From c8ec299ccdfa75dcd041855a819b61a1a55fa710 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 18 Aug 2015 13:39:24 +0200
Subject: [PATCH] Updated documentation

---
 doc/html/_modules/promod3/core/pm3argparse.html | 17 ++++++++++-------
 doc/html/_sources/core/helper.txt               |  4 ++--
 doc/html/core/helper.html                       |  2 +-
 doc/html/core/pm3argparse.html                  |  8 ++++----
 doc/html/searchindex.js                         |  2 +-
 5 files changed, 18 insertions(+), 15 deletions(-)

diff --git a/doc/html/_modules/promod3/core/pm3argparse.html b/doc/html/_modules/promod3/core/pm3argparse.html
index 3dbaa167..01998d8b 100644
--- a/doc/html/_modules/promod3/core/pm3argparse.html
+++ b/doc/html/_modules/promod3/core/pm3argparse.html
@@ -117,10 +117,14 @@
 
 <span class="sd">    :type: :class:`bool`</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-<div class="viewcode-block" id="PM3ArgumentParser.__init__"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.__init__">[docs]</a>    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="bp">True</span><span class="p">,</span> <span class="n">description</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
+<div class="viewcode-block" id="PM3ArgumentParser.__init__"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.__init__">[docs]</a>    <span class="k">def</span> <span class="nf">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">description</span><span class="p">,</span> <span class="n">action</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Create a new instance of :class:`~pm3argparse.PM3ArgumentParser`.</span>
 
+<span class="sd">        :param description: Help text for this script, handed down to</span>
+<span class="sd">                            |descattr|_ of |argpinit|_.</span>
+<span class="sd">        :type description: :class:`str`</span>
+
 <span class="sd">        :param action: Indicates if the calling script is a |project| action.</span>
 <span class="sd">                       This influences |progattr|_ of</span>
 <span class="sd">                       :class:`~argparse.ArgumentParser` by clipping of the</span>
@@ -129,10 +133,6 @@
 <span class="sd">                       :class:`~argparse.ArgumentParser` kicks in.</span>
 <span class="sd">        :type action: :class:`bool`</span>
 
-<span class="sd">        :param description: Help text for this script, handed down to</span>
-<span class="sd">                            |descattr|_ of |argpinit|_.</span>
-<span class="sd">        :type description: :class:`str`</span>
-
 <span class="sd">        :returns: :class:`argparse.ArgumentParser`.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">prog</span> <span class="o">=</span> <span class="bp">None</span>
@@ -154,10 +154,13 @@
 <span class="sd">        function to bend :mod:`argparse` to use :class:`ost.Logger`.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">message</span><span class="p">:</span>
+            <span class="n">no_nl_msg</span> <span class="o">=</span> <span class="n">message</span>
+            <span class="k">if</span> <span class="n">message</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">==</span> <span class="s">&#39;</span><span class="se">\n</span><span class="s">&#39;</span><span class="p">:</span>
+                <span class="n">no_nl_msg</span> <span class="o">=</span> <span class="n">message</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
             <span class="k">if</span> <span class="nb">file</span> <span class="ow">is</span> <span class="bp">None</span> <span class="ow">or</span> <span class="nb">file</span> <span class="ow">is</span> <span class="n">sys</span><span class="o">.</span><span class="n">stderr</span><span class="p">:</span>
-                <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+                <span class="n">ost</span><span class="o">.</span><span class="n">LogError</span><span class="p">(</span><span class="n">no_nl_msg</span><span class="p">)</span>
             <span class="k">else</span><span class="p">:</span>
-                <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="n">message</span><span class="p">)</span>
+                <span class="n">ost</span><span class="o">.</span><span class="n">LogScript</span><span class="p">(</span><span class="n">no_nl_msg</span><span class="p">)</span>
 
 <div class="viewcode-block" id="PM3ArgumentParser.Parse"><a class="viewcode-back" href="../../../core/pm3argparse.html#promod3.core.pm3argparse.PM3ArgumentParser.Parse">[docs]</a>    <span class="k">def</span> <span class="nf">Parse</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">args</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.txt
index 3af02dfc..93ea65eb 100644
--- a/doc/html/_sources/core/helper.txt
+++ b/doc/html/_sources/core/helper.txt
@@ -53,7 +53,7 @@ File Tests
   (fh, fn) = tempfile.mkstemp(suffix='.pdb')
   os.close(fh)
 
-  p = pm3argparse.PM3ArgumentParser()
+  p = pm3argparse.PM3ArgumentParser('Dummy')
   p.add_argument('file', type=str)
   opts = p.Parse([fn])
 
@@ -71,7 +71,7 @@ File Tests
   from promod3.core import helper
   from promod3.core import pm3argparse
 
