Update to v1.8.5

materialsproject · Feb 12, 2019 · be1fe40 · be1fe40
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diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,6 +2,15 @@
 FireWorks Changelog
 ===================
 
+**v1.8.5**
+
+.. caution:: the code to authenticate to databases was changed in this version. If you encounter problems after updating, contact the help group.
+
+* save action in GridFS if Launch document too large (G. Petretto)
+* fixed Jinja functionality in TemplateWriterTask (E. Ateljevich)
+* update authentication method to not use deprecated db.authenticate
+* small updates to tutorials / docs to reflect user questions
+
 **v1.8.4**
 
 .. warning:: this version changes the manner in which one authenticates to the web gui via Python (command line is unaffected). You no longer set environment variables. See docs on the web gui for more information.

diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt
@@ -44,6 +44,7 @@ Additional contributions from:
 * Eric Sivonxay
 * Matt Henderson
 * Steven Torrisi
+* Eli Ateljevich
 * Github user: kpoman
 * Github user: jakirkham
 * Github user: shenjh

diff --git a/docs/_sources/duplicates_tutorial.rst.txt b/docs/_sources/duplicates_tutorial.rst.txt
@@ -113,3 +113,14 @@ The built-in duplicate finder, ``Exact Dupe Finder``, suffers from two limitatio
 * matching is limited to *exact* matches of the Firework spec. You cannot, for example, define two FireWorks to be duplicated if a portion of the spec matches within some numerical tolerance.
 
 In the future, we will include a tutorial on implementing custom Dupe Finders for your application that overcome these limitations. For now, we suggest that you refer to the internal docs or contact us for help. (see :ref:`contributing-label`). You can also try to improve performance by manually adding database indices to :doc:`improve performance <performance_tutorial>`.
+
+Adding a DupeFinder with Python
+===============================
+
+If you are creating a FireWork within Python and want to add in a DupeFinder object, create a key in your spec called ``_dupefinder`` and drop your DupeFinder object in there. For example::
+
+    from fireworks import Firework, ScriptTask
+    from fireworks.user_objects.dupefinders.dupefinder_exact import DupeFinderExact
+
+    fw = Firework([ScriptTask.from_str('echo "hello"')],
+                  spec={"_dupefinder": DupeFinderExact()})
diff --git a/docs/_sources/queue_tutorial.rst.txt b/docs/_sources/queue_tutorial.rst.txt
@@ -247,6 +247,12 @@ More information
     qlaunch singleshot -h
     qlaunch rapidfire -h
 
+
+Submitting to the queue with Python
+===================================
+
+Although most people will submit jobs to the queue with the command line, you can also submit jobs via Python. The example is similar to previous tutorials for running the ``rapidfire`` command, however you want to replace ``fireworks.core.rocket_launcher.rapidfire`` with ``fireworks.core.queue_launcher.rapidfire`` and adjust the parameters accordingly.
+
 Limitations and Next Steps
 ==========================
 

diff --git a/docs/_sources/templatewritertask.rst.txt b/docs/_sources/templatewritertask.rst.txt
@@ -109,7 +109,7 @@ Template files are not restricted to simple variable substitutions with curly br
 
 #. Now, try deleting the line containing the ``optparam`` and repeating the launch process. You'll see that the lines pertaining to the ``OPTIONAL PARAMETER`` are no longer written!
 
-Therefore, with Jinja2's templating language we can write fairly general templates. While variable substitutions, *if/then* statements, and *for loops* should cover the majority of cases, you can see even more features in the `official Jinja2 documentation <http://jinja.pocoo.org>`_. For example, you can use template inheritance or insert templates into other templates.
+Therefore, with Jinja2's templating language we can write fairly general templates. While variable substitutions, *if/then* statements, and *for loops* should cover the majority of cases, you can see even more features in the `official Jinja2 documentation <http://jinja.pocoo.org>`_.
 
