Remove path in usage principles

breimanntools · Sep 20, 2023 · d8db338 · d8db338
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diff --git a/docs/build/doctrees/environment.pickle b/docs/build/doctrees/environment.pickle
diff --git a/docs/build/doctrees/usage_principles.doctree b/docs/build/doctrees/usage_principles.doctree
diff --git a/docs/build/html/_images/social_previews/summary_usage_principles_25466335.png b/docs/build/html/_images/social_previews/summary_usage_principles_25466335.png
diff --git a/docs/build/html/_images/social_previews/summary_usage_principles_94300a05.png b/docs/build/html/_images/social_previews/summary_usage_principles_94300a05.png
diff --git a/docs/build/html/_sources/usage_principles.rst.txt b/docs/build/html/_sources/usage_principles.rst.txt
@@ -15,8 +15,4 @@ Import AAanalysis as:
 .. toctree::
    :maxdepth: 1
 
-   index/usage_principles/data_flow_entry_points
-   index/usage_principles/aaontology
-   index/usage_principles/feature_identification
-   index/usage_principles/pu_learning
-   index/usage_principles/xai
+
diff --git a/docs/build/html/index/CONTRIBUTING_COPY.html b/docs/build/html/index/CONTRIBUTING_COPY.html
@@ -41,7 +41,7 @@
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
     <link rel="next" title="Tutorials" href="../tutorials.html" />
-    <link rel="prev" title="Explainable AI at Sequence Level" href="usage_principles/xai.html" /> 
+    <link rel="prev" title="Usage Principles" href="../usage_principles.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -365,7 +365,7 @@ <h3>Building the Docs<a class="headerlink" href="#building-the-docs" title="Perm
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="usage_principles/xai.html" class="btn btn-neutral float-left" title="Explainable AI at Sequence Level" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="../usage_principles.html" class="btn btn-neutral float-left" title="Usage Principles" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="../tutorials.html" class="btn btn-neutral float-right" title="Tutorials" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

diff --git a/docs/build/html/index/usage_principles/aaontology.html b/docs/build/html/index/usage_principles/aaontology.html
@@ -39,9 +39,7 @@
         <script src="../../_static/design-tabs.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Identifying Physicochemical Signatures using CPP" href="feature_identification.html" />
-    <link rel="prev" title="Data Flow and Enry Points" href="data_flow_entry_points.html" /> 
+    <link rel="search" title="Search" href="../../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -68,16 +66,9 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">OVERVIEW</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="data_flow_entry_points.html">Data Flow and Enry Points</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">AAontology: Classification of amino acid scales</a></li>
-<li class="toctree-l2"><a class="reference internal" href="feature_identification.html">Identifying Physicochemical Signatures using CPP</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pu_learning.html">Learning from unbalanced and small data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="xai.html">Explainable AI at Sequence Level</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../CONTRIBUTING_COPY.html">Contributing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">EXAMPLES</span></p>
@@ -107,7 +98,6 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../../usage_principles.html">Usage Principles</a></li>
       <li class="breadcrumb-item active">AAontology: Classification of amino acid scales</li>
       <li class="wy-breadcrumbs-aside">
               <a href="https://github.com/breimanntools/aaanalysis/blob/master/index/usage_principles/aaontology.rst" class="fa fa-github"> Edit on GitHub</a>
@@ -126,10 +116,7 @@ <h1>AAontology: Classification of amino acid scales<a class="headerlink" href="#
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="data_flow_entry_points.html" class="btn btn-neutral float-left" title="Data Flow and Enry Points" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="feature_identification.html" class="btn btn-neutral float-right" title="Identifying Physicochemical Signatures using CPP" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
 
