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datatractor · May 31, 2024 · 2e138ed · 2e138ed
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diff --git a/index.html b/index.html
diff --git a/main/.buildinfo b/main/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 27126caf861b581f5cca4ac102e36093
+config: ef1c6e478917fc3c6a0743e118ceb0c3
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/main/.doctrees/apidoc/beam.doctree b/main/.doctrees/apidoc/beam.doctree
diff --git a/main/.doctrees/environment.pickle b/main/.doctrees/environment.pickle
diff --git a/main/.doctrees/index.doctree b/main/.doctrees/index.doctree
diff --git a/main/_sources/index.rst.txt b/main/_sources/index.rst.txt
@@ -1,5 +1,5 @@
-Datatractor Beam
-================
+Datatractor Beam: Reference implementation of the Datatractor API
+=================================================================
 
 .. toctree::
    :maxdepth: 3
@@ -10,10 +10,11 @@ Datatractor Beam
    apidoc/beam
 
 
-Documentation of Datatractor Beam, the reference implementation of the Datatractor API,
-published at `Datatractor Yard <https://yard.datatractors.org/>`_.
+Documentation of |beamrepo|_, the reference implementation of the Datatractor API,
+available at |yardsite|_.
+
+Datatractor Beam contains :mod:`beam`, a draft Python 3.10 package, which can be used to:
 
-Datatractor :mod:`beam` is a draft Python 3.10 package, which can be used to:
 - query the registry of `Extractors <https://yard.datatractor.org/extractors/>`_ for extractors that support a given file type,
 - install those extractors in a fresh Python virtual environment environment via `pip`,
 - invoke the extractor either in Python or at the CLI, producing Python objects or files on disk.
@@ -60,17 +61,21 @@ Alternatively, if the ``preferred_mode="cli"`` argument is specified, the extrac
 In this case, the ``ret`` will be empty bytes, and the output of the extractor should appear in the ``output.nc`` file.
 
 
-.. |SchemaRepo| image:: https://badgen.net/static/datatractor/schema/?icon=github
+.. |schemarepo| image:: https://badgen.net/static/datatractor/schema/?icon=github
+
+.. _schemarepo: https://github.com/datatractor/schema/
+
+.. |yardrepo| image:: https://badgen.net/static/datatractor/yard/?icon=github
 
-.. _SchemaRepo: https://github.com/datatractor/schema/
+.. _yardrepo: https://github.com/datatractor/yard/
 
-.. |YardRepo| image:: https://badgen.net/static/datatractor/yard/?icon=github
+.. |yardsite| image:: https://badgen.net/static/%F0%9F%9A%9C%20datatractor/yard
 
-.. _YardRepo: https://github.com/datatractor/yard/
+.. _yardsite: https://yard.datatractor.org/
 
-.. |BeamRepo| image:: https://badgen.net/static/datatractor/beam/?icon=github
+.. |beamrepo| image:: https://badgen.net/static/datatractor/beam/?icon=github
 
-.. _BeamRepo: https://github.com/datatractor/beam/
+.. _beamrepo: https://github.com/datatractor/beam/
 
 .. |LinkML| replace:: :mod:`LinkML`
 

diff --git a/main/_static/custom_theme.css b/main/_static/custom_theme.css
@@ -0,0 +1,6 @@
+.wy-side-nav-search {
+    background: #01152F;
+}
+.wy-side-nav-search > div.version {
+    color: #CF000F;
+}
diff --git a/main/apidoc/beam.html b/main/apidoc/beam.html
@@ -4,10 +4,11 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>beam package &mdash; datatractor-beam main documentation</title>
+  <title>beam package &mdash; Datatractor Beam main documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom_theme.css" type="text/css" />
+    <link rel="shortcut icon" href="https://datatractor.github.io/schema/main/_images/166528759-32x32.png"/>
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -20,7 +21,7 @@
     <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="prev" title="Datatractor Beam" href="../index.html" /> 
+    <link rel="prev" title="Datatractor Beam: Reference implementation of the Datatractor API" href="../index.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -32,7 +33,8 @@
 
