Merge branch 'master' of https://github.com/materialsvirtuallab/pymat…

…gen-analysis-diffusion

.github/workflows/linting.yml

@@ -39,4 +39,4 @@ jobs:
         pydocstyle --count pymatgen
     - name: pylint
       run: |
-        pylint pymatgen
+        pylint pymatgen

.github/workflows/testing.yml

@@ -9,7 +9,7 @@ jobs:
       max-parallel: 20
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: ['3.9']
 
     runs-on: ${{ matrix.os }}
 

.pre-commit-config.yaml

@@ -1,14 +1,56 @@
+exclude: ^(docs|.*test_files|cmd_line|dev_scripts)
+
+default_language_version:
+  python: python3.8
+
+ci:
+  autoupdate_schedule: monthly
+  skip: [flake8, mypy]
+
 repos:
+
+  - repo: https://github.com/myint/autoflake
+    rev: v1.4
+    hooks:
+      - id: autoflake
+        args:
+          - --in-place
+          - --remove-unused-variables
+          - --remove-all-unused-imports
+          - --expand-star-imports
+          - --ignore-init-module-imports
+
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v2.31.0
+    hooks:
+      - id: pyupgrade
+        args: [--py38-plus]
+
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.1.0
     hooks:
       - id: check-yaml
+        exclude: pymatgen/analysis/vesta_cutoffs.yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
-      - id: flake8
-        args: ["--max-line-length=120"]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+
   - repo: https://github.com/psf/black
-    rev: 20.8b1 # Replace by any tag/version: https://github.com/psf/black/tags
+    rev: 22.1.0
+    hooks:
+      - id: black
+
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v0.930
     hooks:
-    - id: black
-      language_version: python3 # Should be a command that runs python3.6+
+      - id: mypy

COPYRIGHT

@@ -31,4 +31,4 @@ THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING,
 BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
 PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, AND
 THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT,
-UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+UPDATES, ENHANCEMENTS, OR MODIFICATIONS.

LICENSE

@@ -24,4 +24,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
-OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.rst

@@ -37,7 +37,7 @@ If you use pymatgen-diffusion in your research, please cite the following
 work::
 
     Deng, Z.; Zhu, Z.; Chu, I.H.; Ong, S. P. Data-Driven First-Principles
-    Methods for the Study and Design of Alkali Superionic Conductors, 
+    Methods for the Study and Design of Alkali Superionic Conductors,
     Chem. Mater., 2016, acs.chemmater.6b02648, doi:10.1021/acs.chemmater.6b02648.
 
 You should also include the following citation for the pymatgen core package
@@ -48,14 +48,14 @@ given that it forms the basis for most of the analyses::
     Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
     Open-Source Python Library for Materials Analysis.* Computational
     Materials Science, 2013, 68, 314-319. doi:10.1016/j.commatsci.2012.10.028.
-    
+
 In addtion, some of the analyses may also have relevant publications that
 you should cite. Please consult the documentation of each module.
 
 Contributing
 ============
 
-We welcome contributions in all forms. If you'd like to contribute, please 
+We welcome contributions in all forms. If you'd like to contribute, please
 fork this repository, make changes and send us a pull request!
 
 Acknowledgements

docs/_modules/index.html

@@ -5,10 +5,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Overview: module code &#8212; pymatgen-diffusion 2021.4.29 documentation</title>
-    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
-    <link rel="stylesheet" href="../_static/flasky.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+    <title>Overview: module code &#8212; pymatgen-diffusion 2022.1.15 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/doctools.js"></script>
@@ -36,7 +36,7 @@ <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 2021.4.29 documentation</a> &#187;</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-this"><a href="">Overview: module code</a></li> 
       </ul>
     </div>  
@@ -85,7 +85,7 @@ <h1>All modules for which code is available</h1>
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>

docs/_modules/pymatgen/analysis/diffusion/aimd/clustering.html

@@ -5,10 +5,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>pymatgen.analysis.diffusion.aimd.clustering &#8212; pymatgen-diffusion 2021.4.29 documentation</title>
-    <link rel="stylesheet" href="../../../../../_static/pygments.css" type="text/css" />
-    <link rel="stylesheet" href="../../../../../_static/flasky.css" type="text/css" />
-    <script id="documentation_options" data-url_root="../../../../../" src="../../../../../_static/documentation_options.js"></script>
+    <title>pymatgen.analysis.diffusion.aimd.clustering &#8212; pymatgen-diffusion 2022.1.15 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/doctools.js"></script>
@@ -36,7 +36,7 @@ <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 2021.4.29 documentation</a> &#187;</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-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.clustering</a></li> 
       </ul>
@@ -48,8 +48,7 @@ <h3>Navigation</h3>
           <div class="body" role="main">
 
   <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="highlight"><pre>
-<span></span><span class="c1"># coding: utf-8</span>
-<span class="c1"># Copyright (c) Materials Virtual Lab.</span>
+<span></span><span class="c1"># Copyright (c) Materials Virtual Lab.</span>
 <span class="c1"># Distributed under the terms of the BSD License.</span>
 
 <span class="sd">&quot;&quot;&quot;</span>
@@ -166,7 +165,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
 <span class="sd">            iterations: Number of iterations thus far.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">iterations</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_iterations</span><span class="p">:</span>
-            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;Max iterations </span><span class="si">%d</span><span class="s2"> reached!&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_iterations</span><span class="p">)</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Max iterations </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">max_iterations</span><span class="si">}</span><span class="s2"> reached!&quot;</span><span class="p">)</span>
             <span class="k">return</span> <span class="kc">True</span>
         <span class="k">if</span> <span class="n">old_centroids</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">return</span> <span class="kc">False</span>
@@ -242,7 +241,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
 <span class="sd">            iterations: Number of iterations thus far.</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">if</span> <span class="n">iterations</span> <span class="o">&gt;</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_iterations</span><span class="p">:</span>
-            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="s2">&quot;Max iterations </span><span class="si">%d</span><span class="s2"> reached!&quot;</span> <span class="o">%</span> <span class="bp">self</span><span class="o">.</span><span class="n">max_iterations</span><span class="p">)</span>
+            <span class="n">warnings</span><span class="o">.</span><span class="n">warn</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Max iterations </span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="n">max_iterations</span><span class="si">}</span><span class="s2"> reached!&quot;</span><span class="p">)</span>
             <span class="k">return</span> <span class="kc">True</span>
         <span class="k">if</span> <span class="n">old_centroids</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
             <span class="k">return</span> <span class="kc">False</span>
@@ -295,7 +294,7 @@ <h1>Source code for pymatgen.analysis.diffusion.aimd.clustering</h1><div class="
   <h3 id="searchlabel">Quick search</h3>
     <div class="searchformwrapper">
     <form class="search" action="../../../../../search.html" method="get">
-      <input type="text" name="q" aria-labelledby="searchlabel" />
+      <input type="text" name="q" aria-labelledby="searchlabel" autocomplete="off" autocorrect="off" autocapitalize="off" spellcheck="false"/>
       <input type="submit" value="Go" />
     </form>
     </div>