Update to v1.9.7

materialsproject · Mar 8, 2021 · 1cb78cf · 1cb78cf
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diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,6 +2,8 @@
 FireWorks Changelog
 ===================
 
+.. caution:: Starting v1.9.7 onwards, the changelog is no longer maintained. Please check the Github commit log for a record of changes.
+
 **v1.9.6**
 
 * avoid checking the number of jobs in the queue if not needed (G. Petretto)

diff --git a/docs/_sources/contributors.rst.txt b/docs/_sources/contributors.rst.txt
@@ -2,6 +2,8 @@
 Contributors
 ============
 
+.. caution:: Starting v1.9.7 onwards, the contributors list is no longer maintained. Please check the Github contributors list instead.
+
 FireWorks was developed primarily by Anubhav Jain at Lawrence Berkeley National Lab, using research funding from Kristin Persson for the `Materials Project <http://www.materialsproject.org>`_.
 
 Additional contributions from:

diff --git a/docs/_sources/fireworks.core.rst.txt b/docs/_sources/fireworks.core.rst.txt
@@ -52,7 +52,6 @@ fireworks.core.rocket\_launcher module
    :undoc-members:
    :show-inheritance:
 
-
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diff --git a/docs/_sources/fireworks.core.tests.rst.txt b/docs/_sources/fireworks.core.tests.rst.txt
@@ -44,7 +44,6 @@ fireworks.core.tests.test\_tracker module
    :undoc-members:
    :show-inheritance:
 
-
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diff --git a/docs/_sources/fireworks.examples.custom_firetasks.hello_world.rst.txt b/docs/_sources/fireworks.examples.custom_firetasks.hello_world.rst.txt
@@ -20,7 +20,6 @@ fireworks.examples.custom\_firetasks.hello\_world.hello\_world\_task module
    :undoc-members:
    :show-inheritance:
 
-
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diff --git a/docs/_sources/fireworks.examples.custom_firetasks.merge_task.rst.txt b/docs/_sources/fireworks.examples.custom_firetasks.merge_task.rst.txt
@@ -12,7 +12,6 @@ fireworks.examples.custom\_firetasks.merge\_task.merge\_task module
    :undoc-members:
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-
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diff --git a/docs/_sources/fireworks.examples.tutorial_examples.rst.txt b/docs/_sources/fireworks.examples.tutorial_examples.rst.txt
@@ -44,7 +44,6 @@ fireworks.examples.tutorial\_examples.workflows module
    :undoc-members:
    :show-inheritance:
 
