-to-qc-selector-s-documentation" title="Permalink to this headline">¶</a></h1>
-<p><a class="reference external" href="https://github.com/theochem/DiverseSelector">DiverseSelector</a> is a free, open-source, and cross-platform Python library designed to help you effortlessly identify the most diverse subset of molecules from your dataset. Please use the following citation in any publication using DiverseSelector library:</p>
+<p><a class="reference external" href="https://github.com/theochem/Selector">selector</a> is a free, open-source, and cross-platform Python library designed to help you effortlessly identify the most diverse subset of molecules from your dataset. Please use the following citation in any publication using selector library:</p>
 <p><strong>“QC-Selector: A Generic Python Package for Subset Selection”</strong>, Fanwang Meng, Alireza Tehrani, Valerii Chuiko, Abigail Broscius, Abdul, Hassan, Maximilian van Zyl, Marco Martínez González, Yang, Ramón Alain Miranda-Quintana, Paul W. Ayers, and Farnaz Heidar-Zadeh”</p>
-<p>The DiverseSelector source code is hosted on <a class="reference external" href="https://github.com/theochem/DiverseSelector">GitHub</a> and is released under the <a class="reference external" href="https://github.com/theochem/DiverseSelector/blob/main/LICENSE">GNU General Public License v3.0</a>. We welcome any contributions to the DiverseSelector library in accordance with our Code of Conduct; please see our <a class="reference external" href="https://qcdevs.org/guidelines/QCDevsCodeOfConduct/">Contributing Guidelines</a>. Please report any issues you encounter while using DiverseSelector library on <a class="reference external" href="https://github.com/theochem/DiverseSelector/issues">GitHub Issues</a>. For further information and inquiries please contact us at <a class="reference external" href="mailto:qcdevs&#37;&#52;&#48;gmail&#46;com">qcdevs<span>&#64;</span>gmail<span>&#46;</span>com</a>.</p>
+<p>The selector source code is hosted on <a class="reference external" href="https://github.com/theochem/Selector">GitHub</a> and is released under the <a class="reference external" href="https://github.com/theochem/Selector/blob/main/LICENSE">GNU General Public License v3.0</a>. We welcome any contributions to the selector library in accordance with our Code of Conduct; please see our <a class="reference external" href="https://qcdevs.org/guidelines/QCDevsCodeOfConduct/">Contributing Guidelines</a>. Please report any issues you encounter while using selector library on <a class="reference external" href="https://github.com/theochem/Selector/issues">GitHub Issues</a>. For further information and inquiries please contact us at <a class="reference external" href="mailto:qcdevs&#37;&#52;&#48;gmail&#46;com">qcdevs<span>&#64;</span>gmail<span>&#46;</span>com</a>.</p>
 <section id="why-qc-selector">
 <h2>Why QC-Selector?<a class="headerlink" href="#why-qc-selector" title="Permalink to this headline">¶</a></h2>
 <p>In the world of chemistry, selecting the right subset of molecules is critical for a wide range of applications, including drug discovery, materials science, and molecular optimization. QC-Selector offers a cutting-edge solution to streamline this process, empowering researchers, scientists, and developers to make smarter decisions faster.</p>
@@ -278,7 +278,7 @@
     {
         requestKernel: true,
         binderOptions: {
-            repo: "theochem/DiverseSelector",
+            repo: "theochem/Selector",
             ref: "main",
         },
         codeMirrorConfig: {
@@ -295,8 +295,8 @@
     <script>kernelName = 'python3'</script>
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
 <div class='prev-next-area'>
     <a class='right-next' id="next-link" href="installation.html" title="next page">
@@ -307,15 +307,15 @@
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     </a>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -325,8 +325,8 @@
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/html/partition.html

@@ -7,11 +7,11 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Partition based methods &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
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     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -19,10 +19,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
-    
+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
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@@ -31,7 +31,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
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     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -57,34 +57,34 @@
     <link rel="prev" title="Dissimilarity based methods" href="dissimilarity.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
-    
+
 
     <!-- Google Analytics -->
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   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
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-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -153,17 +153,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -172,15 +172,15 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
 <div class="dropdown-buttons-trigger">
     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
             class="fas fa-download"></i></button>
 
     <div class="dropdown-buttons">
         <!-- ipynb file if we had a myst markdown file -->
-        
+
         <!-- Download raw file -->
         <a class="dropdown-buttons" href="_sources/partition.rst"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
@@ -198,14 +198,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Fpartition.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Fpartition.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -222,21 +222,21 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
         </div>
     </div>
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
+
   <section id="partition-based-methods">
 <h1>Partition based methods<a class="headerlink" href="#partition-based-methods" title="Permalink to this headline">¶</a></h1>
-<span class="target" id="module-DiverseSelector.partition"></span><p>Module for Partition-Based Selection Methods.</p>
+<span class="target" id="module-selector.partition"></span><p>Module for Partition-Based Selection Methods.</p>
 <dl class="py class">
-<dt class="sig sig-object py" id="DiverseSelector.partition.DirectedSphereExclusion">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">DiverseSelector.partition.</span></span><span class="sig-name descname"><span class="pre">DirectedSphereExclusion</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r0</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_iter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random_seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.partition.DirectedSphereExclusion" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.partition.DirectedSphereExclusion">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">selector.partition.</span></span><span class="sig-name descname"><span class="pre">DirectedSphereExclusion</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r0</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">ref_index</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">p</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">2.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">eps</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">tol</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0.05</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">n_iter</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">10</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random_seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.partition.DirectedSphereExclusion" title="Permalink to this definition">¶</a></dt>
 <dd><p>Select samples using Directed Sphere Exclusion (DISE) algorithm.</p>
 <p>In a nutshell, this algorithm iteratively excludes any sample within a given radius from
 any already selected sample. The radius of the exclusion sphere is an adjustable parameter.
@@ -255,8 +255,8 @@ number of samples.</p>
 Journal of Chemical Information and Computer Sciences,
 43(1), 317–323. <a class="reference external" href="https://doi.org/10.1021/ci025554v">https://doi.org/10.1021/ci025554v</a></p>
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.partition.DirectedSphereExclusion.algorithm">
-<span class="sig-name descname"><span class="pre">algorithm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_size</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.partition.DirectedSphereExclusion.algorithm" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.partition.DirectedSphereExclusion.algorithm">
+<span class="sig-name descname"><span class="pre">algorithm</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_size</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.partition.DirectedSphereExclusion.algorithm" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return selected samples based on directed sphere exclusion algorithm.</p>
 <dl class="simple">
 <dt>X: ndarray of shape (n_samples, n_features)</dt><dd><p>Feature matrix of <cite>n_samples</cite> samples in <cite>n_features</cite> dimensional space.</p>
@@ -271,8 +271,8 @@ Journal of Chemical Information and Computer Sciences,
 </dd></dl>
 
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.partition.DirectedSphereExclusion.select_from_cluster">
-<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.partition.DirectedSphereExclusion.select_from_cluster" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.partition.DirectedSphereExclusion.select_from_cluster">
+<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.partition.DirectedSphereExclusion.select_from_cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Return selected samples from a cluster based on directed sphere exclusion algorithm</p>
 <dl class="simple">
 <dt>X: ndarray of shape (n_samples, n_features)</dt><dd><p>Feature matrix of <cite>n_samples</cite> samples in <cite>n_features</cite> dimensional space.</p>
@@ -291,8 +291,8 @@ Journal of Chemical Information and Computer Sciences,
 </dd></dl>
 
