diff --git a/doc/html/_modules/index.html b/doc/html/_modules/index.html
index cb7a1cc662e84d8c42c40c6eab7c48ae2d45ef31..71f48a347297969fa05bf47a58c120918316f7a2 100644
--- a/doc/html/_modules/index.html
+++ b/doc/html/_modules/index.html
@@ -50,8 +50,7 @@
<h1>All modules for which code is available</h1>
<ul><li><a href="promod3.html">promod3</a></li>
-<ul><li><a href="promod3/core/argcheck.html">promod3.core.argcheck</a></li>
-<li><a href="promod3/core/helper.html">promod3.core.helper</a></li>
+<ul><li><a href="promod3/core/helper.html">promod3.core.helper</a></li>
<li><a href="promod3/core/pm3argparse.html">promod3.core.pm3argparse</a></li>
<li><a href="promod3/rawmodel/_rawmodel.html">promod3.rawmodel._rawmodel</a></li>
</ul><li><a href="test_actions.html">test_actions</a></li>
diff --git a/doc/html/_modules/promod3/core/argcheck.html b/doc/html/_modules/promod3/core/argcheck.html
deleted file mode 100644
index 4d6313888272f91b1479c554c237eafd7f80d4c5..0000000000000000000000000000000000000000
--- a/doc/html/_modules/promod3/core/argcheck.html
+++ /dev/null
@@ -1,199 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
- "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-
-
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
- <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-
- <title>promod3.core.argcheck — ProMod3 0 documentation</title>
-
- <link rel="stylesheet" href="../../../_static/alabaster.css" type="text/css" />
- <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../../../',
- VERSION: '0',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true
- };
- </script>
- <script type="text/javascript" src="../../../_static/jquery.js"></script>
- <script type="text/javascript" src="../../../_static/underscore.js"></script>
- <script type="text/javascript" src="../../../_static/doctools.js"></script>
- <link rel="top" title="ProMod3 0 documentation" href="../../../index.html" />
- <link rel="up" title="promod3" href="../../promod3.html" />
-
-
- <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
-
- </head>
- <body role="document">
- <div class="related" role="navigation" aria-label="related navigation">
- <h3>Navigation</h3>
- <ul>
- <li class="right" style="margin-right: 10px">
- <a href="../../../genindex.html" title="General Index"
- accesskey="I">index</a></li>
- <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">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../../index.html" >Module code</a> »</li>
- <li class="nav-item nav-item-2"><a href="../../promod3.html" accesskey="U">promod3</a> »</li>
- </ul>
- </div>
-
- <div class="document">
- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body" role="main">
-
- <h1>Source code for promod3.core.argcheck</h1><div class="highlight"><pre>
-<span class="sd">"""</span>
-<span class="sd">Basic helpers for arguments.</span>
-<span class="sd">"""</span>
-
-<span class="kn">import</span> <span class="nn">os</span><span class="o">,</span> <span class="nn">sys</span>
-<span class="kn">import</span> <span class="nn">ost</span>
-<span class="kn">import</span> <span class="nn">helper</span>
-
-<div class="viewcode-block" id="FileExists"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExists">[docs]</a><span class="k">def</span> <span class="nf">FileExists</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="nb">file</span><span class="p">):</span>
- <span class="sd">'''</span>
-<span class="sd"> Checks if a file exists, terminates if not. The error message displayed is</span>
-<span class="sd"> fixed and only needs a *prefix* describing the specimen of file.</span>
-
-<span class="sd"> :param prefix: String to put in front of the failure-message</span>
-<span class="sd"> "file does not exist: ``file``".</span>
-<span class="sd"> :type prefix: :class:`str`</span>
-
-<span class="sd"> :param exit_status: Exit code on missing file, ends up in ``$?`` in the</span>
-<span class="sd"> shell. ``0`` is traditionally reserved to successful commands.</span>
-<span class="sd"> :type exit_status: :class:`int`</span>
-
-<span class="sd"> :param file: Path including file name to be checked.</span>
-<span class="sd"> :type file: :class:`str`</span>
-
-<span class="sd"> :returns: No return value, exits script with value ``exit_status`` if file is</span>
-<span class="sd"> missing.</span>
-<span class="sd"> '''</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="nb">file</span><span class="p">):</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="nb">file</span><span class="p">),</span>
- <span class="n">exit_status</span><span class="p">)</span>
-</div>
-<div class="viewcode-block" id="FileExtension"><a class="viewcode-back" href="../../../core/argcheck.html#promod3.core.argcheck.FileExtension">[docs]</a><span class="k">def</span> <span class="nf">FileExtension</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="nb">file</span><span class="p">,</span> <span class="n">extensions</span><span class="p">,</span> <span class="n">gz</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
- <span class="sd">'''</span>
-<span class="sd"> Checks a file to carry a known extension given by a list of strings. Since</span>
-<span class="sd"> files are very often compressed these days, an additional "gz" suffix can be</span>
-<span class="sd"> tracked automatically by this function. Thus, the list of *extensions* only</span>
-<span class="sd"> needs to contain what you are really looking for, e.g. ("pdb") instead of</span>
-<span class="sd"> ("pdb", "pdb.gz"). The *gz* flag also determines the output of this function.</span>
-<span class="sd"> If enabled, a triple is returned: name of the file without extension, its</span>
-<span class="sd"> extension and a Boolean to tell whether the file carries the gzip extension</span>
-<span class="sd"> or not. If *gz* detection is turned of, only a tuple is returned: file name</span>
-<span class="sd"> and extension. If the tested file name has an unrecognised extension, this</span>
-<span class="sd"> function terminates the script.</span>
-
-<span class="sd"> :param prefix: String to put in front of the failure-message</span>
-<span class="sd"> "file extension not supported: ``file``".</span>
-<span class="sd"> :type prefix: :class:`str`</span>
-
-<span class="sd"> :param exit_status: Exit code on missing file, ends up in ``$?`` in the</span>
-<span class="sd"> shell. ``0`` is traditionally reserved to successful commands.</span>
-<span class="sd"> :type exit_status: :class:`int`</span>
-
-<span class="sd"> :param file: Path including file name to be checked.</span>
-<span class="sd"> :type file: :class:`str`</span>
-
-<span class="sd"> :param extensions: List of strings without a leading ".".</span>
-<span class="sd"> :type extensions: :class:`list`</span>
-
-<span class="sd"> :param gz: Indicates whether to check for an additional "gz" extension.</span>
-<span class="sd"> :type gz: :class:`bool`</span>
-
-<span class="sd"> :returns: (base name of ``file`` (:class:`str`), extension of file without a</span>
-<span class="sd"> ".gz" (:class:`str`), flag to indicate an additional ".gz"</span>
-<span class="sd"> (:class:`bool`)) **if** ``gz`` is set, (base name of ``file``</span>
-<span class="sd"> (:class:`str`), extension of file) **if not**.</span>
-<span class="sd"> '''</span>
- <span class="n">filename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="nb">file</span><span class="p">)</span>
