Restructure docs #5 #8

dev/CB_test_modules.ipynb

@@ -2757,7 +2757,9 @@
    "execution_count": null,
    "metadata": {},
    "outputs": [],
-   "source": []
+   "source": [
+    "specimen.hqtb."
+   ]
   }
  ],
  "metadata": {

docs/build/html/_modules/index.html

@@ -51,8 +51,7 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../about-pipeline.html">About SPECIMEN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../run-pipeline.html">Run the Pipeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../overview-pipes.html">Overview of the Pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../specimen.html">Contents of SPECIMEN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../help.html">Help &amp; FAQ</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../dev-notes.html">Notes for Developers</a></li>
@@ -83,17 +82,18 @@
 
   <h1>All modules for which code is available</h1>
 <ul><li><a href="specimen/classes/reports.html">specimen.classes.reports</a></li>
-<li><a href="specimen/core/analysis.html">specimen.core.analysis</a></li>
-<li><a href="specimen/core/bidirectional_blast.html">specimen.core.bidirectional_blast</a></li>
-<li><a href="specimen/core/generate_draft_model.html">specimen.core.generate_draft_model</a></li>
-<li><a href="specimen/core/refinement/annotation.html">specimen.core.refinement.annotation</a></li>
-<li><a href="specimen/core/refinement/cleanup.html">specimen.core.refinement.cleanup</a></li>
-<li><a href="specimen/core/refinement/extension.html">specimen.core.refinement.extension</a></li>
-<li><a href="specimen/core/refinement/smoothing.html">specimen.core.refinement.smoothing</a></li>
-<li><a href="specimen/core/validation.html">specimen.core.validation</a></li>
+<li><a href="specimen/cmpb/workflow.html">specimen.cmpb.workflow</a></li>
+<li><a href="specimen/hqtb/core/analysis.html">specimen.hqtb.core.analysis</a></li>
+<li><a href="specimen/hqtb/core/bidirectional_blast.html">specimen.hqtb.core.bidirectional_blast</a></li>
+<li><a href="specimen/hqtb/core/generate_draft_model.html">specimen.hqtb.core.generate_draft_model</a></li>
+<li><a href="specimen/hqtb/core/refinement/annotation.html">specimen.hqtb.core.refinement.annotation</a></li>
+<li><a href="specimen/hqtb/core/refinement/cleanup.html">specimen.hqtb.core.refinement.cleanup</a></li>
+<li><a href="specimen/hqtb/core/refinement/extension.html">specimen.hqtb.core.refinement.extension</a></li>
+<li><a href="specimen/hqtb/core/refinement/smoothing.html">specimen.hqtb.core.refinement.smoothing</a></li>
+<li><a href="specimen/hqtb/core/validation.html">specimen.hqtb.core.validation</a></li>
+<li><a href="specimen/hqtb/workflow.html">specimen.hqtb.workflow</a></li>
 <li><a href="specimen/util/set_up.html">specimen.util.set_up</a></li>
 <li><a href="specimen/util/util.html">specimen.util.util</a></li>
-<li><a href="specimen/workflow.html">specimen.workflow</a></li>
 </ul>
 
            </div>

docs/build/html/_modules/specimen/classes/reports.html

@@ -51,8 +51,7 @@
               <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../about-pipeline.html">About SPECIMEN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../run-pipeline.html">Run the Pipeline</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../overview-pipes.html">Overview of the Pipelines</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../specimen.html">Contents of SPECIMEN</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../help.html">Help &amp; FAQ</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../dev-notes.html">Notes for Developers</a></li>

docs/build/html/_modules/specimen/core/analysis.html → docs/build/html/_modules/specimen/hqtb/core/analysis.html

@@ -1,31 +1,31 @@
 <!DOCTYPE html>
-<html class="writer-html5" lang="en" data-content_root="../../../">
+<html class="writer-html5" lang="en" data-content_root="../../../../">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>specimen.core.analysis &mdash; SPECIMEN 1.0.0 documentation</title>
-      <link rel="stylesheet" type="text/css" href="../../../_static/pygments.css?v=559046d4" />
-      <link rel="stylesheet" type="text/css" href="../../../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../../../_static/copybutton.css?v=76b2166b" />
-      <link rel="stylesheet" type="text/css" href="../../../_static/custom_theme.css?v=ef5873f9" />
+  <title>specimen.hqtb.core.analysis &mdash; SPECIMEN 1.0.0 documentation</title>
+      <link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=559046d4" />
+      <link rel="stylesheet" type="text/css" href="../../../../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../../../../_static/copybutton.css?v=76b2166b" />
+      <link rel="stylesheet" type="text/css" href="../../../../_static/custom_theme.css?v=ef5873f9" />
 
 
-    <link rel="shortcut icon" href="../../../_static/LogoSPECIMEN.png"/>
+    <link rel="shortcut icon" href="../../../../_static/LogoSPECIMEN.png"/>
   <!--[if lt IE 9]>
-    <script src="../../../_static/js/html5shiv.min.js"></script>
+    <script src="../../../../_static/js/html5shiv.min.js"></script>
   <![endif]-->
 
