Update to v0.3.6

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diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -5,6 +5,14 @@
 matminer Changelog
 ==================
 
+
+**v0.3.6**
+
+* Improve MPDataRetrieval to serialize objects (A. Faghaninia)
+* Some fixes to GDRF and AFS (L. Williams, M. Dylla)
+* Some fixes for Ewald (A. Faghaninia)
+* improve error messages (A. Jain)
+
 **v0.3.5**
 
 * some tools for sklearn Pipeline integration (J. Brenneck)

diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt
@@ -48,3 +48,4 @@ Other
 * Evgeny Blokhin (Tilde Lab)
 * Max Dylla (Snyder Research Group, Northwestern University)
 * David Waroquiers (UC Louvain, Belgium)
+* Logan Williams (U Michigan Ann Arbor)
diff --git a/docs/_sources/matminer.utils.rst.txt b/docs/_sources/matminer.utils.rst.txt
@@ -60,6 +60,14 @@ matminer.utils.pipeline module
  :undoc-members:
  :show-inheritance:
 
+matminer.utils.utils module
+---------------------------
+
+.. automodule:: matminer.utils.utils
+ :members:
+ :undoc-members:
+ :show-inheritance:
+
 
 Module contents
 ---------------

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
  URL_ROOT: '',
- VERSION: '0.3.5',
+ VERSION: '0.3.6',
  LANGUAGE: 'None',
  COLLAPSE_INDEX: false,
  FILE_SUFFIX: '.html',

diff --git a/docs/changelog.html b/docs/changelog.html
@@ -6,7 +6,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>MatMiner Changlog &#8212; matminer 0.3.5 documentation</title>
+ <title>MatMiner Changlog &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -39,6 +39,13 @@ <h3>Navigation</h3>
 
  <div class="section" id="matminer-changelog">
 <h1>matminer Changelog<a class="headerlink" href="#matminer-changelog" title="Permalink to this headline">¶</a></h1>
+<p><strong>v0.3.6</strong></p>
+<ul class="simple">
+<li>Improve MPDataRetrieval to serialize objects (A. Faghaninia)</li>
+<li>Some fixes to GDRF and AFS (L. Williams, M. Dylla)</li>
+<li>Some fixes for Ewald (A. Faghaninia)</li>
+<li>improve error messages (A. Jain)</li>
+</ul>
 <p><strong>v0.3.5</strong></p>
 <ul class="simple">
 <li>some tools for sklearn Pipeline integration (J. Brenneck)</li>
@@ -305,7 +312,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div>
 

diff --git a/docs/contributors.html b/docs/contributors.html
@@ -6,7 +6,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>MatMiner Contributors &#8212; matminer 0.3.5 documentation</title>
+ <title>MatMiner Contributors &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -79,6 +79,7 @@ <h2>Other<a class="headerlink" href="#other" title="Permalink to this headline">
 <li>Evgeny Blokhin (Tilde Lab)</li>
 <li>Max Dylla (Snyder Research Group, Northwestern University)</li>
 <li>David Waroquiers (UC Louvain, Belgium)</li>
+<li>Logan Williams (U Michigan Ann Arbor)</li>
 </ul>
 </div>
 </div>
@@ -132,7 +133,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div>
 

diff --git a/docs/example_bulkmod.html b/docs/example_bulkmod.html
@@ -6,7 +6,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Predicting bulk moduli with matminer &#8212; matminer 0.3.5 documentation</title>
+ <title>Predicting bulk moduli with matminer &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -361,7 +361,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div>
 

diff --git a/docs/featurizer_summary.html b/docs/featurizer_summary.html
@@ -6,7 +6,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Table of Featurizers &#8212; matminer 0.3.5 documentation</title>
+ <title>Table of Featurizers &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -420,7 +420,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div>
 