- <span class="n">is_gz</span> <span class="o">=</span> <span class="bp">False</span>
- <span class="k">if</span> <span class="n">fileext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'.gz'</span><span class="p">:</span>
- <span class="n">is_gz</span> <span class="o">=</span> <span class="bp">True</span>
- <span class="n">filename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
- <span class="k">if</span> <span class="ow">not</span> <span class="n">gz</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
- <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
- <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
- <span class="n">exit_status</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="s">''</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
- <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
- <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
- <span class="n">exit_status</span><span class="p">)</span>
- <span class="n">fileext</span> <span class="o">=</span> <span class="n">fileext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
- <span class="k">for</span> <span class="n">ext</span> <span class="ow">in</span> <span class="n">extensions</span><span class="p">:</span>
- <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="n">ext</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span>
- <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
- <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">),</span> <span class="n">fileext</span><span class="p">,</span> <span class="n">is_gz</span>
- <span class="k">else</span><span class="p">:</span>
- <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">filename</span><span class="p">),</span> <span class="n">fileext</span>
- <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">gz</span><span class="p">:</span>
- <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
- <span class="n">helper</span><span class="o">.</span><span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
- <span class="nb">file</span><span class="p">)</span><span class="o">+</span>
- <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
- <span class="n">exit_status</span><span class="p">)</span>
-</div>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span>
- <span class="s">'FileExists'</span><span class="p">,</span>
- <span class="s">'FileExtension'</span><span class="p">,</span>
-<span class="p">)</span>
-
-<span class="c"># LocalWords: gz pdb gzip bool os sys FileExists FileExtension filename</span>
-<span class="c"># LocalWords: fileext</span>
-</pre></div>
-
- </div>
- </div>
- </div>
- <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
- <div class="sphinxsidebarwrapper">
-<div id="searchbox" style="display: none" role="search">
- <h3>Quick search</h3>
- <form class="search" action="../../../search.html" method="get">
- <input type="text" name="q" />
- <input type="submit" value="Go" />
- <input type="hidden" name="check_keywords" value="yes" />
- <input type="hidden" name="area" value="default" />
- </form>
- <p class="searchtip" style="font-size: 90%">
- Enter search terms or a module, class or function name.
- </p>
-</div>
-<script type="text/javascript">$('#searchbox').show(0);</script>
- </div>
- </div>
- <div class="clearer"></div>
- </div>
- <div class="footer">
- ©2015, Bienchen.
-
- |
- Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
- & <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
-
- </div>
-
-
-
-
- </body>
-</html>
\ No newline at end of file
diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html
index 0773acfb304c2d227ddcca15b6ca218163c410ee..8f7745b6246a8a308ff9440f4ce982cdb5ec7184 100644
--- a/doc/html/_modules/promod3/core/helper.html
+++ b/doc/html/_modules/promod3/core/helper.html
@@ -56,28 +56,123 @@
<span class="sd">Uncategorised functions which may come handy at several places.</span>
<span class="sd">"""</span>
+<span class="kn">import</span> <span class="nn">os</span>
<span class="kn">import</span> <span class="nn">sys</span>
<span class="kn">import</span> <span class="nn">ost</span>
<div class="viewcode-block" id="MsgErrorAndExit"><a class="viewcode-back" href="../../../core/helper.html#promod3.core.helper.MsgErrorAndExit">[docs]</a><span class="k">def</span> <span class="nf">MsgErrorAndExit</span><span class="p">(</span><span class="n">msg</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">):</span>
- <span class="sd">'''</span>
-<span class="sd"> Send a messages to the |ost_s| :ost_docs:`error log <base/logging/>` and exit</span>
-<span class="sd"> the Python interpreter.</span>
+ <span class="sd">'''</span>
+<span class="sd"> Send a messages to the |ost_s| :ost_docs:`error log <base/logging/>` and</span>
+<span class="sd"> exit the Python interpreter.</span>
-<span class="sd"> :param msg: The message.</span>
-<span class="sd"> :type msg: :class:`str`</span>
+<span class="sd"> :param msg: The message.</span>
+<span class="sd"> :type msg: :class:`str`</span>
-<span class="sd"> :param exit_status: Exit code, ends up in ``$?`` in the shell. ``0`` is</span>
+<span class="sd"> :param exit_status: Exit code, ends up in ``$?`` in the shell. ``0`` is</span>
<span class="sd"> traditionally reserved to successful commands.</span>
-<span class="sd"> :type exit_status: :class:`int`</span>
+<span class="sd"> :type exit_status: :class:`int`</span>
-<span class="sd"> :returns: No return value, exits script with value ``exit_status``.</span>
-<span class="sd"> '''</span>
- <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
- <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
+<span class="sd"> :returns: No return value, exits script with value ``exit_status``.</span>
+<span class="sd"> '''</span>
+ <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">msg</span><span class="p">)</span>
+ <span class="n">sys</span><span class="o">.</span><span class="n">exit</span><span class="p">(</span><span class="n">exit_status</span><span class="p">)</span>
+</div>
+<div class="viewcode-block" id="FileExists"><a class="viewcode-back" href="../../../core/helper.html#promod3.core.helper.FileExists">[docs]</a><span class="k">def</span> <span class="nf">FileExists</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="n">filename</span><span class="p">):</span>
+ <span class="sd">'''</span>
+<span class="sd"> Checks if a file exists, terminates if not. The error message displayed is</span>
+<span class="sd"> fixed and only needs a *prefix* describing the specimen of file.</span>
+
+<span class="sd"> :param prefix: String to put in front of the failure-message</span>
+<span class="sd"> "file does not exist: ``file``".</span>
+<span class="sd"> :type prefix: :class:`str`</span>
+
+<span class="sd"> :param exit_status: Exit code on missing file, ends up in ``$?`` in the</span>
+<span class="sd"> shell. ``0`` is traditionally reserved to successful commands.</span>
+<span class="sd"> :type exit_status: :class:`int`</span>
+
+<span class="sd"> :param file: Path including file name to be checked.</span>
+<span class="sd"> :type file: :class:`str`</span>
+
+<span class="sd"> :returns: No return value, exits script with value ``exit_status`` if file</span>
+<span class="sd"> is missing.</span>
+<span class="sd"> '''</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">exists</span><span class="p">(</span><span class="n">filename</span><span class="p">):</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file does not exist: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">filename</span><span class="p">),</span>