 <dl class="py class">
-<dt class="sig sig-object py" id="DiverseSelector.partition.GridPartitioning">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">DiverseSelector.partition.</span></span><span class="sig-name descname"><span class="pre">GridPartitioning</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cells</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grid_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'equisized_independent'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random_seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.partition.GridPartitioning" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.partition.GridPartitioning">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">selector.partition.</span></span><span class="sig-name descname"><span class="pre">GridPartitioning</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">cells</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">grid_method</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'equisized_independent'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_dim</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">random_seed</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">42</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.partition.GridPartitioning" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selecting points using the Grid Partitioning algorithm.</p>
 <p>Points are partitioned into grids using an algorithm (equisized independent or equisized
 dependent). A point is selected from each of the grids while the number of selected points is
@@ -302,8 +302,8 @@ than the number of grids available to select from, the points are chosen from th
 greatest diversity.</p>
 <p>Adapted from <a class="reference external" href="https://doi.org/10.1016/S1093-3263(99)00016-9">https://doi.org/10.1016/S1093-3263(99)00016-9</a>.</p>
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.partition.GridPartitioning.select_from_cluster">
-<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_selected</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.partition.GridPartitioning.select_from_cluster" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.partition.GridPartitioning.select_from_cluster">
+<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_selected</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.partition.GridPartitioning.select_from_cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Grid partitioning algorithm for selecting points from cluster.</p>
 <dl class="simple">
 <dt>arr: np.ndarray</dt><dd><p>Coordinate array of points</p>
@@ -322,8 +322,8 @@ greatest diversity.</p>
 </dd></dl>
 
 <dl class="py class">
-<dt class="sig sig-object py" id="DiverseSelector.partition.Medoid">
-<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">DiverseSelector.partition.</span></span><span class="sig-name descname"><span class="pre">Medoid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">start_id=0</span></em>, <em class="sig-param"><span class="pre">func_distance=&lt;function</span> <span class="pre">Medoid.&lt;lambda&gt;&gt;</span></em>, <em class="sig-param"><span class="pre">scaling=10</span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.partition.Medoid" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.partition.Medoid">
+<em class="property"><span class="pre">class</span> </em><span class="sig-prename descclassname"><span class="pre">selector.partition.</span></span><span class="sig-name descname"><span class="pre">Medoid</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="pre">start_id=0</span></em>, <em class="sig-param"><span class="pre">func_distance=&lt;function</span> <span class="pre">Medoid.&lt;lambda&gt;&gt;</span></em>, <em class="sig-param"><span class="pre">scaling=10</span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.partition.Medoid" title="Permalink to this definition">¶</a></dt>
 <dd><p>Selecting points using an algorithm adapted from KDTree.</p>
 <p>Points are initially used to construct a KDTree. Eucleidean distances are used for this
 algorithm. The first point selected is based on the starting_idx provided and becomes the first
@@ -334,8 +334,8 @@ and is used as the new query point for find_furthest_neighbor, repeating the pro
 upon selecting requested number of points or if all available points exhausted.</p>
 <p>Adapted from: <a class="reference external" href="https://en.wikipedia.org/wiki/K-d_tree#Construction">https://en.wikipedia.org/wiki/K-d_tree#Construction</a></p>
 <dl class="py method">
-<dt class="sig sig-object py" id="DiverseSelector.partition.Medoid.select_from_cluster">
-<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_selected</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.partition.Medoid.select_from_cluster" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.partition.Medoid.select_from_cluster">
+<span class="sig-name descname"><span class="pre">select_from_cluster</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">arr</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_selected</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.partition.Medoid.select_from_cluster" title="Permalink to this definition">¶</a></dt>
 <dd><p>Main function for selecting points using the KDTree algorithm.</p>
 <dl class="simple">
 <dt>arr: np.ndarray</dt><dd><p>Coordinate array of points</p>
@@ -359,7 +359,7 @@ upon selecting requested number of points or if all available points exhausted.<
     {
         requestKernel: true,
         binderOptions: {
-            repo: "theochem/DiverseSelector",
+            repo: "theochem/Selector",
             ref: "main",
         },
         codeMirrorConfig: {
@@ -376,10 +376,10 @@ upon selecting requested number of points or if all available points exhausted.<
     <script>kernelName = 'python3'</script>
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
+<div class='prev-next-area'>
     <a class='left-prev' id="prev-link" href="dissimilarity.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
@@ -395,15 +395,15 @@ upon selecting requested number of points or if all available points exhausted.<
     <i class="fas fa-angle-right"></i>
     </a>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -413,8 +413,8 @@ upon selecting requested number of points or if all available points exhausted.<
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/html/py-modindex.html

@@ -6,11 +6,11 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
     <title>Python Module Index &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
   <link rel="stylesheet"
     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -18,10 +18,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
-    
+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
@@ -30,7 +30,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
+
   <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -48,36 +48,36 @@
 
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
-    
+
 
     <!-- Google Analytics -->
-    
+
 
 
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
 <div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -146,17 +146,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -165,8 +165,8 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
             <!-- Source interaction buttons -->
 
 <div class="dropdown-buttons-trigger">
@@ -174,14 +174,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Fpy-modindex.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Fpy-modindex.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -198,15 +198,15 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
         </div>
     </div>
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
+
 
    <h1>Python Module Index</h1>
 
@@ -222,46 +222,46 @@
        <td><img src="_static/minus.png" class="toggler"
               id="toggle-1" style="display: none" alt="-" /></td>
        <td>
-       <code class="xref">DiverseSelector</code></td><td>
+       <code class="xref">selector</code></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="base.html#module-DiverseSelector.base"><code class="xref">DiverseSelector.base</code></a></td><td>
+       <a href="base.html#module-selector.base"><code class="xref">selector.base</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="dissimilarity.html#module-DiverseSelector.dissimilarity"><code class="xref">DiverseSelector.dissimilarity</code></a></td><td>
+       <a href="dissimilarity.html#module-selector.dissimilarity"><code class="xref">selector.dissimilarity</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="partition.html#module-DiverseSelector.partition"><code class="xref">DiverseSelector.partition</code></a></td><td>
+       <a href="partition.html#module-selector.partition"><code class="xref">selector.partition</code></a></td><td>
        <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
-       <a href="utils.html#module-DiverseSelector.utils"><code class="xref">DiverseSelector.utils</code></a></td><td>
+       <a href="utils.html#module-selector.utils"><code class="xref">selector.utils</code></a></td><td>
        <em></em></td></tr>
    </table>
 
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
 <div class='prev-next-area'>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -271,8 +271,8 @@
 
       </div>
     </div>
-  
+
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book/content/_build/html/search.html

@@ -6,11 +6,11 @@
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+
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@@ -201,17 +201,17 @@
 
         <!-- Table of contents -->
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-            
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     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
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-                
+
   <h1 id="search-documentation">Search</h1>
-  
+
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   <div class="admonition warning">
   <p>
@@ -220,42 +220,42 @@
   </p>
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-  
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+
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     <div class="container">
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           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
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             &copy; Copyright 2022-2023.<br/>
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     </div>
@@ -265,8 +265,8 @@
 
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book/content/_build/html/searchindex.js

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                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
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     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
             class="fas fa-download"></i></button>
 
     <div class="dropdown-buttons">
         <!-- ipynb file if we had a myst markdown file -->
-        
+
         <!-- Download raw file -->
         <a class="dropdown-buttons" href="_sources/starting.ipynb"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
@@ -198,14 +198,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Fstarting.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Fstarting.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -222,24 +222,24 @@
     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn"
         aria-label="Launch interactive content"><i class="fas fa-rocket"></i></button>
     <div class="dropdown-buttons">
-        
-        <a class="binder-button" href="https://mybinder.org/v2/gh/theochem/DiverseSelector/main?urlpath=tree/book/content/starting.ipynb"><button type="button"
+
+        <a class="binder-button" href="https://mybinder.org/v2/gh/theochem/Selector/main?urlpath=tree/book/content/starting.ipynb"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Launch Binder" data-toggle="tooltip"
                 data-placement="left"><img class="binder-button-logo"
                     src="_static/images/logo_binder.svg"
                     alt="Interact on binder">Binder</button></a>
-        
-        
-        
-        <a class="colab-button" href="https://colab.research.google.com/github/theochem/DiverseSelector/blob/main/book/content/starting.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
+
+
+
+        <a class="colab-button" href="https://colab.research.google.com/github/theochem/Selector/blob/main/book/content/starting.ipynb"><button type="button" class="btn btn-secondary topbarbtn"
                 title="Launch Colab" data-toggle="tooltip" data-placement="left"><img class="colab-button-logo"
                     src="_static/images/logo_colab.png"
                     alt="Interact on Colab">Colab</button></a>
-        
+
         <button type="button" class="btn btn-secondary topbarbtn"
             onclick="initThebeSBT()" title="Launch Thebe" data-toggle="tooltip" data-placement="left"><i
                 class="fas fa-play"></i><span style="margin-left: .4em;">Live Code</span></button>
-        
+
     </div>
 </div>
 
