Update to v0.1.3

hackingmaterials · Sep 8, 2017 · 677a124 · 677a124
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diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -194,6 +194,19 @@ A few examples demonstrating usage can be found in the notebook hosted on `Jupyt
 Changelog
 ---------
 
+**v0.1.3**
+
+* remove git-lfs
+* refactor structure descriptors
+* multiple fixes to cohesive energy
+* fixes to data loaders
+* fix complex Mongo retrieval queries, better logic for query projections
+* more unit tests
+* enforce lower case feature names
+* sort data by atomic number not electronegativity in data getters, this will avoid pernicious behavior
+* many minor cleanups, bug fixes, and consistency fixes
+
+
 **v0.1.2**
 
 * Several new structure fingerprint methods (L. Ward, K. Bostrom)

diff --git a/docs/_sources/matminer.datasets.rst.txt b/docs/_sources/matminer.datasets.rst.txt
@@ -0,0 +1,29 @@
+matminer.datasets package
+=========================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    matminer.datasets.test_datasets
+
+Submodules
+----------
+
+matminer.datasets.dataframe_loader module
+-----------------------------------------
+
+.. automodule:: matminer.datasets.dataframe_loader
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: matminer.datasets
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/_sources/matminer.datasets.test_datasets.rst.txt b/docs/_sources/matminer.datasets.test_datasets.rst.txt
@@ -0,0 +1,22 @@
+matminer.datasets.test_datasets package
+=======================================
+
+Submodules
+----------
+
+matminer.datasets.test_datasets.test_datasets module
+----------------------------------------------------
+
+.. automodule:: matminer.datasets.test_datasets.test_datasets
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: matminer.datasets.test_datasets
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/_sources/matminer.rst.txt b/docs/_sources/matminer.rst.txt
@@ -7,6 +7,7 @@ Subpackages
 .. toctree::
 
     matminer.data_retrieval
+    matminer.datasets
     matminer.featurizers
     matminer.figrecipes
     matminer.learners

diff --git a/docs/genindex.html b/docs/genindex.html
diff --git a/docs/index.html b/docs/index.html
@@ -6,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>matminer (Materials Data Mining) &#8212; matminer 0.1.2 documentation</title>
+    <title>matminer (Materials Data Mining) &#8212; matminer 0.1.3 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',
+        VERSION:     '0.1.3',
         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 0.1.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">matminer 0.1.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -202,6 +202,18 @@ <h3>Plotting tools<a class="headerlink" href="#plotting-tools" title="Permalink
 </div>
 <div class="section" id="changelog">
 <h3>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h3>
+<p><strong>v0.1.3</strong></p>
+<ul class="simple">
+<li>remove git-lfs</li>
+<li>refactor structure descriptors</li>
+<li>multiple fixes to cohesive energy</li>
+<li>fixes to data loaders</li>
+<li>fix complex Mongo retrieval queries, better logic for query projections</li>
+<li>more unit tests</li>
+<li>enforce lower case feature names</li>
+<li>sort data by atomic number not electronegativity in data getters, this will avoid pernicious behavior</li>
+<li>many minor cleanups, bug fixes, and consistency fixes</li>
+</ul>
 <p><strong>v0.1.2</strong></p>
 <ul class="simple">
 <li>Several new structure fingerprint methods (L. Ward, K. Bostrom)</li>
@@ -298,7 +310,7 @@ <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 0.1.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="#">matminer 0.1.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">

diff --git a/docs/matminer.data_retrieval.html b/docs/matminer.data_retrieval.html
@@ -6,15 +6,15 @@
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
 
