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docstring edits for PEP8 compliance

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1 parent d3385b7 commit 27562e4a53d5871ab5fda7d6ede7c9cc757a70ea @tyarkoni tyarkoni committed Dec 30, 2014
Showing with 315 additions and 12,991 deletions.
  1. +3 −1 .gitignore
  2. +9 −6 MANIFEST
  3. BIN docs/_build/doctrees/environment.pickle
  4. BIN docs/_build/doctrees/index.doctree
  5. BIN docs/_build/doctrees/neurosynth.analysis.doctree
  6. BIN docs/_build/doctrees/neurosynth.base.doctree
  7. BIN docs/_build/doctrees/neurosynth.doctree
  8. BIN docs/_build/doctrees/neurosynth.tests.doctree
  9. +0 −4 docs/_build/html/.buildinfo
  10. +0 −106 docs/_build/html/_modules/index.html
  11. +0 −131 docs/_build/html/_modules/neurosynth.html
  12. +0 −509 docs/_build/html/_modules/neurosynth/analysis/classify.html
  13. +0 −379 docs/_build/html/_modules/neurosynth/analysis/cluster.html
  14. +0 −295 docs/_build/html/_modules/neurosynth/analysis/decode.html
  15. +0 −296 docs/_build/html/_modules/neurosynth/analysis/meta.html
  16. +0 −135 docs/_build/html/_modules/neurosynth/analysis/network.html
  17. +0 −212 docs/_build/html/_modules/neurosynth/analysis/reduce.html
  18. +0 −163 docs/_build/html/_modules/neurosynth/analysis/stats.html
  19. +0 −707 docs/_build/html/_modules/neurosynth/base/dataset.html
  20. +0 −346 docs/_build/html/_modules/neurosynth/base/imageutils.html
  21. +0 −195 docs/_build/html/_modules/neurosynth/base/lexparser.html
  22. +0 −169 docs/_build/html/_modules/neurosynth/base/mappable.html
  23. +0 −338 docs/_build/html/_modules/neurosynth/base/mask.html
  24. +0 −160 docs/_build/html/_modules/neurosynth/base/transformations.html
  25. +0 −175 docs/_build/html/_modules/neurosynth/tests/test_analysis.html
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  28. +0 −23 docs/_build/html/_sources/index.txt
  29. +0 −78 docs/_build/html/_sources/neurosynth.analysis.txt
  30. +0 −62 docs/_build/html/_sources/neurosynth.base.txt
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  33. +0 −464 docs/_build/html/_static/agogo.css
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  36. BIN docs/_build/html/_static/bgfooter.png
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  39. BIN docs/_build/html/_static/comment-close.png
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  41. BIN docs/_build/html/_static/contents.png
  42. +0 −1 docs/_build/html/_static/css/badge_only.css
  43. +0 −4 docs/_build/html/_static/css/theme.css
  44. +0 −256 docs/_build/html/_static/default.css
  45. +0 −238 docs/_build/html/_static/doctools.js
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  58. +0 −63 docs/_build/html/_static/pygments.css
  59. +0 −622 docs/_build/html/_static/searchtools.js
  60. +0 −159 docs/_build/html/_static/sidebar.js
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  72. BIN docs/_build/html/objects.inv
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  74. +0 −105 docs/_build/html/search.html
  75. +0 −1 docs/_build/html/searchindex.js
  76. +1 −0 docs/conf.py
  77. +7 −0 docs/modules.rst
  78. +294 −225 neurosynth/base/dataset.py
  79. +1 −1 setup.py
View
@@ -4,4 +4,6 @@
build/
dist
dist/*
-.ipynb_checkpoints
+.ipynb_checkpoints
+docs/_*/*
+neurosynth.egg-info
View
@@ -4,41 +4,42 @@ LICENSE
README.md
setup.cfg
setup.py
-examples/.DS_Store
examples/classify_regions_using_features.ipynb
examples/create_a_full_set_of_meta_analysis_images.py
examples/create_a_new_dataset_and_load_features.py
examples/decode_images.py
examples/identify_regions_coactivated_with_ROI.ipynb
examples/neurosynth_demo.ipynb
examples/neurosynth_demo.py
-neurosynth/.DS_Store
+examples/.ipynb_checkpoints/neurosynth_demo-checkpoint.ipynb
neurosynth/__init__.py
neurosynth/__init__.pyc
neurosynth/version.py
neurosynth/version.pyc
-neurosynth/analysis/.DS_Store
neurosynth/analysis/__init__.py
neurosynth/analysis/__init__.pyc
neurosynth/analysis/classify.py
+neurosynth/analysis/classify.pyc
+neurosynth/analysis/cluster.py
+neurosynth/analysis/cluster.pyc
neurosynth/analysis/decode.py
neurosynth/analysis/decode.pyc
neurosynth/analysis/meta.py
-neurosynth/analysis/misc.py
-neurosynth/analysis/ml.py
+neurosynth/analysis/meta.pyc
neurosynth/analysis/network.py
neurosynth/analysis/plotutils.py
neurosynth/analysis/reduce.py
+neurosynth/analysis/reduce.pyc
neurosynth/analysis/stats.py
neurosynth/analysis/stats.pyc
