ver. 0.4.0 and sphinx run

rpoleski · Feb 22, 2018 · 340f7c7 · 340f7c7
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diff --git a/README.md b/README.md
@@ -3,7 +3,7 @@
 <dl>MulensModel is package for modeling microlensing (or &mu;-lensing) 
 events. </dl>
 
-It is still under development. [Latest release: 0.3.1](https://github.com/rpoleski/MulensModel/releases/tag/0.3.1)
+It is still under development. [Latest release: 0.4.0](https://github.com/rpoleski/MulensModel/releases/tag/0.4.0)
 
 MulensModel can generate a microlensing light curve for a given set of microlensing parameters, fit that light curve to some data, and return a chi2 value. That chi2 can then be input into an arbitrary likelihood function to find the best fit parameters.
 
@@ -46,11 +46,11 @@ Future Development:
 3. Unpack the archive.
 4. Add the path to the unpack directory to the PYTHONPATH, e.g., if you've extracted the archive in your home directory (``/home/USER_NAME/``) in tcsh:
 ```
-setenv PYTHONPATH /home/USER_NAME/MulensModel-0.3.1/source\:$PYTHONPATH
+setenv PYTHONPATH /home/USER_NAME/MulensModel-0.4.0/source\:$PYTHONPATH
 ```
 in bash:
 ```
-export PYTHONPATH=/home/USER_NAME/MulensModel-0.3.1/source:$PYTHONPATH
+export PYTHONPATH=/home/USER_NAME/MulensModel-0.4.0/source:$PYTHONPATH
 ```
 In order to have this command invoked every time you open the terminal, please add this command to ``~/.cshrc`` or ``~/.bashrc`` file.
 
@@ -66,5 +66,5 @@ gcc -Wl,-soname,rapper -shared -o VBBinaryLensingLibrary_wrapper.so VBBinaryLens
 ---
 [![astropy](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat)](http://www.astropy.org/)
 
-file revised Jan 2018
+file revised Feb 2018
 
diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # 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: 3e06b7a41d33c1b33b0f22a6a31a75ee
+config: 05bc5a4e3b729650af9049309698e761
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/modules.doctree b/docs/.doctrees/modules.doctree
diff --git a/docs/MulensModel.binarylens.html b/docs/MulensModel.binarylens.html
@@ -1,38 +1,48 @@
-
 <!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>MulensModel.binarylens module &#8212; MulensModel 0.3.1 documentation</title>
+
+    <title>MulensModel.binarylens module &mdash; MulensModel 0.3.1 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:     '0.3.1',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true,
-        SOURCELINK_SUFFIX: '.txt'
+        HAS_SOURCE:  true
       };
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-    <link rel="index" title="Index" href="genindex.html" />
-    <link rel="search" title="Search" href="search.html" />
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="top" title="MulensModel 0.3.1 documentation" href="index.html" />
 
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
 
   </head>
-  <body>
-
+  <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">MulensModel 0.3.1 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
 
     <div class="document">
       <div class="documentwrapper">
@@ -44,7 +54,7 @@
 <dl class="class">
 <dt id="MulensModel.binarylens.BinaryLens">
 <em class="property">class </em><code class="descclassname">MulensModel.binarylens.</code><code class="descname">BinaryLens</code><span class="sig-paren">(</span><em>mass_1=None</em>, <em>mass_2=None</em>, <em>separation=None</em><span class="sig-paren">)</span><a class="headerlink" href="#MulensModel.binarylens.BinaryLens" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference external" href="https://docs.python.org/2/library/functions.html#object" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">object</span></code></a></p>
+<dd><p>Bases: <a class="reference external" href="https://docs.python.org/library/functions.html#object" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">object</span></code></a></p>
 <p>The binary lens equation - its solutions, images, parities,
 magnifications, etc.</p>
 <p>The binary lens equation is a 5th order complex polynomial.</p>
@@ -65,7 +75,7 @@
 </dl>
 <p>Note: mass_1 and mass_2 may be defined as a fraction of some other
 mass than the total mass. This is possible but not recommended -
-make sure you know what you’re doing before you start using this
+make sure you know what you&#8217;re doing before you start using this
 possibility.</p>
 <dl class="method">
 <dt id="MulensModel.binarylens.BinaryLens.point_source_magnification">
@@ -163,16 +173,16 @@
 <dd>Requested accuracy of the result defined as the sum of the area
 of the squares that determine the contour line and 
 the estimated total enclosed area (see sec. 4 of the paper). 
-As M. Dominik states: <em>“this vastly overestimates 
+As M. Dominik states: <em>&#8220;this vastly overestimates 
 the fractional error, and a suitable value should be chosen by
 testing how its variation affects the final results - 
-I recommend starting at acc = 0.1.”</em> It significantly affects 
+I recommend starting at acc = 0.1.&#8221;</em> It significantly affects 
 execution time.</dd>
 <dt>ld_accuracy: <em>float</em>, optional</dt>
-<dd>Requested limb-darkening accuracy. As M. Dominik states: <em>”
+<dd>Requested limb-darkening accuracy. As M. Dominik states: <em>&#8221;
 Fractional uncertainty for the adaptive Simpson integration of
 the limb-darkening profile-related function during application
-of Green’s theorem.”</em> It does not addect execution time so can
+of Green&#8217;s theorem.&#8221;</em> It does not addect execution time so can
 be set to very small value.</dd>
 </dl>
 </dd>
@@ -232,28 +242,25 @@
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
-        <div class="sphinxsidebarwrapper"><div class="relations">
-<h3>Related Topics</h3>
-<ul>
-  <li><a href="index.html">Documentation overview</a><ul>
-  </ul></li>
-</ul>
-</div>
+        <div class="sphinxsidebarwrapper">
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
-      <li><a href="_sources/MulensModel.binarylens.rst.txt"
+      <li><a href="_sources/MulensModel.binarylens.txt"
             rel="nofollow">Show Source</a></li>
     </ul>
    </div>
 <div id="searchbox" style="display: none" role="search">
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-      <div><input type="submit" value="Go" /></div>
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+      <input type="submit" value="Go" />
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@@ -264,12 +271,12 @@ <h3>Quick search</h3>
       &copy;2017, Radek Poleski, Jennifer Yee.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.6.3</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.9</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
 
