-
Notifications
You must be signed in to change notification settings - Fork 0
/
installation.html
226 lines (216 loc) · 12.9 KB
/
installation.html
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
<!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>Installation — PERI 0.1.2 documentation</title>
<link rel="stylesheet" href="_static/nature.css" type="text/css" />
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<script type="text/javascript">
var DOCUMENTATION_OPTIONS = {
URL_ROOT: './',
VERSION: '0.1.2',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
HAS_SOURCE: true,
SOURCELINK_SUFFIX: '.txt'
};
</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>
<script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.0/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
<script type="text/javascript" src="_static/mathconf.js"></script>
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
<link rel="next" title="PERI Walkthrough" href="walkthrough.html" />
<link rel="prev" title="Welcome to PERI’s documentation!" href="index.html" />
</head>
<body>
<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="right" >
<a href="walkthrough.html" title="PERI Walkthrough"
accesskey="N">next</a> |</li>
<li class="right" >
<a href="index.html" title="Welcome to PERI’s documentation!"
accesskey="P">previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">PERI 0.1.2 documentation</a> »</li>
</ul>
</div>
<div class="document">
<div class="documentwrapper">
<div class="bodywrapper">
<div class="body" role="main">
<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<div class="section" id="id1">
<h2>Installation<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h2>
<p>The Python package <code class="docutils literal"><span class="pre">peri</span></code> is compatible with most platforms including Linux,
Mac, and Windows. Currently we are only compatible with Python 2.7.x but very
close to Python 3.x compatibility. In order to run <code class="docutils literal"><span class="pre">peri</span></code> you must have a
modern installation of Python. On all platforms, we recommend using the new
<a class="reference external" href="https://www.continuum.io/downloads">Anaconda</a>. However, any modern
distribution of Python will work. For example, on Linux, you can you the system
Python installed by default (via <code class="docutils literal"><span class="pre">apt-get</span> <span class="pre">install</span> <span class="pre">python</span></code>). On Mac, you can
use the system Python or one installed from macports / brew.</p>
<div class="section" id="quick-install">
<h3>Quick install<a class="headerlink" href="#quick-install" title="Permalink to this headline">¶</a></h3>
<p>Official releases of <code class="docutils literal"><span class="pre">peri</span></code> are provided on <a class="reference external" href="http://pypi.python.org">PyPI.org</a>, a.k.a. the <a class="reference external" href="https://wiki.python.org/moin/CheeseShop">‘cheeseshop’</a>. You can access the source
distribution files there at <a class="reference external" href="https://pypi.python.org/pypi/peri/">peri</a> or
using the common packaging tools provided with Python. The quickest way is to
run:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="n">peri</span>
</pre></div>
</div>
<p>This will install <code class="docutils literal"><span class="pre">peri</span></code> onto your <code class="code docutils literal"><span class="pre">PYTHONPATH</span></code>. Make sure that the
appropriate path is also added to your path so the <code class="docutils literal"><span class="pre">peri</span></code> executable is
available. It can be found in <code class="code docutils literal"><span class="pre">$PYTHONPATH/bin</span></code>.</p>
<p>If you don’t have Python, you’ll first need to install 64-bit Python,
version 2.7. Download <a class="reference external" href="https://www.python.org/downloads/">Python</a>.</p>
<dl class="docutils">
<dt>In addition, you’ll want 64-bit versions of the following packages</dt>
<dd><ul class="first last simple">
<li><code class="docutils literal"><span class="pre">numpy</span></code> (required)</li>
<li><code class="docutils literal"><span class="pre">scipy</span></code> (required)</li>
<li><code class="docutils literal"><span class="pre">matplotlib</span></code> (required)</li>
<li><code class="docutils literal"><span class="pre">pillow</span></code> (required)</li>
<li><code class="docutils literal"><span class="pre">pyfftw</span></code> (makes calculations <em>much</em> faster; all-but-required)</li>
<li><code class="docutils literal"><span class="pre">trackpy</span></code> (useful for analyzing the results and getting initial guesses;
not required)</li>
</ul>
</dd>
</dl>
<p>Running <code class="docutils literal"><span class="pre">pip</span> <span class="pre">install</span> <span class="pre">peri</span></code> should install <code class="docutils literal"><span class="pre">peri</span></code> and its dependencies
automatically. Sometimes I have trouble with dependencies on Windows machines.