   <hr/>
 

diff --git a/docs/build/html/index/usage_principles/data_flow_entry_points.html b/docs/build/html/index/usage_principles/data_flow_entry_points.html
@@ -39,9 +39,7 @@
         <script src="../../_static/design-tabs.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="AAontology: Classification of amino acid scales" href="aaontology.html" />
-    <link rel="prev" title="Usage Principles" href="../../usage_principles.html" /> 
+    <link rel="search" title="Search" href="../../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -68,16 +66,9 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">OVERVIEW</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a><ul class="current">
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Data Flow and Enry Points</a></li>
-<li class="toctree-l2"><a class="reference internal" href="aaontology.html">AAontology: Classification of amino acid scales</a></li>
-<li class="toctree-l2"><a class="reference internal" href="feature_identification.html">Identifying Physicochemical Signatures using CPP</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pu_learning.html">Learning from unbalanced and small data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="xai.html">Explainable AI at Sequence Level</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../CONTRIBUTING_COPY.html">Contributing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">EXAMPLES</span></p>
@@ -107,7 +98,6 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../../usage_principles.html">Usage Principles</a></li>
       <li class="breadcrumb-item active">Data Flow and Enry Points</li>
       <li class="wy-breadcrumbs-aside">
               <a href="https://github.com/breimanntools/aaanalysis/blob/master/index/usage_principles/data_flow_entry_points.rst" class="fa fa-github"> Edit on GitHub</a>
@@ -129,10 +119,7 @@ <h1>Data Flow and Enry Points<a class="headerlink" href="#data-flow-and-enry-poi
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="../../usage_principles.html" class="btn btn-neutral float-left" title="Usage Principles" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="aaontology.html" class="btn btn-neutral float-right" title="AAontology: Classification of amino acid scales" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
 
   <hr/>
 

diff --git a/docs/build/html/index/usage_principles/feature_identification.html b/docs/build/html/index/usage_principles/feature_identification.html
@@ -39,9 +39,7 @@
         <script src="../../_static/design-tabs.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Learning from unbalanced and small data" href="pu_learning.html" />
-    <link rel="prev" title="AAontology: Classification of amino acid scales" href="aaontology.html" /> 
+    <link rel="search" title="Search" href="../../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -68,16 +66,9 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">OVERVIEW</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="data_flow_entry_points.html">Data Flow and Enry Points</a></li>
-<li class="toctree-l2"><a class="reference internal" href="aaontology.html">AAontology: Classification of amino acid scales</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Identifying Physicochemical Signatures using CPP</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pu_learning.html">Learning from unbalanced and small data</a></li>
-<li class="toctree-l2"><a class="reference internal" href="xai.html">Explainable AI at Sequence Level</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../CONTRIBUTING_COPY.html">Contributing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">EXAMPLES</span></p>
@@ -107,7 +98,6 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../../usage_principles.html">Usage Principles</a></li>
       <li class="breadcrumb-item active">Identifying Physicochemical Signatures using CPP</li>
       <li class="wy-breadcrumbs-aside">
               <a href="https://github.com/breimanntools/aaanalysis/blob/master/index/usage_principles/feature_identification.rst" class="fa fa-github"> Edit on GitHub</a>
@@ -127,10 +117,7 @@ <h1>Identifying Physicochemical Signatures using CPP<a class="headerlink" href="
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="aaontology.html" class="btn btn-neutral float-left" title="AAontology: Classification of amino acid scales" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="pu_learning.html" class="btn btn-neutral float-right" title="Learning from unbalanced and small data" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
 
