Commit c8c414e2 authored by Guillaume Sagnol's avatar Guillaume Sagnol

doc+

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......@@ -406,6 +406,10 @@ dl.glossary dt {
font-size: 1.3em;
}
.sig-paren {
font-size: larger;
}
.versionmodified {
font-style: italic;
}
......@@ -471,22 +475,36 @@ table.highlighttable td {
padding: 0 0.5em 0 0.5em;
}
tt.descname {
div.code-block-filename {
padding: 2px 5px;
font-size: small;
}
div.code-block-filename code {
background-color: transparent;
}
div.code-block-filename + pre,
div.code-block-filename + div.highlight > pre {
margin-top: 0;
}
code.descname {
background-color: transparent;
font-weight: bold;
font-size: 1.2em;
}
tt.descclassname {
code.descclassname {
background-color: transparent;
}
tt.xref, a tt {
code.xref, a code {
background-color: transparent;
font-weight: bold;
}
h1 tt, h2 tt, h3 tt, h4 tt, h5 tt, h6 tt {
h1 code, h2 code, h3 code, h4 code, h5 code, h6 code {
background-color: transparent;
}
......
......@@ -13,11 +13,11 @@
.highlight .gr { color: #FF0000 } /* Generic.Error */
.highlight .gh { color: #000080; font-weight: bold } /* Generic.Heading */
.highlight .gi { color: #00A000 } /* Generic.Inserted */
.highlight .go { color: #333333 } /* Generic.Output */
.highlight .go { color: #303030 } /* Generic.Output */
.highlight .gp { color: #c65d09; font-weight: bold } /* Generic.Prompt */
.highlight .gs { font-weight: bold } /* Generic.Strong */
.highlight .gu { color: #800080; font-weight: bold } /* Generic.Subheading */
.highlight .gt { color: #0044DD } /* Generic.Traceback */
.highlight .gt { color: #0040D0 } /* Generic.Traceback */
.highlight .kc { color: #007020; font-weight: bold } /* Keyword.Constant */
.highlight .kd { color: #007020; font-weight: bold } /* Keyword.Declaration */
.highlight .kn { color: #007020; font-weight: bold } /* Keyword.Namespace */
......
......@@ -35,22 +35,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33037163-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body class="wy-body-for-nav" role="document">
......@@ -61,7 +45,9 @@
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="index.html" class="fa fa-home"> picos</a>
<a href="index.html" class="fa fa-home"> Home <img src="_static/picos_big_trans.gif" height="50px" width="200px"/> </a>
<div role="search">
<form id ="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -163,6 +149,7 @@
</ul>
</div>
&nbsp;
</nav>
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......@@ -35,22 +35,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33037163-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body class="wy-body-for-nav" role="document">
......@@ -61,7 +45,9 @@
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="index.html" class="fa fa-home"> picos</a>
<a href="index.html" class="fa fa-home"> Home <img src="_static/picos_big_trans.gif" height="50px" width="200px"/> </a>
<div role="search">
<form id ="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -163,6 +149,7 @@
</ul>
</div>
&nbsp;
</nav>
......@@ -198,19 +185,19 @@
<span id="id1"></span><h1>Download<a class="headerlink" href="#download" title="Permalink to this headline"></a></h1>
<p>The latest version of PICOS can be downloaded here:</p>
<blockquote>
<div><a class="reference external" href="dist/PICOS-1.1.0.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version110']);">picos-1.1.0</a></div></blockquote>
<div><a class="reference external" href="dist/PICOS-1.1.0.tar.gz">picos-1.1.0</a></div></blockquote>
<p>Installation instructions are explained
<a class="reference internal" href="intro.html#requirements"><em>here</em></a>.</p>
<p><strong>Older versions</strong></p>
<blockquote>
<div><p><a class="reference external" href="dist/PICOS-1.0.2.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version102']);">picos-1.0.2</a></p>
<p><a class="reference external" href="dist/PICOS-1.0.1.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version101']);">picos-1.0.1</a></p>
<p><a class="reference external" href="dist/PICOS-1.0.1.dev.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version101']);">picos-1.0.1.dev</a></p>
<p><a class="reference external" href="dist/PICOS-1.0.0.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version100']);">picos-1.0.0</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.3.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version013']);">picos-0.1.3</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.2.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version012']);">picos-0.1.2</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.1.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version011']);">picos-0.1.1</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.0.tar.gz" onClick="javascript: _gaq.push(['_trackPageview', '/downloads/version010']);">picos-0.1.0</a></p>
<div><p><a class="reference external" href="dist/PICOS-1.0.2.tar.gz">picos-1.0.2</a></p>
<p><a class="reference external" href="dist/PICOS-1.0.1.tar.gz">picos-1.0.1</a></p>
<p><a class="reference external" href="dist/PICOS-1.0.1.dev.tar.gz">picos-1.0.1.dev</a></p>
<p><a class="reference external" href="dist/PICOS-1.0.0.tar.gz">picos-1.0.0</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.3.tar.gz">picos-0.1.3</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.2.tar.gz">picos-0.1.2</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.1.tar.gz">picos-0.1.1</a></p>
<p><a class="reference external" href="dist/PICOS-0.1.0.tar.gz">picos-0.1.0</a></p>
</div></blockquote>
</div>
......
