Update to v0.2.8

hackingmaterials · Mar 24, 2018 · 21a2b19 · 21a2b19
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diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -5,6 +5,17 @@
 matminer Changelog
 ==================
 
+**v0.2.8**
+
+* new FunctionFeaturizer to combine features into mini functions (J. Montoya)
+* updates to PlotlyFig (A. Dunn)
+* Update default n_jobs to cpu_count() (A. Dunn)
+* test fixes and updates (A. Dunn, N. Zimmermann, J. Montoya)
+* move Jupyter notebooks to matminer_examples repo, separate from matminer (J. Montoya)
+* add presets for AFS, GRDF featurizes (M. Dylla)
+* update CircleCI testing (A. Dunn)
+* code cleanups (A. Dunn, A. Jain, J. Montoya)
+
 **v0.2.6**
 
 * modify ChemicalRSO to use fit() method (Q. Wang)

diff --git a/docs/_sources/matminer.featurizers.rst.txt b/docs/_sources/matminer.featurizers.rst.txt
@@ -36,6 +36,14 @@ matminer\.featurizers\.dos module
     :undoc-members:
     :show-inheritance:
 
+matminer\.featurizers\.function module
+--------------------------------------
+
+.. automodule:: matminer.featurizers.function
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 matminer\.featurizers\.site module
 ----------------------------------
 

