Merge branch 'master' into dependabot/pip/maggma-0.47.3

materialsvirtuallab · Aug 7, 2022 · 204108d · 204108d
2 parents e672966 + 46758d8
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
           - --ignore-init-module-imports
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v2.34.0
+    rev: v2.37.3
     hooks:
       - id: pyupgrade
         args: [--py38-plus]
@@ -46,11 +46,11 @@ repos:
       - id: black
 
   - repo: https://github.com/PyCQA/flake8
-    rev: 4.0.1
+    rev: 5.0.2
     hooks:
       - id: flake8
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.961
+    rev: v0.971
     hooks:
       - id: mypy
diff --git a/CHANGES.rst b/CHANGES.rst
@@ -1,6 +1,10 @@
 Change Log
 ==========
 
+v2022.4.22
+----------
+* Make MigrationHop MSONAble. (@acrutt)
+
 v2021.4.29
 ----------
 * Fixed msite calc order (@hmlli)

diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -1,16 +1,17 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; pymatgen-diffusion 2022.1.15 documentation</title>
+    <title>Overview: module code &#8212; pymatgen-diffusion 2022.7.21 documentation</title>
     <link rel="stylesheet" type="text/css" href="../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../_static/flasky.css" />
     <script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js"></script>
     <script src="../_static/jquery.js"></script>
     <script src="../_static/underscore.js"></script>
+    <script src="../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../_static/doctools.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -36,7 +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">pymatgen-diffusion 2022.1.15 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../index.html">pymatgen-diffusion 2022.7.21 documentation</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">Overview: module code</a></li> 
       </ul>
     </div>  
@@ -47,8 +48,7 @@ <h3>Navigation</h3>
           <div class="body" role="main">
 
   <h1>All modules for which code is available</h1>
-<ul><li><a href="pymatgen/analysis/diffusion/aimd/clustering.html">pymatgen.analysis.diffusion.aimd.clustering</a></li>
-<li><a href="pymatgen/analysis/diffusion/aimd/pathway.html">pymatgen.analysis.diffusion.aimd.pathway</a></li>
+<ul><li><a href="pymatgen/analysis/diffusion/aimd/pathway.html">pymatgen.analysis.diffusion.aimd.pathway</a></li>
 <li><a href="pymatgen/analysis/diffusion/aimd/rdf.html">pymatgen.analysis.diffusion.aimd.rdf</a></li>
 <li><a href="pymatgen/analysis/diffusion/aimd/tests/test_clustering.html">pymatgen.analysis.diffusion.aimd.tests.test_clustering</a></li>
 <li><a href="pymatgen/analysis/diffusion/aimd/tests/test_pathway.html">pymatgen.analysis.diffusion.aimd.tests.test_pathway</a></li>
@@ -64,6 +64,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="pymatgen/analysis/diffusion/neb/tests/test_io.html">pymatgen.analysis.diffusion.neb.tests.test_io</a></li>
 <li><a href="pymatgen/analysis/diffusion/neb/tests/test_pathfinder.html">pymatgen.analysis.diffusion.neb.tests.test_pathfinder</a></li>
 <li><a href="pymatgen/analysis/diffusion/tests/test_analyzer.html">pymatgen.analysis.diffusion.tests.test_analyzer</a></li>
+<li><a href="pymatgen/analysis/diffusion/tests/test_pathfinder.html">pymatgen.analysis.diffusion.tests.test_pathfinder</a></li>
 <li><a href="pymatgen/analysis/diffusion/utils/edge_data_from_sc.html">pymatgen.analysis.diffusion.utils.edge_data_from_sc</a></li>
 <li><a href="pymatgen/analysis/diffusion/utils/parse_entries.html">pymatgen.analysis.diffusion.utils.parse_entries</a></li>
 <li><a href="pymatgen/analysis/diffusion/utils/supercells.html">pymatgen.analysis.diffusion.utils.supercells</a></li>
@@ -90,7 +91,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/pathway.html
@@ -1,16 +1,17 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.pathway &#8212; pymatgen-diffusion 2022.1.15 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.pathway &#8212; pymatgen-diffusion 2022.7.21 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../../../_static/flasky.css" />
     <script data-url_root="../../../../../" id="documentation_options" src="../../../../../_static/documentation_options.js"></script>
     <script src="../../../../../_static/jquery.js"></script>
     <script src="../../../../../_static/underscore.js"></script>
+    <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../../../../_static/doctools.js"></script>
     <link rel="index" title="Index" href="../../../../../genindex.html" />
     <link rel="search" title="Search" href="../../../../../search.html" />
@@ -36,7 +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">pymatgen-diffusion 2022.1.15 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2022.7.21 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.pathway</a></li> 
       </ul>
@@ -155,7 +156,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.pathway</h1><div class="hig
         <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">n</span> <span class="ow">in</span> <span class="n">count</span><span class="o">.</span><span class="n">most_common</span><span class="p">(</span><span class="n">ngrid</span><span class="p">):</span>
             <span class="n">Pr</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="o">=</span> <span class="nb">float</span><span class="p">(</span><span class="n">n</span><span class="p">)</span> <span class="o">/</span> <span class="n">nsteps</span> <span class="o">/</span> <span class="nb">len</span><span class="p">(</span><span class="n">indices</span><span class="p">)</span> <span class="o">/</span> <span class="n">lattice</span><span class="o">.</span><span class="n">volume</span> <span class="o">*</span> <span class="n">ngrid</span>
 
