Update to v0.9.0

hackingmaterials · Jun 5, 2019 · 6cc0c0e · 6cc0c0e
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diff --git a/atomate/__init__.py b/atomate/__init__.py
@@ -1 +1 @@
-__version__ = "0.8.9"
+__version__ = "0.9.0"
diff --git a/docs/_images/MgO-dos.png b/docs/_images/MgO-dos.png
diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,8 +2,16 @@
 atomate Changelog
 =================
 
+**v0.9.0**
+
+* Fix db authentication issue in v0.8.9 (M. Siron)
+* Change default vasp_cmd and db_file to those in config.py (M. Horton)
+* update plots in docs (A. Ganose)
+
 **v0.8.9**
 
+.. caution:: this version introduced a quirk in the db authentication scheme, you might need to set authsource manually or update to v0.9.0
+
 * fix NSCF run kpoint mesh and Boltztrap workflow to reflect pymatgen updates (A. Ganose)
 * allow "authsource" parameter in db.json files (A. Jain)
 * add powerup for turning off gzip (D. Broberg)

diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt
@@ -7,7 +7,7 @@ atomate development is led by the Hacking Materials research group led by Anubha
 Contributions are provided by:
 
 * Alireza Faghaninia, Alex Dunn, Alex Ganose, and Evan Spotte-Smith through the research group of A. Jain at LBNL.
-* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, Sam Blau, Jimmy Shen, Anne Rutt, and Eric Sivonxay 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, Anne Rutt, Eric Sivonxay, and Martin Siron 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.
 * Tess Smidt through the research group of Prof. Jeff Neaton at UC Berkeley.

diff --git a/docs/_sources/running_workflows.rst.txt b/docs/_sources/running_workflows.rst.txt
@@ -192,8 +192,8 @@ Simply add the following Python script (``bs-analysis.py``) to your folder, **ch
     # Comment out the get_plot and uncomment save_plot if you have no GUI frontend to plot to.
     dos_plotter = DosPlotter()
     dos_plotter.add_dos_dict(complete_dos.get_element_dos())
-    dos_plotter.get_plot(xlim=(-10, 10), ylim=(0, 0.1))
-    #dos_plotter.save_plot('MgO-dos.pdf', img_format='pdf', xlim=(-10, 10), ylim=(0, 0.1))
+    dos_plotter.get_plot(xlim=(-10, 10))
+    #dos_plotter.save_plot('MgO-dos.pdf', img_format='pdf', xlim=(-10, 10))
 
     # print the Fermi energy and bandgap from the DOS:
     print('Fermi energy: {} eV'.format(complete_dos.efermi))

diff --git a/docs/_static/MgO-dos.png b/docs/_static/MgO-dos.png
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: '0.8.9',
+    VERSION: '0.9.0',
     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 0.8.9 documentation</title>
+    <title>atomate.common.firetasks package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.common.firetasks.tests package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -211,7 +211,7 @@ <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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.common package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.feff.firetasks package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.feff.firetasks.tests package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.feff.fireworks package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.feff.fireworks.tests package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.feff package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.feff.workflows package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</title>
+    <title>atomate.feff.workflows.tests package &#8212; atomate 0.9.0 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>
@@ -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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 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 0.8.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.0 documentation</a> &#187;</li> 
       </ul>
     </div>