-neurosynth/base/.DS_Store
neurosynth/base/__init__.py
neurosynth/base/__init__.pyc
neurosynth/base/dataset.py
neurosynth/base/dataset.pyc
neurosynth/base/imageutils.py
neurosynth/base/imageutils.pyc
neurosynth/base/lexparser.py
+neurosynth/base/lexparser.pyc
neurosynth/base/mappable.py
neurosynth/base/mappable.pyc
neurosynth/base/mask.py
@@ -48,6 +49,8 @@ neurosynth/base/transformations.pyc
neurosynth/resources/MNI152_T1_2mm_brain.nii.gz
neurosynth/tests/__init__.py
neurosynth/tests/__init__.pyc
+neurosynth/tests/lextab.pyc
+neurosynth/tests/parsetab.pyc
neurosynth/tests/test_analysis.py
neurosynth/tests/test_analysis.pyc
neurosynth/tests/test_base.py
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@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c98057ac3d0b144629e82e2906711f8b
-tags: 645f666f9bcd5a90fca523b33c5a78b7
@@ -1,106 +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>Overview: module code &mdash; neurosynth documentation</title>
-
- <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
- <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '',
- 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="neurosynth documentation" href="../index.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><a href="../index.html">neurosynth documentation</a> &raquo;</li>
- </ul>
- </div>
- <div class="sphinxsidebar">
- <div class="sphinxsidebarwrapper">
-<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="document">
- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body">
-
- <h1>All modules for which code is available</h1>
-<ul><li><a href="neurosynth.html">neurosynth</a></li>
-<ul><li><a href="neurosynth/analysis/classify.html">neurosynth.analysis.classify</a></li>
-<li><a href="neurosynth/analysis/cluster.html">neurosynth.analysis.cluster</a></li>
-<li><a href="neurosynth/analysis/decode.html">neurosynth.analysis.decode</a></li>
-<li><a href="neurosynth/analysis/meta.html">neurosynth.analysis.meta</a></li>
-<li><a href="neurosynth/analysis/network.html">neurosynth.analysis.network</a></li>
-<li><a href="neurosynth/analysis/reduce.html">neurosynth.analysis.reduce</a></li>
-<li><a href="neurosynth/analysis/stats.html">neurosynth.analysis.stats</a></li>
-<li><a href="neurosynth/base/dataset.html">neurosynth.base.dataset</a></li>
-<li><a href="neurosynth/base/imageutils.html">neurosynth.base.imageutils</a></li>
-<li><a href="neurosynth/base/lexparser.html">neurosynth.base.lexparser</a></li>
-<li><a href="neurosynth/base/mappable.html">neurosynth.base.mappable</a></li>
-<li><a href="neurosynth/base/mask.html">neurosynth.base.mask</a></li>
-<li><a href="neurosynth/base/transformations.html">neurosynth.base.transformations</a></li>
-<li><a href="neurosynth/tests/test_analysis.html">neurosynth.tests.test_analysis</a></li>
-<li><a href="neurosynth/tests/test_base.html">neurosynth.tests.test_base</a></li>
-<li><a href="neurosynth/tests/utils.html">neurosynth.tests.utils</a></li>
-</ul></ul>
-
- </div>
- </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><a href="../index.html">neurosynth documentation</a> &raquo;</li>
- </ul>
- </div>
- <div class="footer">
- &copy; Copyright 2014, Tal Yarkoni.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
- </div>
- </body>
-</html>
@@ -1,131 +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>neurosynth &mdash; neurosynth documentation</title>
-
- <link rel="stylesheet" href="../_static/sphinxdoc.css" type="text/css" />
- <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-
- <script type="text/javascript">
- var DOCUMENTATION_OPTIONS = {
- URL_ROOT: '../',
- VERSION: '',
- 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="neurosynth documentation" href="../index.html" />
- <link rel="up" title="Module code" href="index.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><a href="../index.html">neurosynth documentation</a> &raquo;</li>
- <li><a href="index.html" accesskey="U">Module code</a> &raquo;</li>
- </ul>
- </div>
- <div class="sphinxsidebar">
- <div class="sphinxsidebarwrapper">
-<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="document">
- <div class="documentwrapper">
- <div class="bodywrapper">
- <div class="body">
-
- <h1>Source code for neurosynth</h1><div class="highlight"><pre>
-<span class="c"># emacs: -*- mode: python-mode; py-indent-offset: 4; tab-width: 4; indent-tabs-mode: nil -*-</span>
-<span class="c"># ex: set sts=4 ts=4 sw=4 et:</span>
