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CHANGELOG.md
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......@@ -5,6 +5,14 @@ Changes in Release 3.2.0
* Turn `submit-af2` into Python script
Changes in Release 3.1.1
=================================================================================
* `run_af2` Python package:
* Adapt to new AF2 versioning scheme
* Fallback for picking up the Singularity image automatically
Changes in Release 3.1.0
=================================================================================
......
run_af2/doc/html/.buildinfo
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# Sphinx build info version 1
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config: 80029e49350607596e13800ac8a707b6
config: c4d4f094057515b594fb8499643853e2
tags: 645f666f9bcd5a90fca523b33c5a78b7
run_af2/doc/html/.doctrees/environment.pickle
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run_af2/doc/html/.doctrees/index.doctree
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run_af2/doc/html/_shared.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>_shared &#8212; af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
<title>_shared &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-this"><a href="">_shared</a></li>
</ul>
</div>
......@@ -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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-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 = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '3.0.1.dev0+g6a14f8a.d20220324',
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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 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
<title>Index &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-this"><a href="">Index</a></li>
</ul>
</div>
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run_af2/doc/html/index.html
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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>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
<title>Welcome to af2@scicore/run_af2’s documentation! &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-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 3.0 (release 3.0.1.dev0+g6a14f8a.d20220324)
<p>You are reading the documentation for version 3.1 (release 3.1.1.dev0+ge9ef748.d20220330)
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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-this"><a href="">Welcome to af2&#64;scicore/run_af2’s documentation!</a></li>
</ul>
</div>
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run_af2/doc/html/objects.inv
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run_af2/doc/html/py-modindex.html
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......@@ -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 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
<title>Python Module Index &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 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>
......@@ -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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-this"><a href="">Python Module Index</a></li>
</ul>
</div>
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run_af2/doc/html/run_singularity.html
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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>run_singularity &#8212; af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
<title>run_singularity &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 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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......@@ -29,7 +29,7 @@
<li class="right" >
<a href="_shared.html" title="_shared"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-this"><a href="">run_singularity</a></li>
</ul>
</div>
......@@ -191,7 +191,7 @@ in AF2.</p></li>
<li class="right" >
<a href="_shared.html" title="_shared"
>previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">af2@scicore/run_af2 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-this"><a href="">run_singularity</a></li>
</ul>
</div>
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run_af2/doc/html/search.html
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......@@ -5,7 +5,7 @@
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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 3.0.1.dev0+g6a14f8a.d20220324 documentation</title>
<title>Search &#8212; af2@scicore/run_af2 3.1.1.dev0+ge9ef748.d20220330 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 @@
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<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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-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 3.0.1.dev0+g6a14f8a.d20220324 documentation</a> &#187;</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-this"><a href="">Search</a></li>
</ul>
</div>
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run_af2/src/run_af2/run_singularity.py
+ 5
− 1
View file @ f88d7a71
......@@ -177,7 +177,9 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments
def _determine_af2_image(af2_image_dir):
"""Select an image from a given directory. File name of the images need to
be of form alphafold-<YYYY-MM-DD>.sif. The path to the latest image will be
returned, determined by the '<YYYY-MM-DD>' component of the file name."""
returned, determined by the '<YYYY-MM-DD>' component of the file name. If
the file name is of different form, an arbitrary file ending with '.sif'
will be used."""
lst_mtch = "0000-00-00"
af2_path = ""
af2_files = os.listdir(af2_image_dir)
......@@ -192,6 +194,8 @@ def _determine_af2_image(af2_image_dir):
if mtch.group(1) > lst_mtch:
af2_path = af2_file
lst_mtch = mtch.group(1)
elif af2_file.endswith(".sif"):
af2_path = af2_file
af2_path = os.path.join(af2_image_dir, af2_path)
return af2_path
......
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