Update to v0.8.4

hackingmaterials · Nov 2, 2018 · e98259c · e98259c
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commit e98259c
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diff --git a/atomate/__init__.py b/atomate/__init__.py
@@ -1 +1 @@
-__version__ = "0.8.3"
+__version__ = "0.8.4"
diff --git a/docs/_sources/atomate.qchem.firetasks.rst.txt b/docs/_sources/atomate.qchem.firetasks.rst.txt
@@ -11,6 +11,14 @@ Subpackages
 Submodules
 ----------
 
+atomate.qchem.firetasks.fragmenter module
+-----------------------------------------
+
+.. automodule:: atomate.qchem.firetasks.fragmenter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 atomate.qchem.firetasks.geo\_transformations module
 ---------------------------------------------------
 

diff --git a/docs/_sources/atomate.qchem.firetasks.tests.rst.txt b/docs/_sources/atomate.qchem.firetasks.tests.rst.txt
@@ -4,6 +4,14 @@ atomate.qchem.firetasks.tests package
 Submodules
 ----------
 
+atomate.qchem.firetasks.tests.test\_fragmenter module
+-----------------------------------------------------
+
+.. automodule:: atomate.qchem.firetasks.tests.test_fragmenter
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 atomate.qchem.firetasks.tests.test\_geo\_transformations module
 ---------------------------------------------------------------
 

diff --git a/docs/_sources/atomate.qchem.workflows.base.rst.txt b/docs/_sources/atomate.qchem.workflows.base.rst.txt
@@ -12,6 +12,14 @@ atomate.qchem.workflows.base.double\_FF\_opt module
     :undoc-members:
     :show-inheritance:
 
+atomate.qchem.workflows.base.fragmentation module
+-------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.base.fragmentation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 atomate.qchem.workflows.base.torsion\_potential module
 ------------------------------------------------------
 

diff --git a/docs/_sources/atomate.qchem.workflows.tests.rst.txt b/docs/_sources/atomate.qchem.workflows.tests.rst.txt
@@ -12,6 +12,14 @@ atomate.qchem.workflows.tests.test\_double\_FF\_opt module
     :undoc-members:
     :show-inheritance:
 
+atomate.qchem.workflows.tests.test\_fragmentation module
+--------------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.tests.test_fragmentation
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 atomate.qchem.workflows.tests.test\_parse\_pass\_write module
 -------------------------------------------------------------
 

diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,6 +2,13 @@
 atomate Changelog
 =================
 
+**v0.8.4**
+
+* add some QChem functionality! (S. Blau, E. Spotte-Smith)
+* better credential parsing in CalcDB (A. Rutt)
+* update paramiko for better security (A. Jain)
+* add tasks_settings.yaml to site-packages (A. Jain)
+
 **v0.8.3**
 
 * add CHGCAR and AECAR storage options (J. Shen)

diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt
@@ -6,10 +6,10 @@ atomate development is led by the Hacking Materials research group led by Anubha
 
 Contributions are provided by:
 
-* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, Sam Blau, and Jimmy Shen through the research group of Prof. Kristin Persson at UC Berkeley.
+* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, and Anne Rutt through the research group of Prof. Kristin Persson at UC Berkeley.
 * Hanmei Tang, Prof. Shyue Ping Ong, and the Materials Virtual Lab research group at UC San Diego.
 * Brandon Bocklund, who led the atomate documentation effort, through the research group of Prof. Zi-Kiu Liu at Penn State.
-* Alireza Faghaninia and A. Dunn through the research group of A. Jain at LBNL.
+* Alireza Faghaninia, Alex Dunn, and Evan Spotte-Smith through the research group of A. Jain at LBNL.
 * 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
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: '',
-    VERSION: '0.8.3',
+    VERSION: '0.8.4',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.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>atomate.common.firetasks package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.common.firetasks package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -677,7 +677,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.firetasks.tests.html b/docs/atomate.common.firetasks.tests.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>atomate.common.firetasks.tests package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.common.firetasks.tests package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -161,7 +161,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.html b/docs/atomate.common.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>atomate.common package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.common package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -116,7 +116,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.firetasks.html b/docs/atomate.feff.firetasks.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>atomate.feff.firetasks package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.feff.firetasks package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -452,7 +452,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.firetasks.tests.html b/docs/atomate.feff.firetasks.tests.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>atomate.feff.firetasks.tests package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.feff.firetasks.tests package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -121,7 +121,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.fireworks.html b/docs/atomate.feff.fireworks.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>atomate.feff.fireworks package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.feff.fireworks package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -212,7 +212,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.fireworks.tests.html b/docs/atomate.feff.fireworks.tests.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>atomate.feff.fireworks.tests package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.feff.fireworks.tests package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -116,7 +116,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.html b/docs/atomate.feff.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>atomate.feff package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.feff package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -185,7 +185,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.workflows.html b/docs/atomate.feff.workflows.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>atomate.feff.workflows package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.feff.workflows package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -251,7 +251,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.workflows.tests.html b/docs/atomate.feff.workflows.tests.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>atomate.feff.workflows.tests package &#8212; atomate 0.8.3 documentation</title>
+    <title>atomate.feff.workflows.tests package &#8212; atomate 0.8.4 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">atomate 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -189,7 +189,7 @@ <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 0.8.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.8.4 documentation</a> &#187;</li> 
       </ul>
     </div>