To get around this, try downloading the <a class="reference external" href="https://www.continuum.io/downloads">Anaconda</a> Python distribution,
which includes nearly all of the <code class="docutils literal"><span class="pre">peri</span></code> dependencies. Alternatively, you can
download the dependencies in 64-bit from Christopher Gohlke’s helpful website
<a class="reference external" href="http://www.lfd.uci.edu/~gohlke/pythonlibs/">here</a>.</p>
</div>
<div class="section" id="source-code">
<h3>Source code<a class="headerlink" href="#source-code" title="Permalink to this headline">¶</a></h3>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">Development builds of PERI may be unstable and not suitable for production
use, install at your own risk.</p>
</div>
<p>Alternatively, you may install the development version from source. Currently,
the repository is hosted on <a class="reference external" href="https://github.com/peri-source/peri">GitHub</a>.
To download and install from source you can clone and install:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">peri</span><span class="o">-</span><span class="n">source</span><span class="o">/</span><span class="n">peri</span><span class="o">.</span><span class="n">git</span>
<span class="n">cd</span> <span class="n">peri</span><span class="o">/</span>
<span class="n">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>After that, given you have properly set your <code class="code docutils literal"><span class="pre">PATH</span></code> variables (see
above), you should have <code class="code docutils literal"><span class="pre">peri</span></code> on the command line.</p>
<p>Source releases are also tagged on GitHub and can be accessed from the cloned
repository. To install a particular release, go to the cloned repo and
checkout the desired tags. These tags can be listed from command line:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">tag</span> <span class="o">-</span><span class="n">l</span>
<span class="n">git</span> <span class="n">checkout</span> <span class="o"><</span><span class="n">tag</span> <span class="n">name</span><span class="o">></span>
<span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
</pre></div>
</div>
</div>
</div>
<div class="section" id="contributing">
<h2>Contributing<a class="headerlink" href="#contributing" title="Permalink to this headline">¶</a></h2>
<p>If you find that featuring performance is poor for a particular image or you
encounter a bug / issue, please reach out to the developers.</p>
<div class="section" id="bugs-and-issues">
<h3>Bugs and issues<a class="headerlink" href="#bugs-and-issues" title="Permalink to this headline">¶</a></h3>
<p>Bugs and issues are currently reported through GitHub <a class="reference external" href="https://github.com/peri-source/peri/issues">issues</a>. In order to help us as much as
possible to resolve the issue, please enable the highest verbosity in the
<code class="docutils literal"><span class="pre">peri</span></code> logging system (<a class="reference internal" href="reference/logger.html#module-peri.logger" title="peri.logger"><code class="xref py py-class docutils literal"><span class="pre">logger</span></code></a>) and upload your logs along with a
link to the image and run script / command line to the issue tracker.</p>
</div>
<div class="section" id="id3">
<h3>Contributing<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
<div class="admonition-todo admonition" id="index-0">
<p class="first admonition-title">Todo</p>
<p class="last">Create a contributing doc which describes how to become a developer</p>
</div>
</div>
</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="#">Installation</a><ul>
<li><a class="reference internal" href="#id1">Installation</a><ul>
<li><a class="reference internal" href="#quick-install">Quick install</a></li>
<li><a class="reference internal" href="#source-code">Source code</a></li>
</ul>
</li>
<li><a class="reference internal" href="#contributing">Contributing</a><ul>
<li><a class="reference internal" href="#bugs-and-issues">Bugs and issues</a></li>
<li><a class="reference internal" href="#id3">Contributing</a></li>
</ul>
</li>
</ul>
</li>
</ul>
<h4>Previous topic</h4>
<p class="topless"><a href="index.html"
title="previous chapter">Welcome to PERI’s documentation!</a></p>
<h4>Next topic</h4>
<p class="topless"><a href="walkthrough.html"
title="next chapter">PERI Walkthrough</a></p>
<div role="note" aria-label="source link">
<h3>This Page</h3>
<ul class="this-page-menu">
<li><a href="_sources/installation.rst.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">
<div><input type="text" name="q" /></div>
<div><input type="submit" value="Go" /></div>
<input type="hidden" name="check_keywords" value="yes" />
<input type="hidden" name="area" value="default" />
</form>
</div>
<script type="text/javascript">$('#searchbox').show(0);</script>
</div>
</div>
<div class="clearer"></div>
</div>
<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"
>index</a></li>
<li class="right" >
<a href="py-modindex.html" title="Python Module Index"
>modules</a> |</li>
<li class="right" >
<a href="walkthrough.html" title="PERI Walkthrough"
>next</a> |</li>
<li class="right" >
<a href="index.html" title="Welcome to PERI’s documentation!"
>previous</a> |</li>
<li class="nav-item nav-item-0"><a href="index.html">PERI 0.1.2 documentation</a> »</li>
</ul>
</div>
<div class="footer" role="contentinfo">
© Copyright 2016, Matt Bierbaum, Brian Leahy.
Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.6.2.
</div>
</body>
</html>