Update to v0.7.9

hackingmaterials · Jun 8, 2018 · 2c0b2fa · 2c0b2fa
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diff --git a/atomate/__init__.py b/atomate/__init__.py
@@ -1 +1 @@
-__version__ = "0.7.8"
+__version__ = "0.7.9"
diff --git a/docs/_sources/atomate.qchem.firetasks.rst.txt b/docs/_sources/atomate.qchem.firetasks.rst.txt
@@ -11,6 +11,30 @@ Subpackages
 Submodules
 ----------
 
+atomate.qchem.firetasks.geo\_transformations module
+---------------------------------------------------
+
+.. automodule:: atomate.qchem.firetasks.geo_transformations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.firetasks.parse\_outputs module
+---------------------------------------------
+
+.. automodule:: atomate.qchem.firetasks.parse_outputs
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.firetasks.run\_calc module
+----------------------------------------
+
+.. automodule:: atomate.qchem.firetasks.run_calc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 atomate.qchem.firetasks.write\_inputs module
 --------------------------------------------
 

diff --git a/docs/_sources/atomate.qchem.firetasks.tests.rst.txt b/docs/_sources/atomate.qchem.firetasks.tests.rst.txt
@@ -4,6 +4,22 @@ atomate.qchem.firetasks.tests package
 Submodules
 ----------
 
+atomate.qchem.firetasks.tests.test\_geo\_transformations module
+---------------------------------------------------------------
+
+.. automodule:: atomate.qchem.firetasks.tests.test_geo_transformations
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.firetasks.tests.test\_run\_calc module
+----------------------------------------------------
+
+.. automodule:: atomate.qchem.firetasks.tests.test_run_calc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 atomate.qchem.firetasks.tests.test\_write\_inputs module
 --------------------------------------------------------
 

diff --git a/docs/_sources/atomate.qchem.fireworks.rst.txt b/docs/_sources/atomate.qchem.fireworks.rst.txt
@@ -0,0 +1,22 @@
+atomate.qchem.fireworks package
+===============================
+
+Submodules
+----------
+
+atomate.qchem.fireworks.core module
+-----------------------------------
+
+.. automodule:: atomate.qchem.fireworks.core
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: atomate.qchem.fireworks
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/_sources/atomate.qchem.rst.txt b/docs/_sources/atomate.qchem.rst.txt
@@ -7,6 +7,36 @@ Subpackages
 .. toctree::
 
     atomate.qchem.firetasks
+    atomate.qchem.fireworks
+    atomate.qchem.workflows
+
+Submodules
+----------
+
+atomate.qchem.database module
+-----------------------------
+
+.. automodule:: atomate.qchem.database
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.drones module
+---------------------------
+
+.. automodule:: atomate.qchem.drones
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.powerups module
+-----------------------------
+
+.. automodule:: atomate.qchem.powerups
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
 
 Module contents
 ---------------

diff --git a/docs/_sources/atomate.qchem.workflows.base.rst.txt b/docs/_sources/atomate.qchem.workflows.base.rst.txt
@@ -0,0 +1,30 @@
+atomate.qchem.workflows.base package
+====================================
+
+Submodules
+----------
+
+atomate.qchem.workflows.base.double\_FF\_opt module
+---------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.base.double_FF_opt
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.workflows.base.torsion\_potential module
+------------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.base.torsion_potential
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: atomate.qchem.workflows.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/_sources/atomate.qchem.workflows.rst.txt b/docs/_sources/atomate.qchem.workflows.rst.txt
@@ -0,0 +1,18 @@
+atomate.qchem.workflows package
+===============================
+
+Subpackages
+-----------
+
+.. toctree::
+
+    atomate.qchem.workflows.base
+    atomate.qchem.workflows.tests
+
+Module contents
+---------------
+
+.. automodule:: atomate.qchem.workflows
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/_sources/atomate.qchem.workflows.tests.rst.txt b/docs/_sources/atomate.qchem.workflows.tests.rst.txt
@@ -0,0 +1,38 @@
+atomate.qchem.workflows.tests package
+=====================================
+
+Submodules
+----------
+
+atomate.qchem.workflows.tests.test\_double\_FF\_opt module
+----------------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.tests.test_double_FF_opt
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.workflows.tests.test\_parse\_pass\_write module
+-------------------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.tests.test_parse_pass_write
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+atomate.qchem.workflows.tests.test\_torsion\_potential module
+-------------------------------------------------------------
+
+.. automodule:: atomate.qchem.workflows.tests.test_torsion_potential
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: atomate.qchem.workflows.tests
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,6 +2,12 @@
 atomate Changelog
 =================
 
+**v0.7.9**
+
+* Overhaul and update of QChem in atomate (B. Wood, S. Blau)
+* Fix integration tests (A. Dunn)
+* Stop officially supporting Py2
+
 **v0.7.8**
 
 * some QChem tasks and workflows (B. Wood)

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, and Patrick Huck through the research group of Prof. Kristin Persson at UC Berkeley.
+* Kiran Mathew, Shyam Dwaraknath, Joey Montoya, Murat Aykol, Patrick Huck, Brandon Wood, and Sam Blau 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 through the research group of A. Jain at LBNL.
+* Alireza Faghaninia and A. Dunn 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
diff --git a/docs/_sources/installation.rst.txt b/docs/_sources/installation.rst.txt
@@ -125,8 +125,10 @@ Installing atomate includes installation of codes, configuration files, and vari
 
 .. _Create a Python virtual environment:
 
-Create a Python virtual environment
-===================================
+Create a Python 3 virtual environment
+=====================================
+
+.. note:: Make sure to create Python 3 environment (ideally Python 3.6 and higher) as recent versions of atomate only support Py3 and higher.
 
 We highly recommended that you organize your installation of the atomate and the other Python codes using a virtual environment (e.g. ``virtualenv`` or similar tool such as anaconda).
 Ultimately, whether you want to use a virtual environment is optional and you don't have to use one if you know what you are doing.
@@ -175,7 +177,7 @@ To set up your virtual environment:
 Install Python packages
 =======================
 
-You have successfully set up an environment in which to install atomate!
+You have successfully set up an Python 3 environment in which to install atomate!
 Next, we will download and install all of the atomate-related Python packages.
 
 You can install these packages automatically or in "development mode". Development mode installation makes it easier to view and modify the source code to your needs, but requires a few more steps to set up and maintain.

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: '',
-    VERSION: '0.7.8',
+    VERSION: '0.7.9',
     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 0.7.8 documentation</title>
+    <title>atomate.common.firetasks package &#8212; atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</title>
+    <title>atomate.common.firetasks.tests package &#8212; atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</title>
+    <title>atomate.common package &#8212; atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</title>
+    <title>atomate.feff.firetasks package &#8212; atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</title>
+    <title>atomate.feff.firetasks.tests package &#8212; atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 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 0.7.8 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.9 documentation</a> &#187;</li> 
       </ul>
     </div>