Update dev docs

materialsproject · Jun 11, 2018 · 607aae1 · 607aae1
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diff --git a/custodian/__init__.py b/custodian/__init__.py
@@ -2,6 +2,6 @@
 
 __author__ = "Shyue Ping Ong, William Davidson Richards, Stephen Dacek, " \
              "Xiaohui Qu"
-__version__ = "2018.3.10"
+__version__ = "2018.6.11"
 
 from .custodian import Custodian
diff --git a/docs/_modules/custodian/ansible/actions.html b/docs/_modules/custodian/ansible/actions.html
diff --git a/docs/_modules/custodian/ansible/interpreter.html b/docs/_modules/custodian/ansible/interpreter.html
@@ -6,10 +6,10 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>custodian.ansible.interpreter &#8212; custodian 2018.3.10 documentation</title>
+    <title>custodian.ansible.interpreter &#8212; custodian 2018.6.11 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" src="../../../_static/documentation_options.js"></script>
+    <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></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>
@@ -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">custodian 2018.3.10 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2018.6.11 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -132,8 +132,8 @@ <h1>Source code for custodian.ansible.interpreter</h1><div class="highlight"><pr
             <span class="k">if</span> <span class="n">action</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">supported_actions</span><span class="p">:</span>
                 <span class="bp">self</span><span class="o">.</span><span class="n">supported_actions</span><span class="p">[</span><span class="n">action</span><span class="p">]</span><span class="o">.</span><span class="fm">__call__</span><span class="p">(</span><span class="n">obj</span><span class="p">,</span> <span class="n">settings</span><span class="p">)</span>
             <span class="k">elif</span> <span class="bp">self</span><span class="o">.</span><span class="n">strict</span><span class="p">:</span>
-                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{}</span><span class="s2"> is not a supported action!&quot;</span></div>
-                                 <span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">action</span><span class="p">))</span>
+                <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="s2">&quot;</span><span class="si">{}</span><span class="s2"> is not a supported action!&quot;</span>
+                                 <span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="n">action</span><span class="p">))</span></div>
 
 <div class="viewcode-block" id="Modder.modify_object"><a class="viewcode-back" href="../../../custodian.ansible.html#custodian.ansible.interpreter.Modder.modify_object">[docs]</a>    <span class="k">def</span> <span class="nf">modify_object</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">modification</span><span class="p">,</span> <span class="n">obj</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;</span>
@@ -145,8 +145,8 @@ <h1>Source code for custodian.ansible.interpreter</h1><div class="highlight"><pr
 <span class="sd">            obj (object): Object to modify</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="n">d</span> <span class="o">=</span> <span class="n">obj</span><span class="o">.</span><span class="n">as_dict</span><span class="p">()</span>
-        <span class="bp">self</span><span class="o">.</span><span class="n">modify</span><span class="p">(</span><span class="n">modification</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span></div></div>
-        <span class="k">return</span> <span class="n">obj</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">d</span><span class="p">)</span>
+        <span class="bp">self</span><span class="o">.</span><span class="n">modify</span><span class="p">(</span><span class="n">modification</span><span class="p">,</span> <span class="n">d</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">obj</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">d</span><span class="p">)</span></div></div>
 
 
 <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>

diff --git a/docs/_modules/custodian/cli/converge_geometry.html b/docs/_modules/custodian/cli/converge_geometry.html
@@ -6,10 +6,10 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>custodian.cli.converge_geometry &#8212; custodian 2018.3.10 documentation</title>
+    <title>custodian.cli.converge_geometry &#8212; custodian 2018.6.11 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" src="../../../_static/documentation_options.js"></script>
+    <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></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>
@@ -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">custodian 2018.3.10 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2018.6.11 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -121,17 +121,17 @@ <h1>Source code for custodian.cli.converge_geometry</h1><div class="highlight"><
                      <span class="s2">&quot;action&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;_file_copy&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;dest&quot;</span><span class="p">:</span> <span class="s2">&quot;POSCAR&quot;</span><span class="p">}}}]</span>
 
         <span class="n">job_number</span> <span class="o">+=</span> <span class="mi">1</span>
-        <span class="k">yield</span> <span class="n">VaspJob</span><span class="p">(</span><span class="n">vasp_command</span><span class="p">,</span> <span class="n">final</span><span class="o">=</span><span class="n">converged</span><span class="p">,</span> <span class="n">backup</span><span class="o">=</span><span class="n">backup</span><span class="p">,</span></div>
-                      <span class="n">suffix</span><span class="o">=</span><span class="n">suffix</span><span class="p">,</span> <span class="n">settings_override</span><span class="o">=</span><span class="n">settings</span><span class="p">)</span>
+        <span class="k">yield</span> <span class="n">VaspJob</span><span class="p">(</span><span class="n">vasp_command</span><span class="p">,</span> <span class="n">final</span><span class="o">=</span><span class="n">converged</span><span class="p">,</span> <span class="n">backup</span><span class="o">=</span><span class="n">backup</span><span class="p">,</span>
+                      <span class="n">suffix</span><span class="o">=</span><span class="n">suffix</span><span class="p">,</span> <span class="n">settings_override</span><span class="o">=</span><span class="n">settings</span><span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="do_run"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.converge_geometry.do_run">[docs]</a><span class="k">def</span> <span class="nf">do_run</span><span class="p">(</span><span class="n">args</span><span class="p">):</span>
     <span class="n">handlers</span> <span class="o">=</span> <span class="p">[</span><span class="n">VaspErrorHandler</span><span class="p">(),</span> <span class="n">MeshSymmetryErrorHandler</span><span class="p">(),</span>
                 <span class="n">UnconvergedErrorHandler</span><span class="p">(),</span> <span class="n">NonConvergingErrorHandler</span><span class="p">(),</span>
                 <span class="n">PotimErrorHandler</span><span class="p">()]</span>
     <span class="n">c</span> <span class="o">=</span> <span class="n">Custodian</span><span class="p">(</span><span class="n">handlers</span><span class="p">,</span> <span class="n">get_runs</span><span class="p">(</span><span class="n">args</span><span class="p">),</span> <span class="n">max_errors</span><span class="o">=</span><span class="mi">10</span><span class="p">,</span> <span class="n">gzipped_output</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">gzip</span><span class="p">)</span>
-    <span class="n">c</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
-    <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Geometry optimization complete&quot;</span><span class="p">)</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+    <span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="s2">&quot;Geometry optimization complete&quot;</span><span class="p">)</span></div>
 