+ <span class="n">exit_status</span><span class="p">)</span>
+</div>
+<div class="viewcode-block" id="FileExtension"><a class="viewcode-back" href="../../../core/helper.html#promod3.core.helper.FileExtension">[docs]</a><span class="k">def</span> <span class="nf">FileExtension</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span> <span class="n">exit_status</span><span class="p">,</span> <span class="n">filename</span><span class="p">,</span> <span class="n">extensions</span><span class="p">,</span> <span class="n">gzip</span><span class="o">=</span><span class="bp">False</span><span class="p">):</span>
+ <span class="sd">'''</span>
+<span class="sd"> Checks a file to carry a known extension given by a list of strings. Since</span>
+<span class="sd"> files are very often compressed these days, an additional "gz" suffix can be</span>
+<span class="sd"> tracked automatically by this function. Thus, the list of *extensions* only</span>
+<span class="sd"> needs to contain what you are really looking for, e.g. ("pdb") instead of</span>
+<span class="sd"> ("pdb", "pdb.gz"). The *gzip* flag also determines the output of this</span>
+<span class="sd"> function. If enabled, a triple is returned: name of the file without</span>
+<span class="sd"> extension, its extension and a Boolean to tell whether the file carries the</span>
+<span class="sd"> gzip extension or not. If *gzip* detection is turned of, only a tuple is</span>
+<span class="sd"> returned: file name and extension. If the tested file name has an</span>
+<span class="sd"> unrecognised extension, this function terminates the script.</span>
+
+<span class="sd"> :param prefix: String to put in front of the failure-message</span>
+<span class="sd"> "file extension not supported: ``filename``".</span>
+<span class="sd"> :type prefix: :class:`str`</span>
+
+<span class="sd"> :param exit_status: Exit code on missing file, ends up in ``$?`` in the</span>
+<span class="sd"> shell. ``0`` is traditionally reserved to successful commands.</span>
+<span class="sd"> :type exit_status: :class:`int`</span>
+
+<span class="sd"> :param filename: Path including file name to be checked.</span>
+<span class="sd"> :type filename: :class:`str`</span>
+
+<span class="sd"> :param extensions: List of strings without a leading ".".</span>
+<span class="sd"> :type extensions: :class:`list`</span>
+
+<span class="sd"> :param gzip: Indicates whether to check for an additional "gz" extension.</span>
+<span class="sd"> :type gzip: :class:`bool`</span>
+
+<span class="sd"> :returns: (base name of ``filename`` (:class:`str`), extension of file</span>
+<span class="sd"> without a ".gz" (:class:`str`), flag to indicate an additional</span>
+<span class="sd"> ".gz" (:class:`bool`)) **if** ``gzip`` is set, (base name of</span>
+<span class="sd"> ``filename`` (:class:`str`), extension of file) **if not**.</span>
+<span class="sd"> '''</span>
+ <span class="n">pfilename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">filename</span><span class="p">)</span>
+ <span class="n">is_gz</span> <span class="o">=</span> <span class="bp">False</span>
+ <span class="k">if</span> <span class="n">fileext</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span> <span class="o">==</span> <span class="s">'.gz'</span><span class="p">:</span>
+ <span class="n">is_gz</span> <span class="o">=</span> <span class="bp">True</span>
+ <span class="n">pfilename</span><span class="p">,</span> <span class="n">fileext</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">splitext</span><span class="p">(</span><span class="n">pfilename</span><span class="p">)</span>
+ <span class="k">if</span> <span class="ow">not</span> <span class="n">gzip</span><span class="p">:</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">filename</span><span class="p">)</span><span class="o">+</span>
+ <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+ <span class="n">exit_status</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="s">''</span><span class="p">:</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">gzip</span><span class="p">:</span>
+ <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span><span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">filename</span><span class="p">)</span><span class="o">+</span>
+ <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+ <span class="n">exit_status</span><span class="p">)</span>
+ <span class="n">fileext</span> <span class="o">=</span> <span class="n">fileext</span><span class="p">[</span><span class="mi">1</span><span class="p">:]</span><span class="o">.</span><span class="n">lower</span><span class="p">()</span>
+ <span class="k">for</span> <span class="n">ext</span> <span class="ow">in</span> <span class="n">extensions</span><span class="p">:</span>
+ <span class="k">if</span> <span class="n">fileext</span> <span class="o">==</span> <span class="n">ext</span><span class="o">.</span><span class="n">lower</span><span class="p">():</span>
+ <span class="k">if</span> <span class="n">gzip</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">pfilename</span><span class="p">),</span> <span class="n">fileext</span><span class="p">,</span> <span class="n">is_gz</span>
+ <span class="k">else</span><span class="p">:</span>
+ <span class="k">return</span> <span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">basename</span><span class="p">(</span><span class="n">pfilename</span><span class="p">),</span> <span class="n">fileext</span>
+ <span class="n">extension_string</span> <span class="o">=</span> <span class="s">', '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">gzip</span><span class="p">:</span>
+ <span class="n">extension_string</span> <span class="o">+=</span> <span class="s">', '</span> <span class="o">+</span> <span class="s">'.gz, '</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">extensions</span><span class="p">)</span> <span class="o">+</span> <span class="s">'.gz'</span>
+ <span class="n">MsgErrorAndExit</span><span class="p">(</span><span class="s">'</span><span class="si">%s</span><span class="s"> file extension not supported: </span><span class="si">%s</span><span class="s">. '</span> <span class="o">%</span> <span class="p">(</span><span class="n">prefix</span><span class="p">,</span>
+ <span class="n">filename</span><span class="p">)</span><span class="o">+</span>
+ <span class="s">'Allowed extensions are: </span><span class="si">%s</span><span class="se">\n</span><span class="s">'</span> <span class="o">%</span> <span class="n">extension_string</span><span class="p">,</span>
+ <span class="n">exit_status</span><span class="p">)</span>
</div>
<span class="n">__all__</span> <span class="o">=</span> <span class="p">(</span>
- <span class="s">'MsgErrorAndExit'</span><span class="p">,</span>
+ <span class="s">'MsgErrorAndExit'</span><span class="p">,</span>
+ <span class="s">'FileExists'</span><span class="p">,</span>
+ <span class="s">'FileExtension'</span><span class="p">,</span>
<span class="p">)</span>
</pre></div>
diff --git a/doc/html/_sources/core/argcheck.txt b/doc/html/_sources/core/argcheck.txt
index b9a35a624353e75b40ec545830da812d07b5aeff..2968e9ef3f6307b7e688f9a7de9e1e174be675a3 100644
--- a/doc/html/_sources/core/argcheck.txt
+++ b/doc/html/_sources/core/argcheck.txt
@@ -59,8 +59,6 @@ here. All tests are designed to exit a script on failure.