......@@ -35,22 +35,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33037163-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body class="wy-body-for-nav" role="document">
......@@ -61,7 +45,9 @@
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="index.html" class="fa fa-home"> picos</a>
<a href="index.html" class="fa fa-home"> Home <img src="_static/picos_big_trans.gif" height="50px" width="200px"/> </a>
<div role="search">
<form id ="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -163,6 +149,7 @@
</ul>
</div>
&nbsp;
</nav>
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......@@ -34,22 +34,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33037163-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body class="wy-body-for-nav" role="document">
......@@ -60,7 +44,9 @@
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="index.html" class="fa fa-home"> picos</a>
<a href="index.html" class="fa fa-home"> Home <img src="_static/picos_big_trans.gif" height="50px" width="200px"/> </a>
<div role="search">
<form id ="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -162,6 +148,7 @@
</ul>
</div>
&nbsp;
</nav>
......
......@@ -36,22 +36,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33037163-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body class="wy-body-for-nav" role="document">
......@@ -62,7 +46,9 @@
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="index.html" class="fa fa-home"> picos</a>
<a href="index.html" class="fa fa-home"> Home <img src="_static/picos_big_trans.gif" height="50px" width="200px"/> </a>
<div role="search">
<form id ="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -164,6 +150,7 @@
</ul>
</div>
&nbsp;
</nav>
......@@ -209,12 +196,12 @@ are recquired.</p>
<p class="last">Since Picos 1.0.1, it is possible to define flows on a graph
(i.e., a <a class="reference external" href="http://networkx.lanl.gov/index.html">networkx</a> object)
with the function
<a class="reference internal" href="tools.html#picos.tools.flow_Constraint" title="picos.tools.flow_Constraint"><tt class="xref py py-func docutils literal"><span class="pre">flow_Constraint()</span></tt></a>. It creates an object of the class
<tt class="xref py py-class docutils literal"><span class="pre">_Flow_Constraint</span></tt> that can be passed to a problem
with <a class="reference internal" href="problem.html#picos.Problem.add_constraint" title="picos.Problem.add_constraint"><tt class="xref py py-func docutils literal"><span class="pre">add_constraint()</span></tt></a>.
<a class="reference internal" href="tools.html#picos.tools.flow_Constraint" title="picos.tools.flow_Constraint"><code class="xref py py-func docutils literal"><span class="pre">flow_Constraint()</span></code></a>. It creates an object of the class
<code class="xref py py-class docutils literal"><span class="pre">_Flow_Constraint</span></code> that can be passed to a problem
with <a class="reference internal" href="problem.html#picos.Problem.add_constraint" title="picos.Problem.add_constraint"><code class="xref py py-func docutils literal"><span class="pre">add_constraint()</span></code></a>.
This automatically inserts a constraint for the flow conservation at each node
and the capacity constraints for each edge. We have included an example
using the function <a class="reference internal" href="tools.html#picos.tools.flow_Constraint" title="picos.tools.flow_Constraint"><tt class="xref py py-func docutils literal"><span class="pre">flow_Constraint()</span></tt></a>
using the function <a class="reference internal" href="tools.html#picos.tools.flow_Constraint" title="picos.tools.flow_Constraint"><code class="xref py py-func docutils literal"><span class="pre">flow_Constraint()</span></code></a>
for the max-flow problem below, see <a class="reference internal" href="#newversion"><em>here</em></a>.</p>
</div>
<p>We use an arbitrary graph generated by the LCF generator of the networkx package.