-    <title>matminer.data_retrieval package &#8212; matminer 0.1.2 documentation</title>
+    <title>matminer.data_retrieval package &#8212; matminer 0.1.3 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',
+        VERSION:     '0.1.3',
         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 0.1.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.1.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -61,7 +61,11 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <code class="descname">__init__</code><span class="sig-paren">(</span><em>api_key=None</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_Citrine.CitrineDataRetrieval.__init__" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="docutils">
 <dt>Args:</dt>
-<dd>api_key: (str) Your Citrine API key, or None if you&#8217;ve set the CITRINE_KEY environment variable</dd>
+<dd><dl class="first last docutils">
+<dt>api_key: (str) Your Citrine API key, or None if you&#8217;ve set the</dt>
+<dd>CITRINE_KEY environment variable</dd>
+</dl>
+</dd>
 </dl>
 <p>Returns: None</p>
 </dd></dl>
@@ -70,27 +74,35 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dt id="matminer.data_retrieval.retrieve_Citrine.CitrineDataRetrieval.get_dataframe">
 <code class="descname">get_dataframe</code><span class="sig-paren">(</span><em>formula=None</em>, <em>property=None</em>, <em>data_type=None</em>, <em>reference=None</em>, <em>min_measurement=None</em>, <em>max_measurement=None</em>, <em>from_record=None</em>, <em>data_set_id=None</em>, <em>max_results=None</em>, <em>show_columns=None</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_Citrine.CitrineDataRetrieval.get_dataframe" title="Permalink to this definition">¶</a></dt>
 <dd><p>Gets data from Citrine in a dataframe format.
-See client docs at <a class="reference external" href="http://citrineinformatics.github.io/api-documentation/">http://citrineinformatics.github.io/api-documentation/</a> for more details on these parameters.</p>
+See client docs at
+<a class="reference external" href="http://citrineinformatics.github.io/api-documentation/">http://citrineinformatics.github.io/api-documentation/</a> for more details
+on these parameters.</p>
 <dl class="docutils">
 <dt>Args:</dt>
 <dd><dl class="first docutils">
-<dt>formula: (str) filter for the chemical formula field; only those results that have chemical formulas that</dt>
-<dd>contain this string will be returned</dd>
+<dt>formula: (str) filter for the chemical formula field; only those</dt>
+<dd>results that have chemical formulas that contain this string
+will be returned</dd>
 </dl>
 <p>property: (str) name of the property to search for
-data_type: (str) &#8216;EXPERIMENTAL&#8217;/&#8217;COMPUTATIONAL&#8217;/&#8217;MACHINE_LEARNING&#8217;; filter for properties obtained from</p>
+data_type: (str) &#8216;EXPERIMENTAL&#8217;/&#8217;COMPUTATIONAL&#8217;/&#8217;MACHINE_LEARNING&#8217;;</p>
 <blockquote>
-<div>experimental work, computational methods, or machine learning.</div></blockquote>
+<div>filter for properties obtained from experimental work,
+computational methods, or machine learning.</div></blockquote>
 <dl class="docutils">
-<dt>reference: (str) filter for the reference field; only those results that have contributors that</dt>
-<dd>contain this string will be returned</dd>
+<dt>reference: (str) filter for the reference field; only those results</dt>
+<dd>that have contributors that contain this string will be returned</dd>
 </dl>
-<p class="last">min_measurement: (str/num) minimum of the property value range
+<p>min_measurement: (str/num) minimum of the property value range
 max_measurement: (str/num) maximum of the property value range
-from_record: (int) index of the first record to return (indexed from 0)
-data_set_id: (int) id of the particular data set to search on
+from_record: (int) index of the first record to return (indexed</p>
+<blockquote>
+<div>from 0)</div></blockquote>
+<p>data_set_id: (int) id of the particular data set to search on
 max_results: (int) number of records to limit the results to
-show_columns: (list) list of columns to show from the resulting dataframe</p>
+show_columns: (list) list of columns to show from the resulting</p>
+<blockquote class="last">
+<div>dataframe</div></blockquote>
 </dd>
 </dl>
 <p>Returns: (object) Pandas dataframe object containing the results</p>
@@ -153,51 +165,46 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dl class="class">
 <dt id="matminer.data_retrieval.retrieve_MP.MPDataRetrieval">
 <em class="property">class </em><code class="descclassname">matminer.data_retrieval.retrieve_MP.</code><code class="descname">MPDataRetrieval</code><span class="sig-paren">(</span><em>api_key=None</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MP.MPDataRetrieval" title="Permalink to this definition">¶</a></dt>
-<dd><p>MPDataRetrieval is used to retrieve data from the Materials Project database, print the results, and convert them
-into an indexed/unindexed Pandas dataframe.</p>
+<dd><p>MPDataRetrieval is used to retrieve data from the Materials Project
+database, print the results, and convert them into an indexed Pandas
+dataframe.</p>
 <dl class="method">
 <dt id="matminer.data_retrieval.retrieve_MP.MPDataRetrieval.__init__">
 <code class="descname">__init__</code><span class="sig-paren">(</span><em>api_key=None</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MP.MPDataRetrieval.__init__" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="docutils">
 <dt>Args:</dt>
-<dd>api_key: (str) Your Materials Project API key, or None if you&#8217;ve set the MAPI_KEY environment variable</dd>
+<dd><dl class="first last docutils">
+<dt>api_key: (str) Your Materials Project API key, or None if you&#8217;ve</dt>
+<dd>set up your pymatgen config.</dd>
+</dl>
+</dd>
 </dl>
-<p>Returns: None</p>
 </dd></dl>
 