@@ -247,7 +247,7 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
             <div class="tocsection onthispage pt-5 pb-3">
                 <i class="fas fa-list"></i> Contents
             </div>
@@ -330,9 +330,9 @@
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
+
   <section class="tex2jax_ignore mathjax_ignore" id="getting-started">
 <h1>Getting started<a class="headerlink" href="#getting-started" title="Permalink to this headline">¶</a></h1>
 <section id="demo-dissimilarity-based-selection-synthetic-data">
@@ -343,8 +343,8 @@
 <h2>Generating Synthetic Data<a class="headerlink" href="#generating-synthetic-data" title="Permalink to this headline">¶</a></h2>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># install the DiverseSelector module</span>
-<span class="o">!</span>pip install git+https://github.com/theochem/DiverseSelector
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># install the selector module</span>
+<span class="o">!</span>pip install git+https://github.com/theochem/Selector
 <span class="o">!</span>pip install rdkit
 </pre></div>
 </div>
@@ -352,7 +352,7 @@
 </div>
 <div class="cell docutils container">
 <div class="cell_input docutils container">
-<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">DiverseSelector</span>
+<div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">selector</span>
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Tuple</span><span class="p">,</span> <span class="n">Union</span>
@@ -482,8 +482,8 @@
 <div class="cell docutils container">
 <div class="cell_input docutils container">
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># MaxMin method</span>
-<span class="kn">from</span> <span class="nn">DiverseSelector.methods.partition</span> <span class="kn">import</span> <span class="o">*</span>
-<span class="kn">from</span> <span class="nn">DiverseSelector.methods.dissimilarity</span> <span class="kn">import</span> <span class="o">*</span>
+<span class="kn">from</span> <span class="nn">selector.methods.partition</span> <span class="kn">import</span> <span class="o">*</span>
+<span class="kn">from</span> <span class="nn">selector.methods.dissimilarity</span> <span class="kn">import</span> <span class="o">*</span>
 
 <span class="c1"># diverse subset selection from randomly generated data points</span>
 <span class="n">selector</span> <span class="o">=</span> <span class="n">MaxMin</span><span class="p">()</span>
@@ -556,8 +556,8 @@
 <div class="highlight-ipython3 notranslate"><div class="highlight"><pre><span></span><span class="c1"># diverse subset selection from randomly generated data points</span>
 <span class="n">selected_id7</span> <span class="o">=</span> <span class="n">GridPartitioning</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s2">&quot;equisized_independent&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span> <span class="mi">12</span><span class="p">)</span>
 <span class="c1"># diverse subset selection from data points with obvious patterns (different clusters)</span>
-<span class="n">selected_id8</span> <span class="o">=</span> <span class="n">GridPartitioning</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s2">&quot;equisized_independent&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">coords_cluster</span><span class="p">,</span> 
-                                                                   <span class="n">size</span><span class="o">=</span><span class="mi">12</span><span class="p">,</span> 
+<span class="n">selected_id8</span> <span class="o">=</span> <span class="n">GridPartitioning</span><span class="p">(</span><span class="mi">2</span><span class="p">,</span> <span class="s2">&quot;equisized_independent&quot;</span><span class="p">)</span><span class="o">.</span><span class="n">select</span><span class="p">(</span><span class="n">coords_cluster</span><span class="p">,</span>
+                                                                   <span class="n">size</span><span class="o">=</span><span class="mi">12</span><span class="p">,</span>
                                                                    <span class="n">labels</span><span class="o">=</span><span class="n">class_labels_cluster</span><span class="p">)</span>
 
 <span class="n">graph_data</span><span class="p">(</span><span class="n">coords</span><span class="p">,</span><span class="n">selected_id7</span><span class="p">)</span>
@@ -750,7 +750,7 @@
     {
         requestKernel: true,
         binderOptions: {
-            repo: "theochem/DiverseSelector",
+            repo: "theochem/Selector",
             ref: "main",
         },
         codeMirrorConfig: {
@@ -767,10 +767,10 @@
     <script>kernelName = 'python3'</script>
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
+<div class='prev-next-area'>
     <a class='left-prev' id="prev-link" href="installation.html" title="previous page">
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         <div class="prev-next-info">
@@ -786,15 +786,15 @@
     <i class="fas fa-angle-right"></i>
     </a>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -804,8 +804,8 @@
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/html/utils.html

@@ -7,11 +7,11 @@
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
     <title>Utilities &#8212; Ayers Lab</title>
-    
+
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
-    
+
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     href="_static/vendor/fontawesome/5.13.0/css/all.min.css">
   <link rel="preload" as="font" type="font/woff2" crossorigin
@@ -19,10 +19,10 @@
   <link rel="preload" as="font" type="font/woff2" crossorigin
     href="_static/vendor/fontawesome/5.13.0/webfonts/fa-brands-400.woff2">
 
-    
-      
 
-    
+
+
+
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="_static/sphinx-book-theme.css?digest=c3fdc42140077d1ad13ad2f1588a4309" />
     <link rel="stylesheet" type="text/css" href="_static/togglebutton.css" />
@@ -31,7 +31,7 @@
     <link rel="stylesheet" type="text/css" href="_static/sphinx-thebe.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-main.c949a650a448cc0ae9fd3441c0e17fb0.css" />
     <link rel="stylesheet" type="text/css" href="_static/panels-variables.06eb56fa6e07937060861dad626602ad.css" />
-    
+
   <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -56,34 +56,34 @@
     <link rel="prev" title="Partition based methods" href="partition.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
     <meta name="docsearch:language" content="None">
-    
+
 
     <!-- Google Analytics -->
-    
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
-    
+
     <div class="container-fluid" id="banner"></div>
 
-    
+
 
     <div class="container-xl">
       <div class="row">
-          
+
 <div class="col-12 col-md-3 bd-sidebar site-navigation show" id="site-navigation">
-    
+
         <div class="navbar-brand-box">
     <a class="navbar-brand text-wrap" href="index.html">
-      
+
         <!-- `logo` is deprecated in Sphinx 4.0, so remove this when we stop supporting 3 -->
-        
-      
-      
+
+
+
       <img src="_static/selector_logo.png" class="logo" alt="logo">
-      
-      
+
+
       <h1 class="site-logo" id="site-title">Ayers Lab</h1>
-      
+
     </a>
 </div><form class="bd-search d-flex align-items-center" action="search.html" method="get">
   <i class="icon fas fa-search"></i>
@@ -152,17 +152,17 @@
 </div>
 
 
-          
 
 
-          
+
+
 <main class="col py-md-3 pl-md-4 bd-content overflow-auto" role="main">
-    
+
     <div class="topbar container-xl fixed-top">
     <div class="topbar-contents row">
         <div class="col-12 col-md-3 bd-topbar-whitespace site-navigation show"></div>
         <div class="col pl-md-4 topbar-main">
-            
+
             <button id="navbar-toggler" class="navbar-toggler ml-0" type="button" data-toggle="collapse"
                 data-toggle="tooltip" data-placement="bottom" data-target=".site-navigation" aria-controls="navbar-menu"
                 aria-expanded="true" aria-label="Toggle navigation" aria-controls="site-navigation"
@@ -171,15 +171,15 @@
                 <i class="fas fa-arrow-left"></i>
                 <i class="fas fa-arrow-up"></i>
             </button>
-            
-            
+
+
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     <button id="dropdown-buttons-trigger" class="btn btn-secondary topbarbtn" aria-label="Download this page"><i
             class="fas fa-download"></i></button>
 
