Update to v0.9.4

hackingmaterials · Sep 18, 2019 · b4a9ac0 · b4a9ac0
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diff --git a/atomate/__init__.py b/atomate/__init__.py
@@ -1 +1 @@
-__version__ = "0.9.3"
+__version__ = "0.9.4"
diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,6 +2,11 @@
 atomate Changelog
 =================
 
+**v0.9.4**
+
+* Fixes for new pymatgen (S. Blau, S.P. Ong)
+
+
 **v0.9.3**
 
 * Minor change to enforce storing chgcars, clean up old kwargs in MagneticOrderings workflow (M. Horton)

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: '0.9.3',
+    VERSION: '0.9.4',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common.firetasks package &#8212; atomate 0.9.3 documentation</title>
+    <title>atomate.common.firetasks package &#8212; atomate 0.9.4 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">atomate 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -44,7 +44,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="atomate.common.firetasks.tests.html">atomate.common.firetasks.tests package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#submodules">Submodules</a></li>
-<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_glue_tasks">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#atomate-common-firetasks-tests-test-glue-tasks-module">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_parse_outputs">atomate.common.firetasks.tests.test_parse_outputs module</a></li>
 <li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests">Module contents</a></li>
 </ul>
@@ -292,7 +292,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dt>Required params:</dt><dd><p>name (str): descriptive name for this calculation file/dir</p>
 </dd>
 <dt>Optional params:</dt><dd><dl class="simple">
-<dt>filesystem (str or custom user format): name of filesystem. Supports env_chk. </dt><dd><p>defaults to None</p>
+<dt>filesystem (str or custom user format): name of filesystem. Supports env_chk.</dt><dd><p>defaults to None</p>
 </dd>
 <dt>path (str): The path to the directory containing the calculation. defaults to</dt><dd><p>current working directory.</p>
 </dd>
@@ -354,10 +354,10 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 to designate the stress from the last ionic_step. If the value
 is not a string or does not begin with “&gt;&gt;”, it is passed as is.</p>
 </dd>
-<dt>parse_class (str): string representation of complete path to a class </dt><dd><p>with which to parse the output, e. g. pymatgen.io.vasp.Vasprun
+<dt>parse_class (str): string representation of complete path to a class</dt><dd><p>with which to parse the output, e. g. pymatgen.io.vasp.Vasprun
 or pymatgen.io.feff.LDos.from_file, class must be MSONable</p>
 </dd>
-<dt>parse_kwargs (str): dict of kwargs for the parse class,</dt><dd><p>e. g. {“filename”: “vasprun.xml”, “parse_dos”: False, 
+<dt>parse_kwargs (str): dict of kwargs for the parse class,</dt><dd><p>e. g. {“filename”: “vasprun.xml”, “parse_dos”: False,
 “parse_eigen”: False}</p>
 </dd>
 </dl>
@@ -658,7 +658,7 @@ <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 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.firetasks.tests.html b/docs/atomate.common.firetasks.tests.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common.firetasks.tests package &#8212; atomate 0.9.3 documentation</title>
+    <title>atomate.common.firetasks.tests package &#8212; atomate 0.9.4 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">atomate 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -41,58 +41,8 @@ <h1>atomate.common.firetasks.tests package<a class="headerlink" href="#atomate-c
 <div class="section" id="submodules">
 <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
 </div>
-<div class="section" id="module-atomate.common.firetasks.tests.test_glue_tasks">
-<span id="atomate-common-firetasks-tests-test-glue-tasks-module"></span><h2>atomate.common.firetasks.tests.test_glue_tasks module<a class="headerlink" href="#module-atomate.common.firetasks.tests.test_glue_tasks" title="Permalink to this headline">¶</a></h2>
-<dl class="class">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc">
-<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestCopyFilesFromCalcLoc</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
-<dl class="method">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.setUpClass">
-<em class="property">classmethod </em><code class="sig-name descname">setUpClass</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.setUpClass" title="Permalink to this definition">¶</a></dt>
-<dd><p>Hook method for setting up class fixture before running tests in the class.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.test_copyfilesfromcalcloc">
-<code class="sig-name descname">test_copyfilesfromcalcloc</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.test_copyfilesfromcalcloc" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder">
-<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestCreateFolder</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
-<dl class="method">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder.test_createfolder">
-<code class="sig-name descname">test_createfolder</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestCreateFolder.test_createfolder" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles">
-<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestDeleteFiles</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
-<dl class="method">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles.test_cleanupfiles">
-<code class="sig-name descname">test_cleanupfiles</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestDeleteFiles.test_cleanupfiles" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
-<dl class="class">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs">