-<span class="sd">&quot;&quot;&quot;NeuroSynth -- large-scale synthesis of functional neuroimaging data.</span>
-
-<span class="sd">&quot;&quot;&quot;</span>
-<span class="n">__all__</span> <span class="o">=</span> <span class="p">[</span><span class="s">&quot;analysis&quot;</span><span class="p">,</span> <span class="s">&quot;base&quot;</span><span class="p">,</span> <span class="s">&quot;set_logging_level&quot;</span><span class="p">,</span> <span class="s">&quot;__version__&quot;</span><span class="p">]</span>
-
-<span class="kn">import</span> <span class="nn">logging</span>
-<span class="kn">import</span> <span class="nn">sys</span>
-<span class="kn">import</span> <span class="nn">os</span>
-
-<span class="kn">from</span> <span class="nn">version</span> <span class="kn">import</span> <span class="n">__version__</span>
-
-<span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s">&quot;neurosynth&quot;</span><span class="p">)</span>
-
-<div class="viewcode-block" id="set_logging_level"><a class="viewcode-back" href="../neurosynth.html#neurosynth.set_logging_level">[docs]</a><span class="k">def</span> <span class="nf">set_logging_level</span><span class="p">(</span><span class="n">level</span><span class="o">=</span><span class="bp">None</span><span class="p">):</span>
- <span class="sd">&quot;&quot;&quot;Set neurosynth&#39;s logging level</span>
-
-<span class="sd"> Args</span>
-<span class="sd"> level : str</span>
-<span class="sd"> Name of the logging level (warning, error, info, etc) known</span>
-<span class="sd"> to logging module. If no level provided, it would get that one</span>
-<span class="sd"> from environment variable NEUROSYNTH_LOGLEVEL</span>
-<span class="sd"> &quot;&quot;&quot;</span>
- <span class="k">if</span> <span class="n">level</span> <span class="ow">is</span> <span class="bp">None</span><span class="p">:</span>
- <span class="n">level</span> <span class="o">=</span> <span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s">&#39;NEUROSYNTH_LOGLEVEL&#39;</span><span class="p">,</span> <span class="s">&#39;warn&#39;</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">level</span> <span class="ow">is</span> <span class="ow">not</span> <span class="bp">None</span><span class="p">:</span>
- <span class="n">logger</span><span class="o">.</span><span class="n">setLevel</span><span class="p">(</span><span class="nb">getattr</span><span class="p">(</span><span class="n">logging</span><span class="p">,</span> <span class="n">level</span><span class="o">.</span><span class="n">upper</span><span class="p">()))</span>
- <span class="k">return</span> <span class="n">logger</span><span class="o">.</span><span class="n">getEffectiveLevel</span><span class="p">()</span>
-</div>
-<span class="k">def</span> <span class="nf">_setup_logger</span><span class="p">(</span><span class="n">logger</span><span class="p">):</span>
- <span class="c"># Basic logging setup</span>
- <span class="n">console</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">StreamHandler</span><span class="p">(</span><span class="n">sys</span><span class="o">.</span><span class="n">stdout</span><span class="p">)</span>
- <span class="n">console</span><span class="o">.</span><span class="n">setFormatter</span><span class="p">(</span><span class="n">logging</span><span class="o">.</span><span class="n">Formatter</span><span class="p">(</span><span class="s">&quot;</span><span class="si">%(levelname)-6s</span><span class="s"> </span><span class="si">%(module)-7s</span><span class="s"> </span><span class="si">%(message)s</span><span class="s">&quot;</span><span class="p">))</span>
- <span class="n">logger</span><span class="o">.</span><span class="n">addHandler</span><span class="p">(</span><span class="n">console</span><span class="p">)</span>
- <span class="n">set_logging_level</span><span class="p">()</span>
-
-<span class="c"># Setup neurosynth&#39;s logger</span>
-<span class="n">_setup_logger</span><span class="p">(</span><span class="n">logger</span><span class="p">)</span>
-</pre></div>
-
- </div>
- </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><a href="../index.html">neurosynth documentation</a> &raquo;</li>
- <li><a href="index.html" >Module code</a> &raquo;</li>
- </ul>
- </div>
- <div class="footer">
- &copy; Copyright 2014, Tal Yarkoni.
- Created using <a href="http://sphinx-doc.org/">Sphinx</a> 1.2.3.
- </div>
- </body>
-</html>
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