python-pebl-doc 1.0.2-3 / usr / share / doc / python-pebl / html / config.html

This file is indexed.

/usr/share/doc/python-pebl/html/config.html is in python-pebl-doc 1.0.2-3.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below. 

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
<!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>config – Pebl’s configuration system &mdash; Pebl 1.0.1 documentation</title>
    
    <link rel="stylesheet" href="_static/default.css" type="text/css" />
    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
    
    <script type="text/javascript">
      var DOCUMENTATION_OPTIONS = {
        URL_ROOT:    './',
        VERSION:     '1.0.1',
        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="Pebl 1.0.1 documentation" href="index.html" />
    <link rel="up" title="API Reference" href="apiref.html" />
    <link rel="next" title="cpd – Conditional probability distributions" href="cpd.html" />
    <link rel="prev" title="API Reference" href="apiref.html" /> 
  </head>
  <body>
    <div class="related">
      <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="right" >
          <a href="cpd.html" title="cpd – Conditional probability distributions"
             accesskey="N">next</a> |</li>
        <li class="right" >
          <a href="apiref.html" title="API Reference"
             accesskey="P">previous</a> |</li>
        <li><a href="index.html">Pebl 1.0.1 documentation</a> &raquo;</li>
          <li><a href="apiref.html" accesskey="U">API Reference</a> &raquo;</li> 
      </ul>
    </div>  

    <div class="document">
      <div class="documentwrapper">
        <div class="bodywrapper">
          <div class="body">
            
  <div class="section" id="module-pebl.config">
<span id="config-pebl-s-configuration-system"></span><h1><tt class="xref py py-mod docutils literal"><span class="pre">config</span></tt> &#8211; Pebl&#8217;s configuration system<a class="headerlink" href="#module-pebl.config" title="Permalink to this headline"></a></h1>
<p>The config module defines a set of parameter types and functions to validate
user input. A module or class can define a parameter by creating an instance of
one of the Parameter classes &#8211; it is automatically registered with the config
module. Many modules provide a fromconfig() factory function that create and
return a parametrized object.</p>
<div class="section" id="specifying-parameters">
<h2>Specifying Parameters<a class="headerlink" href="#specifying-parameters" title="Permalink to this headline"></a></h2>
<p>A Parameter definition requires the following:</p>
<blockquote>
<div><ul>
<li><p class="first">a name of the form section.option
(examples: data.filename, result.format)</p>
</li>
<li><p class="first">a short description</p>
</li>
<li><p class="first">a validator function</p>
<p>The function has one argument: the string value of the parameter. It
should return true if the value is valid and false otherwise.  The config
module includes several factory functions that create
validator functions. See section on validator factories.</p>
</li>
<li><p class="first">a default value specified as a string</p>
</li>
</ul>
</div></blockquote>
<div class="section" id="example-parameter-definitions">
<h3>Example parameter definitions<a class="headerlink" href="#example-parameter-definitions" title="Permalink to this headline"></a></h3>
<p>From the pebl.data module:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">_pfilename</span> <span class="o">=</span> <span class="n">config</span><span class="o">.</span><span class="n">StringParameter</span><span class="p">(</span>
    <span class="s">&#39;data.filename&#39;</span><span class="p">,</span>
    <span class="s">&#39;File to read data from.&#39;</span><span class="p">,</span>
    <span class="n">config</span><span class="o">.</span><span class="n">fileexists</span><span class="p">(),</span>
<span class="p">)</span>
</pre></div>
</div>
<p>In the above example, the config.fileexists() function returns a validator
function that checks whether the file exists.</p>
<p>From the pebl.result module:</p>
<div class="highlight-python"><div class="highlight"><pre>_psize = config.IntParameter(
    &#39;result.numnetworks&#39;,
    \&quot;\&quot;\&quot;Number of top-scoring networks to save. Specify 0 to indicate that
    all scored networks should be saved.\&quot;\&quot;\&quot;,
    default=1000
)
</pre></div>
</div>
<p>In the above example, The IntParameter subclass of Parameter automatically
checks whether the parameter value is an integer and raises an error if it is
not. It thus does not require an additional validator.</p>
</div>
</div>
<div class="section" id="parameter-types">
<h2>Parameter Types<a class="headerlink" href="#parameter-types" title="Permalink to this headline"></a></h2>
<dl class="class">
<dt id="pebl.config.StringParameter">
<em class="property">class </em><tt class="descclassname">pebl.config.</tt><tt class="descname">StringParameter</tt><big>(</big><em>name</em>, <em>description</em>, <em>validator=&lt;function default_validator at 0x7f94304de578&gt;</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#pebl.config.StringParameter" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="class">
<dt id="pebl.config.IntParameter">
<em class="property">class </em><tt class="descclassname">pebl.config.</tt><tt class="descname">IntParameter</tt><big>(</big><em>name</em>, <em>description</em>, <em>validator=&lt;function default_validator at 0x7f94304de578&gt;</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#pebl.config.IntParameter" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="class">
<dt id="pebl.config.FloatParameter">
<em class="property">class </em><tt class="descclassname">pebl.config.</tt><tt class="descname">FloatParameter</tt><big>(</big><em>name</em>, <em>description</em>, <em>validator=&lt;function default_validator at 0x7f94304de578&gt;</em>, <em>default=None</em><big>)</big><a class="headerlink" href="#pebl.config.FloatParameter" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

