Update to v1.9.5

docs/_sources/changelog.rst.txt

@@ -2,6 +2,19 @@
 FireWorks Changelog
 ===================
 
+**v1.9.5**
+
+* document new help forum!
+* ability to add custom kwargs to the LaunchPad MongoClient using the YAML format (thanks to I. Kondov for pointing in this direction)
+* restore "text_mode" for anyone having problems with the new binary FilePad
+* rework lostruns recovery
+* actually use launch_dir in update_checkpoint (hopefully shouldn't change any behavior)
+* prevent "zombie" reruns of offline runs when marking them as fizzled or rerun. (thanks to jotelha for suggestion)
+* Use mod_spec instead of update_spec to pass on out-/infiles along Fireworks (J. Hörmann)
+* allow binary files in FilePad / handle filepad files as binary always (J. Hörmann)
+* update SLURM job id parsing (G. Petretto)
+* update dependencies
+
 **v1.9.4**
 
 * filepad tasks to get files by query (Github user: J. Hörmann)

docs/_sources/index.rst.txt

@@ -259,7 +259,7 @@ Want to see something added or changed? There are many ways to make that a reali
 * Point us to areas of the code that are difficult to understand or use.
 * Contribute code! If you are interested in this option, please see our :doc:`contribution guidelines</contributing>`.
 
-Please submit questions, issues / bug reports, and all other communication through the `FireWorks Google Groups <https://groups.google.com/forum/#!forum/fireworkflows>`_.
+Please submit questions, issues / bug reports, and all other communication through the `FireWorks Discourse forum <https://discuss.matsci.org/c/fireworks>`_.
 
 Make contributions through GitHub using our `Contribution Guidelines. <https://github.com/materialsproject/fireworks/blob/master/CONTRIBUTING.md>`_
 

docs/_sources/installation.rst.txt

@@ -2,7 +2,7 @@
 Installing FireWorks
 ====================
 
-.. note:: We suggest that you use Python 2.7.3 or higher, especially in production. There is a `bug <https://groups.google.com/forum/#!topic/modwsgi/DW-SlIb07rE>`_ in Python 2.7.2 that could affect FireWorks (although we haven't seen any problems yet). As of FireWorks v0.7, Python 3.3 and higher should also work.
+.. note:: We suggest that you use Python 3.7 or higher, especially in production. There is a `bug <https://groups.google.com/forum/#!topic/modwsgi/DW-SlIb07rE>`_ in Python 2.7.2 that could affect FireWorks (although we haven't seen any problems yet).
 
 Install MongoDB
 ===============
@@ -22,15 +22,15 @@ Preparing to Install FireWorks (Python and pip)
 ===============================================
 To prepare for installation, you should:
 
-#. Install `Python <http://www.python.org>`_ - either Python 2.7+ or Python 3 should work.
+#. Install `Python <http://www.python.org>`_ - use Python 3.3+ (and ideally the latest version) as Python 2 has been discontinued. FireWorks may continue to work with Python 2.7.x for some time, but this is no longer guaranteed.
 #. Install `pip <http://www.pip-installer.org/en/latest/installing.html>`_, if not already packaged with your system (this sometimes comes bundled with your Python install). This will allow you to download required dependencies.
 
 .. tip:: if you have easy_install configured, e.g. through `setuptools <http://pypi.python.org/pypi/setuptools>`_, you should be able to install pip using the command ``easy_install pip``. You should make sure that setuptools is installed using the proper Python version and probably without the ``--user`` option if running ``ez_setup.py``.
 
