Update to v0.9.3

hackingmaterials · Aug 30, 2019 · 7520471 · 7520471
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diff --git a/atomate/__init__.py b/atomate/__init__.py
@@ -1 +1 @@
-__version__ = "0.9.2"
+__version__ = "0.9.3"
diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,6 +2,11 @@
 atomate Changelog
 =================
 
+**v0.9.3**
+
+* Minor change to enforce storing chgcars, clean up old kwargs in MagneticOrderings workflow (M. Horton)
+* Improve speed of large file copying in CopyVaspOutputs (T.M. Boland)
+
 **v0.9.2**
 
 * fix CalcDB authentication issue (M. Bercx)

diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt
@@ -12,4 +12,4 @@ Contributions are provided by:
 * Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State.
 * Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley.
 * Danny Broberg through the research group of Prof. Mark Asta at UC Berkeley.
-* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx
+* External contributors: specter119, M. Dias Costa, S. Torrisi, Max Dylla, Marnik Bercx, Tara Maria Boland
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.9.2',
+    VERSION: '0.9.3',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common.firetasks package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.common.firetasks package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <h3>Navigation</h3>
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           <a href="py-modindex.html" title="Python Module Index"
              >modules</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -658,7 +658,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.firetasks.tests.html b/docs/atomate.common.firetasks.tests.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common.firetasks.tests package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.common.firetasks.tests package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
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@@ -207,7 +207,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.html b/docs/atomate.common.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.common package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
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@@ -113,7 +113,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.firetasks.html b/docs/atomate.feff.firetasks.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.firetasks package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.feff.firetasks package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -442,7 +442,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.firetasks.tests.html b/docs/atomate.feff.firetasks.tests.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.firetasks.tests package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.feff.firetasks.tests package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -118,7 +118,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.fireworks.html b/docs/atomate.feff.fireworks.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.fireworks package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.feff.fireworks package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -209,7 +209,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.fireworks.tests.html b/docs/atomate.feff.fireworks.tests.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.fireworks.tests package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.feff.fireworks.tests package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -113,7 +113,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.html b/docs/atomate.feff.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.feff package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -182,7 +182,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.workflows.html b/docs/atomate.feff.workflows.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.workflows package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.feff.workflows package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -252,7 +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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.workflows.tests.html b/docs/atomate.feff.workflows.tests.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.workflows.tests package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.feff.workflows.tests package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -186,7 +186,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.html b/docs/atomate.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
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@@ -423,7 +423,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
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diff --git a/docs/atomate.lammps.firetasks.html b/docs/atomate.lammps.firetasks.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.lammps.firetasks package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.lammps.firetasks package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -461,7 +461,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.lammps.fireworks.html b/docs/atomate.lammps.fireworks.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.lammps.fireworks package &#8212; atomate 0.9.2 documentation</title>
+    <title>atomate.lammps.fireworks package &#8212; atomate 0.9.3 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" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
@@ -27,7 +27,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
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@@ -196,7 +196,7 @@ <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">atomate 0.9.2 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.3 documentation</a> &#187;</li> 
       </ul>
     </div>