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Commit d3a33a2f authored by Bienchen's avatar Bienchen
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Update documentation

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# 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: 28b0c8014ab9635fcc7ca0d345e21e72
config: b9aa92d5a319ad1e85a69d45f2e2182e
tags: 645f666f9bcd5a90fca523b33c5a78b7
run_af2/doc/html/.doctrees/environment.pickle
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run_af2/doc/html/.doctrees/run_singularity.doctree
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......@@ -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 1.0.5 documentation</title>
<title>_shared &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">_shared</a></li>
</ul>
</div>
......@@ -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 v3.9)"><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 v3.10)"><code class="xref py py-class docutils literal notranslate"><span class="pre">argparse.ArgumentParser</span></code></a> object. Run the parser and return the
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 v3.9)"><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 v3.10)"><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 v3.9)"><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 v3.10)"><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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">_shared</a></li>
</ul>
</div>
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run_af2/doc/html/_static/documentation_options.js
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var DOCUMENTATION_OPTIONS = {
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BUILDER: 'html',
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run_af2/doc/html/genindex.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Index &#8212; af2@scicore/run_af2 1.0.5 documentation</title>
<title>Index &#8212; af2@scicore/run_af2 2.0.0 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>
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<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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Index</a></li>
</ul>
</div>
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run_af2/doc/html/index.html
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<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 1.0.5 documentation</title>
<title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 2.0.0 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 1.0 (release 1.0.5)
<p>You are reading the documentation for version 2.0 (release 2.0.0)
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" >
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>next</a> |</li>
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<li class="nav-item nav-item-0"><a href="#">af2@scicore/run_af2 2.0.0 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>
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<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 1.0.5 documentation</title>
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<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>
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<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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Python Module Index</a></li>
</ul>
</div>
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<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Search &#8212; af2@scicore/run_af2 1.0.5 documentation</title>
<title>Search &#8212; af2@scicore/run_af2 2.0.0 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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<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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Search</a></li>
</ul>
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......@@ -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 1.0.5 documentation</a> &#187;</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 2.0.0 documentation</a> &#187;</li>
<li class="nav-item nav-item-this"><a href="">Search</a></li>
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