-        <span class="n">Pr</span> <span class="o">=</span> <span class="n">Pr</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">lens</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">lens</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">lens</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>
+        <span class="n">Pr</span> <span class="o">=</span> <span class="n">Pr</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">lens</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span> <span class="n">lens</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span> <span class="n">lens</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span>  <span class="c1"># pylint: disable=E1121</span>
 
         <span class="bp">self</span><span class="o">.</span><span class="n">structure</span> <span class="o">=</span> <span class="n">structure</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">trajectories</span> <span class="o">=</span> <span class="n">trajectories</span>
@@ -421,7 +422,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/rdf.html
@@ -1,16 +1,17 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.rdf &#8212; pymatgen-diffusion 2022.1.15 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.rdf &#8212; pymatgen-diffusion 2022.7.21 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../../../_static/flasky.css" />
     <script data-url_root="../../../../../" id="documentation_options" src="../../../../../_static/documentation_options.js"></script>
     <script src="../../../../../_static/jquery.js"></script>
     <script src="../../../../../_static/underscore.js"></script>
+    <script src="../../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../../../../_static/doctools.js"></script>
     <link rel="index" title="Index" href="../../../../../genindex.html" />
     <link rel="search" title="Search" href="../../../../../search.html" />
@@ -36,7 +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">pymatgen-diffusion 2022.1.15 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../index.html">pymatgen-diffusion 2022.7.21 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.rdf</a></li> 
       </ul>
@@ -557,7 +558,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_clustering.html
@@ -1,16 +1,17 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.tests.test_clustering &#8212; pymatgen-diffusion 2022.1.15 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.tests.test_clustering &#8212; pymatgen-diffusion 2022.7.21 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../../../../_static/flasky.css" />
     <script data-url_root="../../../../../../" id="documentation_options" src="../../../../../../_static/documentation_options.js"></script>
     <script src="../../../../../../_static/jquery.js"></script>
     <script src="../../../../../../_static/underscore.js"></script>
+    <script src="../../../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../../../../../_static/doctools.js"></script>
     <link rel="index" title="Index" href="../../../../../../genindex.html" />
     <link rel="search" title="Search" href="../../../../../../search.html" />
@@ -36,7 +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">pymatgen-diffusion 2022.1.15 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2022.7.21 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.tests.test_clustering</a></li> 
       </ul>
@@ -133,7 +134,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_pathway.html
@@ -1,16 +1,17 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.tests.test_pathway &#8212; pymatgen-diffusion 2022.1.15 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.tests.test_pathway &#8212; pymatgen-diffusion 2022.7.21 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../../../../_static/flasky.css" />
     <script data-url_root="../../../../../../" id="documentation_options" src="../../../../../../_static/documentation_options.js"></script>
     <script src="../../../../../../_static/jquery.js"></script>
     <script src="../../../../../../_static/underscore.js"></script>
+    <script src="../../../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../../../../../_static/doctools.js"></script>
     <link rel="index" title="Index" href="../../../../../../genindex.html" />
     <link rel="search" title="Search" href="../../../../../../search.html" />
@@ -36,7 +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">pymatgen-diffusion 2022.1.15 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2022.7.21 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.tests.test_pathway</a></li> 
       </ul>
@@ -191,7 +192,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>