File Tests
--------------------------------------------------------------------------------
-.. autofunction:: FileExists
-
.. autofunction:: FileExtension
.. LocalWords: currentmodule py howto argparse testcode argcheck os promod
diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.txt
index 3d9413f97bc22b455aca6a9bf7f9dd45a22bf19e..5de671aed8587d79f96b2995becd0d05f25de59f 100644
--- a/doc/html/_sources/core/helper.txt
+++ b/doc/html/_sources/core/helper.txt
@@ -39,3 +39,50 @@ Messages
.. autofunction:: MsgErrorAndExit
+File Tests
+--------------------------------------------------------------------------------
+
+.. testcode:: helper
+ :hide:
+
+ import os
+ import tempfile
+ from promod3.core import helper
+ from promod3.core import pm3argparse
+
+ (fh, fn) = tempfile.mkstemp(suffix='.pdb')
+ os.close(fh)
+
+ p = pm3argparse.PM3ArgumentParser()
+ p.add_argument('file', type=str)
+ opts = p.Parse([fn])
+
+ helper.FileExists('Test file', 1, opts.file)
+
+ opts.name, opts.ext, opts.gz = helper.FileExtension('Test file', 2,
+ opts.file,
+ ('pdb', 'mmcif'),
+ gzip=True)
+
+ os.remove(fn)
+
+.. doctest:: helper
+
+ from promod3.core import helper
+ from promod3.core import pm3argparse
+
+ p = pm3argparse.PM3ArgumentParser()
+ p.add_argument('file', type=str)
+ opts = p.Parse()
+
+ helper.FileExists('Test file', 1, opts.file)
+
+ opts.name, opts.ext, opts.gz = helper.FileExtension('Test file', 2,
+ opts.file,
+ ('pdb', 'mmcif'),
+ gzip=True)
+
+
+.. autofunction:: FileExists
+
+.. autofunction:: FileExtension
diff --git a/doc/html/_sources/core/index.txt b/doc/html/_sources/core/index.txt
index 8adefa269ed7f4f9bcdfdceff447a23649ccee35..904e46a8b44899eccf980857b40fde819be59a33 100644
--- a/doc/html/_sources/core/index.txt
+++ b/doc/html/_sources/core/index.txt
@@ -12,8 +12,6 @@ modeling per se but cover standard programming issues.
pm3argparse
- argcheck
-
helper
.. LocalWords: promod se toctree maxdepth argcheck
diff --git a/doc/html/_static/classic.css b/doc/html/_static/classic.css
deleted file mode 100644
index 2da923464d37ff4fc5d8461dcb81b0d4aba52493..0000000000000000000000000000000000000000
--- a/doc/html/_static/classic.css
+++ /dev/null
@@ -1,261 +0,0 @@
-/*
- * default.css_t
- * ~~~~~~~~~~~~~
- *
- * Sphinx stylesheet -- default theme.
- *
- * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-@import url("basic.css");
-
-/* -- page layout ----------------------------------------------------------- */
-
-body {
- font-family: sans-serif;
- font-size: 100%;
- background-color: #11303d;
- color: #000;
- margin: 0;
- padding: 0;
-}
-
-div.document {
- background-color: #1c4e63;
-}
-
-div.documentwrapper {
- float: left;
- width: 100%;
-}
-
-div.bodywrapper {
- margin: 0 0 0 230px;
-}
-
-div.body {
- background-color: #ffffff;
- color: #000000;
- padding: 0 20px 30px 20px;
-}
-
-div.footer {
- color: #ffffff;
- width: 100%;
- padding: 9px 0 9px 0;
- text-align: center;
- font-size: 75%;
-}
-
-div.footer a {
- color: #ffffff;
- text-decoration: underline;
-}
-
-div.related {
- background-color: #133f52;
- line-height: 30px;
- color: #ffffff;
-}
-
-div.related a {
- color: #ffffff;
-}
-
-div.sphinxsidebar {
-}
-
-div.sphinxsidebar h3 {
- font-family: 'Trebuchet MS', sans-serif;
- color: #ffffff;
- font-size: 1.4em;
- font-weight: normal;
- margin: 0;
- padding: 0;
-}
-
-div.sphinxsidebar h3 a {
- color: #ffffff;
-}
-
-div.sphinxsidebar h4 {
- font-family: 'Trebuchet MS', sans-serif;
- color: #ffffff;
- font-size: 1.3em;
- font-weight: normal;
- margin: 5px 0 0 0;
- padding: 0;
-}
-
-div.sphinxsidebar p {
- color: #ffffff;
-}
-
-div.sphinxsidebar p.topless {
- margin: 5px 10px 10px 10px;
-}
-
-div.sphinxsidebar ul {
- margin: 10px;
- padding: 0;
- color: #ffffff;
-}
-
-div.sphinxsidebar a {
- color: #98dbcc;
-}
-
-div.sphinxsidebar input {
- border: 1px solid #98dbcc;
- font-family: sans-serif;
- font-size: 1em;
-}
-
-
-
-/* -- hyperlink styles ------------------------------------------------------ */
-
-a {
- color: #355f7c;
- text-decoration: none;
-}
-
-a:visited {
- color: #355f7c;
- text-decoration: none;
-}
-
-a:hover {
- text-decoration: underline;
-}
-
-
-
-/* -- body styles ----------------------------------------------------------- */
-
-div.body h1,
-div.body h2,
-div.body h3,
-div.body h4,
-div.body h5,
-div.body h6 {
- font-family: 'Trebuchet MS', sans-serif;
- background-color: #f2f2f2;
- font-weight: normal;
- color: #20435c;
- border-bottom: 1px solid #ccc;
- margin: 20px -20px 10px -20px;
- padding: 3px 0 3px 10px;
-}
-
-div.body h1 { margin-top: 0; font-size: 200%; }
-div.body h2 { font-size: 160%; }
-div.body h3 { font-size: 140%; }
-div.body h4 { font-size: 120%; }
-div.body h5 { font-size: 110%; }
-div.body h6 { font-size: 100%; }
-
-a.headerlink {
- color: #c60f0f;
- font-size: 0.8em;
- padding: 0 4px 0 4px;
- text-decoration: none;