   <hr/>
 

diff --git a/docs/build/html/index/usage_principles/pu_learning.html b/docs/build/html/index/usage_principles/pu_learning.html
@@ -39,9 +39,7 @@
         <script src="../../_static/design-tabs.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Explainable AI at Sequence Level" href="xai.html" />
-    <link rel="prev" title="Identifying Physicochemical Signatures using CPP" href="feature_identification.html" /> 
+    <link rel="search" title="Search" href="../../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -68,19 +66,9 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">OVERVIEW</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="data_flow_entry_points.html">Data Flow and Enry Points</a></li>
-<li class="toctree-l2"><a class="reference internal" href="aaontology.html">AAontology: Classification of amino acid scales</a></li>
-<li class="toctree-l2"><a class="reference internal" href="feature_identification.html">Identifying Physicochemical Signatures using CPP</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Learning from unbalanced and small data</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#what-is-pu-learning">What is PU learning?</a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="xai.html">Explainable AI at Sequence Level</a></li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../CONTRIBUTING_COPY.html">Contributing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">EXAMPLES</span></p>
@@ -110,7 +98,6 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../../usage_principles.html">Usage Principles</a></li>
       <li class="breadcrumb-item active">Learning from unbalanced and small data</li>
       <li class="wy-breadcrumbs-aside">
               <a href="https://github.com/breimanntools/aaanalysis/blob/master/index/usage_principles/pu_learning.rst" class="fa fa-github"> Edit on GitHub</a>
@@ -141,10 +128,7 @@ <h2>What is PU learning?<a class="headerlink" href="#what-is-pu-learning" title=
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="feature_identification.html" class="btn btn-neutral float-left" title="Identifying Physicochemical Signatures using CPP" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="xai.html" class="btn btn-neutral float-right" title="Explainable AI at Sequence Level" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
 
   <hr/>
 

diff --git a/docs/build/html/index/usage_principles/xai.html b/docs/build/html/index/usage_principles/xai.html
@@ -39,9 +39,7 @@
         <script src="../../_static/design-tabs.js"></script>
     <script src="../../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../../genindex.html" />
-    <link rel="search" title="Search" href="../../search.html" />
-    <link rel="next" title="Contributing" href="../CONTRIBUTING_COPY.html" />
-    <link rel="prev" title="Learning from unbalanced and small data" href="pu_learning.html" /> 
+    <link rel="search" title="Search" href="../../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -68,19 +66,9 @@
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption" role="heading"><span class="caption-text">OVERVIEW</span></p>
-<ul class="current">
+<ul>
 <li class="toctree-l1"><a class="reference internal" href="../introduction.html">Introduction</a></li>
-<li class="toctree-l1 current"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="data_flow_entry_points.html">Data Flow and Enry Points</a></li>
-<li class="toctree-l2"><a class="reference internal" href="aaontology.html">AAontology: Classification of amino acid scales</a></li>
-<li class="toctree-l2"><a class="reference internal" href="feature_identification.html">Identifying Physicochemical Signatures using CPP</a></li>
-<li class="toctree-l2"><a class="reference internal" href="pu_learning.html">Learning from unbalanced and small data</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">Explainable AI at Sequence Level</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#what-is-explainable-ai">What is explainable AI?</a></li>
-</ul>
-</li>
-</ul>
-</li>
+<li class="toctree-l1"><a class="reference internal" href="../../usage_principles.html">Usage Principles</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../CONTRIBUTING_COPY.html">Contributing</a></li>
 </ul>
 <p class="caption" role="heading"><span class="caption-text">EXAMPLES</span></p>
@@ -110,7 +98,6 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="../../index.html" class="icon icon-home" aria-label="Home"></a></li>
-          <li class="breadcrumb-item"><a href="../../usage_principles.html">Usage Principles</a></li>
       <li class="breadcrumb-item active">Explainable AI at Sequence Level</li>
       <li class="wy-breadcrumbs-aside">
               <a href="https://github.com/breimanntools/aaanalysis/blob/master/index/usage_principles/xai.rst" class="fa fa-github"> Edit on GitHub</a>
@@ -132,10 +119,7 @@ <h2>What is explainable AI?<a class="headerlink" href="#what-is-explainable-ai"
 
            </div>
           </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="pu_learning.html" class="btn btn-neutral float-left" title="Learning from unbalanced and small data" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="../CONTRIBUTING_COPY.html" class="btn btn-neutral float-right" title="Contributing" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
-    </div>
+          <footer>
 
   <hr/>
 

diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js