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -7,7 +7,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Index &#8212; matminer 0.3.5 documentation</title>
+ <title>Index &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -29,7 +29,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -927,7 +927,7 @@ <h2 id="H">H</h2>
 </li>
  <li><a href="matminer.featurizers.html#matminer.featurizers.stats.PropertyStats.holder_mean">holder_mean() (matminer.featurizers.stats.PropertyStats static method)</a>
 </li>
- <li><a href="matminer.utils.html#matminer.utils.conversions.homogenize_multiindex">homogenize_multiindex() (in module matminer.utils.conversions)</a>
+ <li><a href="matminer.utils.html#matminer.utils.utils.homogenize_multiindex">homogenize_multiindex() (in module matminer.utils.utils)</a>
 </li>
  </ul></td>
 </tr></table>
@@ -1143,10 +1143,10 @@ <h2 id="M">M</h2>
 </li>
  <li><a href="matminer.figrecipes.html#module-matminer.figrecipes.plot">matminer.figrecipes.plot (module)</a>
 </li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="matminer.utils.html#module-matminer.utils">matminer.utils (module)</a>
 </li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="matminer.utils.html#module-matminer.utils.caching">matminer.utils.caching (module)</a>
 </li>
  <li><a href="matminer.utils.html#module-matminer.utils.conversions">matminer.utils.conversions (module)</a>
@@ -1172,6 +1172,8 @@ <h2 id="M">M</h2>
  <li><a href="matminer.utils.tests.html#module-matminer.utils.tests.test_data">matminer.utils.tests.test_data (module)</a>
 </li>
  <li><a href="matminer.utils.tests.html#module-matminer.utils.tests.test_flatten_dict">matminer.utils.tests.test_flatten_dict (module)</a>
+</li>
+ <li><a href="matminer.utils.html#module-matminer.utils.utils">matminer.utils.utils (module)</a>
 </li>
  <li><a href="matminer.featurizers.html#matminer.featurizers.stats.PropertyStats.maximum">maximum() (matminer.featurizers.stats.PropertyStats static method)</a>
 </li>
@@ -1351,10 +1353,10 @@ <h2 id="T">T</h2>
  </ul></li>
  <li><a href="matminer.utils.tests.html#matminer.utils.tests.test_conversions.TestConversions.test_json_to_object">test_json_to_object() (matminer.utils.tests.test_conversions.TestConversions method)</a>
 </li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="matminer.datasets.test_datasets.html#matminer.datasets.test_datasets.test_datasets.DataSetTest.test_piezoelectric_tensor">test_piezoelectric_tensor() (matminer.datasets.test_datasets.test_datasets.DataSetTest method)</a>
 </li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="matminer.utils.tests.html#matminer.utils.tests.test_conversions.TestConversions.test_str_to_composition">test_str_to_composition() (matminer.utils.tests.test_conversions.TestConversions method)</a>
 </li>
  <li><a href="matminer.utils.tests.html#matminer.utils.tests.test_conversions.TestConversions.test_structure_to_composition">test_structure_to_composition() (matminer.utils.tests.test_conversions.TestConversions method)</a>
@@ -1386,6 +1388,8 @@ <h2 id="T">T</h2>
 </li>
  </ul></li>
  <li><a href="matminer.figrecipes.html#matminer.figrecipes.plot.PlotlyFig.triangle">triangle() (matminer.figrecipes.plot.PlotlyFig method)</a>
+</li>
+ <li><a href="matminer.data_retrieval.html#matminer.data_retrieval.retrieve_MP.MPDataRetrieval.try_get_prop_by_material_id">try_get_prop_by_material_id() (matminer.data_retrieval.retrieve_MP.MPDataRetrieval method)</a>
 </li>
  </ul></td>
 </tr></table>
@@ -1456,7 +1460,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div>
 

diff --git a/docs/index.html b/docs/index.html
@@ -6,7 +6,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>matminer (Materials Data Mining) &#8212; matminer 0.3.5 documentation</title>
+ <title>matminer (Materials Data Mining) &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
  <li class="right" >
  <a href="py-modindex.html" title="Python Module Index"
  >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="#">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="#">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -229,7 +229,7 @@ <h3>Navigation</h3>
  <li class="right" >
  <a href="py-modindex.html" title="Python Module Index"
  >modules</a> |</li>
- <li class="nav-item nav-item-0"><a href="#">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="#">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div>
 

