diff --git a/doc/html/_modules/promod3/core/helper.html b/doc/html/_modules/promod3/core/helper.html index 8f7745b6246a8a308ff9440f4ce982cdb5ec7184..26a25b8bccbc719d9b953ba8e1badfe18f0fb53d 100644 --- a/doc/html/_modules/promod3/core/helper.html +++ b/doc/html/_modules/promod3/core/helper.html @@ -100,6 +100,41 @@ <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="FileGzip"><a class="viewcode-back" href="../../../core/helper.html#promod3.core.helper.FileGzip">[docs]</a><span class="k">def</span> <span class="nf">FileGzip</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">allowed</span><span class="o">=</span><span class="bp">True</span><span class="p">):</span> + <span class="sd">'''</span> +<span class="sd"> See if a file is gzipped or not. This is basically done by checking for a</span> +<span class="sd"> "gz" suffix. May also be used to verify that a file is not compressed where</span> +<span class="sd"> it does not apply. That is where *allowed* comes in. If "gz" is not allowed,</span> +<span class="sd"> terminates the script on gzip files.</span> + +<span class="sd"> :param prefix: String to put in front of the failure-message where gzip</span> +<span class="sd"> files are not allowed.</span> +<span class="sd"> :type prefix: :class:`str`</span> + +<span class="sd"> :param exit_status: Exit code on gzip files to be avoided, ends up in</span> +<span class="sd"> ``$?`` in the shell. ``0`` is traditionally reserved to</span> +<span class="sd"> 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 allowed: Set to ``False`` if gzipped files are not allowed. Then the</span> +<span class="sd"> script will terminate if a gzip file is found.</span> +<span class="sd"> :type allowed: :class:`bool`</span> + +<span class="sd"> :returns: Flag to indicate if file is gzipped (:class:`bool`).</span> +<span class="sd"> '''</span> + <span class="n">_</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="k">if</span> <span class="ow">not</span> <span class="n">allowed</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 in Gzip 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="n">exit_status</span><span class="p">)</span> + <span class="k">return</span> <span class="n">is_gz</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> @@ -174,6 +209,8 @@ <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: gzipped gz param str gzip bool</span> </pre></div> </div> diff --git a/doc/html/_sources/changelog.txt b/doc/html/_sources/changelog.txt index d0336bb6c605f6eef99d72f5a79aa195e1731ba1..9c9ba86de73c69b98b8e46e93abced278a4a3f8a 100644 --- a/doc/html/_sources/changelog.txt +++ b/doc/html/_sources/changelog.txt @@ -16,4 +16,8 @@ Changes in Release 0.2 * added html documentation to repository * meld renamed to rawmodel +Changes in Release 0.3 (to be released) +------------------------------------------------------------------------------- + * merged argcheck into the helper module + .. LocalWords: Changelog reStructuredText changelog txt diff --git a/doc/html/_sources/core/argcheck.txt b/doc/html/_sources/core/argcheck.txt deleted file mode 100644 index 2968e9ef3f6307b7e688f9a7de9e1e174be675a3..0000000000000000000000000000000000000000 --- a/doc/html/_sources/core/argcheck.txt +++ /dev/null @@ -1,66 +0,0 @@ -:mod:`~promod3.core.argcheck` - Standard Tests For Command Line Arguments -================================================================================ - -.. currentmodule:: promod3.core.argcheck - -Introduction --------------------------------------------------------------------------------- - -For parsing command line arguments - -:py_docs:`optional <howto/argparse.html#introducing-optional-arguments>` and -:py_docs:`positional <howto/argparse.html#introducing-positional-arguments>` - -|project| tools should utilise its own -:mod:`~promod3.core.pm3argparse` module. While this comes with a lot -of functionality to fetch values from the command line comfortably, it has no -means in checking/ verifying input. Some of the most common tests are covered -here. All tests are designed to exit a script on failure. - -.. testcode:: argcheck - :hide: - - import os - import argparse - import tempfile - from promod3.core import argcheck - - (fh, fn) = tempfile.mkstemp(suffix='.pdb') - os.close(fh) - - p = argparse.ArgumentParser() - p.add_argument('file', type=str) - opts = p.parse_args([fn]) - - argcheck.FileExists('Test file', 1, opts.file) - - opts.name, opts.ext, opts.gz = argcheck.FileExtension('Test file', 2, - opts.file, - ('pdb', 'mmcif'), - gz=True) - - os.remove(fn) - -.. doctest:: argcheck - - import argparse - from promod3.core import argcheck - - p = argparse.ArgumentParser() - p.add_argument('file', type=str) - opts = p.parse_args() - - argcheck.FileExists('Test file', 1, opts.file) - - opts.name, opts.ext, opts.gz = argcheck.FileExtension('Test file', 2, - opts.file, - ('pdb', 'mmcif'), - gz=True) - - -File Tests --------------------------------------------------------------------------------- - -.. autofunction:: FileExtension - -.. LocalWords: currentmodule py howto argparse testcode argcheck os promod -.. LocalWords: tempfile fh fn ArgumentParser str args FileExists gz pdb -.. LocalWords: FileExtension mmcif doctest autofunction diff --git a/doc/html/_sources/core/helper.txt b/doc/html/_sources/core/helper.txt index 5de671aed8587d79f96b2995becd0d05f25de59f..3af02dfc72096745f22f1d7ab323f02100942ab8 100644 --- a/doc/html/_sources/core/helper.txt +++ b/doc/html/_sources/core/helper.txt @@ -86,3 +86,5 @@ File Tests .. autofunction:: FileExists .. autofunction:: FileExtension + +.. autofunction:: FileGzip diff --git a/doc/html/changelog.html b/doc/html/changelog.html index 25bc202bf2b266d153c186a4b92dba8d016a9639..8611701ec36c4833374e9d30e056ad31f3887971 100644 --- a/doc/html/changelog.html +++ b/doc/html/changelog.html @@ -73,6 +73,14 @@ </ul> </div></blockquote> </div> +<div class="section" id="changes-in-release-0-3-to-be-released"> +<h2>Changes in Release 0.3 (to be released)<a class="headerlink" href="#changes-in-release-0-3-to-be-released" title="Permalink to this headline">¶</a></h2> +<blockquote> +<div><ul class="simple"> +<li>merged argcheck into the helper module</li> +</ul> +</div></blockquote> +</div> </div> @@ -86,6 +94,7 @@ <li><a class="reference internal" href="#">Changelog</a><ul> <li><a class="reference internal" href="#changes-in-release-0-1">Changes in Release 0.1</a></li> <li><a class="reference internal" href="#changes-in-release-0-2">Changes in Release 0.2</a></li> +<li><a class="reference internal" href="#changes-in-release-0-3-to-be-released">Changes in Release 0.3 (to be released)</a></li> </ul> </li> </ul> diff --git a/doc/html/core/argcheck.html b/doc/html/core/argcheck.html deleted file mode 100644 index b8b373c453b3057c47c2614d6f7a6844dc61557a..0000000000000000000000000000000000000000 --- a/doc/html/core/argcheck.html +++ /dev/null @@ -1,139 +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>argcheck - Standard Tests For Command Line Arguments — 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" /> - - - <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> - </ul> - </div> - - <div class="document"> - <div class="documentwrapper"> - <div class="bodywrapper"> - <div class="body" role="main"> - - <div class="section" id="argcheck-standard-tests-for-command-line-arguments"> -<h1><code class="xref py py-mod docutils literal"><span class="pre">argcheck</span></code> - Standard Tests For Command Line Arguments<a class="headerlink" href="#argcheck-standard-tests-for-command-line-arguments" title="Permalink to this headline">¶</a></h1> -<div class="section" id="introduction"> -<h2>Introduction<a class="headerlink" href="#introduction" title="Permalink to this headline">¶</a></h2> -<p>For parsing command line arguments - -<a class="reference external" href="https://docs.python.org/2.7/howto/argparse.html#introducing-optional-arguments">optional</a> and -<a class="reference external" href="https://docs.python.org/2.7/howto/argparse.html#introducing-positional-arguments">positional</a> - -ProMod3 tools should utilise its own -<a class="reference internal" href="pm3argparse.html#module-promod3.core.pm3argparse" title="promod3.core.pm3argparse"><code class="xref py py-mod docutils literal"><span class="pre">pm3argparse</span></code></a> module. While this comes with a lot -of functionality to fetch values from the command line comfortably, it has no -means in checking/ verifying input. Some of the most common tests are covered -here. All tests are designed to exit a script on failure.</p> -<div class="highlight-python"><div class="highlight"><pre><span class="kn">import</span> <span class="nn">argparse</span> -<span class="kn">from</span> <span class="nn">promod3.core</span> <span class="kn">import</span> <span class="n">argcheck</span> - -<span class="n">p</span> <span class="o">=</span> <span class="n">argparse</span><span class="o">.