Updated documentation

9e35f56c · Bienchen · d00e723d · 9e35f56c · 9e35f56c · 9e35f56c
Commit 9e35f56c authored 2 years ago by Bienchen
--- a/run_af2/doc/html/.buildinfo
+++ b/run_af2/doc/html/.buildinfo
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 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
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+config: 6325d903612a71b0cf84ff2096c98a7c
 tags: 645f666f9bcd5a90fca523b33c5a78b7
--- a/run_af2/doc/html/.doctrees/environment.pickle
+++ b/run_af2/doc/html/.doctrees/environment.pickle
--- a/run_af2/doc/html/.doctrees/index.doctree
+++ b/run_af2/doc/html/.doctrees/index.doctree
--- a/run_af2/doc/html/.doctrees/run_singularity.doctree
+++ b/run_af2/doc/html/.doctrees/run_singularity.doctree
--- a/run_af2/doc/html/_shared.html
+++ b/run_af2/doc/html/_shared.html
@@ -6,7 +6,7 @@
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />

-    <title>_shared &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>_shared &#8212; af2@scicore/run_af2 0.0.0 documentation</title>
    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
    <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -33,7 +33,7 @@
        <li class="right" >
          <a href="index.html" title="Welcome to af2@scicore/run_af2’s documentation!"
             accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">_shared</a></li> 
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@@ -67,12 +67,12 @@ creates the version file.</p>
 <span class="sig-prename descclassname"><span class="pre">run_af2._shared.</span></span><span class="sig-name descname"><span class="pre">parse_af2_arguments</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">parser</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#run_af2._shared.parse_af2_arguments" title="Permalink to this definition">¶</a></dt>
 <dd><p>AF2 pipeline arguments parsing capabilities.</p>
 <p>Add arguments common for running the AF2 pipeline to an existing
-<a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a> object. Run the parser and return the
+<a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.ArgumentParser" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a> object. Run the parser and return the
 result. That way tools can implement their own description for the parser
-and run tests on input with the <a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object.</p>
+and run tests on input with the <a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Returns</dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object from
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/argparse.html#argparse.Namespace" title="(in Python v3.11)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.Namespace</span></code></a> object from
 <cite>argparse.ArgumentParser.parse_args</cite>.</p>
 </dd>
 </dl>
@@ -129,7 +129,7 @@ and run tests on input with the <a class="reference external" href="https://docs
        <li class="right" >
          <a href="index.html" title="Welcome to af2@scicore/run_af2’s documentation!"
             >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">_shared</a></li> 
      </ul>
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--- a/run_af2/doc/html/_static/documentation_options.js
+++ b/run_af2/doc/html/_static/documentation_options.js
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    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '3.1.1.dev0+ge9ef748.d20220330',
+    VERSION: '0.0.0',
    LANGUAGE: 'None',
    COLLAPSE_INDEX: false,
    BUILDER: 'html',

--- a/run_af2/doc/html/genindex.html
+++ b/run_af2/doc/html/genindex.html
@@ -5,7 +5,7 @@
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Index &#8212; af2@scicore/run_af2 0.0.0 documentation</title>
    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
    <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -24,7 +24,7 @@
        <li class="right" >
          <a href="py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Index</a></li> 
      </ul>
    </div>  
@@ -132,7 +132,7 @@
        <li class="right" >
          <a href="py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Index</a></li> 
      </ul>
    </div>

--- a/run_af2/doc/html/index.html
+++ b/run_af2/doc/html/index.html
@@ -6,7 +6,7 @@
    <meta charset="utf-8" />
    <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 af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 0.0.0 documentation</title>
    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
    <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
    <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
@@ -29,7 +29,7 @@
        <li class="right" >
          <a href="_shared.html" title="_shared"
             accesskey="N">next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Welcome to af2&#64;scicore/run_af2’s documentation!</a></li> 
      </ul>
    </div>  
@@ -41,7 +41,7 @@
            
  <section id="welcome-to-af2-scicore-run-af2-s-documentation">
 <h1>Welcome to af2&#64;scicore/run_af2’s documentation!<a class="headerlink" href="#welcome-to-af2-scicore-run-af2-s-documentation" title="Permalink to this headline">¶</a></h1>
-<p>You are reading the documentation for version 3.1 (release 3.1.1.dev0+ge9ef748.d20220330)
+<p>You are reading the documentation for version 0.0 (release 0.0.0)
 of <strong>run_af2</strong>.</p>
 <p><strong>run_af2</strong> is a Python package to run the <a class="reference external" href="https://github.com/deepmind/alphafold">AlphaFold 2 (AF2) pipeline</a> on the sciCORE cluster.</p>
 <p>The package comes with two major parts: userland commands to just execute the
@@ -114,7 +114,7 @@ Python modules is here:</p>
        <li class="right" >
          <a href="_shared.html" title="_shared"
             >next</a> |</li>
-        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Welcome to af2&#64;scicore/run_af2’s documentation!</a></li> 
      </ul>
    </div>

--- a/run_af2/doc/html/objects.inv
+++ b/run_af2/doc/html/objects.inv
--- a/run_af2/doc/html/py-modindex.html
+++ b/run_af2/doc/html/py-modindex.html
@@ -5,7 +5,7 @@
  <head>
    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Python Module Index &#8212; af2@scicore/run_af2 0.0.0 documentation</title>
    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
    <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
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@@ -27,7 +27,7 @@
        <li class="right" >
          <a href="#" title="Python Module Index"
             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Python Module Index</a></li> 
      </ul>
    </div>  
@@ -96,7 +96,7 @@
        <li class="right" >
          <a href="#" title="Python Module Index"
             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Python Module Index</a></li> 
      </ul>
    </div>

--- a/run_af2/doc/html/run_singularity.html
+++ b/run_af2/doc/html/run_singularity.html
--- a/run_af2/doc/html/search.html
+++ b/run_af2/doc/html/search.html
@@ -5,7 +5,7 @@
  <head>
    <meta charset="utf-8" />
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-    <title>Search &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</title>
+    <title>Search &#8212; af2@scicore/run_af2 0.0.0 documentation</title>
    <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
    <link rel="stylesheet" type="text/css" href="_static/sphinxdoc.css" />
    
@@ -30,7 +30,7 @@
        <li class="right" >
          <a href="py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Search</a></li> 
      </ul>
    </div>  
@@ -89,7 +89,7 @@
        <li class="right" >
          <a href="py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 0.0.0 documentation</a> &#187;</li>
        <li class="nav-item nav-item-this"><a href="">Search</a></li> 
      </ul>
    </div>

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