</div>
<div class="section" id="validator-factories">
<h2>Validator Factories<a class="headerlink" href="#validator-factories" title="Permalink to this headline"></a></h2>
<p>The following functions create validator functions.</p>
<dl class="function">
<dt id="pebl.config.between">
<tt class="descclassname">pebl.config.</tt><tt class="descname">between</tt><big>(</big><em>min</em>, <em>max</em><big>)</big><a class="headerlink" href="#pebl.config.between" title="Permalink to this definition"></a></dt>
<dd><p>Returns validator that checks whether value is between min and max.</p>
</dd></dl>

<dl class="function">
<dt id="pebl.config.oneof">
<tt class="descclassname">pebl.config.</tt><tt class="descname">oneof</tt><big>(</big><em>*values</em><big>)</big><a class="headerlink" href="#pebl.config.oneof" title="Permalink to this definition"></a></dt>
<dd><p>Returns validator that checks whether value is in approved list.</p>
</dd></dl>

<dl class="function">
<dt id="pebl.config.atleast">
<tt class="descclassname">pebl.config.</tt><tt class="descname">atleast</tt><big>(</big><em>min</em><big>)</big><a class="headerlink" href="#pebl.config.atleast" title="Permalink to this definition"></a></dt>
<dd><p>Returns validator that checks whether value is &gt; min.</p>
</dd></dl>

<dl class="function">
<dt id="pebl.config.atmost">
<tt class="descclassname">pebl.config.</tt><tt class="descname">atmost</tt><big>(</big><em>max</em><big>)</big><a class="headerlink" href="#pebl.config.atmost" title="Permalink to this definition"></a></dt>
<dd><p>Returns validator that checks whether value is &lt; max.</p>
</dd></dl>

<dl class="function">
<dt id="pebl.config.fileexists">
<tt class="descclassname">pebl.config.</tt><tt class="descname">fileexists</tt><big>(</big><big>)</big><a class="headerlink" href="#pebl.config.fileexists" title="Permalink to this definition"></a></dt>
<dd><p>Returns validator that checks whether value is an existing file.</p>
</dd></dl>

</div>
<div class="section" id="using-parameters">
<h2>Using Parameters<a class="headerlink" href="#using-parameters" title="Permalink to this headline"></a></h2>
<p>Parameters can be set with the config.set function or in a configuration file.
The config file should be in a format compatible with Python&#8217;s ConfigParser
module.</p>
<p>Specifying parameter values using a config file:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="p">[</span><span class="n">data</span><span class="p">]</span>
<span class="n">filename</span> <span class="o">=</span> <span class="n">example_data</span><span class="o">.</span><span class="n">txt</span>

<span class="p">[</span><span class="n">result</span><span class="p">]</span>
<span class="n">format</span><span class="o">=</span><span class="n">html</span>
</pre></div>
</div>
<p>Specifying parameter values using config.set:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">pebl</span> <span class="kn">import</span> <span class="n">config</span>
<span class="n">config</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&#39;data.filename&#39;</span><span class="p">,</span> <span class="s">&#39;example_data.txt&#39;</span><span class="p">)</span>
<span class="n">config</span><span class="o">.</span><span class="n">set</span><span class="p">(</span><span class="s">&#39;result.format&#39;</span><span class="p">,</span> <span class="s">&#39;html&#39;</span><span class="p">)</span>
</pre></div>
</div>
<dl class="function">
<dt id="pebl.config.set">
<tt class="descclassname">pebl.config.</tt><tt class="descname">set</tt><big>(</big><em>name</em>, <em>value</em>, <em>source='config.set'</em><big>)</big><a class="headerlink" href="#pebl.config.set" title="Permalink to this definition"></a></dt>
<dd><p>Set a parameter value.</p>
<ul class="simple">
<li>name should be of the form &#8220;section.name&#8221;.</li>
<li>value can be a string which will be casted to the required datatype.</li>
<li>source specifies where this parameter value was specified (config file,
command line, interactive shell, etc).</li>
</ul>
</dd></dl>