-}
-
-a.headerlink:hover {
- background-color: #c60f0f;
- color: white;
-}
-
-div.body p, div.body dd, div.body li {
- text-align: justify;
- line-height: 130%;
-}
-
-div.admonition p.admonition-title + p {
- display: inline;
-}
-
-div.admonition p {
- margin-bottom: 5px;
-}
-
-div.admonition pre {
- margin-bottom: 5px;
-}
-
-div.admonition ul, div.admonition ol {
- margin-bottom: 5px;
-}
-
-div.note {
- background-color: #eee;
- border: 1px solid #ccc;
-}
-
-div.seealso {
- background-color: #ffc;
- border: 1px solid #ff6;
-}
-
-div.topic {
- background-color: #eee;
-}
-
-div.warning {
- background-color: #ffe4e4;
- border: 1px solid #f66;
-}
-
-p.admonition-title {
- display: inline;
-}
-
-p.admonition-title:after {
- content: ":";
-}
-
-pre {
- padding: 5px;
- background-color: #eeffcc;
- color: #333333;
- line-height: 120%;
- border: 1px solid #ac9;
- border-left: none;
- border-right: none;
-}
-
-code {
- background-color: #ecf0f3;
- padding: 0 1px 0 1px;
- font-size: 0.95em;
-}
-
-th {
- background-color: #ede;
-}
-
-.warning code {
- background: #efc2c2;
-}
-
-.note code {
- background: #d6d6d6;
-}
-
-.viewcode-back {
- font-family: sans-serif;
-}
-
-div.viewcode-block:target {
- background-color: #f4debf;
- border-top: 1px solid #ac9;
- border-bottom: 1px solid #ac9;
-}
-
-div.code-block-caption {
- color: #efefef;
- background-color: #1c4e63;
-}
\ No newline at end of file
diff --git a/doc/html/_static/sidebar.js b/doc/html/_static/sidebar.js
deleted file mode 100644
index 5882ecfa32a95db4e78c498653fc5cbbb2311817..0000000000000000000000000000000000000000
--- a/doc/html/_static/sidebar.js
+++ /dev/null
@@ -1,159 +0,0 @@
-/*
- * sidebar.js
- * ~~~~~~~~~~
- *
- * This script makes the Sphinx sidebar collapsible.
- *
- * .sphinxsidebar contains .sphinxsidebarwrapper. This script adds
- * in .sphixsidebar, after .sphinxsidebarwrapper, the #sidebarbutton
- * used to collapse and expand the sidebar.
- *
- * When the sidebar is collapsed the .sphinxsidebarwrapper is hidden
- * and the width of the sidebar and the margin-left of the document
- * are decreased. When the sidebar is expanded the opposite happens.
- * This script saves a per-browser/per-session cookie used to
- * remember the position of the sidebar among the pages.
- * Once the browser is closed the cookie is deleted and the position
- * reset to the default (expanded).
- *
- * :copyright: Copyright 2007-2015 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
- */
-
-$(function() {
-
-
-
-
-
-
-
-
- // global elements used by the functions.
- // the 'sidebarbutton' element is defined as global after its
- // creation, in the add_sidebar_button function
- var bodywrapper = $('.bodywrapper');
- var sidebar = $('.sphinxsidebar');
- var sidebarwrapper = $('.sphinxsidebarwrapper');
-
- // for some reason, the document has no sidebar; do not run into errors
- if (!sidebar.length) return;
-
- // original margin-left of the bodywrapper and width of the sidebar
- // with the sidebar expanded
- var bw_margin_expanded = bodywrapper.css('margin-left');
- var ssb_width_expanded = sidebar.width();
-
- // margin-left of the bodywrapper and width of the sidebar
- // with the sidebar collapsed
- var bw_margin_collapsed = '.8em';
- var ssb_width_collapsed = '.8em';
-
- // colors used by the current theme
- var dark_color = $('.related').css('background-color');
- var light_color = $('.document').css('background-color');
-
- function sidebar_is_collapsed() {
- return sidebarwrapper.is(':not(:visible)');
- }
-
- function toggle_sidebar() {
- if (sidebar_is_collapsed())
- expand_sidebar();
- else
- collapse_sidebar();
- }
-
- function collapse_sidebar() {
- sidebarwrapper.hide();
- sidebar.css('width', ssb_width_collapsed);
- bodywrapper.css('margin-left', bw_margin_collapsed);
- sidebarbutton.css({
- 'margin-left': '0',
- 'height': bodywrapper.height()
- });
- sidebarbutton.find('span').text('»');
- sidebarbutton.attr('title', _('Expand sidebar'));
- document.cookie = 'sidebar=collapsed';
- }
-
- function expand_sidebar() {
- bodywrapper.css('margin-left', bw_margin_expanded);
- sidebar.css('width', ssb_width_expanded);
- sidebarwrapper.show();
- sidebarbutton.css({
- 'margin-left': ssb_width_expanded-12,
- 'height': bodywrapper.height()
- });
- sidebarbutton.find('span').text('«');
- sidebarbutton.attr('title', _('Collapse sidebar'));
- document.cookie = 'sidebar=expanded';
- }
-
- function add_sidebar_button() {
- sidebarwrapper.css({
- 'float': 'left',
- 'margin-right': '0',
- 'width': ssb_width_expanded - 28
- });
- // create the button
- sidebar.append(
- '<div id="sidebarbutton"><span>«</span></div>'
- );
- var sidebarbutton = $('#sidebarbutton');
- light_color = sidebarbutton.css('background-color');
- // find the height of the viewport to center the '<<' in the page
- var viewport_height;