 
           <a href="../index.html" class="icon icon-home">
-            datatractor-beam
+            Datatractor Beam
+              <img src="https://avatars.githubusercontent.com/u/166528759" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 main
@@ -62,7 +64,7 @@
 
     <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">datatractor-beam</a>
+          <a href="../index.html">Datatractor Beam</a>
       </nav>
 
       <div class="wy-nav-content">
@@ -72,7 +74,7 @@
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">beam package</li>
       <li class="wy-breadcrumbs-aside">
-            <a href="../_sources/apidoc/beam.rst.txt" rel="nofollow"> View page source</a>
+              <a href="https://github.com/datatractor/beam/blob/main/docs/source/apidoc/beam.rst" class="fa fa-github"> Edit on GitHub</a>
       </li>
   </ul>
   <hr/>
@@ -85,10 +87,9 @@ <h1>beam package<a class="headerlink" href="#beam-package" title="Link to this h
 <section id="module-beam">
 <span id="module-contents"></span><h2>Module contents<a class="headerlink" href="#module-beam" title="Link to this heading"></a></h2>
 <p>This script is intended as an example usage and reference implementation of the
-API endpoints exposed on the <a class="reference external" href="https://yard.datatractor.org/">datatractor yard</a>.
-Currently, it can be used to:</p>
+API endpoints exposed on the <a class="reference external" href="https://yard.datatractor.org/"><img alt="yardsite" src="https://badgen.net/static/%F0%9F%9A%9C%20datatractor/yard" /></a>. Currently, it can be used to:</p>
 <ul class="simple">
-<li><p>query the registry of <a class="reference external" href="https://yard.datatractors.org/extractors/">Extractors</a> for
+<li><p>query the registry of <a class="reference external" href="https://yard.datatractor.org/extractors/">Extractors</a> for
 extractors that support a given file type,</p></li>
 <li><p>install those extractors in a fresh Python virtual environment environment via <cite>pip</cite>,</p></li>
 <li><p>invoke the extractor either in Python or at the CLI, producing Python objects or files
@@ -115,7 +116,7 @@ <h1>beam package<a class="headerlink" href="#beam-package" title="Link to this h
 <li><p><strong>extractor_definition</strong> (<span class="sphinx_autodoc_typehints-type"><code class="xref py py-data docutils literal notranslate"><span class="pre">Optional</span></code>[<code class="xref py py-class docutils literal notranslate"><span class="pre">dict</span></code>]</span>) – A dictionary containing the extractor definition to use instead
 of a registry lookup.</p></li>
 <li><p><strong>registry_base_url</strong> (<span class="sphinx_autodoc_typehints-type"><code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code></span>) – The base URL of the registry to use. Defaults to the
-datatractor yard.</p></li>
+<a class="reference external" href="https://yard.datatractor.org/"><img alt="yardsite" src="https://badgen.net/static/%F0%9F%9A%9C%20datatractor/yard" /></a>.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Return type<span class="colon">:</span></dt>
@@ -134,7 +135,7 @@ <h1>beam package<a class="headerlink" href="#beam-package" title="Link to this h
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="../index.html" class="btn btn-neutral float-left" title="Datatractor Beam" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="../index.html" class="btn btn-neutral float-left" title="Datatractor Beam: Reference implementation of the Datatractor API" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
     </div>
 
   <hr/>

diff --git a/main/apidoc/modules.html b/main/apidoc/modules.html
@@ -4,10 +4,11 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>beam &mdash; datatractor-beam main documentation</title>
+  <title>beam &mdash; Datatractor Beam main documentation</title>
       <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="../_static/custom_theme.css" type="text/css" />
+    <link rel="shortcut icon" href="https://datatractor.github.io/schema/main/_images/166528759-32x32.png"/>
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -31,7 +32,8 @@
 