-
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diff --git a/docs/_sources/fireworks.features.rst.txt b/docs/_sources/fireworks.features.rst.txt
@@ -60,7 +60,6 @@ fireworks.features.stats module
    :undoc-members:
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-
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diff --git a/docs/_sources/fireworks.features.tests.rst.txt b/docs/_sources/fireworks.features.tests.rst.txt
@@ -12,7 +12,6 @@ fireworks.features.tests.test\_introspect module
    :undoc-members:
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-
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diff --git a/docs/_sources/fireworks.flask_site.rst.txt b/docs/_sources/fireworks.flask_site.rst.txt
@@ -36,7 +36,6 @@ fireworks.flask\_site.util module
    :undoc-members:
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diff --git a/docs/_sources/fireworks.queue.rst.txt b/docs/_sources/fireworks.queue.rst.txt
@@ -20,7 +20,6 @@ fireworks.queue.queue\_launcher module
    :undoc-members:
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diff --git a/docs/_sources/fireworks.rst.txt b/docs/_sources/fireworks.rst.txt
@@ -28,7 +28,6 @@ fireworks.fw\_config module
    :undoc-members:
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diff --git a/docs/_sources/fireworks.scripts.rst.txt b/docs/_sources/fireworks.scripts.rst.txt
@@ -36,7 +36,6 @@ fireworks.scripts.rlaunch\_run module
    :undoc-members:
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diff --git a/docs/_sources/fireworks.tests.rst.txt b/docs/_sources/fireworks.tests.rst.txt
@@ -52,7 +52,6 @@ fireworks.tests.test\_workflow module
    :undoc-members:
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diff --git a/docs/_sources/fireworks.user_objects.dupefinders.rst.txt b/docs/_sources/fireworks.user_objects.dupefinders.rst.txt
@@ -12,7 +12,6 @@ fireworks.user\_objects.dupefinders.dupefinder\_exact module
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diff --git a/docs/_sources/fireworks.user_objects.firetasks.rst.txt b/docs/_sources/fireworks.user_objects.firetasks.rst.txt
@@ -60,7 +60,6 @@ fireworks.user\_objects.firetasks.unittest\_tasks module
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diff --git a/docs/_sources/fireworks.user_objects.firetasks.tests.rst.txt b/docs/_sources/fireworks.user_objects.firetasks.tests.rst.txt
@@ -44,7 +44,6 @@ fireworks.user\_objects.firetasks.tests.test\_templatewriter\_task module
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-
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diff --git a/docs/_sources/fireworks.user_objects.queue_adapters.rst.txt b/docs/_sources/fireworks.user_objects.queue_adapters.rst.txt
@@ -28,7 +28,6 @@ fireworks.user\_objects.queue\_adapters.pbs\_newt\_adapter module
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-
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diff --git a/docs/_sources/fireworks.user_objects.queue_adapters.tests.rst.txt b/docs/_sources/fireworks.user_objects.queue_adapters.tests.rst.txt
@@ -12,7 +12,6 @@ fireworks.user\_objects.queue\_adapters.tests.test\_common\_adapter module
    :undoc-members:
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-
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diff --git a/docs/_sources/fireworks.utilities.rst.txt b/docs/_sources/fireworks.utilities.rst.txt
@@ -60,7 +60,6 @@ fireworks.utilities.update\_collection module
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-
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diff --git a/docs/_sources/fireworks.utilities.tests.rst.txt b/docs/_sources/fireworks.utilities.tests.rst.txt
@@ -36,7 +36,6 @@ fireworks.utilities.tests.test\_update\_collection module
    :undoc-members:
    :show-inheritance:
 
-
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diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
@@ -211,6 +211,7 @@ Misc
     qadapter_programming
     update_text
     filepad_tutorial
+    json_schema
 
 Reference
 =========

diff --git a/docs/_sources/json_schema.rst.txt b/docs/_sources/json_schema.rst.txt
@@ -0,0 +1,79 @@
+=================
+Using JSON Schema
+=================
+
+.. note:: If you only use FireWorks with Python and provide your fireworks and workflows in Python only (not in YAML or JSON) you might want to skip this topic.
+
+Why should I use JSON schema?
+=============================
+
+The input for FireWorks is often provided in JSON and YAML and generated by
+third-party software that is unaware of the valid data types in FireWorks. Latent
+mismatches of data types may produce run-time errors, such as missing keywords
+or wrong data types, that are more difficult to handle than a validation of the
+initial input.
+
+JSON schema provides a formal human- and machine-readable description of
+the data types used in classes in FireWorks. Additionally, a function is provided
+that checks the validity of JSON and YAML inputs immediately before deserialization.
+
+To use the schema the `fireworks_schema` package must be installed.
+
+There are three ways to activate JSON schema validation:
+
+* Call the schema validator explicitly
+* Activate automatic schema validation
+* Modify the list of classes for automatic validation
+
+
+Call the schema validator explicitly
+====================================
+
+This is the case when you use Python but read JSON/YAML serialized objects
+provided externally. In the following example, a serialized workflow object is
+loaded from a YAML file and validated against the Workflow schema:
+
+.. code-block:: python
+
+  import yaml
+  import fireworks_schema
+  from fireworks import Workflow
+
+  with open('empty_fws.yaml', 'rt') as yf:
+      dct = yaml.safe_load(yf)
+  fireworks_schema.validate(dct, 'Workflow')
+  wf = Workflow.from_dict(dct)
+
+
+Activate automatic schema validation
+====================================
+
+To activate automatic schema validation you must specify:
+
+.. code-block:: yaml
+
+  JSON_SCHEMA_VALIDATE: true
+
+in your FWConfig file. For more details about managing your FWConfig file see the
+:doc:`FW Config tutorial <config_tutorial>`.
+
+The default value of ``JSON_SCHEMA_VALIDATE`` is ``false``.
+
+If automatic validation is turned on, i.e. ``JSON_SCHEMA_VALIDATE`` is ``true``,
+then validation is performed only for built-in classes specified in the list
+``JSON_SCHEMA_VALIDATE_LIST``, whenever an object of these
+classes is loaded from file. You can find the default
+``JSON_SCHEMA_VALIDATE_LIST`` in ``fw_config.py`` file in the FireWorks source.
+
+
+Modify the list of classes for automatic validation
+===================================================
+
+You can modify the default ``JSON_SCHEMA_VALIDATE_LIST`` in your FWConfig file.
+For example, to turn on automatic validation for serialized ``Firework`` and
+``Workflow`` objects only:
+
+.. code-block:: yaml
+
+  JSON_SCHEMA_VALIDATE: true
+  JSON_SCHEMA_VALIDATE_LIST: [Firework, Workflow]
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -693,7 +693,7 @@ pre {
     overflow-y: hidden;  /* fixes display issues on Chrome browsers */
 }
 