 Virtualenv installation option
 ------------------------------
 
-Virtualenv is a tool that allows you to separate your FireWorks installation from your other Python installations. For example, you might want to use Python 2.7 for FireWorks, but Python 3+ for other Python codes you're interested in using. Or, you might have different versions of Python libraries supporting FireWorks and your other installations. This is often the case on shared machines. if you're interested in this option, you might consider a :doc:`virtualenv install </virtualenv_tutorial>`. Otherwise, just follow the installation instructions below. A simpler option to setting up virtualenv that accomplishes some of the same goals is to use the ``--user`` flag when running ``python setup.py develop`` in the the Git version of installation (see Installation Method 2).
+Virtualenv is a tool that allows you to separate your FireWorks installation from your other Python installations. If you're interested in this option, you might consider a :doc:`virtualenv install </virtualenv_tutorial>`. Otherwise, just follow the installation instructions below. A simpler option to setting up virtualenv that accomplishes some of the same goals is to use the ``--user`` flag when running ``python setup.py develop`` in the the Git version of installation (see Installation Method 2).
 
 Installation Method 1: Use Pip
 ==============================

docs/_sources/security_tutorial.rst.txt

@@ -71,9 +71,23 @@ If the MongoDB server is configured with TLS/SSL launchpad file
 ``my_launchpad.yaml`` (or whatever launchpad file is specified after the ``-l`` option or in the configuration file) has to include further information in the following lines::
 
     ssl: <bool> # whether to use TLS/SSL for connection to MongoDB, default: false
-    ssl_ca_certs: <path to the CA certificate to be used for connection>
-    ssl_certfile: <path to the client certificate to be used for connection>
-    ssl_keyfile: <path to the client private key (optional)>
-    ssl_pem_passphrase: <passphrase for the client private key (optional)>
+    ssl_ca_certs: <string> # path to the CA certificate to be used for connection
+    ssl_certfile: <string> # path to the client certificate (optional)
+    ssl_keyfile: <string> # path to the client private key (optional)
+    ssl_pem_passphrase: <string> # passphrase for the client private key (optional)
+    authsource: <string> # alternative authentication database (optional)
+    mongoclient_kwargs:
+        authMechanism: <string> # alternative authentication mechanism (optional)
 
-.. note:: If ``ssl`` is ``false`` or omitted then all remaining TLS/SSL settings **must** be omitted. If ``ssl`` is ``true`` then the connection will be encrypted and the remaining TLS/SSL settings are optional, depending on the specific server policies.
+.. note:: If ``ssl`` is ``false`` or omitted then all remaining TLS/SSL settings **must** be omitted. If ``ssl`` is ``true`` then the connection will be encrypted, ``ssl_ca_certs`` must be set and the remaining TLS/SSL settings are optional, depending on the specific server policies.
+
+.. note:: If ``ssl_certfile`` is set and ``ssl_keyfile`` is not set then the file specified by ``ssl_certfile`` must contain the private key.
+
+.. note:: If the private key is encrypted and  ``ssl_pem_passphrase`` is not set then **lpad**, **rlaunch** and **qlaunch** will prompt for the passphase.
+
+.. note:: If ``authmechanism`` is ``MONGODB-X509`` then ``authsource`` must be set to ``$external``, and ``username`` and ``password`` must not be set.
+
+Other Mongoclient options
+=========================
+
+The ``mongoclient_kwargs`` option can be used to set any other desired options for the MongoClient. The format is a dictionary (see ``authMechanism`` above for an example).

docs/_sources/virtualenv_tutorial.rst.txt

@@ -7,7 +7,7 @@ In this tutorial, we'll cover just the basics of setting up a *virtualenv* for y
 Introduction to virtualenv
 ==========================
 
-Your virtualenv is stored inside a user-specified directory on your system. That directory will contain the Python 2.7.3 executable needed for FireWorks as well as all dependencies for the FireWorks code. When you activate your virtualenv, your "normal" Python executable will be bypassed in favor of the one in this directory. In addition, your normal "site packages" directory that contains your external Python libraries will be bypassed in favor of the one you set up in your virtualenv. Finally, your "pip" and "easy_install" will be bypassed so that they install packages to your virtualenv. When you deactivate your virtualenv, things will return back to their usual state.
+Your virtualenv is stored inside a user-specified directory on your system. That directory will contain the Python executable needed for FireWorks as well as all dependencies for the FireWorks code. When you activate your virtualenv, your "normal" Python executable will be bypassed in favor of the one in this directory. In addition, your normal "site packages" directory that contains your external Python libraries will be bypassed in favor of the one you set up in your virtualenv. Finally, your "pip" and "easy_install" will be bypassed so that they install packages to your virtualenv. When you deactivate your virtualenv, things will return back to their usual state.
 