</span><span class="n">ArgumentParser</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_args</span><span class="p">()</span> - -<span class="n">argcheck</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">argcheck</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">gz</span><span class="o">=</span><span class="bp">True</span><span class="p">)</span> -</pre></div> -</div> -</div> -<div class="section" id="file-tests"> -<h2>File Tests<a class="headerlink" href="#file-tests" title="Permalink to this headline">¶</a></h2> -</div> -</div> - - - </div> - </div> - </div> - <div class="sphinxsidebar" role="navigation" aria-label="main navigation"> - <div class="sphinxsidebarwrapper"> - <h3><a href="../index.html">Table Of Contents</a></h3> - <ul> -<li><a class="reference internal" href="#"><code class="docutils literal"><span class="pre">argcheck</span></code> - Standard Tests For Command Line Arguments</a><ul> -<li><a class="reference internal" href="#introduction">Introduction</a></li> -<li><a class="reference internal" href="#file-tests">File Tests</a></li> -</ul> -</li> -</ul> - - <div role="note" aria-label="source link"> - <h3>This Page</h3> - <ul class="this-page-menu"> - <li><a href="../_sources/core/argcheck.txt" - rel="nofollow">Show Source</a></li> - </ul> - </div> -<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> - - | - <a href="../_sources/core/argcheck.txt" - rel="nofollow">Page source</a></li> - </div> - - - - - </body> -</html> \ No newline at end of file diff --git a/doc/html/core/helper.html b/doc/html/core/helper.html index 1a5ccdd11af6e50776ed2f0bcb64c3c72aa9d2da..248f14588e8a21948f1ed45a50c3421468d7b8e6 100644 --- a/doc/html/core/helper.html +++ b/doc/html/core/helper.html @@ -178,6 +178,36 @@ without a ”.gz” (<a class="reference external" href="https://docs.py </table> </dd></dl> +<dl class="function"> +<dt id="promod3.core.helper.FileGzip"> +<code class="descclassname">promod3.core.helper.</code><code class="descname">FileGzip</code><span class="sig-paren">(</span><em>prefix</em>, <em>exit_status</em>, <em>filename</em>, <em>allowed=True</em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/promod3/core/helper.html#FileGzip"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#promod3.core.helper.FileGzip" title="Permalink to this definition">¶</a></dt> +<dd><p>See if a file is gzipped or not. This is basically done by checking for a +“gz” suffix. May also be used to verify that a file is not compressed where +it does not apply. That is where <em>allowed</em> comes in. If “gz” is not allowed, +terminates the script on gzip files.</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 where gzip +files are not allowed.</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 gzip files to be avoided, 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>allowed</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>) – Set to <code class="docutils literal"><span class="pre">False</span></code> if gzipped files are not allowed. Then the +script will terminate if a gzip file is found.</li> +</ul> +</td> +</tr> +<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">Flag to indicate if file is gzipped (<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>).</p> +</td> +</tr> +</tbody> +</table> +</dd></dl> + </div> </div> diff --git a/doc/html/genindex.html b/doc/html/genindex.html index 63ddd0cf605661089ae8e7e4ca7ab495000d672a..c2b808b91e0350723ae5c6374feb7c3e1f7ba635 100644 --- a/doc/html/genindex.html +++ b/doc/html/genindex.html @@ -160,10 +160,14 @@ <dt><a href="core/helper.html#promod3.core.helper.FileExists">FileExists() (in module promod3.core.helper)</a> </dt> + + <dt><a href="core/helper.html#promod3.core.helper.FileExtension">FileExtension() (in module promod3.core.helper)</a> + </dt> + </dl></td> <td style="width: 33%" valign="top"><dl> - <dt><a href="core/helper.html#promod3.core.helper.FileExtension">FileExtension() (in module promod3.core.helper)</a> + <dt><a href="core/helper.html#promod3.core.helper.FileGzip">FileGzip() (in module promod3.core.helper)</a> </dt> </dl></td> diff --git a/doc/html/index.html b/doc/html/index.html index 76891b1cf946d941b6d6655b9a99818daca9943d..48254575ac08fe6e1f353ffcd173283460e8b4fe 100644 --- a/doc/html/index.html +++ b/doc/html/index.html @@ -71,6 +71,7 @@ <li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul> <li class="toctree-l2"><a class="reference internal" href="changelog.html#changes-in-release-0-1">Changes in Release 0.1</a></li> <li class="toctree-l2"><a class="reference internal" href="changelog.html#changes-in-release-0-2">Changes in Release 0.2</a></li> +<li class="toctree-l2"><a class="reference internal" href="changelog.html#changes-in-release-0-3-to-be-released">Changes in Release 0.3 (to be released)</a></li> </ul> </li> </ul> diff --git a/doc/html/objects.inv b/doc/html/objects.inv index 77c570a218fc0d6f3a2094f0e07de7b3b61388a4..97e919fbb3e76fc22fd69ebca7e0532a5eca0d82 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 5a2a7f8ca58d73266ab40404623ddbbd5fa3209c..cf991d0c7654bc363532cf4140fa1b4aea4b026e 100644 --- a/doc/html/searchindex.js +++ b/doc/html/searchindex.js @@ -1 +1 @@ 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