diff --git a/docs/changelog.html b/docs/changelog.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>MatMiner Changlog &#8212; matminer 0.2.6 documentation</title>
+    <title>MatMiner Changlog &#8212; matminer 0.2.8 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:     '0.2.6',
+        VERSION:     '0.2.8',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -48,6 +48,17 @@ <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>v0.2.8</strong></p>
+<ul class="simple">
+<li>new FunctionFeaturizer to combine features into mini functions (J. Montoya)</li>
+<li>updates to PlotlyFig (A. Dunn)</li>
+<li>Update default n_jobs to cpu_count() (A. Dunn)</li>
+<li>test fixes and updates (A. Dunn, N. Zimmermann, J. Montoya)</li>
+<li>move Jupyter notebooks to matminer_examples repo, separate from matminer (J. Montoya)</li>
+<li>add presets for AFS, GRDF featurizes (M. Dylla)</li>
+<li>update CircleCI testing (A. Dunn)</li>
+<li>code cleanups (A. Dunn, A. Jain, J. Montoya)</li>
+</ul>
 <p><strong>v0.2.6</strong></p>
 <ul class="simple">
 <li>modify ChemicalRSO to use fit() method (Q. Wang)</li>
@@ -241,7 +252,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/contributors.html b/docs/contributors.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>MatMiner Contributors &#8212; matminer 0.2.6 documentation</title>
+    <title>MatMiner Contributors &#8212; matminer 0.2.8 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:     '0.2.6',
+        VERSION:     '0.2.8',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -137,7 +137,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/example_bulkmod.html b/docs/example_bulkmod.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Predicting bulk moduli with matminer &#8212; matminer 0.2.6 documentation</title>
+    <title>Predicting bulk moduli with matminer &#8212; matminer 0.2.8 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:     '0.2.6',
+        VERSION:     '0.2.8',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -368,7 +368,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -6,13 +6,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Index &#8212; matminer 0.2.6 documentation</title>
+    <title>Index &#8212; matminer 0.2.8 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:     '0.2.6',
+        VERSION:     '0.2.8',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -38,7 +38,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -115,6 +115,8 @@ <h2 id="_">_</h2>
         <li><a href="matminer.featurizers.html#matminer.featurizers.composition.ValenceOrbital.__init__">(matminer.featurizers.composition.ValenceOrbital method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.dos.DOSFeaturizer.__init__">(matminer.featurizers.dos.DOSFeaturizer method)</a>
+</li>
+        <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.__init__">(matminer.featurizers.function.FunctionFeaturizer method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.site.AGNIFingerprints.__init__">(matminer.featurizers.site.AGNIFingerprints method)</a>
 </li>
@@ -263,6 +265,8 @@ <h2 id="C">C</h2>
         <li><a href="matminer.featurizers.html#matminer.featurizers.composition.TMetalFraction.citations">(matminer.featurizers.composition.TMetalFraction method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.composition.ValenceOrbital.citations">(matminer.featurizers.composition.ValenceOrbital method)</a>
+</li>
+        <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.citations">(matminer.featurizers.function.FunctionFeaturizer method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.site.AGNIFingerprints.citations">(matminer.featurizers.site.AGNIFingerprints method)</a>
 </li>
@@ -396,6 +400,8 @@ <h2 id="E">E</h2>
       <li><a href="matminer.featurizers.html#matminer.featurizers.structure.EwaldEnergy">EwaldEnergy (class in matminer.featurizers.structure)</a>
 </li>
       <li><a href="matminer.featurizers.html#matminer.featurizers.site.EwaldSiteEnergy">EwaldSiteEnergy (class in matminer.featurizers.site)</a>
+</li>
+      <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.exp_dict">exp_dict (matminer.featurizers.function.FunctionFeaturizer attribute)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -441,6 +447,8 @@ <h2 id="F">F</h2>
         <li><a href="matminer.featurizers.html#matminer.featurizers.composition.ValenceOrbital.feature_labels">(matminer.featurizers.composition.ValenceOrbital method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.dos.DOSFeaturizer.feature_labels">(matminer.featurizers.dos.DOSFeaturizer method)</a>
+</li>
+        <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.feature_labels">(matminer.featurizers.function.FunctionFeaturizer method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.site.AGNIFingerprints.feature_labels">(matminer.featurizers.site.AGNIFingerprints method)</a>
 </li>
@@ -529,6 +537,8 @@ <h2 id="F">F</h2>
         <li><a href="matminer.featurizers.html#matminer.featurizers.composition.ValenceOrbital.featurize">(matminer.featurizers.composition.ValenceOrbital method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.dos.DOSFeaturizer.featurize">(matminer.featurizers.dos.DOSFeaturizer method)</a>
+</li>
+        <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.featurize">(matminer.featurizers.function.FunctionFeaturizer method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.site.AGNIFingerprints.featurize">(matminer.featurizers.site.AGNIFingerprints method)</a>
 </li>
@@ -582,7 +592,11 @@ <h2 id="F">F</h2>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="matminer.featurizers.html#matminer.featurizers.base.BaseFeaturizer.featurize_dataframe">featurize_dataframe() (matminer.featurizers.base.BaseFeaturizer method)</a>
+
+      <ul>
+        <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.featurize_dataframe">(matminer.featurizers.function.FunctionFeaturizer method)</a>
 </li>
+      </ul></li>
       <li><a href="matminer.featurizers.html#matminer.featurizers.base.BaseFeaturizer.featurize_many">featurize_many() (matminer.featurizers.base.BaseFeaturizer method)</a>
 </li>
       <li><a href="matminer.featurizers.html#matminer.featurizers.base.BaseFeaturizer.featurize_wrapper">featurize_wrapper() (matminer.featurizers.base.BaseFeaturizer method)</a>
@@ -629,6 +643,8 @@ <h2 id="F">F</h2>
         <li><a href="matminer.featurizers.html#matminer.featurizers.structure.SiteStatsFingerprint.from_preset">(matminer.featurizers.structure.SiteStatsFingerprint static method)</a>
 </li>
       </ul></li>
+      <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer">FunctionFeaturizer (class in matminer.featurizers.function)</a>
+</li>
   </ul></td>
 </tr></table>
 