 <dl class="method">
 <dt id="matminer.data_retrieval.retrieve_MP.MPDataRetrieval.get_dataframe">
 <code class="descname">get_dataframe</code><span class="sig-paren">(</span><em>criteria</em>, <em>properties</em>, <em>mp_decode=False</em>, <em>index_mpid=True</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MP.MPDataRetrieval.get_dataframe" title="Permalink to this definition">¶</a></dt>
 <dd><p>Gets data from MP in a dataframe format.
-See API docs at <a class="reference external" href="https://materialsproject.org/wiki/index.php/The_Materials_API">https://materialsproject.org/wiki/index.php/The_Materials_API</a> for more details.</p>
+See API docs at
+<a class="reference external" href="https://materialsproject.org/wiki/index.php/The_Materials_API">https://materialsproject.org/wiki/index.php/The_Materials_API</a>
+for more details.</p>
 <dl class="docutils">
 <dt>Args:</dt>
-<dd><dl class="first docutils">
-<dt>criteria: (str/dict) Criteria of the query as a string or mongo-style dict. If string, it supports a</dt>
-<dd><p class="first">powerful but simple string criteria. E.g., &#8220;Fe2O3&#8221; means search for materials with reduced_formula
-Fe2O3. Wild cards are also supported. E.g., &#8220;*2O&#8221; means get all materials whose formula can be formed
-as *2O, e.g., Li2O, K2O, etc.</p>
-<dl class="docutils">
-<dt>Other syntax examples:</dt>
-<dd>mp-1234: Interpreted as a Materials ID.
-Fe2O3 or *2O3: Interpreted as reduced formulas.
-Li-Fe-O or *-Fe-O: Interpreted as chemical systems.</dd>
+<dd><dl class="first last docutils">
+<dt>criteria: (str/dict) see MPRester.query() for a description of this</dt>
+<dd>parameter. String examples: &#8220;mp-1234&#8221;, &#8220;Fe2O3&#8221;, &#8220;Li-Fe-O&#8217;,
+&#8220;*2O3&#8221;. Dict example: {&#8220;band_gap&#8221;: {&#8220;$gt&#8221;: 1}}</dd>
+<dt>properties: (list) see MPRester.query() for a description of this</dt>
+<dd>parameter. Example: [&#8220;formula&#8221;, &#8220;formation_energy_per_atom&#8221;]</dd>
+<dt>mp_decode: (bool) see MPRester.query() for a description of this</dt>
+<dd>parameter. Whether to decode to a Pymatgen object where
+possible.</dd>
+<dt>index_mpid: (bool) Whether to set the materials_id as the dataframe</dt>
+<dd>index.</dd>
 </dl>
-<p>You can mix and match with spaces, which are interpreted as &#8220;OR&#8221;. E.g. &#8220;mp-1234 FeO&#8221; means query for
-all compounds with reduced formula FeO or with materials_id mp-1234.</p>
-<p class="last">Using a full dict syntax, even more powerful queries can be constructed. For example,
-{&#8220;elements&#8221;:{&#8220;$in&#8221;:[&#8220;Li&#8221;, &#8220;Na&#8221;, &#8220;K&#8221;], &#8220;$all&#8221;: [&#8220;O&#8221;]}, &#8220;nelements&#8221;:2} selects all Li, Na and K oxides.
-{&#8220;band_gap&#8221;: {&#8220;$gt&#8221;: 1}} selects all materials with band gaps greater than 1 eV.</p>
 </dd>
-<dt>properties: (list) Properties to request for as a list. For example,</dt>
-<dd>[&#8220;formula&#8221;, &#8220;formation_energy_per_atom&#8221;] returns the formula and formation energy per atom.</dd>
-<dt>mp_decode: (bool) Whether to do a decoding to a Pymatgen object where possible. In some cases, it might be</dt>
-<dd>useful to just get the raw python dict, i.e., set to False.</dd>
 </dl>
-<p class="last">index_mpid: (bool) Whether to set the materials_id as the dataframe index.</p>
-</dd>
-</dl>
-<p>Returns: A Pandas dataframe object</p>
+<p>Returns: A pandas Dataframe object</p>
 </dd></dl>
 