......@@ -261,7 +248,7 @@ such that:</p>
<div class="math">
<p><img src="_images/math/8b3fa43e388cf37f2c6338689a67db1525ddbb11.png" alt="\mathrm{value} (f) = \sum_{(s,j)\in E} f((s,j)) - \sum_{(i,s)\in E} f((i,s)) = \sum_{(i,t)\in E} f((i,t)) - \sum_{(t,j)\in E} f((t,j))."/></p>
</div><p>This problem clearly has a linear programming formulation, which
we solve below for <tt class="docutils literal"><span class="pre">s=16</span></tt> and <tt class="docutils literal"><span class="pre">t=10</span></tt>:</p>
we solve below for <code class="docutils literal"><span class="pre">s=16</span></code> and <code class="docutils literal"><span class="pre">t=10</span></code>:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">maxflow</span><span class="o">=</span><span class="n">pic</span><span class="o">.</span><span class="n">Problem</span><span class="p">()</span>
<span class="c">#source and sink nodes</span>
<span class="n">s</span><span class="o">=</span><span class="mi">16</span>
......@@ -341,7 +328,7 @@ The optimal flow has value 15.0
</pre></div>
</div>
<p id="newversion">An equivalent and faster way to define this problem is to use the
function <a class="reference internal" href="tools.html#picos.tools.flow_Constraint" title="picos.tools.flow_Constraint"><tt class="xref py py-func docutils literal"><span class="pre">flow_Constraint()</span></tt></a>:</p>
function <a class="reference internal" href="tools.html#picos.tools.flow_Constraint" title="picos.tools.flow_Constraint"><code class="xref py py-func docutils literal"><span class="pre">flow_Constraint()</span></code></a>:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">maxflow2</span><span class="o">=</span><span class="n">pic</span><span class="o">.</span><span class="n">Problem</span><span class="p">()</span>
<span class="c"># Flow variable</span>
<span class="n">f</span><span class="o">=</span><span class="p">{}</span>
......@@ -447,7 +434,7 @@ In fact, the matrix defining this LP is <em>totally unimodular</em>, from
which we know that every extreme point of the polyhedron defining the
feasible region is integral, and hence the simplex algorithm
will return a minimum cut.</p>
<p>We solve the mincut problem below, for <tt class="docutils literal"><span class="pre">s=16</span></tt> and <tt class="docutils literal"><span class="pre">t=10</span></tt>:</p>
<p>We solve the mincut problem below, for <code class="docutils literal"><span class="pre">s=16</span></code> and <code class="docutils literal"><span class="pre">t=10</span></code>:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">mincut</span><span class="o">=</span><span class="n">pic</span><span class="o">.</span><span class="n">Problem</span><span class="p">()</span>
<span class="c">#source and sink nodes</span>
......
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......@@ -35,22 +35,6 @@
<script src="https://cdnjs.cloudflare.com/ajax/libs/modernizr/2.6.2/modernizr.min.js"></script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-33037163-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
</head>
<body class="wy-body-for-nav" role="document">
......@@ -61,7 +45,9 @@
<nav data-toggle="wy-nav-shift" class="wy-nav-side">
<div class="wy-side-nav-search">
<a href="index.html" class="fa fa-home"> picos</a>
<a href="index.html" class="fa fa-home"> Home <img src="_static/picos_big_trans.gif" height="50px" width="200px"/> </a>
<div role="search">
<form id ="rtd-search-form" class="wy-form" action="search.html" method="get">
......@@ -163,6 +149,7 @@
</ul>
</div>
&nbsp;
</nav>
......@@ -424,12 +411,12 @@ features that are <em>not handled by PICOS</em>.</p>
</ul>
</div></blockquote>
<p>To use one of these solver, make sure that the python interface to this solver is correctly
installed and linked in your <tt class="docutils literal"><span class="pre">PYTHONPATH</span></tt> variable. The sites of the solvers
installed and linked in your <code class="docutils literal"><span class="pre">PYTHONPATH</span></code> variable. The sites of the solvers
give instructions to do this, except for <em>zibopt</em>, for which you must install
a separate interface: <a class="reference external" href="http://code.google.com/p/python-zibopt/">python-zibopt</a>.