     <div class="dropdown-buttons">
         <!-- ipynb file if we had a myst markdown file -->
-        
+
         <!-- Download raw file -->
         <a class="dropdown-buttons" href="_sources/utils.rst"><button type="button"
                 class="btn btn-secondary topbarbtn" title="Download source file" data-toggle="tooltip"
@@ -197,14 +197,14 @@
         aria-label="Connect with source repository"><i class="fab fa-github"></i></button>
     <div class="dropdown-buttons sourcebuttons">
         <a class="repository-button"
-            href="https://github.com/theochem/DiverseSelector"><button type="button" class="btn btn-secondary topbarbtn"
+            href="https://github.com/theochem/Selector"><button type="button" class="btn btn-secondary topbarbtn"
                 data-toggle="tooltip" data-placement="left" title="Source repository"><i
                     class="fab fa-github"></i>repository</button></a>
         <a class="issues-button"
-            href="https://github.com/theochem/DiverseSelector/issues/new?title=Issue%20on%20page%20%2Futils.html&body=Your%20issue%20content%20here."><button
+            href="https://github.com/theochem/Selector/issues/new?title=Issue%20on%20page%20%2Futils.html&body=Your%20issue%20content%20here."><button
                 type="button" class="btn btn-secondary topbarbtn" data-toggle="tooltip" data-placement="left"
                 title="Open an issue"><i class="fas fa-lightbulb"></i>open issue</button></a>
-        
+
     </div>
 </div>
 
@@ -221,21 +221,21 @@
 
         <!-- Table of contents -->
         <div class="d-none d-md-block col-md-2 bd-toc show">
-            
+
         </div>
     </div>
 </div>
     <div id="main-content" class="row">
         <div class="col-12 col-md-9 pl-md-3 pr-md-0">
-        
+
               <div>
-                
-  <section id="module-DiverseSelector.utils">
-<span id="utilities"></span><h1>Utilities<a class="headerlink" href="#module-DiverseSelector.utils" title="Permalink to this headline">¶</a></h1>
+
+  <section id="module-selector.utils">
+<span id="utilities"></span><h1>Utilities<a class="headerlink" href="#module-selector.utils" title="Permalink to this headline">¶</a></h1>
 <p>Module for Selection Utilities.</p>
 <dl class="py function">
-<dt class="sig sig-object py" id="DiverseSelector.utils.optimize_radius">
-<span class="sig-prename descclassname"><span class="pre">DiverseSelector.utils.</span></span><span class="sig-name descname"><span class="pre">optimize_radius</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#DiverseSelector.utils.optimize_radius" title="Permalink to this definition">¶</a></dt>
+<dt class="sig sig-object py" id="selector.utils.optimize_radius">
+<span class="sig-prename descclassname"><span class="pre">selector.utils.</span></span><span class="sig-name descname"><span class="pre">optimize_radius</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">obj</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">X</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">size</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cluster_ids</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#selector.utils.optimize_radius" title="Permalink to this definition">¶</a></dt>
 <dd><p>Algorithm that uses sphere exclusion for selecting points from cluster.</p>
 <p>Iteratively searches for the optimal radius to obtain the correct number
 of selected samples. If the radius cannot converge to return <cite>size</cite> points,
@@ -262,7 +262,7 @@ the function returns the closest number of samples to <cite>size</cite> as possi
     {
         requestKernel: true,
         binderOptions: {
-            repo: "theochem/DiverseSelector",
+            repo: "theochem/Selector",
             ref: "main",
         },
         codeMirrorConfig: {
@@ -279,10 +279,10 @@ the function returns the closest number of samples to <cite>size</cite> as possi
     <script>kernelName = 'python3'</script>
 
               </div>
-              
-        
+
+
             <!-- Previous / next buttons -->
-<div class='prev-next-area'> 
+<div class='prev-next-area'>
     <a class='left-prev' id="prev-link" href="partition.html" title="previous page">
         <i class="fas fa-angle-left"></i>
         <div class="prev-next-info">
@@ -291,15 +291,15 @@ the function returns the closest number of samples to <cite>size</cite> as possi
         </div>
     </a>
 </div>
-        
+
         </div>
     </div>
     <footer class="footer">
     <div class="container">
       <p>
-        
+
           By The QC-Dev Community with the support of Digital Research Alliance of Canada and The Jupyter Book Community<br/>
-        
+
             &copy; Copyright 2022-2023.<br/>
       </p>
     </div>
@@ -309,8 +309,8 @@ the function returns the closest number of samples to <cite>size</cite> as possi
 
       </div>
     </div>
-  
+
   <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
 
   </body>
-</html>
+</html>

book/content/_build/jupyter_execute/installation.ipynb

@@ -16,7 +16,7 @@
     "We are preparing a 1.0 release. Until then, these instructions for installing a stable release will not work yet. If you enjoy living on the edge, try the development release as explained in the “Latest git revision” section below.\n",
     "</div>\n",
     "\n",
-    "The following dependencies are required to run DiverseSelector properly,\n",
+    "The following dependencies are required to run selector properly,\n",
     "\n",
     "* Python >= 3.6: http://www.python.org/ \n",
     "* NumPy >= 1.21.5: http://www.numpy.org/\n",
@@ -29,7 +29,7 @@
     "\n",
     "## Installation with Ana- or Miniconda:\n",
     "\n",
-    "1. To install DiverseSelector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:\n",
+    "1. To install selector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:\n",
     "\n",
     "```\n",
     "# Activate your main conda environment if it is not loaded in your .bashrc.\n",
@@ -96,20 +96,20 @@
     "\n",
     "## Latest git revision\n",
     "\n",
-    "This section shows how one can install the latest revision of DiverseSelector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.\n",
+    "This section shows how one can install the latest revision of selector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.\n",
     "\n",
     "There are two installation methods:\n",
     "\n",
     "1. **Quick and dirty.** Of this method, there are four variants, depending on the correctness of your `PATH` variable and the presence of a virtual or conda environment. These different scenarios are explained in more detail in the previous section.\n",
     "```\n",
     "# with env, correct PATH\n",
-    "pip install git+https://github.com/theochem/DiverseSelector.git\n",
+    "pip install git+https://github.com/theochem/Selector.git\n",
     "# with env, broken PATH\n",
-    "python -m pip install git+https://github.com/theochem/DiverseSelector.git\n",
+    "python -m pip install git+https://github.com/theochem/Selector.git\n",
     "# without env, correct PATH\n",
-    "pip install git+https://github.com/theochem/DiverseSelector.git --user\n",
+    "pip install git+https://github.com/theochem/Selector.git --user\n",
     "# without env, broken PATH\n",
-    "python -m pip install git+https://github.com/theochem/DiverseSelector.git --user\n",
+    "python -m pip install git+https://github.com/theochem/Selector.git --user\n",
     "```\n",
     "\n",
     "2. **Slow and Smart.** In addition to the four variations in the quick and dirty method, the slow and smart can be used with `pip` or just with `setup.py`. You also have the options to use SSH or HTTPS protocols to clone the git repository. Pick whichever works best for you.\n",
@@ -117,9 +117,9 @@
     "# A) Clone git repo with https OR ssh:\n",
     "# The second one only works if you have ssh set up for Github\n",
     "#  A1) https\n",
-    "git clone https://github.com/theochem/DiverseSelector.git\n",
+    "git clone https://github.com/theochem/Selector.git\n",
     "#  A2) ssh\n",
-    "git clone [email protected]:theochem/DiverseSelector.git\n",
+    "git clone [email protected]:theochem/Selector.git\n",
     "# B) Optionally write the version string\n",
     "pip install roberto  # or any of the three other ways of running pip, see above.\n",
     "rob write-version\n",
@@ -148,7 +148,7 @@
     "# Install pytest in your conda env.\n",
     "conda install pytest pytest-xdist\n",
     "# Then run the tests.\n",
-    "pytest --pyargs diverseselector -n auto\n",
+    "pytest --pyargs selector -n auto\n",
     "```\n",
     "\n",
     "With Pip:\n",
@@ -157,13 +157,13 @@
     "pip install pytest pytest-xdist\n",
     "# .. and refresh the virtual environment.\n",
     "# This is a venv quirk. Without it, pytest may not find IOData.\n",
-    "deactivate && source ~/diverseselector/activate\n",
+    "deactivate && source ~/selector/activate\n",
     "\n",
     "# Alternatively, install pytest in your home directory.\n",
     "pip install pytest pytest-xdist --user\n",
     "\n",
     "# Finally, run the tests.\n",
-    "pytest --pyargs diverseselector -n auto\n",
+    "pytest --pyargs selector -n auto\n",
     "```"
    ]
   }
@@ -189,4 +189,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