<p>The following functions are used for reading, getting, writing and listing
parameters.</p>
<dl class="function">
<dt id="pebl.config.read">
<tt class="descclassname">pebl.config.</tt><tt class="descname">read</tt><big>(</big><em>filename</em><big>)</big><a class="headerlink" href="#pebl.config.read" title="Permalink to this definition"></a></dt>
<dd><p>Reads parameter from config file.</p>
<p>Config files should conform to the format specified in the ConfigParser
module from Python&#8217;s standard library. A Parameter&#8217;s name has two parts:
the section and the option name.  These correspond to &#8216;section&#8217; and
&#8216;option&#8217; as defined in ConfigParser.</p>
<p>For example, parameter &#8216;foo.bar&#8217; would be specified in the config file as:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="p">[</span><span class="n">foo</span><span class="p">]</span>
<span class="n">bar</span> <span class="o">=</span> <span class="mi">5</span>
</pre></div>
</div>
</dd></dl>

<dl class="function">
<dt id="pebl.config.get">
<tt class="descclassname">pebl.config.</tt><tt class="descname">get</tt><big>(</big><em>name</em><big>)</big><a class="headerlink" href="#pebl.config.get" title="Permalink to this definition"></a></dt>
<dd><p>Returns value of parameter.</p>
<p>Raises KeyError if parameter not found.
Examples:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="kn">from</span> <span class="nn">pebl</span> <span class="kn">import</span> <span class="n">config</span>
<span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;data.filename&#39;</span><span class="p">)</span>
<span class="n">config</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;result.format&#39;</span><span class="p">)</span>
</pre></div>
</div>
<p>The value returned could be the default value or the latest value set using
config.set or config.read</p>
</dd></dl>

<dl class="function">
<dt id="pebl.config.write">
<tt class="descclassname">pebl.config.</tt><tt class="descname">write</tt><big>(</big><em>filename</em>, <em>include_defaults=False</em><big>)</big><a class="headerlink" href="#pebl.config.write" title="Permalink to this definition"></a></dt>
<dd><p>Writes parameters to config file.</p>
<p>If include_default is True, writes all parameters. Else, only writes
parameters that were specifically set (via config file, command line, etc).</p>
</dd></dl>

<dl class="function">
<dt id="pebl.config.parameters">
<tt class="descclassname">pebl.config.</tt><tt class="descname">parameters</tt><big>(</big><em>section=None</em><big>)</big><a class="headerlink" href="#pebl.config.parameters" title="Permalink to this definition"></a></dt>
<dd><p>Returns list of parameters.</p>
<p>If section is specified, returns parameters for that section only.
section can be a section name or a search string to use with
string.startswith(..)</p>
</dd></dl>

<dl class="function">
<dt id="pebl.config.configobj">
<tt class="descclassname">pebl.config.</tt><tt class="descname">configobj</tt><big>(</big><em>params</em><big>)</big><a class="headerlink" href="#pebl.config.configobj" title="Permalink to this definition"></a></dt>
<dd><p>Given a list of parameters, returns a ConfigParser object.</p>
<p>This function can be used to convert a list of parameters to a config
object which can then be written to file.</p>
</dd></dl>

</div>
</div>


          </div>
        </div>
      </div>
      <div class="sphinxsidebar">
        <div class="sphinxsidebarwrapper">
  <h3><a href="index.html">Table Of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#"><tt class="docutils literal"><span class="pre">config</span></tt> &#8211; Pebl&#8217;s configuration system</a><ul>
<li><a class="reference internal" href="#specifying-parameters">Specifying Parameters</a><ul>
<li><a class="reference internal" href="#example-parameter-definitions">Example parameter definitions</a></li>
</ul>
</li>
<li><a class="reference internal" href="#parameter-types">Parameter Types</a></li>
<li><a class="reference internal" href="#validator-factories">Validator Factories</a></li>
<li><a class="reference internal" href="#using-parameters">Using Parameters</a></li>
</ul>
</li>
</ul>

  <h4>Previous topic</h4>
  <p class="topless"><a href="apiref.html"
                        title="previous chapter">API Reference</a></p>
  <h4>Next topic</h4>
  <p class="topless"><a href="cpd.html"
                        title="next chapter"><tt class="docutils literal"><span class="pre">cpd</span></tt> &#8211; Conditional probability distributions</a></p>
  <h3>This Page</h3>
  <ul class="this-page-menu">
    <li><a href="_sources/config.txt"
           rel="nofollow">Show Source</a></li>
  </ul>
<div id="searchbox" style="display: none">
  <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="related">
      <h3>Navigation</h3>
      <ul>
        <li class="right" style="margin-right: 10px">
          <a href="genindex.html" title="General Index"
             >index</a></li>
        <li class="right" >
          <a href="py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
        <li class="right" >
          <a href="cpd.html" title="cpd – Conditional probability distributions"
             >next</a> |</li>
        <li class="right" >
          <a href="apiref.html" title="API Reference"
             >previous</a> |</li>
        <li><a href="index.html">Pebl 1.0.1 documentation</a> &raquo;</li>
          <li><a href="apiref.html" >API Reference</a> &raquo;</li> 
      </ul>
    </div>
    <div class="footer">
        &copy; Copyright 2008, Abhik Shah.
      Last updated on Aug 18, 2015.
      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
    </div>
  </body>
</html>

APT Browse - Built by Thomas Orozco.