- if (window.innerHeight)
- viewport_height = window.innerHeight;
- else
- viewport_height = $(window).height();
- sidebarbutton.find('span').css({
- 'display': 'block',
- 'margin-top': (viewport_height - sidebar.position().top - 20) / 2
- });
-
- sidebarbutton.click(toggle_sidebar);
- sidebarbutton.attr('title', _('Collapse sidebar'));
- sidebarbutton.css({
- 'color': '#FFFFFF',
- 'border-left': '1px solid ' + dark_color,
- 'font-size': '1.2em',
- 'cursor': 'pointer',
- 'height': bodywrapper.height(),
- 'padding-top': '1px',
- 'margin-left': ssb_width_expanded - 12
- });
-
- sidebarbutton.hover(
- function () {
- $(this).css('background-color', dark_color);
- },
- function () {
- $(this).css('background-color', light_color);
- }
- );
- }
-
- function set_position_from_cookie() {
- if (!document.cookie)
- return;
- var items = document.cookie.split(';');
- for(var k=0; k<items.length; k++) {
- var key_val = items[k].split('=');
- var key = key_val[0].replace(/ /, ""); // strip leading spaces
- if (key == 'sidebar') {
- var value = key_val[1];
- if ((value == 'collapsed') && (!sidebar_is_collapsed()))
- collapse_sidebar();
- else if ((value == 'expanded') && (sidebar_is_collapsed()))
- expand_sidebar();
- }
- }
- }
-
- add_sidebar_button();
- var sidebarbutton = $('#sidebarbutton');
- set_position_from_cookie();
-});
\ No newline at end of file
diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html
index 3ecd6b1b1e52dae0a4e6b3e13d4b7137e18f6f57..b8b373c453b3057c47c2614d6f7a6844dc61557a 100644
--- a/doc/html/core/argcheck.html
+++ b/doc/html/core/argcheck.html
@@ -24,9 +24,6 @@
<script type="text/javascript" src="../_static/underscore.js"></script>
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
- <link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
- <link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
- <link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
@@ -42,15 +39,7 @@
<li class="right" >
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
- <li class="right" >
- <a href="helper.html" title="helper - Shared Functionality For the Everything"
- accesskey="N">next</a> |</li>
- <li class="right" >
- <a href="pm3argparse.html" title="pm3argparse - Parsing Command Lines"
- accesskey="P">previous</a> |</li>
- <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
- <li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
- <li class="nav-item nav-item-2"><a href="index.html" accesskey="U"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a> »</li>
+ <li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
</ul>
</div>
@@ -89,70 +78,6 @@ here. All tests are designed to exit a script on failure.</p>
</div>
<div class="section" id="file-tests">
<h2>File Tests<a class="headerlink" href="#file-tests" title="Permalink to this headline">¶</a></h2>
-<dl class="function">
-<dt id="promod3.core.argcheck.FileExists">
-<code class="descclassname">promod3.core.argcheck.</code><code class="descname">FileExists</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>file</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/argcheck.html#FileExists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.argcheck.FileExists" title="Permalink to this definition">¶</a></dt>
-<dd><p>Checks if a file exists, terminates if not. The error message displayed is
-fixed and only needs a <em>prefix</em> describing the specimen of file.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
-“file does not exist: <code class="docutils literal"><span class="pre">file</span></code>”.</li>
-<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal"><span class="pre">$?</span></code> in the
-shell. <code class="docutils literal"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
-<li><strong>file</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">No return value, exits script with value <code class="docutils literal"><span class="pre">exit_status</span></code> if file is
-missing.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="promod3.core.argcheck.FileExtension">
-<code class="descclassname">promod3.core.argcheck.</code><code class="descname">FileExtension</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>file</em>, <em>extensions</em>, <em>gz=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/argcheck.html#FileExtension"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.argcheck.FileExtension" title="Permalink to this definition">¶</a></dt>
-<dd><p>Checks a file to carry a known extension given by a list of strings. Since
-files are very often compressed these days, an additional “gz” suffix can be
-tracked automatically by this function. Thus, the list of <em>extensions</em> only
-needs to contain what you are really looking for, e.g. (“pdb”) instead of
-(“pdb”, “pdb.gz”). The <em>gz</em> flag also determines the output of this function.