book/content/_build/jupyter_execute/installation.py

@@ -1,44 +1,43 @@
 #!/usr/bin/env python
-# coding: utf-8
 
 # # Installation
-# 
+#
 # ## Stable releases
-# 
+#
 # <div class="alert alert-block alert-warning">
 # <b>Warning:
 # </b>
-#     
+#
 # We are preparing a 1.0 release. Until then, these instructions for installing a stable release will not work yet. If you enjoy living on the edge, try the development release as explained in the “Latest git revision” section below.
 # </div>
-# 
-# The following dependencies are required to run DiverseSelector properly,
-# 
-# * Python >= 3.6: http://www.python.org/ 
+#
+# The following dependencies are required to run selector properly,
+#
+# * Python >= 3.6: http://www.python.org/
 # * NumPy >= 1.21.5: http://www.numpy.org/
 # * SciPy >= 1.5.0: http://www.scipy.org/
 # * PyTest >= 5.3.4: https://docs.pytest.org/
 # * PyTest-Cov >= 2.8.0: https://pypi.org/project/pytest-cov
-# 
+#
 # Normally, you don’t need to install these dependencies manually. They will be installed automatically when you follow the instructions below.
-# 
-# 
+#
+#
 # ## Installation with Ana- or Miniconda:
-# 
-# 1. To install DiverseSelector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:
-# 
+#
+# 1. To install selector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:
+#
 # ```
 # # Activate your main conda environment if it is not loaded in your .bashrc.
 # # E.g. run the following if you have miniconda installed in e.g. ~/miniconda3
 # source ~/miniconda3/bin/activate
-# 
+#
 # # Create a horton3 conda environment. (optional, recommended)
 # conda create -n horton3
 # source activate horton3
-# 
+#
 # # Install the stable release.
 # conda install -c theochem qc-selector
-# 
+#
 # # Unstable releases
 # # (Only do this if you understand the implications.)
 # # Install the testing release. (beta)
@@ -46,76 +45,76 @@
 # # Install the development release. (alpha)
 # conda install -c theochem/label/dev qc-selector
 # ```
-# 
+#
 # ## Installation with Pip
-# 
+#
 # 1. You can work in a [virtual environment](https://docs.python.org/3/tutorial/venv.html):
-# 
+#
 # ```
 # # Create a virtual environment in ~/horton3
 # # Feel free to change the path.
 # python3 -m venv ~/horton3
-# 
+#
 # # Activate the virtual environemnt.
 # source ~/horton3/bin/activate
-# 
+#
 # # Install the stable release in the venv horton3.
 # pip3 install qc-selector
 # # alternative: python3 -m pip install qc-selector
-# 
+#
 # # For developers, install a pre-release (alpha or beta).
 # # (Only do this if you understand the implications.)
 # pip3 install --pre qc-selector
 # # alternative: python3 -m pip install --pre qc-selector
 # ```
-# 
-# 
+#
+#
 # 2. You can install into your `{$HOME}` directory without creating a virtual environment
-# 
+#
 # ```
 # # Install the stable release in your home directory.
 # pip3 install qc-selector --user
 # # alternative: python3 -m pip install qc-selector --user
-# 
+#
 # # For developers, install a pre-release (alpha or beta).
 # # (Only do this if you understand the implications.)
 # pip3 install --pre qc-selector --user
 # # alternative: python3 -m pip install --pre qc-selector --user
 # ```
-# 
+#
 # This is by far the simplest method, ideal to get started, but you have only one home directory. If the installation breaks due to some experimentation, it is harder to make a clean start in comparison to the other options.
-#     
+#
 # In case the `pip3` executable is not found, pip may be installed in a directory which is not included in your `${PATH}` variable. This seems to be a common issue on macOS. A simple workaround is to replace `pip3` by `python3 -m pip`.
-# 
-# In case Python and your operating system are up to date, you may also use `pip` instead of `pip3` or `python` instead of `python3`. The `3` is only used to avoid potential confusion with Python 2. Note that the `3` is only present in names of executables, not names of 
+#
+# In case Python and your operating system are up to date, you may also use `pip` instead of `pip3` or `python` instead of `python3`. The `3` is only used to avoid potential confusion with Python 2. Note that the `3` is only present in names of executables, not names of
 # Python modules.
-# 
+#
 # ## Latest git revision
-# 
-# This section shows how one can install the latest revision of DiverseSelector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.
-# 
+#
+# This section shows how one can install the latest revision of selector from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.
+#
 # There are two installation methods:
-# 
+#
 # 1. **Quick and dirty.** Of this method, there are four variants, depending on the correctness of your `PATH` variable and the presence of a virtual or conda environment. These different scenarios are explained in more detail in the previous section.
 # ```
 # # with env, correct PATH
-# pip install git+https://github.com/theochem/DiverseSelector.git
+# pip install git+https://github.com/theochem/Selector.git
 # # with env, broken PATH
-# python -m pip install git+https://github.com/theochem/DiverseSelector.git
+# python -m pip install git+https://github.com/theochem/Selector.git
 # # without env, correct PATH
-# pip install git+https://github.com/theochem/DiverseSelector.git --user
+# pip install git+https://github.com/theochem/Selector.git --user
 # # without env, broken PATH
-# python -m pip install git+https://github.com/theochem/DiverseSelector.git --user
+# python -m pip install git+https://github.com/theochem/Selector.git --user
 # ```
-# 
+#
 # 2. **Slow and Smart.** In addition to the four variations in the quick and dirty method, the slow and smart can be used with `pip` or just with `setup.py`. You also have the options to use SSH or HTTPS protocols to clone the git repository. Pick whichever works best for you.
 # ```
 # # A) Clone git repo with https OR ssh:
 # # The second one only works if you have ssh set up for Github
 # #  A1) https
-# git clone https://github.com/theochem/DiverseSelector.git
+# git clone https://github.com/theochem/Selector.git
 # #  A2) ssh
-# git clone [email protected]:theochem/DiverseSelector.git
+# git clone [email protected]:theochem/Selector.git
 # # B) Optionally write the version string
 # pip install roberto  # or any of the three other ways of running pip, see above.
 # rob write-version
@@ -133,31 +132,31 @@
 # #  C6) pip, without env, broken PATH
 # python -m pip install . --user
 # ```
-# 
-# 
+#
+#
 # ## Testing
-# 
+#
 # The tests are automatically run when we build packages with conda, but you may try them again on your own machine after installation.
-# 
+#
 # With Ana- or Miniconda:
 # ```
 # # Install pytest in your conda env.
 # conda install pytest pytest-xdist
 # # Then run the tests.
-# pytest --pyargs diverseselector -n auto
+# pytest --pyargs selector -n auto
 # ```
-# 
+#
 # With Pip:
 # ```
 # # Install pytest in your conda env ...
 # pip install pytest pytest-xdist
 # # .. and refresh the virtual environment.
 # # This is a venv quirk. Without it, pytest may not find IOData.
-# deactivate && source ~/diverseselector/activate
-# 
+# deactivate && source ~/selector/activate
+#
 # # Alternatively, install pytest in your home directory.
 # pip install pytest pytest-xdist --user
-# 
+#
 # # Finally, run the tests.
-# pytest --pyargs diverseselector -n auto
+# pytest --pyargs selector -n auto
 # ```