diff --git a/docs/installation.html b/docs/installation.html
@@ -6,7 +6,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>Installing matminer &#8212; matminer 0.3.5 documentation</title>
+ <title>Installing matminer &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -120,7 +120,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div>
 

diff --git a/docs/matminer.data_retrieval.html b/docs/matminer.data_retrieval.html
@@ -6,7 +6,7 @@
  <head>
  <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
- <title>matminer.data_retrieval package &#8212; matminer 0.3.5 documentation</title>
+ <title>matminer.data_retrieval package &#8212; matminer 0.3.6 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" src="_static/documentation_options.js"></script>
@@ -28,7 +28,7 @@ <h3>Navigation</h3>
  <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">matminer 0.3.5 documentation</a> &#187;</li> 
+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
  </div> 
 
@@ -326,12 +326,46 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dd><p>Gets data from MP in a dataframe format. See api_link for more details.</p>
 <dl class="docutils">
 <dt>Args:</dt>
-<dd>all arguments including criteria, properties and index_mpid are the
-same as in get_data</dd>
+<dd><p class="first">criteria (dict): the same as in get_data
+properties ([str]): the same properties supported as in get_data</p>
+<blockquote>
+<div>plus: “structure”, “initial_structure”, “final_structure”,
+“bandstructure” (line mode), “bandstructure_uniform”,
+“phonon_bandstructure”, “phonon_ddb”, “phonon_bandstructure”,
+“phonon_dos”. Note that for a long list of compounds, it may
+take a long time to retrieve some of these objects.</div></blockquote>
+<p class="last">index_mpid (bool): the same as in get_data
+kwargs (dict): the same keyword arguments as in get_data</p>
+</dd>
 </dl>
 <p>Returns (pandas.Dataframe):</p>
 </dd></dl>
 
+<dl class="method">
+<dt id="matminer.data_retrieval.retrieve_MP.MPDataRetrieval.try_get_prop_by_material_id">
+<code class="descname">try_get_prop_by_material_id</code><span class="sig-paren">(</span><em>prop</em>, <em>material_id_list</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MP.MPDataRetrieval.try_get_prop_by_material_id" title="Permalink to this definition">¶</a></dt>
+<dd><p>Call the relevant get_prop_by_material_id. “prop” is a property such
+as bandstructure that is not readily available in supported properties
+of the get_data function but via the get_bandstructure_by_material_id
+method for example.</p>
+<dl class="docutils">
+<dt>Args:</dt>
+<dd><dl class="first docutils">
+<dt>prop (str): the name of the property. Options are:</dt>
+<dd>“bandstructure”, “dos”, “phonon_dos”, “phonon_bandstructure”,
+“phonon_ddb”</dd>
+</dl>
+<p>material_id_list ([str]): list of material_id of compounds
+kwargs (dict): other keyword arguments that get_*_by_material_id</p>
+<blockquote class="last">
+<div>may have; e.g. line_mode in get_bandstructure_by_material_id</div></blockquote>
+</dd>
+<dt>Returns ([target prop object or NaN]):</dt>
+<dd>If the target property is not available for a certain material_id,
+NaN is returned.</dd>
+</dl>
+</dd></dl>
+
 </dd></dl>
 
 </div>
@@ -420,7 +454,7 @@ <h2>matminer.data_retrieval.retrieve_MPDS module<a class="headerlink" href="#mat
 <dl class="class">
 <dt id="matminer.data_retrieval.retrieve_base.BaseDataRetrieval">
 <em class="property">class </em><code class="descclassname">matminer.data_retrieval.retrieve_base.</code><code class="descname">BaseDataRetrieval</code><a class="headerlink" href="#matminer.data_retrieval.retrieve_base.BaseDataRetrieval" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.6)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
+<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.7)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
 <p>Abstract class to retrieve data from various material APIs while adhering to
 a quasi-standard format for querying.</p>
 <p>## Implementing a new DataRetrieval class</p>
@@ -564,7 +598,7 @@ <h3>Navigation</h3>
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  >modules</a> |</li>
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+ <li class="nav-item nav-item-0"><a href="index.html">matminer 0.3.6 documentation</a> &#187;</li> 
  </ul>
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