-<em class="property">class </em><code class="sig-prename descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="sig-name descname">TestPassCalcLocs</code><span class="sig-paren">(</span><em class="sig-param">methodName='runTest'</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <a class="reference internal" href="atomate.utils.html#atomate.utils.testing.AtomateTest" title="atomate.utils.testing.AtomateTest"><code class="xref py py-class docutils literal notranslate"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
-<dl class="method">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs.test_passcalclocs">
-<code class="sig-name descname">test_passcalclocs</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#atomate.common.firetasks.tests.test_glue_tasks.TestPassCalcLocs.test_passcalclocs" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
-
-</dd></dl>
-
+<div class="section" id="atomate-common-firetasks-tests-test-glue-tasks-module">
+<h2>atomate.common.firetasks.tests.test_glue_tasks module<a class="headerlink" href="#atomate-common-firetasks-tests-test-glue-tasks-module" title="Permalink to this headline">¶</a></h2>
 </div>
 <div class="section" id="module-atomate.common.firetasks.tests.test_parse_outputs">
 <span id="atomate-common-firetasks-tests-test-parse-outputs-module"></span><h2>atomate.common.firetasks.tests.test_parse_outputs module<a class="headerlink" href="#module-atomate.common.firetasks.tests.test_parse_outputs" title="Permalink to this headline">¶</a></h2>
@@ -170,7 +120,7 @@ <h3><a href="index.html">Table of Contents</a></h3>
   <ul>
 <li><a class="reference internal" href="#">atomate.common.firetasks.tests package</a><ul>
 <li><a class="reference internal" href="#submodules">Submodules</a></li>
-<li><a class="reference internal" href="#module-atomate.common.firetasks.tests.test_glue_tasks">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
+<li><a class="reference internal" href="#atomate-common-firetasks-tests-test-glue-tasks-module">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
 <li><a class="reference internal" href="#module-atomate.common.firetasks.tests.test_parse_outputs">atomate.common.firetasks.tests.test_parse_outputs module</a></li>
 <li><a class="reference internal" href="#module-atomate.common.firetasks.tests">Module contents</a></li>
 </ul>
@@ -207,7 +157,7 @@ <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 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.html b/docs/atomate.common.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.common package &#8212; atomate 0.9.3 documentation</title>
+    <title>atomate.common package &#8212; atomate 0.9.4 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">atomate 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -46,7 +46,7 @@ <h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to thi
 <li class="toctree-l2"><a class="reference internal" href="atomate.common.firetasks.html#subpackages">Subpackages</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="atomate.common.firetasks.tests.html">atomate.common.firetasks.tests package</a><ul>
 <li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#submodules">Submodules</a></li>
-<li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_glue_tasks">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
+<li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#atomate-common-firetasks-tests-test-glue-tasks-module">atomate.common.firetasks.tests.test_glue_tasks module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests.test_parse_outputs">atomate.common.firetasks.tests.test_parse_outputs module</a></li>
 <li class="toctree-l4"><a class="reference internal" href="atomate.common.firetasks.tests.html#module-atomate.common.firetasks.tests">Module contents</a></li>
 </ul>
@@ -113,7 +113,7 @@ <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 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.firetasks.html b/docs/atomate.feff.firetasks.html
@@ -4,7 +4,7 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta charset="utf-8" />
-    <title>atomate.feff.firetasks package &#8212; atomate 0.9.3 documentation</title>
+    <title>atomate.feff.firetasks package &#8212; atomate 0.9.4 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">atomate 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -220,6 +220,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 </div>
 <div class="section" id="module-atomate.feff.firetasks.run_calc">
 <span id="atomate-feff-firetasks-run-calc-module"></span><h2>atomate.feff.firetasks.run_calc module<a class="headerlink" href="#module-atomate.feff.firetasks.run_calc" title="Permalink to this headline">¶</a></h2>
+<p>This module defines tasks to run FEFF.</p>
 <dl class="class">
 <dt id="atomate.feff.firetasks.run_calc.RunFeffDirect">
 <em class="property">class </em><code class="sig-prename descclassname">atomate.feff.firetasks.run_calc.</code><code class="sig-name descname">RunFeffDirect</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.feff.firetasks.run_calc.RunFeffDirect" title="Permalink to this definition">¶</a></dt>
@@ -264,6 +265,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 </div>
 <div class="section" id="module-atomate.feff.firetasks.write_inputs">
 <span id="atomate-feff-firetasks-write-inputs-module"></span><h2>atomate.feff.firetasks.write_inputs module<a class="headerlink" href="#module-atomate.feff.firetasks.write_inputs" title="Permalink to this headline">¶</a></h2>
+<p>This module defines tasks for writing FEFF input sets.</p>
 <dl class="class">
 <dt id="atomate.feff.firetasks.write_inputs.WriteEXAFSPaths">
 <em class="property">class </em><code class="sig-prename descclassname">atomate.feff.firetasks.write_inputs.</code><code class="sig-name descname">WriteEXAFSPaths</code><span class="sig-paren">(</span><em class="sig-param">*args</em>, <em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomate.feff.firetasks.write_inputs.WriteEXAFSPaths" title="Permalink to this definition">¶</a></dt>
@@ -442,7 +444,7 @@ <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 0.9.3 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.9.4 documentation</a> &#187;</li> 
       </ul>
     </div>