book/content/_build/jupyter_execute/starting.ipynb

@@ -32,8 +32,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# install the DiverseSelector module\n",
-    "!pip install git+https://github.com/theochem/DiverseSelector\n",
+    "# install the selector module\n",
+    "!pip install git+https://github.com/theochem/Selector\n",
     "!pip install rdkit"
    ]
   },
@@ -44,7 +44,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import DiverseSelector\n",
+    "import selector\n",
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "from typing import Any, Tuple, Union\n",
@@ -170,7 +170,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_6_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_6_0.png"
       },
       "needs_background": "light"
      },
@@ -185,7 +185,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_6_1.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_6_1.png"
       },
       "needs_background": "light"
      },
@@ -221,8 +221,8 @@
    "outputs": [],
    "source": [
     "# MaxMin method\n",
-    "from DiverseSelector.methods.partition import *\n",
-    "from DiverseSelector.methods.dissimilarity import *\n",
+    "from selector.methods.partition import *\n",
+    "from selector.methods.dissimilarity import *\n",
     "\n",
     "# diverse subset selection from randomly generated data points\n",
     "selector = MaxMin()\n",
@@ -248,7 +248,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_10_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_10_0.png"
       },
       "needs_background": "light"
      },
@@ -263,7 +263,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_10_1.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_10_1.png"
       },
       "needs_background": "light"
      },
@@ -302,7 +302,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_12_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_12_0.png"
       },
       "needs_background": "light"
      },
@@ -317,7 +317,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_12_1.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_12_1.png"
       },
       "needs_background": "light"
      },
@@ -361,7 +361,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_14_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_14_0.png"
       },
       "needs_background": "light"
      },
@@ -376,7 +376,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_14_1.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_14_1.png"
       },
       "needs_background": "light"
      },
@@ -420,7 +420,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_16_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_16_0.png"
       },
       "needs_background": "light"
      },
@@ -435,7 +435,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_16_1.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_16_1.png"
       },
       "needs_background": "light"
      },
@@ -486,7 +486,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_18_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_18_0.png"
       },
       "needs_background": "light"
      },
@@ -518,7 +518,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_19_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_19_0.png"
       },
       "needs_background": "light"
      },
@@ -593,7 +593,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_22_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_22_0.png"
       },
       "needs_background": "light"
      },
@@ -643,7 +643,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_25_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_25_0.png"
       },
       "needs_background": "light"
      },
@@ -693,7 +693,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_28_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_28_0.png"
       },
       "needs_background": "light"
      },
@@ -742,7 +742,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_31_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_31_0.png"
       },
       "needs_background": "light"
      },
@@ -791,7 +791,7 @@
      },
      "metadata": {
       "filenames": {
-       "image/png": "/Users/valeriichuiko/Desktop/projects/DiverseSelector/book/content/_build/jupyter_execute/starting_34_0.png"
+       "image/png": "/Users/valeriichuiko/Desktop/projects/selector/book/content/_build/jupyter_execute/starting_34_0.png"
       },
       "needs_background": "light"
      },
@@ -824,4 +824,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 5
-}
+}

book/content/_build/jupyter_execute/starting.py

@@ -1,5 +1,4 @@
 #!/usr/bin/env python
-# coding: utf-8
 
 # # Getting started
 # ## Demo - Dissimilarity Based Selection Synthetic Data
@@ -11,33 +10,35 @@
 # In[ ]:
 
 
-# install the DiverseSelector module
-get_ipython().system('pip install git+https://github.com/theochem/DiverseSelector')
-get_ipython().system('pip install rdkit')
+# install the selector module
+from selector.methods.dissimilarity import *
+from selector.methods.partition import *
+from sklearn.metrics import pairwise_distances
+from sklearn.datasets import make_blobs
+from typing import Any, Tuple, Union
+import numpy as np
+import matplotlib.pyplot as plt
+import selector
+
+get_ipython().system("pip install git+https://github.com/theochem/Selector")
+get_ipython().system("pip install rdkit")
 
 
 # In[1]:
 
 
-import DiverseSelector
-import matplotlib.pyplot as plt
-import numpy as np
-from typing import Any, Tuple, Union
-from sklearn.datasets import make_blobs
-from sklearn.metrics import pairwise_distances
-
-def generate_synthetic_data(n_samples: int = 100,
-                            n_features: int = 2,
-                            n_clusters: int = 2,
-                            cluster_std: float = 1.0,
-                            center_box: Tuple[float, float] = (-10.0, 10.0),
-                            metric: str = "euclidean",
-                            shuffle: bool = True,
-                            random_state: int = 42,
-                            pairwise_dist: bool = False,
-                            **kwargs: Any,
-                            ) -> Union[Tuple[np.ndarray, np.ndarray],
-                                       Tuple[np.ndarray, np.ndarray, np.ndarray]]:
+def generate_synthetic_data(
+    n_samples: int = 100,
+    n_features: int = 2,
+    n_clusters: int = 2,
+    cluster_std: float = 1.0,
+    center_box: Tuple[float, float] = (-10.0, 10.0),
+    metric: str = "euclidean",
+    shuffle: bool = True,
+    random_state: int = 42,
+    pairwise_dist: bool = False,
+    **kwargs: Any,
+) -> Union[Tuple[np.ndarray, np.ndarray], Tuple[np.ndarray, np.ndarray, np.ndarray]]:
     """Generate synthetic data.
 
     Parameters
@@ -78,21 +79,23 @@ def generate_synthetic_data(n_samples: int = 100,
 
     """
     # pylint: disable=W0632
-    syn_data, class_labels = make_blobs(n_samples=n_samples,
-                                        n_features=n_features,
-                                        centers=n_clusters,
-                                        cluster_std=cluster_std,
-                                        center_box=center_box,
-                                        shuffle=shuffle,
-                                        random_state=random_state,
-                                        return_centers=False,
-                                        )
+    syn_data, class_labels = make_blobs(
+        n_samples=n_samples,
+        n_features=n_features,
+        centers=n_clusters,
+        cluster_std=cluster_std,
+        center_box=center_box,
+        shuffle=shuffle,
+        random_state=random_state,
+        return_centers=False,
+    )
     if pairwise_dist:
-        dist = pairwise_distances(X=syn_data,
-                                  Y=None,
-                                  metric=metric,
-                                  **kwargs,
-                                  )
+        dist = pairwise_distances(
+            X=syn_data,
+            Y=None,
+            metric=metric,
+            **kwargs,
+        )
         return syn_data, class_labels, dist
     else:
         return syn_data, class_labels
@@ -101,28 +104,34 @@ def generate_synthetic_data(n_samples: int = 100,
 # In[2]:
 
 
-coords, class_labels, arr_dist = generate_synthetic_data(n_samples=100,
-                                                         n_features=2,
-                                                         n_clusters=1,
-                                                         pairwise_dist=True,
-                                                         metric="euclidean",
-                                                         random_state=42)
+coords, class_labels, arr_dist = generate_synthetic_data(
+    n_samples=100,
+    n_features=2,
+    n_clusters=1,
+    pairwise_dist=True,
+    metric="euclidean",
+    random_state=42,
+)
+
+coords_cluster, class_labels_cluster, arr_dist_cluster = generate_synthetic_data(
+    n_samples=100,
+    n_features=2,
+    n_clusters=3,
+    pairwise_dist=True,
+    metric="euclidean",
+    random_state=42,
+)
+
 