-pre, div[class|="highlight"] {
+pre, div[class*="highlight-"] {
     clear: both;
 }
 
@@ -704,7 +704,7 @@ span.pre {
     hyphens: none;
 }
 
-div[class^="highlight-"] {
+div[class*="highlight-"] {
     margin: 1em 0;
 }
 

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: '1.9.6',
+    VERSION: '1.9.7',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_static/pygments.css b/docs/_static/pygments.css
@@ -1,5 +1,10 @@
+pre { line-height: 125%; }
+td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 .highlight .hll { background-color: #ffffcc }
-.highlight  { background: #eeffcc; }
+.highlight { background: #eeffcc; }
 .highlight .c { color: #408090; font-style: italic } /* Comment */
 .highlight .err { border: 1px solid #FF0000 } /* Error */
 .highlight .k { color: #007020; font-weight: bold } /* Keyword */

diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -166,8 +166,7 @@ var Search = {
           objectterms.push(tmp[i].toLowerCase());
       }
 
-      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i].match(/^\d+$/) ||
-          tmp[i] === "") {
+      if ($u.indexOf(stopwords, tmp[i].toLowerCase()) != -1 || tmp[i] === "") {
         // skip this "word"
         continue;
       }

diff --git a/docs/backgroundtask.html b/docs/backgroundtask.html
@@ -4,8 +4,8 @@
 <html>
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>Running Tasks in the Background &#8212; FireWorks 1.9.6 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Running Tasks in the Background &#8212; FireWorks 1.9.7 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script 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 1.9.6 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.7 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Running Tasks in the Background</a></li> 
       </ul>
     </div>  
@@ -188,14 +188,14 @@ <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 1.9.6 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.7 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Running Tasks in the Background</a></li> 
       </ul>
     </div>
 
     <div class="footer" role="contentinfo">
         &#169; Copyright 2013, Anubhav Jain.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.1.2.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
 <script>
   (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){

diff --git a/docs/basesite_tutorial.html b/docs/basesite_tutorial.html
@@ -4,8 +4,8 @@
 <html>
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0">
-    <title>Using the Web GUI &#8212; FireWorks 1.9.6 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+    <title>Using the Web GUI &#8212; FireWorks 1.9.7 documentation</title>
     <link rel="stylesheet" href="_static/nature.css" type="text/css" />
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <script 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 1.9.6 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.7 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Using the Web GUI</a></li> 
       </ul>
     </div>  
@@ -154,14 +154,14 @@ <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 1.9.6 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="index.html">FireWorks 1.9.7 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Using the Web GUI</a></li> 
       </ul>
     </div>
 
     <div class="footer" role="contentinfo">
         &#169; Copyright 2013, Anubhav Jain.
-      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.1.2.
+      Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 3.2.1.
     </div>
 <script>
   (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
-Original file line number
+Diff line change
@@ Expand Up / @@ -52,7 +52,6 @@ fireworks.core.rocket\_launcher module @@
        :undoc-members:
        :show-inheritance:
     Module contents
     ---------------
@@ Expand Down @@