added cite to doc website

doc/_build/html/_sources/index.rst.txt

@@ -59,6 +59,20 @@ Code Documentation
 See the :ref:`api_doc` for examples and a full list of modules and functions.
 
 
+Cite
+----
+
+To cite the latest TEMUL Toolkit version, use the following DOI:
+
+.. image:: https://www.zenodo.org/badge/203785298.svg
+   :target: https://www.zenodo.org/badge/latestdoi/203785298
+
+For example: Eoghan O'Connell, Michael Hennessy, & Eoin Moynihan. (2020, November 2). PinkShnack/TEMUL: Initial Temul-Toolkit Release (Version 0.1.1). Zenodo. http://doi.org/10.5281/zenodo.4185974
+
+If you wish to cite an older release of the TEMUL Toolkit, click on the above
+badge to find the relevant version.
+
+
 Contribute
 ----------
 

doc/_build/html/_static/pygments.css

@@ -1,5 +1,10 @@
+pre { line-height: 125%; margin: 0; }
+td.linenos pre { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+span.linenos { color: #000000; background-color: #f0f0f0; padding-left: 5px; padding-right: 5px; }
+td.linenos pre.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
+span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; }
 .highlight .hll { background-color: #ffffcc }
-.highlight  { background: #f8f8f8; }
+.highlight { background: #f8f8f8; }
 .highlight .c { color: #408080; font-style: italic } /* Comment */
 .highlight .err { border: 1px solid #FF0000 } /* Error */
 .highlight .k { color: #008000; font-weight: bold } /* Keyword */

doc/_build/html/dg_visualiser_tutorial.html

@@ -185,7 +185,7 @@
 <h2>Load the Experimental Image<a class="headerlink" href="#load-the-experimental-image" title="Permalink to this headline">¶</a></h2>
 <p>Here we load an example experimental atomic resolution image stored in the
 TEMUL package.</p>
-<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">temul.signal_processing</span> <span class="kn">as</span> <span class="nn">tmlsig</span>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="kn">import</span> <span class="nn">temul.signal_processing</span> <span class="k">as</span> <span class="nn">tmlsig</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="kn">from</span> <span class="nn">temul.example_data</span> <span class="kn">import</span> <span class="n">load_Se_implanted_MoS2_data</span>
 <span class="gp">&gt;&gt;&gt; </span><span class="n">image</span> <span class="o">=</span> <span class="n">load_Se_implanted_MoS2_data</span><span class="p">()</span>
 </pre></div>

doc/_build/html/index.html

@@ -223,14 +223,14 @@ <h1>Welcome to TEMUL Toolkit’s documentation!<a class="headerlink" href="#welc
 <p><code class="code bash docutils literal notranslate"><span class="pre">$</span> <span class="pre">pip</span> <span class="pre">install</span> <span class="pre">temul-toolkit</span></code></p>
 <p>Then, it can be imported with the name “temul”. For example, to import the
 <code class="code python docutils literal notranslate"><span class="name"><span class="pre">polarisation</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> module, use:</p>
-<p><code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">temul.polarisation</span></span> <span class="keyword namespace"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">tmlpol</span></span></code></p>
+<p><code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">temul.polarisation</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">tmlpol</span></span></code></p>
 <p>Note 1: If you wish to use the <code class="code python docutils literal notranslate"><span class="name"><span class="pre">simulations</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code> or <code class="code python docutils literal notranslate"><span class="name"><span class="pre">model_refiner</span></span><span class="operator"><span class="pre">.</span></span><span class="name"><span class="pre">py</span></span></code>
 modules, you will need to install PyPrismatic.</p>
 <p>Note 2: If you’re using any of the functions or classes that require element quantification:</p>
 <blockquote>
 <div><ul class="simple">
 <li>navigate to the “temul/external” directory, copy the “atomap_devel_012” folder and paste that in your “site-packages” directory.</li>
-<li>Then, when using atomap to create sublattices and quantify elements call atomap like this: <code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">atomap_devel_012.api</span></span> <span class="keyword namespace"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">am</span></span></code>.</li>
+<li>Then, when using atomap to create sublattices and quantify elements call atomap like this: <code class="code python docutils literal notranslate"><span class="keyword namespace"><span class="pre">import</span></span> <span class="name namespace"><span class="pre">atomap_devel_012.api</span></span> <span class="keyword"><span class="pre">as</span></span> <span class="name namespace"><span class="pre">am</span></span></code>.</li>
 <li>This development version is slowly being folded into the master branch here: <a class="reference external" href="https://gitlab.com/atomap/atomap/-/issues/93">https://gitlab.com/atomap/atomap/-/issues/93</a> and any help or tips on implementation are welcome!</li>
 </ul>
 </div></blockquote>
@@ -247,6 +247,14 @@ <h1>Welcome to TEMUL Toolkit’s documentation!<a class="headerlink" href="#welc
 <h2>Code Documentation<a class="headerlink" href="#code-documentation" title="Permalink to this headline">¶</a></h2>
 <p>See the <a class="reference internal" href="api_doc.html#api-doc"><span class="std std-ref">API documentation</span></a> for examples and a full list of modules and functions.</p>
 </div>
+<div class="section" id="cite">
+<h2>Cite<a class="headerlink" href="#cite" title="Permalink to this headline">¶</a></h2>
+<p>To cite the latest TEMUL Toolkit version, use the following DOI:</p>
+<a class="reference external image-reference" href="https://www.zenodo.org/badge/latestdoi/203785298"><img alt="https://www.zenodo.org/badge/203785298.svg" src="https://www.zenodo.org/badge/203785298.svg" /></a>
+<p>For example: Eoghan O’Connell, Michael Hennessy, &amp; Eoin Moynihan. (2020, November 2). PinkShnack/TEMUL: Initial Temul-Toolkit Release (Version 0.1.1). Zenodo. <a class="reference external" href="http://doi.org/10.5281/zenodo.4185974">http://doi.org/10.5281/zenodo.4185974</a></p>
+<p>If you wish to cite an older release of the TEMUL Toolkit, click on the above
+badge to find the relevant version.</p>
+</div>
 <div class="section" id="contribute">
 <h2>Contribute<a class="headerlink" href="#contribute" title="Permalink to this headline">¶</a></h2>
 <ul class="simple">

doc/index.rst

@@ -59,6 +59,20 @@ Code Documentation
 See the :ref:`api_doc` for examples and a full list of modules and functions.
 
 
+Cite
+----
+
+To cite the latest TEMUL Toolkit version, use the following DOI:
+
+.. image:: https://www.zenodo.org/badge/203785298.svg
+   :target: https://www.zenodo.org/badge/latestdoi/203785298
+
+For example: Eoghan O'Connell, Michael Hennessy, & Eoin Moynihan. (2020, November 2). PinkShnack/TEMUL: Initial Temul-Toolkit Release (Version 0.1.1). Zenodo. http://doi.org/10.5281/zenodo.4185974
+
+If you wish to cite an older release of the TEMUL Toolkit, click on the above
+badge to find the relevant version.
+
+
 Contribute
 ----------