Updated documenation, experimenting with automatic doc build.

README.md

@@ -35,10 +35,11 @@ input_soap = soap_desc.create(mol, positions=[0])
 
 # Installation
 The package is compatible both with Python 2 and Python 3 (tested on 2.7 and
-3.6). The exact list of dependencies are given in setup.py and all of them will
-be automatically installed during setup.
+3.6). We currently only support Unix-based systems, including Linux and macOS.
+The exact list of dependencies are given in setup.py and all of them will be
+automatically installed during setup.
 
-The latest stable release is available through pip: (use the -\-user flag if
+The latest stable release is available through pip: (add the -\-user flag if
 root access is not available)
 
 ```sh

doc.sh

@@ -10,4 +10,4 @@ git config --global user.email "travis@travis-ci.org"
 git config --global user.name "Travis CI"
 git add ./docs
 git commit -m "Travis documentation build: $TRAVIS_BUILD_NUMBER"
-git push --quiet
+git push --quiet https://SINGROUP:$GH_TOKEN@github.com/SINGROUP/dscribe development &>/dev/null

docs/_modules/dscribe/core/lattice.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 

docs/_modules/dscribe/core/system.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 
@@ -332,7 +333,9 @@ <h1>Source code for dscribe.core.system</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="System.get_distance_matrix"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.system.System.get_distance_matrix">[docs]</a>    <span class="k">def</span> <span class="nf">get_distance_matrix</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Calculates the distance matrix A defined as:</span>
 
-<span class="sd">            A_ij = |r_i - r_j|</span>
+<span class="sd">        .. math::</span>
+
+<span class="sd">            A_{ij} = \lvert \mathbf{r}_i - \mathbf{r}_j \\rvert</span>
 
 <span class="sd">        For periodic systems the distance of an atom from itself is the</span>
 <span class="sd">        smallest displacement of an atom from one of it&#39;s periodic copies, and</span>
@@ -349,7 +352,9 @@ <h1>Source code for dscribe.core.system</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="System.get_inverse_distance_matrix"><a class="viewcode-back" href="../../../doc/dscribe.core.html#dscribe.core.system.System.get_inverse_distance_matrix">[docs]</a>    <span class="k">def</span> <span class="nf">get_inverse_distance_matrix</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Calculates the inverse distance matrix A defined as:</span>
 
-<span class="sd">            A_ij = 1/|r_i - r_j|</span>
+<span class="sd">        .. math::</span>
+
+<span class="sd">            A_{ij} = \\frac{1}{\lvert \mathbf{r}_i - \mathbf{r}_j \\rvert }</span>
 
 <span class="sd">        For periodic systems the distance of an atom from itself is the</span>
 <span class="sd">        smallest displacement of an atom from one of it&#39;s periodic copies, and</span>

docs/_modules/dscribe/descriptors/acsf.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 
@@ -153,7 +154,8 @@
            <div itemprop="articleBody">
 
   <h1>Source code for dscribe.descriptors.acsf</h1><div class="highlight"><pre>
-<span></span><span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">unicode_literals</span>
+<span></span><span class="c1"># -*- coding: utf-8 -*-</span>
+<span class="kn">from</span> <span class="nn">__future__</span> <span class="k">import</span> <span class="n">absolute_import</span><span class="p">,</span> <span class="n">division</span><span class="p">,</span> <span class="n">print_function</span><span class="p">,</span> <span class="n">unicode_literals</span>
 <span class="kn">from</span> <span class="nn">builtins</span> <span class="k">import</span> <span class="p">(</span><span class="nb">bytes</span><span class="p">,</span> <span class="nb">str</span><span class="p">,</span> <span class="nb">open</span><span class="p">,</span> <span class="nb">super</span><span class="p">,</span> <span class="nb">range</span><span class="p">,</span> <span class="nb">zip</span><span class="p">,</span> <span class="nb">round</span><span class="p">,</span> <span class="nb">input</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">pow</span><span class="p">,</span> <span class="nb">object</span><span class="p">)</span>
 <span class="kn">import</span> <span class="nn">os</span>
 <span class="kn">import</span> <span class="nn">glob</span>

docs/_modules/dscribe/descriptors/coulombmatrix.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 

docs/_modules/dscribe/descriptors/descriptor.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 

docs/_modules/dscribe/descriptors/elementaldistribution.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 

docs/_modules/dscribe/descriptors/ewaldmatrix.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 

docs/_modules/dscribe/descriptors/lmbtr.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 

docs/_modules/dscribe/descriptors/matrixdescriptor.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 

docs/_modules/dscribe/descriptors/mbtr.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>
 
@@ -455,7 +456,7 @@ <h1>Source code for dscribe.descriptors.mbtr</h1><div class="highlight"><pre>
                     <span class="k">assert</span> <span class="n">info</span><span class="p">[</span><span class="s2">&quot;min&quot;</span><span class="p">]</span> <span class="o">&lt;</span> <span class="n">info</span><span class="p">[</span><span class="s2">&quot;max&quot;</span><span class="p">],</span> \
                         <span class="s2">&quot;The min value should be smaller than the max values&quot;</span></div>
 
-<div class="viewcode-block" id="MBTR.create"><a class="viewcode-back" href="../../../tutorials/mbtr.html#dscribe.descriptors.mbtr.MBTR.create">[docs]</a>    <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">system</span><span class="p">):</span>
+<div class="viewcode-block" id="MBTR.create"><a class="viewcode-back" href="../../../doc/dscribe.descriptors.html#dscribe.descriptors.mbtr.MBTR.create">[docs]</a>    <span class="k">def</span> <span class="nf">create</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">system</span><span class="p">):</span>
         <span class="sd">&quot;&quot;&quot;Return the many-body tensor representation for the given system.</span>
 
 <span class="sd">        Args:</span>

docs/_modules/dscribe/descriptors/sinematrix.html

@@ -89,6 +89,7 @@
 <li class="toctree-l1"><a class="reference internal" href="../../../install.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../tutorials/tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../doc/modules.html">Documentation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../../../citing.html">Citing DScribe</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../../../about.html">About</a></li>
 </ul>