 
 <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>

diff --git a/docs/_modules/custodian/cli/converge_kpoints.html b/docs/_modules/custodian/cli/converge_kpoints.html
@@ -6,10 +6,10 @@
   <head>
     <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>custodian.cli.converge_kpoints &#8212; custodian 2018.3.10 documentation</title>
+    <title>custodian.cli.converge_kpoints &#8212; custodian 2018.6.11 documentation</title>
     <link rel="stylesheet" href="../../../_static/flasky.css" type="text/css" />
     <link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
-    <script type="text/javascript" src="../../../_static/documentation_options.js"></script>
+    <script type="text/javascript" id="documentation_options" data-url_root="../../../" src="../../../_static/documentation_options.js"></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>
@@ -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">custodian 2018.3.10 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../index.html">custodian 2018.6.11 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../index.html" accesskey="U">Module code</a> &#187;</li> 
       </ul>
     </div>  
@@ -108,17 +108,17 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
                     <span class="p">{</span><span class="s2">&quot;filename&quot;</span><span class="p">:</span> <span class="s2">&quot;CONTCAR&quot;</span><span class="p">,</span>
                      <span class="s2">&quot;action&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;_file_copy&quot;</span><span class="p">:</span> <span class="p">{</span><span class="s2">&quot;dest&quot;</span><span class="p">:</span> <span class="s2">&quot;POSCAR&quot;</span><span class="p">}}}]</span>
         <span class="k">yield</span> <span class="n">VaspJob</span><span class="p">(</span><span class="n">vasp_command</span><span class="p">,</span> <span class="n">final</span><span class="o">=</span><span class="kc">False</span><span class="p">,</span> <span class="n">backup</span><span class="o">=</span><span class="n">backup</span><span class="p">,</span>
-                      <span class="n">suffix</span><span class="o">=</span><span class="s2">&quot;.kpoints.</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">&quot;x&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">m</span><span class="p">))),</span></div>
-                      <span class="n">settings_override</span><span class="o">=</span><span class="n">settings</span><span class="p">)</span>
+                      <span class="n">suffix</span><span class="o">=</span><span class="s2">&quot;.kpoints.</span><span class="si">{}</span><span class="s2">&quot;</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="s2">&quot;x&quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="nb">map</span><span class="p">(</span><span class="nb">str</span><span class="p">,</span> <span class="n">m</span><span class="p">))),</span>
+                      <span class="n">settings_override</span><span class="o">=</span><span class="n">settings</span><span class="p">)</span></div>
 
 
 <div class="viewcode-block" id="do_run"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.converge_kpoints.do_run">[docs]</a><span class="k">def</span> <span class="nf">do_run</span><span class="p">(</span><span class="n">args</span><span class="p">):</span>
     <span class="n">handlers</span> <span class="o">=</span> <span class="p">[</span><span class="n">VaspErrorHandler</span><span class="p">(),</span> <span class="n">UnconvergedErrorHandler</span><span class="p">()]</span>
     <span class="n">c</span> <span class="o">=</span> <span class="n">Custodian</span><span class="p">(</span><span class="n">handlers</span><span class="p">,</span> <span class="n">get_runs</span><span class="p">(</span><span class="n">vasp_command</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">command</span><span class="o">.</span><span class="n">split</span><span class="p">(),</span>
                                      <span class="n">target</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">target</span><span class="p">,</span> <span class="n">mode</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">mode</span><span class="p">,</span>
                                      <span class="n">max_steps</span><span class="o">=</span><span class="n">args</span><span class="o">.</span><span class="n">max_steps</span><span class="p">),</span>
-                  <span class="n">max_errors</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span></div>
-    <span class="n">c</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
+                  <span class="n">max_errors</span><span class="o">=</span><span class="mi">10</span><span class="p">)</span>
+    <span class="n">c</span><span class="o">.</span><span class="n">run</span><span class="p">()</span></div>
 
 
 <div class="viewcode-block" id="main"><a class="viewcode-back" href="../../../custodian.cli.html#custodian.cli.converge_kpoints.main">[docs]</a><span class="k">def</span> <span class="nf">main</span><span class="p">():</span>
@@ -168,8 +168,8 @@ <h1>Source code for custodian.cli.converge_kpoints</h1><div class="highlight"><p
              <span class="s2">&quot;until a converged of 1meV is reached.&quot;</span>
     <span class="p">)</span>
 
-    <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span></div>
-    <span class="n">do_run</span><span class="p">(</span><span class="n">args</span><span class="p">)</span>
+    <span class="n">args</span> <span class="o">=</span> <span class="n">parser</span><span class="o">.</span><span class="n">parse_args</span><span class="p">()</span>
+    <span class="n">do_run</span><span class="p">(</span><span class="n">args</span><span class="p">)</span></div>
 
 
 <span class="k">if</span> <span class="vm">__name__</span> <span class="o">==</span> <span class="s2">&quot;__main__&quot;</span><span class="p">:</span>