-coords_cluster, class_labels_cluster, arr_dist_cluster = generate_synthetic_data(n_samples=100,
-                                                         n_features=2,
-                                                         n_clusters=3,
-                                                         pairwise_dist=True,
-                                                         metric="euclidean",
-                                                         random_state=42)
 def graph_data(coords, selected=None, reference=False):
     plt.figure(dpi=150)
     plt.scatter(coords[:, 0], coords[:, 1])
     if selected:
         for i, mol_id in enumerate(selected):
-            plt.scatter(coords[mol_id, 0], coords[mol_id, 1], c='r')
-            plt.text(coords[mol_id,0], coords[mol_id,1], str(i+1))
+            plt.scatter(coords[mol_id, 0], coords[mol_id, 1], c="r")
+            plt.text(coords[mol_id, 0], coords[mol_id, 1], str(i + 1))
     if reference:
-        plt.scatter(coords[0, 0], coords[0, 1], c='black')
+        plt.scatter(coords[0, 0], coords[0, 1], c="black")
     plt.show()
 
 
@@ -141,8 +150,6 @@ graph_data(coords_cluster)
 
 
 # MaxMin method
-from DiverseSelector.methods.partition import *
-from DiverseSelector.methods.dissimilarity import *
 
 # diverse subset selection from randomly generated data points
 selector = MaxMin()
@@ -156,8 +163,8 @@ selected_ids2 = selector.select(arr=arr_dist_cluster, labels=class_labels_cluste
 # In[9]:
 
 
-graph_data(coords,selected_ids1)
-graph_data(coords_cluster,selected_ids2)
+graph_data(coords, selected_ids1)
+graph_data(coords_cluster, selected_ids2)
 
 
 # ### Adapted Optimizable K-Dissimilarity Selection (OptiSim)
@@ -170,8 +177,8 @@ selected_id3 = OptiSim().select(coords, 12)
 # diverse subset selection from data points with obvious patterns (different clusters)
 selected_id4 = OptiSim().select(coords_cluster, size=12, labels=class_labels_cluster)
 
-graph_data(coords,selected_id3)
-graph_data(coords_cluster,selected_id4)
+graph_data(coords, selected_id3)
+graph_data(coords_cluster, selected_id4)
 
 
 # ### Directed Sphere Exclusion
@@ -182,10 +189,12 @@ graph_data(coords_cluster,selected_id4)
 # diverse subset selection from randomly generated data points
 selected_id5 = DirectedSphereExclusion().select(coords, 12)
 # diverse subset selection from data points with obvious patterns (different clusters)
-selected_id6 = DirectedSphereExclusion().select(coords_cluster, size=12, labels=class_labels_cluster)
+selected_id6 = DirectedSphereExclusion().select(
+    coords_cluster, size=12, labels=class_labels_cluster
+)
 
-graph_data(coords,selected_id5)
-graph_data(coords_cluster,selected_id6)
+graph_data(coords, selected_id5)
+graph_data(coords_cluster, selected_id6)
 
 
 # ### Grid Partitioning Method
@@ -196,12 +205,12 @@ graph_data(coords_cluster,selected_id6)
 # diverse subset selection from randomly generated data points
 selected_id7 = GridPartitioning(2, "equisized_independent").select(coords, 12)
 # diverse subset selection from data points with obvious patterns (different clusters)
-selected_id8 = GridPartitioning(2, "equisized_independent").select(coords_cluster, 
-                                                                   size=12, 
-                                                                   labels=class_labels_cluster)
+selected_id8 = GridPartitioning(2, "equisized_independent").select(
+    coords_cluster, size=12, labels=class_labels_cluster
+)
 
-graph_data(coords,selected_id7)
-graph_data(coords_cluster,selected_id8)
+graph_data(coords, selected_id7)
+graph_data(coords_cluster, selected_id8)
 # 20, 5, 3, "equisized_independent"
 
 
@@ -218,18 +227,14 @@ graph_data(coords_cluster, selected_ids)
 # In[12]:
 
 
-import numpy as np
-from sklearn.metrics import pairwise_distances
 np.random.seed(42)
-cluster_one = np.random.normal(0, 1, (3,2))
-cluster_two = np.random.normal(10, 1, (6,2))
-cluster_three = np.random.normal(20, 1, (7,2))
-labels_mocked = np.hstack([[0 for i in range(3)],
-                          [1 for i in range(6)],
-                          [2 for i in range(7)]])
+cluster_one = np.random.normal(0, 1, (3, 2))
+cluster_two = np.random.normal(10, 1, (6, 2))
+cluster_three = np.random.normal(20, 1, (7, 2))
+labels_mocked = np.hstack([[0 for i in range(3)], [1 for i in range(6)], [2 for i in range(7)]])
 
 mocked_cluster_coords = np.vstack([cluster_one, cluster_two, cluster_three])
-selector = MaxMin(lambda x: pairwise_distances(x, metric='euclidean'))
+selector = MaxMin(lambda x: pairwise_distances(x, metric="euclidean"))
 selected_mocked = selector.select(mocked_cluster_coords, size=15, labels=labels_mocked)
 
 graph_data(mocked_cluster_coords, selected_mocked)
@@ -242,10 +247,9 @@ selected_mocked
 # In[6]:
 
 
-selector = DissimilaritySelection(num_selected=12,
-                                  arr_dist=arr_dist,
-                                  random_seed=42,
-                                  method="maxsum")
+selector = DissimilaritySelection(
+    num_selected=12, arr_dist=arr_dist, random_seed=42, method="maxsum"
+)
 selector.starting_idx = 0
 selected_ids2 = selector.select()
 
@@ -261,11 +265,13 @@ graph_data(selected_ids2)
 # In[8]:
 
 
-selector = DissimilaritySelection(features=coords,
-                                  num_selected=12,
-                                  arr_dist=arr_dist,
-                                  grid_method="grid_partioning",
-                                  random_seed=42)
+selector = DissimilaritySelection(
+    features=coords,
+    num_selected=12,
+    arr_dist=arr_dist,
+    grid_method="grid_partioning",
+    random_seed=42,
+)
 selector.starting_idx = 0
 selected_ids3 = selector.select()
 
@@ -281,11 +287,13 @@ graph_data(selected_ids3)
 # In[10]:
 
 
-selector = DissimilaritySelection(num_selected=12,
-                                  features = coords,
-                                  random_seed=42,
-                                  dissim_func="grid_partitioning",
-                                  grid_method="equisized_dependent")
+selector = DissimilaritySelection(
+    num_selected=12,
+    features=coords,
+    random_seed=42,
+    dissim_func="grid_partitioning",
+    grid_method="equisized_dependent",
+)
 selector.starting_idx = 0
 selected_ids4 = selector.select()
 
@@ -301,10 +309,9 @@ graph_data(selected_ids4)
 # In[12]:
 
 
-selector = DissimilaritySelection(num_selected=12,
-                                  features=coords,
-                                  dissim_func="sphere_exclusion",
-                                  random_seed=42)
+selector = DissimilaritySelection(
+    num_selected=12, features=coords, dissim_func="sphere_exclusion", random_seed=42
+)
 selector.starting_idx = 0
 selected_ids5 = selector.select()
 
@@ -320,10 +327,9 @@ graph_data(selected_ids5, True)
 # In[14]:
 
 
-selector = DissimilaritySelection(num_selected=12,
-                                  features=coords,
-                                  dissim_func="optisim",
-                                  random_seed=42)
+selector = DissimilaritySelection(
+    num_selected=12, features=coords, dissim_func="optisim", random_seed=42
+)
 selector.starting_idx = 0
 selected_ids6 = selector.select()
 
@@ -332,4 +338,3 @@ selected_ids6 = selector.select()
 
 
 graph_data(selected_ids6)
-

book/content/_config.yml

@@ -20,7 +20,7 @@ sphinx:
   - 'sphinx.ext.autodoc'
   config:
     mathjax_path: https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js
-    
+
 
 #Read LaTeX
 parse:
@@ -46,7 +46,7 @@ bibtex_bibfiles:
 
 # Information about where the book exists on the web
 repository:
-  url: https://github.com/theochem/DiverseSelector  # Online location of your book
+  url: https://github.com/theochem/Selector  # Online location of your book
   path_to_book: book/content  # Optional path to your book, relative to the repository root
   branch: main  # Which branch of the repository should be used when creating links (optional)
 