 Writing your own templates
 ==========================

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: '1.8.4',
+    VERSION: '1.8.5',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/backgroundtask.html b/docs/backgroundtask.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>Running Tasks in the Background &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Running Tasks in the Background &#8212; FireWorks 1.8.5 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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="duplicates_tutorial.html" title="Handling Duplicates Automatically"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -188,7 +188,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="duplicates_tutorial.html" title="Handling Duplicates Automatically"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/basesite_tutorial.html b/docs/basesite_tutorial.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>Using the Web GUI &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Using the Web GUI &#8212; FireWorks 1.8.5 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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="query_tutorial.html" title="Querying FireWorks and Workflows / Generating Reports"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -154,7 +154,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="query_tutorial.html" title="Querying FireWorks and Workflows / Generating Reports"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/changelog.html b/docs/changelog.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>FireWorks Changelog &#8212; FireWorks 1.8.4 documentation</title>
+    <title>FireWorks Changelog &#8212; FireWorks 1.8.5 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>
@@ -32,7 +32,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="guide_to_writing_firetasks.html" title="The Comprehensive Guide to Writing Firetasks with Python"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -43,6 +43,17 @@ <h3>Navigation</h3>
 
   <div class="section" id="fireworks-changelog">
 <h1>FireWorks Changelog<a class="headerlink" href="#fireworks-changelog" title="Permalink to this headline">¶</a></h1>
+<p><strong>v1.8.5</strong></p>
+<div class="admonition caution">
+<p class="first admonition-title">Caution</p>
+<p class="last">the code to authenticate to databases was changed in this version. If you encounter problems after updating, contact the help group.</p>
+</div>
+<ul class="simple">
+<li>save action in GridFS if Launch document too large (G. Petretto)</li>
+<li>fixed Jinja functionality in TemplateWriterTask (E. Ateljevich)</li>
+<li>update authentication method to not use deprecated db.authenticate</li>
+<li>small updates to tutorials / docs to reflect user questions</li>
+</ul>
 <p><strong>v1.8.4</strong></p>
 <div class="admonition warning">
 <p class="first admonition-title">Warning</p>
@@ -1098,7 +1109,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="guide_to_writing_firetasks.html" title="The Comprehensive Guide to Writing Firetasks with Python"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/config_tutorial.html b/docs/config_tutorial.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>Modifying the FW Config &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Modifying the FW Config &#8212; FireWorks 1.8.5 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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="security_tutorial.html" title="Configuring Security"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -213,7 +213,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="security_tutorial.html" title="Configuring Security"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/contributing.html b/docs/contributing.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>Contributing Code to FireWorks &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Contributing Code to FireWorks &#8212; FireWorks 1.8.5 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">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -138,7 +138,7 @@ <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">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/contributors.html b/docs/contributors.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>Contributors &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Contributors &#8212; FireWorks 1.8.5 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">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -80,6 +80,7 @@ <h1>Contributors<a class="headerlink" href="#contributors" title="Permalink to t
 <li>Eric Sivonxay</li>
 <li>Matt Henderson</li>
 <li>Steven Torrisi</li>
+<li>Eli Ateljevich</li>
 <li>Github user: kpoman</li>
 <li>Github user: jakirkham</li>
 <li>Github user: shenjh</li>
@@ -134,7 +135,7 @@ <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">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/controlworker.html b/docs/controlworker.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>Controlling the directory and Worker of execution &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Controlling the directory and Worker of execution &#8212; FireWorks 1.8.5 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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="dataflow_tasks.html" title="Using the dataflow Firetasks"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -209,7 +209,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="dataflow_tasks.html" title="Using the dataflow Firetasks"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/dataflow_tasks.html b/docs/dataflow_tasks.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>Using the dataflow Firetasks &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Using the dataflow Firetasks &#8212; FireWorks 1.8.5 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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="filepad_tasks.html" title="Using the built-in FilePad Tasks"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -394,7 +394,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="filepad_tasks.html" title="Using the built-in FilePad Tasks"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/defuse_tutorial.html b/docs/defuse_tutorial.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>Canceling (pausing), restarting, and deleting Workflows &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Canceling (pausing), restarting, and deleting Workflows &#8212; FireWorks 1.8.5 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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="priority_tutorial.html" title="Assigning job priority"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -192,7 +192,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="priority_tutorial.html" title="Assigning job priority"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/design_tips.html b/docs/design_tips.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>Tips for designing Firetasks, FireWorks, and Workflows &#8212; FireWorks 1.8.4 documentation</title>
+    <title>Tips for designing Firetasks, FireWorks, and Workflows &#8212; FireWorks 1.8.5 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>
@@ -36,7 +36,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="dynamic_wf_tutorial.html" title="Dynamic Workflows"
              accesskey="P">previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -201,7 +201,7 @@ <h3>Navigation</h3>
         <li class="right" >
           <a href="dynamic_wf_tutorial.html" title="Dynamic Workflows"
              >previous</a> |</li>
-        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.8.5 documentation</a> &#187;</li> 
       </ul>
     </div>