 
           <a href="../index.html" class="icon icon-home">
-            datatractor-beam
+            Datatractor Beam
+              <img src="https://avatars.githubusercontent.com/u/166528759" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 main
@@ -55,7 +57,7 @@
 
     <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">datatractor-beam</a>
+          <a href="../index.html">Datatractor Beam</a>
       </nav>
 
       <div class="wy-nav-content">
@@ -65,7 +67,7 @@
       <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">beam</li>
       <li class="wy-breadcrumbs-aside">
-            <a href="../_sources/apidoc/modules.rst.txt" rel="nofollow"> View page source</a>
+              <a href="https://github.com/datatractor/beam/blob/main/docs/source/apidoc/modules.rst" class="fa fa-github"> Edit on GitHub</a>
       </li>
   </ul>
   <hr/>

diff --git a/main/genindex.html b/main/genindex.html
@@ -3,10 +3,11 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Index &mdash; datatractor-beam main documentation</title>
+  <title>Index &mdash; Datatractor Beam main documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/custom_theme.css" type="text/css" />
+    <link rel="shortcut icon" href="https://datatractor.github.io/schema/main/_images/166528759-32x32.png"/>
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -30,7 +31,8 @@
 
 
           <a href="index.html" class="icon icon-home">
-            datatractor-beam
+            Datatractor Beam
+              <img src="https://avatars.githubusercontent.com/u/166528759" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 main
@@ -54,7 +56,7 @@
 
     <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">datatractor-beam</a>
+          <a href="index.html">Datatractor Beam</a>
       </nav>
 
       <div class="wy-nav-content">
@@ -64,6 +66,7 @@
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
       <li class="breadcrumb-item active">Index</li>
       <li class="wy-breadcrumbs-aside">
+              <a href="https://github.com/datatractor/beam/blob/main/docs/source/genindex" class="fa fa-github"> Edit on GitHub</a>
       </li>
   </ul>
   <hr/>

diff --git a/main/index.html b/main/index.html
@@ -4,10 +4,11 @@
   <meta charset="utf-8" /><meta name="generator" content="Docutils 0.18.1: http://docutils.sourceforge.net/" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Datatractor Beam &mdash; datatractor-beam main documentation</title>
+  <title>Datatractor Beam: Reference implementation of the Datatractor API &mdash; Datatractor Beam main documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/custom_theme.css" type="text/css" />
+    <link rel="shortcut icon" href="https://datatractor.github.io/schema/main/_images/166528759-32x32.png"/>
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -32,7 +33,8 @@
 
 
           <a href="#" class="icon icon-home">
-            datatractor-beam
+            Datatractor Beam
+              <img src="https://avatars.githubusercontent.com/u/166528759" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 main
@@ -56,34 +58,36 @@
 