 If you'd like more details on virtualenv, you can read the `official documentation <https://pypi.python.org/pypi/virtualenv>`_ or see some basic setup instructions `here <http://pythoncentral.org/setting-up-the-python-environment-with-virtualenv/>`_, `or here <http://iamzed.com/2009/05/07/a-primer-on-virtualenv/>`_, `or also here <http://simononsoftware.com/virtualenv-tutorial/>`_.
 

docs/_static/documentation_options.js

@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '1.9.4',
+    VERSION: '1.9.5',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

docs/backgroundtask.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>Running Tasks in the Background &#8212; FireWorks 1.9.4 documentation</title>
+    <title>Running Tasks in the Background &#8212; FireWorks 1.9.5 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>
@@ -35,7 +35,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -185,7 +185,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/basesite_tutorial.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>Using the Web GUI &#8212; FireWorks 1.9.4 documentation</title>
+    <title>Using the Web GUI &#8212; FireWorks 1.9.5 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>
@@ -35,7 +35,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -151,7 +151,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/changelog.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>FireWorks Changelog &#8212; FireWorks 1.9.4 documentation</title>
+    <title>FireWorks Changelog &#8212; FireWorks 1.9.5 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>
@@ -31,7 +31,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -42,6 +42,19 @@ <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>v1.9.5</strong></p>
+<ul class="simple">
+<li><p>document new help forum!</p></li>
+<li><p>ability to add custom kwargs to the LaunchPad MongoClient using the YAML format (thanks to I. Kondov for pointing in this direction)</p></li>
+<li><p>restore “text_mode” for anyone having problems with the new binary FilePad</p></li>
+<li><p>rework lostruns recovery</p></li>
+<li><p>actually use launch_dir in update_checkpoint (hopefully shouldn’t change any behavior)</p></li>
+<li><p>prevent “zombie” reruns of offline runs when marking them as fizzled or rerun. (thanks to jotelha for suggestion)</p></li>
+<li><p>Use mod_spec instead of update_spec to pass on out-/infiles along Fireworks (J. Hörmann)</p></li>
+<li><p>allow binary files in FilePad / handle filepad files as binary always (J. Hörmann)</p></li>
+<li><p>update SLURM job id parsing (G. Petretto)</p></li>
+<li><p>update dependencies</p></li>
+</ul>
 <p><strong>v1.9.4</strong></p>
 <ul class="simple">
 <li><p>filepad tasks to get files by query (Github user: J. Hörmann)</p></li>
@@ -1156,7 +1169,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/config_tutorial.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>Modifying the FW Config &#8212; FireWorks 1.9.4 documentation</title>
+    <title>Modifying the FW Config &#8212; FireWorks 1.9.5 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>
@@ -35,7 +35,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -209,7 +209,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/contributing.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>Contributing Code to FireWorks &#8212; FireWorks 1.9.4 documentation</title>
+    <title>Contributing Code to FireWorks &#8212; FireWorks 1.9.5 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>
@@ -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">FireWorks 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -135,7 +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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>
 

docs/contributors.html

@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>Contributors &#8212; FireWorks 1.9.4 documentation</title>
+    <title>Contributors &#8212; FireWorks 1.9.5 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>
@@ -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">FireWorks 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -136,7 +136,7 @@ <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 1.9.4 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.5 documentation</a> &#187;</li> 
       </ul>
     </div>