-If enabled, a triple is returned: name of the file without extension, its
-extension and a Boolean to tell whether the file carries the gzip extension
-or not. If <em>gz</em> detection is turned of, only a tuple is returned: file name
-and extension. If the tested file name has an unrecognised extension, this
-function terminates the script.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
-“file extension not supported: <code class="docutils literal"><span class="pre">file</span></code>”.</li>
-<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal"><span class="pre">$?</span></code> in the
-shell. <code class="docutils literal"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
-<li><strong>file</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
-<li><strong>extensions</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of strings without a leading ”.”.</li>
-<li><strong>gz</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Indicates whether to check for an additional “gz” extension.</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(base name of <code class="docutils literal"><span class="pre">file</span></code> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), extension of file without a
-”.gz” (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), flag to indicate an additional ”.gz”
-(<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>)) <strong>if</strong> <code class="docutils literal"><span class="pre">gz</span></code> is set, (base name of <code class="docutils literal"><span class="pre">file</span></code>
-(<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), extension of file) <strong>if not</strong>.</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
</div>
</div>
@@ -171,12 +96,6 @@ shell. <code class="docutils literal"><span class="pre">0</span></code> is tradi
</li>
</ul>
- <h4>Previous topic</h4>
- <p class="topless"><a href="pm3argparse.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></p>
- <h4>Next topic</h4>
- <p class="topless"><a href="helper.html"
- title="next chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></p>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index baa64fba46d13bc53e65c66c7e905131a73893e2..1a5ccdd11af6e50776ed2f0bcb64c3c72aa9d2da 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -26,7 +26,7 @@
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
<link rel="next" title="rawmodel - Coordinate Modeling" href="../rawmodel/index.html" />
- <link rel="prev" title="argcheck - Standard Tests For Command Line Arguments" href="argcheck.html" />
+ <link rel="prev" title="pm3argparse - Parsing Command Lines" href="pm3argparse.html" />
<meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
@@ -46,7 +46,7 @@
<a href="../rawmodel/index.html" title="rawmodel - Coordinate Modeling"
accesskey="N">next</a> |</li>
<li class="right" >
- <a href="argcheck.html" title="argcheck - Standard Tests For Command Line Arguments"
+ <a href="pm3argparse.html" title="pm3argparse - Parsing Command Lines"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="../index.html">ProMod3 0 documentation</a> »</li>
<li class="nav-item nav-item-1"><a href="../developers.html" >Documentation For Developes</a> »</li>
@@ -76,8 +76,8 @@ rather empty modules left alone.</p>
<dl class="function">
<dt id="promod3.core.helper.MsgErrorAndExit">
<code class="descclassname">promod3.core.helper.</code><code class="descname">MsgErrorAndExit</code><span class="sig-paren">(</span><em>msg</em>, <em>exit_status</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/helper.html#MsgErrorAndExit"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.helper.MsgErrorAndExit" title="Permalink to this definition">¶</a></dt>
-<dd><p>Send a messages to the OST <a class="reference external" href="http://www.openstructure.org/docs/1.3/base/logging/">error log</a> and exit
-the Python interpreter.</p>
+<dd><p>Send a messages to the OST <a class="reference external" href="http://www.openstructure.org/docs/1.3/base/logging/">error log</a> and
+exit the Python interpreter.</p>
<table class="docutils field-list" frame="void" rules="none">
<col class="field-name" />
<col class="field-body" />
@@ -96,6 +96,88 @@ traditionally reserved to successful commands.</li>
</table>
</dd></dl>
+</div>
+<div class="section" id="file-tests">
+<h2>File Tests<a class="headerlink" href="#file-tests" title="Permalink to this headline">¶</a></h2>
+<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">helper</span>
+<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">pm3argparse</span>
+
+<span class="n">p</span> <span class="o">=</span> <span class="n">pm3argparse</span><span class="o">.</span><span class="n">PM3ArgumentParser</span><span class="p">()</span>
+<span class="n">p</span><span class="o">.</span><span class="n">add_argument</span><span class="p">(</span><span class="s">'file'</span><span class="p">,</span> <span class="nb">type</span><span class="o">=</span><span class="nb">str</span><span class="p">)</span>
+<span class="n">opts</span> <span class="o">=</span> <span class="n">p</span><span class="o">.</span><span class="n">Parse</span><span class="p">()</span>
+
+<span class="n">helper</span><span class="o">.</span><span class="n">FileExists</span><span class="p">(</span><span class="s">'Test file'</span><span class="p">,</span> <span class="mi">1</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">file</span><span class="p">)</span>
+
+<span class="n">opts</span><span class="o">.</span><span class="n">name</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">ext</span><span class="p">,</span> <span class="n">opts</span><span class="o">.</span><span class="n">gz</span> <span class="o">=</span> <span class="n">helper</span><span class="o">.</span><span class="n">FileExtension</span><span class="p">(</span><span class="s">'Test file'</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span>
+ <span class="n">opts</span><span class="o">.</span><span class="n">file</span><span class="p">,</span>
+ <span class="p">(</span><span class="s">'pdb'</span><span class="p">,</span> <span class="s">'mmcif'</span><span class="p">),</span>
+ <span class="n">gzip</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span>
+</pre></div>
+</div>
+<dl class="function">
+<dt id="promod3.core.helper.FileExists">
+<code class="descclassname">promod3.core.helper.</code><code class="descname">FileExists</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/helper.html#FileExists"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.helper.FileExists" title="Permalink to this definition">¶</a></dt>
+<dd><p>Checks if a file exists, terminates if not. The error message displayed is
+fixed and only needs a <em>prefix</em> describing the specimen of file.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
+“file does not exist: <code class="docutils literal"><span class="pre">file</span></code>”.</li>
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal"><span class="pre">$?</span></code> in the
+shell. <code class="docutils literal"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
+<li><strong>file</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">No return value, exits script with value <code class="docutils literal"><span class="pre">exit_status</span></code> if file
+is missing.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="function">
+<dt id="promod3.core.helper.FileExtension">
+<code class="descclassname">promod3.core.helper.</code><code class="descname">FileExtension</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em>, <em>extensions</em>, <em>gzip=False</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/helper.html#FileExtension"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.helper.FileExtension" title="Permalink to this definition">¶</a></dt>
+<dd><p>Checks a file to carry a known extension given by a list of strings. Since
+files are very often compressed these days, an additional “gz” suffix can be
+tracked automatically by this function. Thus, the list of <em>extensions</em> only
+needs to contain what you are really looking for, e.g. (“pdb”) instead of
+(“pdb”, “pdb.gz”). The <em>gzip</em> flag also determines the output of this
+function. If enabled, a triple is returned: name of the file without
+extension, its extension and a Boolean to tell whether the file carries the
+gzip extension or not. If <em>gzip</em> detection is turned of, only a tuple is
+returned: file name and extension. If the tested file name has an