To check your installation, you can simply verify that
<tt class="docutils literal"><span class="pre">import</span> <span class="pre">cvxopt</span></tt> (resp. <tt class="docutils literal"><span class="pre">smcp</span></tt>, <tt class="docutils literal"><span class="pre">mosek</span></tt>, <tt class="docutils literal"><span class="pre">cplex</span></tt>, <tt class="docutils literal"><span class="pre">zibopt</span></tt>, <tt class="docutils literal"><span class="pre">gurobipy</span></tt>) does
not raise an <tt class="docutils literal"><span class="pre">ImportError</span></tt>. The command</p>
<code class="docutils literal"><span class="pre">import</span> <span class="pre">cvxopt</span></code> (resp. <code class="docutils literal"><span class="pre">smcp</span></code>, <code class="docutils literal"><span class="pre">mosek</span></code>, <code class="docutils literal"><span class="pre">cplex</span></code>, <code class="docutils literal"><span class="pre">zibopt</span></code>, <code class="docutils literal"><span class="pre">gurobipy</span></code>) does
not raise an <code class="docutils literal"><span class="pre">ImportError</span></code>. The command</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">picos</span><span class="p">;</span><span class="n">picos</span><span class="o">.</span><span class="n">tools</span><span class="o">.</span><span class="n">available_solvers</span><span class="p">()</span>
</pre></div>
</div>
......@@ -441,7 +428,7 @@ not raise an <tt class="docutils literal"><span class="pre">ImportError</span></
and
<a class="reference external" href="http://abel.ee.ucla.edu/cvxopt/">cvxopt</a>. (cvxopt is needed even if you
do not use the cvxopt solvers, because picos relies on the
<tt class="xref py py-func docutils literal"><span class="pre">sparse</span> <span class="pre">matrices</span></tt> defined in cvxopt.)</p>
<code class="xref py py-func docutils literal"><span class="pre">sparse</span> <span class="pre">matrices</span></code> defined in cvxopt.)</p>
<p>In addition, you must install separately the python interfaces to each <a class="reference internal" href="#solvers"><em>solver</em></a>
you want to use.</p>
</div>
......@@ -450,27 +437,27 @@ you want to use.</p>
<p>After having <a class="reference internal" href="download.html#download"><em>downloaded</em></a> the latest version of picos,
and extracted it in the directory of your choice,
you can install it by typing the following line as root in a terminal:</p>
<div class="highlight-guess"><div class="highlight"><pre><span class="err">$</span> <span class="n">python</span> <span class="n">setup</span><span class="p">.</span><span class="n">py</span> <span class="n">install</span>
<div class="highlight-guess"><div class="highlight"><pre><span class="nv">$</span> <span class="nv">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
</pre></div>
</div>
<p>If you do not have administrator rights, you can also do a local
installation of picos with the <em>prefix scheme</em>. For example:</p>
<div class="highlight-guess"><div class="highlight"><pre><span class="err">$</span> <span class="n">python</span> <span class="n">setup</span><span class="p">.</span><span class="n">py</span> <span class="n">install</span> <span class="o">--</span><span class="n">prefix</span> <span class="o">~/</span><span class="n">python</span>
<div class="highlight-guess"><div class="highlight"><pre><span class="nv">$</span> <span class="nv">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span> <span class="o">--</span><span class="n">prefix</span> <span class="o">~/</span><span class="n">python</span>
</pre></div>
</div>
<p>and make sure that <tt class="docutils literal"><span class="pre">$HOME'/python/lib/python2.x/site-packages/'</span></tt>
is in your <tt class="docutils literal"><span class="pre">PYTHONPATH</span></tt> variable.</p>
<p>and make sure that <code class="docutils literal"><span class="pre">$HOME'/python/lib/python2.x/site-packages/'</span></code>
is in your <code class="docutils literal"><span class="pre">PYTHONPATH</span></code> variable.</p>
<p>To test your installation, you can run the test file:</p>
<div class="highlight-guess"><div class="highlight"><pre><span class="err">$</span> <span class="n">python</span> <span class="n">picos</span><span class="o">/</span><span class="n">test_picos</span><span class="p">.</span><span class="n">py</span>
<div class="highlight-guess"><div class="highlight"><pre><span class="nv">$</span> <span class="nv">python</span> <span class="n">picos</span><span class="o">/</span><span class="n">test_picos</span><span class="o">.</span><span class="n">py</span>
</pre></div>
</div>
<p>This will generate a table with a list of results
for each available solver and class of optimization problems.</p>
<p>Alternatively, you can clone the latest development version from <a class="reference external" href="http://github.com/gsagnol/picos">github</a>:</p>
<div class="highlight-guess"><div class="highlight"><pre><span class="err">$</span> <span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="o">:</span><span class="c1">//github.com/gsagnol/picos.git</span>
<div class="highlight-guess"><div class="highlight"><pre><span class="nv">$</span> <span class="nv">git</span> <span class="n">clone</span> <span class="n">https:</span><span class="sr">//gi</span><span class="n">thub</span><span class="o">.</span><span class="n">com</span><span class="sr">/gsagnol/</span><span class="n">picos</span><span class="o">.</span><span class="n">git</span>
</pre></div>
</div>
<p>in a directory that lies in your <tt class="docutils literal"><span class="pre">PYTHONPATH</span></tt>.</p>
<p>in a directory that lies in your <code class="docutils literal"><span class="pre">PYTHONPATH</span></code>.</p>
</div>
<div class="section" id="license">
<h2>License<a class="headerlink" href="#license" title="Permalink to this headline"></a></h2>
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