       |
-      <a href="_sources/MulensModel.binarylens.rst.txt"
-          rel="nofollow">Page source</a>
+      <a href="_sources/MulensModel.binarylens.txt"
+          rel="nofollow">Page source</a></li>
     </div>
 
 

diff --git a/docs/MulensModel.caustics.html b/docs/MulensModel.caustics.html
@@ -1,38 +1,48 @@
-
 <!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>MulensModel.caustics module &#8212; MulensModel 0.3.1 documentation</title>
+
+    <title>MulensModel.caustics module &mdash; MulensModel 0.3.1 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:     '0.3.1',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
-        HAS_SOURCE:  true,
-        SOURCELINK_SUFFIX: '.txt'
+        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>
-    <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-    <link rel="index" title="Index" href="genindex.html" />
-    <link rel="search" title="Search" href="search.html" />
+    <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+    <link rel="top" title="MulensModel 0.3.1 documentation" href="index.html" />
 
-  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
-
 
-  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9">
 
   </head>
-  <body>
-
+  <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">MulensModel 0.3.1 documentation</a> &raquo;</li> 
+      </ul>
+    </div>  
 
     <div class="document">
       <div class="documentwrapper">
@@ -44,7 +54,7 @@
 <dl class="class">
 <dt id="MulensModel.caustics.Caustics">
 <em class="property">class </em><code class="descclassname">MulensModel.caustics.</code><code class="descname">Caustics</code><span class="sig-paren">(</span><em>q</em>, <em>s</em><span class="sig-paren">)</span><a class="headerlink" href="#MulensModel.caustics.Caustics" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference external" href="https://docs.python.org/2/library/functions.html#object" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">object</span></code></a></p>
+<dd><p>Bases: <a class="reference external" href="https://docs.python.org/library/functions.html#object" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">object</span></code></a></p>
 <p>Class for the caustic structure corresponding to a given (<em>q</em>, <em>s</em>),
 i.e. mass ratio and separation. Implemented for 2-body lenses only.</p>
 <dl class="docutils">
@@ -106,7 +116,7 @@
 <dl class="class">
 <dt id="MulensModel.caustics.Caustics.CriticalCurve">
 <em class="property">class </em><code class="descname">CriticalCurve</code><a class="headerlink" href="#MulensModel.caustics.Caustics.CriticalCurve" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference external" href="https://docs.python.org/2/library/functions.html#object" title="(in Python v2.7)"><code class="xref py py-class docutils literal"><span class="pre">object</span></code></a></p>
+<dd><p>Bases: <a class="reference external" href="https://docs.python.org/library/functions.html#object" title="(in Python v3.6)"><code class="xref py py-class docutils literal"><span class="pre">object</span></code></a></p>
 <p>Internal class of <a class="reference internal" href="#MulensModel.caustics.Caustics" title="MulensModel.caustics.Caustics"><code class="xref py py-class docutils literal"><span class="pre">Caustics</span></code></a>. Defines the critical
 curve (in the lens plane). Origin is center of mass with
 larger mass on the left (<em>q</em> &lt; 1).</p>
@@ -130,28 +140,25 @@
         </div>
       </div>
       <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
-        <div class="sphinxsidebarwrapper"><div class="relations">
-<h3>Related Topics</h3>
-<ul>
-  <li><a href="index.html">Documentation overview</a><ul>
-  </ul></li>
-</ul>
-</div>
+        <div class="sphinxsidebarwrapper">
   <div role="note" aria-label="source link">
     <h3>This Page</h3>
     <ul class="this-page-menu">
-      <li><a href="_sources/MulensModel.caustics.rst.txt"
+      <li><a href="_sources/MulensModel.caustics.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="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>
@@ -162,12 +169,12 @@ <h3>Quick search</h3>
       &copy;2017, Radek Poleski, Jennifer Yee.
 
       |
-      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.6.3</a>
-      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.9</a>
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.3.1</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.3</a>
 
       |
-      <a href="_sources/MulensModel.caustics.rst.txt"
-          rel="nofollow">Page source</a>
+      <a href="_sources/MulensModel.caustics.txt"
+          rel="nofollow">Page source</a></li>
     </div>