+unrecognised extension, this function terminates the script.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>prefix</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – String to put in front of the failure-message
+“file extension not supported: <code class="docutils literal"><span class="pre">filename</span></code>”.</li>
+<li><strong>exit_status</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#int" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">int</span></code></a>) – Exit code on missing file, ends up in <code class="docutils literal"><span class="pre">$?</span></code> in the
+shell. <code class="docutils literal"><span class="pre">0</span></code> is traditionally reserved to successful commands.</li>
+<li><strong>filename</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>) – Path including file name to be checked.</li>
+<li><strong>extensions</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#list" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">list</span></code></a>) – List of strings without a leading ”.”.</li>
+<li><strong>gzip</strong> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>) – Indicates whether to check for an additional “gz” extension.</li>
+</ul>
+</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">(base name of <code class="docutils literal"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), extension of file
+without a ”.gz” (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), flag to indicate an additional
+”.gz” (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#bool" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">bool</span></code></a>)) <strong>if</strong> <code class="docutils literal"><span class="pre">gzip</span></code> is set, (base name of
+<code class="docutils literal"><span class="pre">filename</span></code> (<a class="reference external" href="https://docs.python.org/2.7/library/functions.html#str" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">str</span></code></a>), extension of file) <strong>if not</strong>.</p>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
</div>
</div>
@@ -110,13 +192,14 @@ traditionally reserved to successful commands.</li>
<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a><ul>
<li><a class="reference internal" href="#introduction">Introduction</a></li>
<li><a class="reference internal" href="#messages">Messages</a></li>
+<li><a class="reference internal" href="#file-tests">File Tests</a></li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
- <p class="topless"><a href="argcheck.html"
- title="previous chapter"><code class="docutils literal"><span class="pre">argcheck</span></code> - Standard Tests For Command Line Arguments</a></p>
+ <p class="topless"><a href="pm3argparse.html"
+ title="previous chapter"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="../rawmodel/index.html"
title="next chapter"><code class="docutils literal"><span class="pre">rawmodel</span></code> - Coordinate Modeling</a></p>
diff --git a/doc/html/core/index.html b/doc/html/core/index.html
index aca0f41d3cbdfdbf61f6a452a6985720e437ee95..a916e4415a772584ca5361a705167a96560a03da 100644
--- a/doc/html/core/index.html
+++ b/doc/html/core/index.html
@@ -69,14 +69,10 @@ modeling per se but cover standard programming issues.</p>
<li class="toctree-l2"><a class="reference internal" href="pm3argparse.html#argument-parser">Argument Parser</a></li>
</ul>
</li>
-<li class="toctree-l1"><a class="reference internal" href="argcheck.html"><code class="docutils literal"><span class="pre">argcheck</span></code> - Standard Tests For Command Line Arguments</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="argcheck.html#introduction">Introduction</a></li>
-<li class="toctree-l2"><a class="reference internal" href="argcheck.html#file-tests">File Tests</a></li>
-</ul>
-</li>
<li class="toctree-l1"><a class="reference internal" href="helper.html"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a><ul>
<li class="toctree-l2"><a class="reference internal" href="helper.html#introduction">Introduction</a></li>
<li class="toctree-l2"><a class="reference internal" href="helper.html#messages">Messages</a></li>
+<li class="toctree-l2"><a class="reference internal" href="helper.html#file-tests">File Tests</a></li>
</ul>
</li>
</ul>
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index c43e12fe229e829e792993fd25fb2eead929df31..f5035485b5216c03ffa7596dc340d4f1011db805 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -25,7 +25,7 @@
<script type="text/javascript" src="../_static/doctools.js"></script>
<link rel="top" title="ProMod3 0 documentation" href="../index.html" />
<link rel="up" title="core - ProMod3 Core Functionality" href="index.html" />
- <link rel="next" title="argcheck - Standard Tests For Command Line Arguments" href="argcheck.html" />
+ <link rel="next" title="helper - Shared Functionality For the Everything" href="helper.html" />
<link rel="prev" title="core - ProMod3 Core Functionality" href="index.html" />
@@ -43,7 +43,7 @@
<a href="../py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
- <a href="argcheck.html" title="argcheck - Standard Tests For Command Line Arguments"
+ <a href="helper.html" title="helper - Shared Functionality For the Everything"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="index.html" title="core - ProMod3 Core Functionality"
@@ -176,8 +176,8 @@ first 3 characters of the file name of the script. If
<p class="topless"><a href="index.html"
title="previous chapter"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a></p>
<h4>Next topic</h4>
- <p class="topless"><a href="argcheck.html"
- title="next chapter"><code class="docutils literal"><span class="pre">argcheck</span></code> - Standard Tests For Command Line Arguments</a></p>
+ <p class="topless"><a href="helper.html"
+ title="next chapter"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></p>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
diff --git a/doc/html/developers.html b/doc/html/developers.html
index fe4c5efbec7cdf2a34bd07fc640fe432178e584f..bffc7cd96b0898f4af66076ee2f949ee1b7d857f 100644
--- a/doc/html/developers.html
+++ b/doc/html/developers.html
@@ -64,7 +64,6 @@
<li class="toctree-l1"><a class="reference internal" href="core/setcompoundschemlib.html"><code class="docutils literal"><span class="pre">SetCompoundsChemlib()</span></code></a></li>
<li class="toctree-l1"><a class="reference internal" href="core/index.html"><code class="docutils literal"><span class="pre">core</span></code> - ProMod3 Core Functionality</a><ul>
<li class="toctree-l2"><a class="reference internal" href="core/pm3argparse.html"><code class="docutils literal"><span class="pre">pm3argparse</span></code> - Parsing Command Lines</a></li>
-<li class="toctree-l2"><a class="reference internal" href="core/argcheck.html"><code class="docutils literal"><span class="pre">argcheck</span></code> - Standard Tests For Command Line Arguments</a></li>
<li class="toctree-l2"><a class="reference internal" href="core/helper.html"><code class="docutils literal"><span class="pre">helper</span></code> - Shared Functionality For the Everything</a></li>
</ul>
</li>
diff --git a/doc/html/genindex.html b/doc/html/genindex.html
index b5a5942ca6c433cc2546836200be857d89e42736..63ddd0cf605661089ae8e7e4ca7ab495000d672a 100644
--- a/doc/html/genindex.html
+++ b/doc/html/genindex.html
@@ -157,13 +157,13 @@
<table style="width: 100%" class="indextable genindextable"><tr>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="core/argcheck.html#promod3.core.argcheck.FileExists">FileExists() (in module promod3.core.argcheck)</a>
+ <dt><a href="core/helper.html#promod3.core.helper.FileExists">FileExists() (in module promod3.core.helper)</a>
</dt>
</dl></td>
<td style="width: 33%" valign="top"><dl>
- <dt><a href="core/argcheck.html#promod3.core.argcheck.FileExtension">FileExtension() (in module promod3.core.argcheck)</a>
+ <dt><a href="core/helper.html#promod3.core.helper.FileExtension">FileExtension() (in module promod3.core.helper)</a>
</dt>
</dl></td>
diff --git a/doc/html/objects.inv b/doc/html/objects.inv
index 766bd3e3e580e3cae68902a296510d9251ec0bd4..77c570a218fc0d6f3a2094f0e07de7b3b61388a4 100644
Binary files a/doc/html/objects.inv and b/doc/html/objects.inv differ
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index 739678d5d1743f1569e8b2fe0000c7b562ef7407..5a2a7f8ca58d73266ab40404623ddbbd5fa3209c 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
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