 </dd></dl>
@@ -214,10 +221,12 @@ <h2>matminer.data_retrieval.retrieve_MPDS module<a class="headerlink" href="#mat
 <dd><dl class="method">
 <dt id="matminer.data_retrieval.retrieve_MongoDB.MongoDataRetrieval.__init__">
 <code class="descname">__init__</code><span class="sig-paren">(</span><em>coll</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MongoDB.MongoDataRetrieval.__init__" title="Permalink to this definition">¶</a></dt>
-<dd><p>Tool to retrieve data from a MongoDB collection and reformat for data analysis
-Args:</p>
-<blockquote>
-<div>coll: A MongoDB collection object</div></blockquote>
+<dd><p>Tool to retrieve data from a MongoDB collection and put into a pandas
+Dataframe object</p>
+<dl class="docutils">
+<dt>Args:</dt>
+<dd>coll: A MongoDB collection object</dd>
+</dl>
 </dd></dl>
 
 <dl class="method">
@@ -226,14 +235,16 @@ <h2>matminer.data_retrieval.retrieve_MPDS module<a class="headerlink" href="#mat
 <dd><dl class="docutils">
 <dt>Args:</dt>
 <dd><dl class="first docutils">
-<dt>projection: (list) - a list of str fields to grab; dot-notation is allowed.</dt>
-<dd>Set to &#8220;None&#8221; to try to auto-detect the fields.</dd>
+<dt>projection: (list) - a list of str fields to grab; dot-notation is</dt>
+<dd>allowed. Set to &#8220;None&#8221; to try to auto-detect the fields.</dd>
 </dl>
-<p class="last">query: (JSON) - a pymongo-style query to restrict data being gathered
+<p>query: (JSON) - a pymongo-style query to filter data records
 sort: (tuple) - pymongo-style sort option
-limit: (int) - int to limit the number of entries
-idx_field: (str) - name of field to use as index field (must be unique)
-strict: (bool) - if False, replaces missing values with NaN</p>
+limit: (int) - max number of entries
+idx_field: (str) - name of field to use as index (must have unique</p>
+<blockquote>
+<div>entries)</div></blockquote>
+<p class="last">strict: (bool) - if False, replaces missing values with NaN</p>
 </dd>
 </dl>
 </dd></dl>
@@ -243,21 +254,22 @@ <h2>matminer.data_retrieval.retrieve_MPDS module<a class="headerlink" href="#mat
 <dl class="function">
 <dt id="matminer.data_retrieval.retrieve_MongoDB.clean_projection">
 <code class="descclassname">matminer.data_retrieval.retrieve_MongoDB.</code><code class="descname">clean_projection</code><span class="sig-paren">(</span><em>projection</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MongoDB.clean_projection" title="Permalink to this definition">¶</a></dt>
-<dd><p>Projecting on e.g. &#8216;a.b.&#8217; and &#8216;a&#8217; is disallowed. Project inclusively.
+<dd><p>Projecting on e.g. &#8216;a.b.&#8217; and &#8216;a&#8217; is disallowed in MongoDb, so project
+inclusively. See unit tests for examples of what this is doing.
 Args:</p>
 <blockquote>
 <div>projection: (list) - list of fields to grab; dot-notation is allowed.</div></blockquote>
 </dd></dl>
 
-<dl class="function">
-<dt id="matminer.data_retrieval.retrieve_MongoDB.is_int">
-<code class="descclassname">matminer.data_retrieval.retrieve_MongoDB.</code><code class="descname">is_int</code><span class="sig-paren">(</span><em>x</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MongoDB.is_int" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
 <dl class="function">
 <dt id="matminer.data_retrieval.retrieve_MongoDB.remove_ints">
 <code class="descclassname">matminer.data_retrieval.retrieve_MongoDB.</code><code class="descname">remove_ints</code><span class="sig-paren">(</span><em>projection</em><span class="sig-paren">)</span><a class="headerlink" href="#matminer.data_retrieval.retrieve_MongoDB.remove_ints" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
+<dd><p>Transforms a string like &#8220;a.1.x&#8221; to &#8220;a.x&#8221; - for Mongo projection purposes
+Args:</p>
+<blockquote>
+<div>projection: (str) the projection to remove ints from</div></blockquote>
+<p>Returns:</p>
+</dd></dl>
 
 </div>
 <div class="section" id="module-matminer.data_retrieval">
@@ -314,7 +326,7 @@ <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 0.1.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">matminer 0.1.3 documentation</a> &#187;</li> 
       </ul>
     </div>
     <div class="footer" role="contentinfo">