@@ -644,6 +660,10 @@ <h2 id="G">G</h2>
       <li><a href="matminer.featurizers.html#matminer.featurizers.site.GaussianSymmFunc">GaussianSymmFunc (class in matminer.featurizers.site)</a>
 </li>
       <li><a href="matminer.featurizers.html#matminer.featurizers.site.GeneralizedRadialDistributionFunction">GeneralizedRadialDistributionFunction (class in matminer.featurizers.site)</a>
+</li>
+      <li><a href="matminer.featurizers.html#matminer.featurizers.function.generate_expressions_combinations">generate_expressions_combinations() (in module matminer.featurizers.function)</a>
+</li>
+      <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.generate_string_expressions">generate_string_expressions() (matminer.featurizers.function.FunctionFeaturizer method)</a>
 </li>
       <li><a href="matminer.featurizers.html#matminer.featurizers.stats.PropertyStats.geom_std_dev">geom_std_dev() (matminer.featurizers.stats.PropertyStats static method)</a>
 </li>
@@ -675,10 +695,10 @@ <h2 id="G">G</h2>
         <li><a href="matminer.data_retrieval.html#matminer.data_retrieval.retrieve_MongoDB.MongoDataRetrieval.get_dataframe">(matminer.data_retrieval.retrieve_MongoDB.MongoDataRetrieval method)</a>
 </li>
       </ul></li>
-      <li><a href="matminer.data_retrieval.html#matminer.data_retrieval.retrieve_MDF.MDFDataRetrieval.get_dataframe_by_query">get_dataframe_by_query() (matminer.data_retrieval.retrieve_MDF.MDFDataRetrieval method)</a>
-</li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="matminer.data_retrieval.html#matminer.data_retrieval.retrieve_MDF.MDFDataRetrieval.get_dataframe_by_query">get_dataframe_by_query() (matminer.data_retrieval.retrieve_MDF.MDFDataRetrieval method)</a>
+</li>
       <li><a href="matminer.utils.html#matminer.utils.data.AbstractData.get_elemental_properties">get_elemental_properties() (matminer.utils.data.AbstractData method)</a>
 </li>
       <li><a href="matminer.utils.html#matminer.utils.data.AbstractData.get_elemental_property">get_elemental_property() (matminer.utils.data.AbstractData method)</a>
@@ -781,6 +801,8 @@ <h2 id="I">I</h2>
         <li><a href="matminer.featurizers.html#matminer.featurizers.composition.ValenceOrbital.implementors">(matminer.featurizers.composition.ValenceOrbital method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.dos.DOSFeaturizer.implementors">(matminer.featurizers.dos.DOSFeaturizer method)</a>
+</li>
+        <li><a href="matminer.featurizers.html#matminer.featurizers.function.FunctionFeaturizer.implementors">(matminer.featurizers.function.FunctionFeaturizer method)</a>
 </li>
         <li><a href="matminer.featurizers.html#matminer.featurizers.site.AGNIFingerprints.implementors">(matminer.featurizers.site.AGNIFingerprints method)</a>
 </li>
@@ -910,15 +932,17 @@ <h2 id="M">M</h2>
       <li><a href="matminer.featurizers.html#module-matminer.featurizers.composition">matminer.featurizers.composition (module)</a>
 </li>
       <li><a href="matminer.featurizers.html#module-matminer.featurizers.dos">matminer.featurizers.dos (module)</a>
+</li>
+      <li><a href="matminer.featurizers.html#module-matminer.featurizers.function">matminer.featurizers.function (module)</a>
 </li>
       <li><a href="matminer.featurizers.html#module-matminer.featurizers.site">matminer.featurizers.site (module)</a>
 </li>
       <li><a href="matminer.featurizers.html#module-matminer.featurizers.stats">matminer.featurizers.stats (module)</a>
-</li>
-      <li><a href="matminer.featurizers.html#module-matminer.featurizers.structure">matminer.featurizers.structure (module)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="matminer.featurizers.html#module-matminer.featurizers.structure">matminer.featurizers.structure (module)</a>
+</li>
       <li><a href="matminer.figrecipes.html#module-matminer.figrecipes">matminer.figrecipes (module)</a>
 </li>
       <li><a href="matminer.figrecipes.html#module-matminer.figrecipes.plot">matminer.figrecipes.plot (module)</a>
@@ -1187,7 +1211,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/index.html b/docs/index.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>matminer (Materials Data Mining) &#8212; matminer 0.2.6 documentation</title>
+    <title>matminer (Materials Data Mining) &#8212; matminer 0.2.8 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:     '0.2.6',
+        VERSION:     '0.2.8',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -214,7 +214,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/installation.html b/docs/installation.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>Installing matminer &#8212; matminer 0.2.6 documentation</title>
+    <title>Installing matminer &#8212; matminer 0.2.8 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:     '0.2.6',
+        VERSION:     '0.2.8',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -127,7 +127,7 @@ <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 0.2.6 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.2.8 documentation</a> &#187;</li> 
       </ul>
     </div>