-  p = pm3argparse.PM3ArgumentParser()
+  p = pm3argparse.PM3ArgumentParser(__doc__)
   p.add_argument('file', type=str)
   opts = p.Parse()
 
diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html
index 248f1458..08382933 100644
--- a/doc/html/core/helper.html
+++ b/doc/html/core/helper.html
@@ -102,7 +102,7 @@ traditionally reserved to successful commands.</li>
 <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">pm3argparse</span><span class="o">.</span><span class="n">PM3ArgumentParser</span><span class="p">(</span><span class="n">__doc__</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">&#39;file&#39;</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>
 
diff --git a/doc/html/core/pm3argparse.html b/doc/html/core/pm3argparse.html
index c3c1ed5c..fab963bf 100644
--- a/doc/html/core/pm3argparse.html
+++ b/doc/html/core/pm3argparse.html
@@ -77,7 +77,7 @@ input.</p>
 <h2>Argument Parser<a class="headerlink" href="#argument-parser" title="Permalink to this headline">¶</a></h2>
 <dl class="class">
 <dt id="promod3.core.pm3argparse.PM3ArgumentParser">
-<em class="property">class </em><code class="descclassname">promod3.core.pm3argparse.</code><code class="descname">PM3ArgumentParser</code><span class="sig-paren">(</span><em>action=True</em>, <em>description=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="Permalink to this definition">¶</a></dt>
+<em class="property">class </em><code class="descclassname">promod3.core.pm3argparse.</code><code class="descname">PM3ArgumentParser</code><span class="sig-paren">(</span><em>description</em>, <em>action=True</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser" title="Permalink to this definition">¶</a></dt>
 <dd><p>This class is a child of <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">argparse.ArgumentParser</span></code></a>. It provides a
 set of standard arguments which can be activated, rather than added via the
 traditional way. This helps keeping up a common naming scheme throughout
@@ -105,21 +105,21 @@ called on unrecognised arguments, the script exits with a code 2 by
 </table>
 <dl class="method">
 <dt id="promod3.core.pm3argparse.PM3ArgumentParser.__init__">
-<code class="descname">__init__</code><span class="sig-paren">(</span><em>action=True</em>, <em>description=None</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.__init__" title="Permalink to this definition">¶</a></dt>
+<code class="descname">__init__</code><span class="sig-paren">(</span><em>description</em>, <em>action=True</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/pm3argparse.html#PM3ArgumentParser.__init__"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.pm3argparse.PM3ArgumentParser.__init__" title="Permalink to this definition">¶</a></dt>
 <dd><p>Create a new instance of <code class="xref py py-class docutils literal"><span class="pre">PM3ArgumentParser</span></code>.</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>description</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>) &#8211; Help text for this script, handed down to
+<a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#description"><code class="xref py py-attr docutils literal"><span class="pre">description</span></code></a> of <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.ArgumentParser"><code class="xref py py-meth docutils literal"><span class="pre">argparse.ArgumentParser.__init__()</span></code></a>.</li>
 <li><strong>action</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>) &#8211; Indicates if the calling script is a ProMod3 action.
 This influences <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#prog"><code class="xref py py-attr docutils literal"><span class="pre">prog</span></code></a> of
 <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">ArgumentParser</span></code></a> by clipping of the
 first 3 characters of the file name of the script. If
 <code class="docutils literal"><span class="pre">False</span></code>, default behaviour of
 <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.ArgumentParser" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">ArgumentParser</span></code></a> kicks in.</li>
-<li><strong>description</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>) &#8211; Help text for this script, handed down to
-<a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#description"><code class="xref py py-attr docutils literal"><span class="pre">description</span></code></a> of <a class="reference external" href="https://docs.python.org/2.7/library/argparse.html#argparse.ArgumentParser"><code class="xref py py-meth docutils literal"><span class="pre">argparse.ArgumentParser.__init__()</span></code></a>.</li>
 </ul>
 </td>
 </tr>
diff --git a/doc/html/searchindex.js b/doc/html/searchindex.js
index b25dbdce..f019de0b 100644
--- a/doc/html/searchindex.js
+++ b/doc/html/searchindex.js
@@ -1 +1 @@
-Search.setIndex({envversion:46,filenames:["actions/index_dev","buildsystem","changelog","cmake/index","contributing","core/helper","core/index","core/pm3argparse","core/setcompoundschemlib","developers","index","rawmodel/index","users"],objects:{"":{"command:add_doc_dependency":[3,0,1,""],"command:add_doc_source":[3,0,1,""],"command:pm_action":[3,0,1,""],"command:promod3_unittest":[3,0,1,""],test_actions:[0,1,0,"-"]},"promod3.core":{pm3argparse:[7,1,0,"-"]},"promod3.core.helper":{FileExists:[5,3,1,""],FileExtension:[5,3,1,""],FileGzip:[5,3,1,""],MsgErrorAndExit:[5,3,1,""]},"promod3.core.pm3argparse":{PM3ArgumentParser:[7,5,1,""]},"promod3.core.pm3argparse.PM3ArgumentParser":{"__init__":[7,2,1,""],AddAlignment:[7,2,1,""],AssembleParser:[7,2,1,""],Parse:[7,2,1,""],action:[7,4,1,""]},"promod3.rawmodel":{BuildRawModel:[11,3,1,""],RawModelingResult:[11,5,1,""]},"promod3.rawmodel.RawModelingResult":{gaps:[11,4,1,""],model:[11,4,1,""]},"test_actions.ActionTestCase":{RunAction:[0,2,1,""],RunExitStatusTest:[0,2,1,""],pm_action:[0,4,1,""],pm_bin:[0,4,1,""],testPMExists:[0,2,1,""]},promod3:{SetCompoundsChemlib:[8,3,1,""],core:[6,1,0,"-"],rawmodel:[11,1,0,"-"]},test_actions:{ActionTestCase:[0,5,1,""]}},objnames:{"0":["cmake","command","CMake 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GitLab