-        <script src="../../../_static/jquery.js?v=5d32c60e"></script>
-        <script src="../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../../../_static/documentation_options.js?v=8d563738"></script>
-        <script src="../../../_static/doctools.js?v=888ff710"></script>
-        <script src="../../../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../../../_static/clipboard.min.js?v=a7894cd8"></script>
-        <script src="../../../_static/copybutton.js?v=7859de39"></script>
+        <script src="../../../../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../../../../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../../../../_static/documentation_options.js?v=8d563738"></script>
+        <script src="../../../../_static/doctools.js?v=888ff710"></script>
+        <script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../../../../_static/clipboard.min.js?v=a7894cd8"></script>
+        <script src="../../../../_static/copybutton.js?v=7859de39"></script>
         <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.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" /> 
+    <script src="../../../../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../../../../genindex.html" />
+    <link rel="search" title="Search" href="../../../../search.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -36,12 +36,12 @@
 
 
 
-          <a href="../../../index.html">
+          <a href="../../../../index.html">
 
-              <img src="../../../_static/LogoSPECIMEN.png" class="logo" alt="Logo"/>
+              <img src="../../../../_static/LogoSPECIMEN.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
-  <form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
+  <form id="rtd-search-form" class="wy-form" action="../../../../search.html" method="get">
     <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
     <input type="hidden" name="check_keywords" value="yes" />
     <input type="hidden" name="area" value="default" />
@@ -50,12 +50,11 @@
         </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">Contents:</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../../../installation.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../about-pipeline.html">About SPECIMEN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../run-pipeline.html">Run the Pipeline</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../specimen.html">Contents of SPECIMEN</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../help.html">Help &amp; FAQ</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../../../dev-notes.html">Notes for Developers</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../installation.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../overview-pipes.html">Overview of the Pipelines</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../specimen.html">Contents of SPECIMEN</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../help.html">Help &amp; FAQ</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../../dev-notes.html">Notes for Developers</a></li>
 </ul>
 
         </div>
@@ -64,16 +63,16 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../../../index.html">SPECIMEN</a>
+          <a href="../../../../index.html">SPECIMEN</a>
       </nav>
 
       <div class="wy-nav-content">
         <div class="rst-content">
           <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="../../index.html">Module code</a></li>
-      <li class="breadcrumb-item active">specimen.core.analysis</li>
+      <li><a href="../../../../index.html" class="icon icon-home" aria-label="Home"></a></li>
+          <li class="breadcrumb-item"><a href="../../../index.html">Module code</a></li>
+      <li class="breadcrumb-item active">specimen.hqtb.core.analysis</li>
       <li class="wy-breadcrumbs-aside">
       </li>
   </ul>
@@ -82,7 +81,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <h1>Source code for specimen.core.analysis</h1><div class="highlight"><pre>
+  <h1>Source code for specimen.hqtb.core.analysis</h1><div class="highlight"><pre>
 <span></span><span class="sd">&quot;&quot;&quot;Analyse a model (part 5 of the workflow).</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
@@ -104,7 +103,7 @@ <h1>Source code for specimen.core.analysis</h1><div class="highlight"><pre>
 <span class="kn">from</span> <span class="nn">refinegems.curation.pathways</span> <span class="kn">import</span> <span class="n">kegg_pathway_analysis</span>
 <span class="kn">from</span> <span class="nn">refinegems.curation.biomass</span> <span class="kn">import</span> <span class="n">test_biomass_presence</span>
 
-<span class="kn">from</span> <span class="nn">..classes.reports</span> <span class="kn">import</span> <span class="n">SpecimenModelInfoReport</span>
+<span class="kn">from</span> <span class="nn">...classes.reports</span> <span class="kn">import</span> <span class="n">SpecimenModelInfoReport</span>
 
 <span class="c1">################################################################################</span>
 <span class="c1"># functions</span>
@@ -114,7 +113,7 @@ <h1>Source code for specimen.core.analysis</h1><div class="highlight"><pre>
 <span class="c1"># -------------</span>
 
 <div class="viewcode-block" id="run">
-<a class="viewcode-back" href="../../../modules/core.html#specimen.core.analysis.run">[docs]</a>
+<a class="viewcode-back" href="../../../../modules/core.html#specimen.hqtb.core.analysis.run">[docs]</a>
 <span class="k">def</span> <span class="nf">run</span><span class="p">(</span><span class="n">model_path</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> <span class="nb">dir</span><span class="p">:</span><span class="nb">str</span><span class="p">,</span> 
         <span class="n">media_path</span><span class="p">:</span><span class="nb">str</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">namespace</span><span class="p">:</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;BiGG&#39;</span><span class="p">]</span><span class="o">=</span><span class="s1">&#39;BiGG&#39;</span><span class="p">,</span>
         <span class="n">pc_model_path</span><span class="p">:</span><span class="nb">str</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">pc_based_on</span><span class="p">:</span><span class="n">Literal</span><span class="p">[</span><span class="s1">&#39;id&#39;</span><span class="p">]</span><span class="o">=</span><span class="s1">&#39;id&#39;</span><span class="p">,</span>