     <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="#">datatractor-beam</a>
+          <a href="#">Datatractor Beam</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="#" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active">Datatractor Beam</li>
+      <li class="breadcrumb-item active">Datatractor Beam: Reference implementation of the Datatractor API</li>
       <li class="wy-breadcrumbs-aside">
-            <a href="_sources/index.rst.txt" rel="nofollow"> View page source</a>
+              <a href="https://github.com/datatractor/beam/blob/main/docs/source/index.rst" class="fa fa-github"> Edit on GitHub</a>
       </li>
   </ul>
   <hr/>
 </div>
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <section id="datatractor-beam">
-<h1>Datatractor Beam<a class="headerlink" href="#datatractor-beam" title="Link to this heading"></a></h1>
+  <section id="datatractor-beam-reference-implementation-of-the-datatractor-api">
+<h1>Datatractor Beam: Reference implementation of the Datatractor API<a class="headerlink" href="#datatractor-beam-reference-implementation-of-the-datatractor-api" title="Link to this heading"></a></h1>
 <div class="toctree-wrapper compound">
 </div>
-<p>Documentation of Datatractor Beam, the reference implementation of the Datatractor API,
-published at <a class="reference external" href="https://yard.datatractors.org/">Datatractor Yard</a>.</p>
-<p>Datatractor <a class="reference internal" href="apidoc/beam.html#module-beam" title="beam"><code class="xref py py-mod docutils literal notranslate"><span class="pre">beam</span></code></a> is a draft Python 3.10 package, which can be used to:
-- query the registry of <a class="reference external" href="https://yard.datatractor.org/extractors/">Extractors</a> for extractors that support a given file type,
-- install those extractors in a fresh Python virtual environment environment via <cite>pip</cite>,
-- invoke the extractor either in Python or at the CLI, producing Python objects or files on disk.</p>
+<p>Documentation of <a class="reference external" href="https://github.com/datatractor/beam/"><img alt="beamrepo" src="https://badgen.net/static/datatractor/beam/?icon=github" /></a>, the reference implementation of the Datatractor API,
+available at <a class="reference external" href="https://yard.datatractor.org/"><img alt="yardsite" src="https://badgen.net/static/%F0%9F%9A%9C%20datatractor/yard" /></a>.</p>
+<p>Datatractor Beam contains <a class="reference internal" href="apidoc/beam.html#module-beam" title="beam"><code class="xref py py-mod docutils literal notranslate"><span class="pre">beam</span></code></a>, a draft Python 3.10 package, which can be used to:</p>
+<ul class="simple">
+<li><p>query the registry of <a class="reference external" href="https://yard.datatractor.org/extractors/">Extractors</a> for extractors that support a given file type,</p></li>
+<li><p>install those extractors in a fresh Python virtual environment environment via <cite>pip</cite>,</p></li>
+<li><p>invoke the extractor either in Python or at the CLI, producing Python objects or files on disk.</p></li>
+</ul>
 <section id="installation">
 <h2>Installation<a class="headerlink" href="#installation" title="Link to this heading"></a></h2>
 <div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>[email protected]:datatractor/beam.git

diff --git a/main/objects.inv b/main/objects.inv
diff --git a/main/py-modindex.html b/main/py-modindex.html
@@ -3,10 +3,11 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Python Module Index &mdash; datatractor-beam main documentation</title>
+  <title>Python Module Index &mdash; Datatractor Beam main documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/custom_theme.css" type="text/css" />
+    <link rel="shortcut icon" href="https://datatractor.github.io/schema/main/_images/166528759-32x32.png"/>
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
   <![endif]-->
@@ -37,7 +38,8 @@
 
 
           <a href="index.html" class="icon icon-home">
-            datatractor-beam
+            Datatractor Beam
+              <img src="https://avatars.githubusercontent.com/u/166528759" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 main
@@ -61,7 +63,7 @@
 
     <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">datatractor-beam</a>
+          <a href="index.html">Datatractor Beam</a>
       </nav>
 
       <div class="wy-nav-content">

diff --git a/main/search.html b/main/search.html
@@ -3,10 +3,11 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Search &mdash; datatractor-beam main documentation</title>
+  <title>Search &mdash; Datatractor Beam main documentation</title>
       <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
       <link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
       <link rel="stylesheet" href="_static/custom_theme.css" type="text/css" />
+    <link rel="shortcut icon" href="https://datatractor.github.io/schema/main/_images/166528759-32x32.png"/>
 
   <!--[if lt IE 9]>
     <script src="_static/js/html5shiv.min.js"></script>
@@ -33,7 +34,8 @@
 
 
           <a href="index.html" class="icon icon-home">
-            datatractor-beam
+            Datatractor Beam
+              <img src="https://avatars.githubusercontent.com/u/166528759" class="logo" alt="Logo"/>
           </a>
               <div class="version">
                 main
@@ -57,7 +59,7 @@
 
     <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">datatractor-beam</a>
+          <a href="index.html">Datatractor Beam</a>
       </nav>
 
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