Update to v0.7.0

hackingmaterials · Feb 9, 2018 · 186f3ae · 186f3ae
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diff --git a/atomate/__init__.py b/atomate/__init__.py
@@ -1 +1 @@
-__version__ = "0.6.9"
+__version__ = "0.7.0"
diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
@@ -2,6 +2,14 @@
 atomate Changelog
 =================
 
+**v0.7.0**
+
+* change default behavior when a run looks OK but is unconverged (A. Jain)
+* Some test and code cleanups (S. Dwaraknath, J. Montoya)
+* update to FW names when no structure provided (S. Dwaraknath)
+* remove boltons dependency (A. Faghaninia)
+* fix max_force check for selective dynamics (J. Montoya)
+
 **v0.6.9**
 
 * update requirements to include boltons

diff --git a/docs/atomate.common.firetasks.html b/docs/atomate.common.firetasks.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>atomate.common.firetasks package &#8212; atomate 0.6.9 documentation</title>
+    <title>atomate.common.firetasks package &#8212; atomate 0.7.0 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">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.6.9',
+        VERSION:     '0.7.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -54,7 +54,7 @@ <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>
@@ -495,7 +495,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.firetasks.tests.html b/docs/atomate.common.firetasks.tests.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>atomate.common.firetasks.tests package &#8212; atomate 0.6.9 documentation</title>
+    <title>atomate.common.firetasks.tests package &#8212; atomate 0.7.0 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">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.6.9',
+        VERSION:     '0.7.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -51,57 +51,8 @@ <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="descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="descname">TestCopyFilesFromCalcLoc</code><span class="sig-paren">(</span><em>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"><span class="pre">atomate.utils.testing.AtomateTest</span></code></a></p>
-<dl class="classmethod">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.setUpClass">
-<em class="property">classmethod </em><code class="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></dd></dl>
-
-<dl class="method">
-<dt id="atomate.common.firetasks.tests.test_glue_tasks.TestCopyFilesFromCalcLoc.test_copyfilesfromcalcloc">
-<code class="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="descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="descname">TestCreateFolder</code><span class="sig-paren">(</span><em>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"><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="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="descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="descname">TestDeleteFiles</code><span class="sig-paren">(</span><em>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"><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="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="descclassname">atomate.common.firetasks.tests.test_glue_tasks.</code><code class="descname">TestPassCalcLocs</code><span class="sig-paren">(</span><em>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"><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="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>
@@ -153,7 +104,7 @@ <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>
@@ -190,7 +141,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.common.html b/docs/atomate.common.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>atomate.common package &#8212; atomate 0.6.9 documentation</title>
+    <title>atomate.common package &#8212; atomate 0.7.0 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">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.6.9',
+        VERSION:     '0.7.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -56,7 +56,7 @@ <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>
@@ -123,7 +123,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.firetasks.html b/docs/atomate.feff.firetasks.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>atomate.feff.firetasks package &#8212; atomate 0.6.9 documentation</title>
+    <title>atomate.feff.firetasks package &#8212; atomate 0.7.0 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">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.6.9',
+        VERSION:     '0.7.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -333,7 +333,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.firetasks.tests.html b/docs/atomate.feff.firetasks.tests.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>atomate.feff.firetasks.tests package &#8212; atomate 0.6.9 documentation</title>
+    <title>atomate.feff.firetasks.tests package &#8212; atomate 0.7.0 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">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.6.9',
+        VERSION:     '0.7.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -126,7 +126,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>
 

diff --git a/docs/atomate.feff.fireworks.html b/docs/atomate.feff.fireworks.html
@@ -5,13 +5,13 @@
 <html xmlns="http://www.w3.org/1999/xhtml">
   <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <title>atomate.feff.fireworks package &#8212; atomate 0.6.9 documentation</title>
+    <title>atomate.feff.fireworks package &#8212; atomate 0.7.0 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">
       var DOCUMENTATION_OPTIONS = {
         URL_ROOT:    './',
-        VERSION:     '0.6.9',
+        VERSION:     '0.7.0',
         COLLAPSE_INDEX: false,
         FILE_SUFFIX: '.html',
         HAS_SOURCE:  true,
@@ -37,7 +37,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>  
 
@@ -219,7 +219,7 @@ <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 0.6.9 documentation</a> &#187;</li> 
+        <li class="nav-item nav-item-0"><a href="index.html">atomate 0.7.0 documentation</a> &#187;</li> 
       </ul>
     </div>