@@ -55,11 +55,11 @@ repository:
 launch_buttons:
   thebe                  : true
   colab_url: "https://colab.research.google.com"
-  
+
 copyright: "2022-2023"
-  
+
 html:
   use_issues_button: true
   use_repository_button: true
   favicon: "selector_logo.png"
-  use_multitoc_numbering: false
+  use_multitoc_numbering: false

book/content/_toc.yml

@@ -13,4 +13,4 @@ parts:
     - file: base.rst
     - file: dissimilarity.rst
     - file: partition.rst
-    - file: utils.rst
+    - file: utils.rst

book/content/base.rst

@@ -1,4 +1,4 @@
 Base class
 =============
-.. automodule:: DiverseSelector.base
-    :members:
+.. automodule:: selector.base
+    :members:

book/content/dissimilarity.rst

@@ -1,4 +1,4 @@
 Dissimilarity based methods
 =============
-.. automodule:: DiverseSelector.dissimilarity
-    :members:
+.. automodule:: selector.dissimilarity
+    :members:

book/content/installation.ipynb

@@ -16,7 +16,7 @@
     "We are preparing a 1.0 release. Until then, these instructions for installing a stable release will not work yet. If you enjoy living on the edge, try the development release as explained in the “Latest Git Revision” section below.\n",
     "</div>\n",
     "\n",
-    "The following dependencies are required to run DiverseSelector properly,\n",
+    "The following dependencies are required to run selector properly,\n",
     "\n",
     "* Python >= 3.6: http://www.python.org/ \n",
     "* NumPy >= 1.21.5: http://www.numpy.org/\n",
@@ -29,7 +29,7 @@
     "\n",
     "## Installation with Anaconda or Miniconda:\n",
     "\n",
-    "1. To install DiverseSelector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:\n",
+    "1. To install selector using the conda package management system, install [miniconda](https://conda.io/miniconda.html) or [anaconda](https://www.anaconda.com/download) first, and then:\n",
     "\n",
     "```\n",
     "# Activate your main conda environment if it is not loaded in your .bashrc.\n",
@@ -98,20 +98,20 @@
     "\n",
     "## Latest git revision\n",
     "\n",
-    "This section shows how one can install the latest revision of `DiverseSelector` from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.\n",
+    "This section shows how one can install the latest revision of `selector` from the git repository. This kind of installation comes with some risks (sudden API changes, bugs, …) and so be prepared to accept them when using the following installation instructions.\n",
     "\n",
     "There are two installation methods:\n",
     "\n",
     "1. **Quick and dirty.** Of this method, there are four variants, depending on the correctness of your `PATH` variable and the presence of a virtual or conda environment. These different scenarios are explained in more detail in the previous section.\n",
     "```\n",
     "# with env, correct PATH\n",
-    "pip install git+https://github.com/theochem/DiverseSelector.git\n",
+    "pip install git+https://github.com/theochem/Selector.git\n",
     "# with env, broken PATH\n",
-    "python -m pip install git+https://github.com/theochem/DiverseSelector.git\n",
+    "python -m pip install git+https://github.com/theochem/Selector.git\n",
     "# without env, correct PATH\n",
-    "pip install git+https://github.com/theochem/DiverseSelector.git --user\n",
+    "pip install git+https://github.com/theochem/Selector.git --user\n",
     "# without env, broken PATH\n",
-    "python -m pip install git+https://github.com/theochem/DiverseSelector.git --user\n",
+    "python -m pip install git+https://github.com/theochem/Selector.git --user\n",
     "```\n",
     "\n",
     "2. **Slow and Smart.** In addition to the four variations in the quick and dirty method, the slow and smart can be used with `pip` or just with `setup.py`. You also have the options to use SSH or HTTPS protocols to clone the git repository. Pick whichever works best for you.\n",
@@ -119,9 +119,9 @@
     "# A) Clone git repo with https OR ssh:\n",
     "# The second one only works if you have ssh set up for Github\n",
     "#  A1) https\n",
-    "git clone https://github.com/theochem/DiverseSelector.git\n",
+    "git clone https://github.com/theochem/Selector.git\n",
     "#  A2) ssh\n",
-    "git clone [email protected]:theochem/DiverseSelector.git\n",
+    "git clone [email protected]:theochem/Selector.git\n",
     "# B) Optionally write the version string\n",
     "pip install roberto  # or any of the three other ways of running pip, see above.\n",
     "rob write-version\n",
@@ -150,7 +150,7 @@
     "# Install pytest in your conda env.\n",
     "conda install pytest pytest-xdist\n",
     "# Then run the tests.\n",
-    "pytest --pyargs diverseselector -n auto\n",
+    "pytest --pyargs selector -n auto\n",
     "```\n",
     "\n",
     "With Pip:\n",
@@ -159,13 +159,13 @@
     "pip install pytest pytest-xdist\n",
     "# .. and refresh the virtual environment.\n",
     "# This is a venv quirk. Without it, pytest may not find IOData.\n",
-    "deactivate && source ~/diverseselector/activate\n",
+    "deactivate && source ~/selector/activate\n",
     "\n",
     "# Alternatively, install pytest in your home directory.\n",
     "pip install pytest pytest-xdist --user\n",
     "\n",
     "# Finally, run the tests.\n",
-    "pytest --pyargs diverseselector -n auto\n",
+    "pytest --pyargs selector -n auto\n",
     "```"
    ]
   },

book/content/intro.md

@@ -1,11 +1,11 @@
 <!-- #region -->
 # Welcome to QC-Selector's Documentation!
 
-[DiverseSelector](https://github.com/theochem/DiverseSelector) is a free, open-source, and cross-platform Python library designed to help you effortlessly identify the most diverse subset of molecules from your dataset. Please use the following citation in any publication using DiverseSelector library:
+[selector](https://github.com/theochem/Selector) is a free, open-source, and cross-platform Python library designed to help you effortlessly identify the most diverse subset of molecules from your dataset. Please use the following citation in any publication using selector library:
 
 **"QC-Selector: A Generic Python Package for Subset Selection"**, Fanwang Meng, Alireza Tehrani, Valerii Chuiko, Abigail Broscius, Abdul, Hassan, Maximilian van Zyl, Marco Martínez González, Yang, Ramón Alain Miranda-Quintana, Paul W. Ayers, and Farnaz Heidar-Zadeh"
 
-The DiverseSelector source code is hosted on [GitHub](https://github.com/theochem/DiverseSelector) and is released under the [GNU General Public License v3.0](https://github.com/theochem/DiverseSelector/blob/main/LICENSE). We welcome any contributions to the DiverseSelector library in accordance with our Code of Conduct; please see our [Contributing Guidelines](https://qcdevs.org/guidelines/QCDevsCodeOfConduct/). Please report any issues you encounter while using DiverseSelector library on [GitHub Issues](https://github.com/theochem/DiverseSelector/issues). For further information and inquiries please contact us at [email protected].
+The selector source code is hosted on [GitHub](https://github.com/theochem/Selector) and is released under the [GNU General Public License v3.0](https://github.com/theochem/Selector/blob/main/LICENSE). We welcome any contributions to the selector library in accordance with our Code of Conduct; please see our [Contributing Guidelines](https://qcdevs.org/guidelines/QCDevsCodeOfConduct/). Please report any issues you encounter while using selector library on [GitHub Issues](https://github.com/theochem/Selector/issues). For further information and inquiries please contact us at [email protected].
 
 
 ## Why QC-Selector?

book/content/partition.rst

@@ -1,5 +1,5 @@
 Partition based methods
 =============
 
-.. automodule:: DiverseSelector.partition
-    :members:
+.. automodule:: selector.partition
+    :members:

book/content/references.bib

@@ -1,7 +1,7 @@
 ---
 ---
-@article{diverseselector,
-  title={DiverseSelector: A Novel Approach for Selecting Diverse Molecular Subsets},
+@article{selector,
+  title={selector: A Novel Approach for Selecting Diverse Molecular Subsets},
   author={QC-Devs},
   journal={Nature Chemistry},
   year={2023},