diff --git a/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html b/docs/_modules/pymatgen/analysis/diffusion/aimd/tests/test_rdf.html
@@ -1,16 +1,17 @@
 
 <!DOCTYPE html>
 
-<html>
+<html lang="en">
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.tests.test_rdf &#8212; pymatgen-diffusion 2022.1.15 documentation</title>
+    <title>pymatgen.analysis.diffusion.aimd.tests.test_rdf &#8212; pymatgen-diffusion 2022.7.21 documentation</title>
     <link rel="stylesheet" type="text/css" href="../../../../../../_static/pygments.css" />
     <link rel="stylesheet" type="text/css" href="../../../../../../_static/flasky.css" />
     <script data-url_root="../../../../../../" id="documentation_options" src="../../../../../../_static/documentation_options.js"></script>
     <script src="../../../../../../_static/jquery.js"></script>
     <script src="../../../../../../_static/underscore.js"></script>
+    <script src="../../../../../../_static/_sphinx_javascript_frameworks_compat.js"></script>
     <script src="../../../../../../_static/doctools.js"></script>
     <link rel="index" title="Index" href="../../../../../../genindex.html" />
     <link rel="search" title="Search" href="../../../../../../search.html" />
@@ -36,7 +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">pymatgen-diffusion 2022.1.15 documentation</a> &#187;</li>
+        <li class="nav-item nav-item-0"><a href="../../../../../../index.html">pymatgen-diffusion 2022.7.21 documentation</a> &#187;</li>
           <li class="nav-item nav-item-1"><a href="../../../../../index.html" accesskey="U">Module code</a> &#187;</li>
         <li class="nav-item nav-item-this"><a href="">pymatgen.analysis.diffusion.aimd.tests.test_rdf</a></li> 
       </ul>
@@ -70,7 +71,6 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.tests.test_rdf</h1><div cla
             <span class="n">structure_list</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">s</span><span class="p">)</span>
             <span class="k">if</span> <span class="n">i</span> <span class="o">==</span> <span class="mi">9</span><span class="p">:</span>
                 <span class="k">break</span>
-        <span class="n">species</span> <span class="o">=</span> <span class="p">[</span><span class="s2">&quot;Na&quot;</span><span class="p">,</span> <span class="s2">&quot;P&quot;</span><span class="p">,</span> <span class="s2">&quot;S&quot;</span><span class="p">]</span>
 
         <span class="c1"># Test from_species</span>
         <span class="n">obj</span> <span class="o">=</span> <span class="n">RadialDistributionFunctionFast</span><span class="p">(</span><span class="n">structures</span><span class="o">=</span><span class="n">structure_list</span><span class="p">,</span> <span class="n">ngrid</span><span class="o">=</span><span class="mi">101</span><span class="p">,</span> <span class="n">rmax</span><span class="o">=</span><span class="mf">10.0</span><span class="p">,</span> <span class="n">sigma</span><span class="o">=</span><span class="mf">0.1</span><span class="p">)</span>
@@ -115,7 +115,7 @@ <h3 id="searchlabel">Quick search</h3>
     </form>
     </div>
 </div>
-<script>$('#searchbox').show(0);</script>
+<script>document.getElementById('searchbox').style.display = "block"</script>
         </div>
       </div>
       <div class="clearer"></div>