Merge branch 'develop' into bug-fix

SMTG-Bham · Aug 16, 2023 · a6eb49f · a6eb49f
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diff --git a/README.rst b/README.rst
@@ -1,56 +1,56 @@
 .. image:: figures/tp-logo-header.png
-    :alt: The ThermoPlotter logo, which looks like "TP"
-    :target: https://smtg-ucl.github.io/ThermoPlotter/
+    :alt: The ThermoParser logo, which looks like "TP"
+    :target: https://smtg-ucl.github.io/ThermoParser/
     :align: center
 
 .. code-block::
 
      ________
     ///// \\\\
-    \________/_______________________________________________________________
-    |_____                            : ___                                  \
-    | |   |                           :|   \ |           |     |             /
-    | |   |__   __  |___  |_____   __ :|___/ |    ___  __|__ __|__  __  |__  \
-    | |   |  | /  \ |   \ |  |  | /  \:|     |   /   \   |     |   /  \ |  \ /
-    | |   |  | |__/ |     |  |  | |  |:|     |   |   |   |     |   |__/ |    \_____
-    | |   |  | \__  |     |  |  | \__/:|     \__ \___/   \__   \__ \__  |    :2.3.0\
-    |_________________________________:______________________________________:_____/
+    \________/________________________________________________________________
+    |_____                               : ___                                \
+    | |   |                              :|   \                               /
+    | |   |___   ___  |___  |_____   ___ :|___/  ___   |___   ___   ___  |___ \
+    | |   |   | /   \ |   \ |  |  | /   \:|     /   |  |   \ /     /   \ |   \/
+    | |   |   | |___/ |     |  |  | |   |:|     |   |  |     \___  |___/ |    \_____
+    | |   |   | \___  |     |  |  | \___/:|     \___|_ |         \ \___  |    :3.0.0\
+    |____________________________________:_______________________/____________:_____/
 
 
-.. image:: https://travis-ci.com/SMTG-UCL/ThermoPlotter.svg?branch=master
+.. image:: https://travis-ci.com/SMTG-UCL/ThermoParser.svg?branch=master
     :alt: The travis-ci badge
-    :target: https://travis-ci.com/SMTG-UCL/ThermoPlotter
+    :target: https://travis-ci.com/SMTG-UCL/ThermoParser
 
-ThermoPlotter is a toolkit used to simplify the analysis of data
+ThermoParser is a toolkit used to simplify the analysis of data
 produced by specialist materials science codes, centred around
 thermoelectrics, but also useful for anything pertaining to electronic
-and/ or phononic transport. ThermoPlotter is a Python library which
+and/ or phononic transport. ThermoParser is a Python library which
 contains functions for data retrieval, manipulation and plotting, which
 can be easily used with a little Python knowlege to generate a wide
-array of high-quality plots in only a few lines of code. ThermoPlotter
+array of high-quality plots in only a few lines of code. ThermoParser
 also contains a suite of command-line tools which can retrieve specific
 data, save derived properties and plot graphs in a single command.
 
 Click on the image to go to the `gallery`_!
 
 .. image:: figures/wideband.png
    :alt: A phonon dispersion where widened bands show phonon scattering
-   :target: https://smtg-ucl.github.io/ThermoPlotter/gallery.html
+   :target: https://smtg-ucl.github.io/ThermoParser/gallery.html
 
-.. _gallery: https://smtg-ucl.github.io/ThermoPlotter/gallery.html
+.. _gallery: https://smtg-ucl.github.io/ThermoParser/gallery.html
 
 Installation
 ------------
 
-ThermoPlotter can easily be installed with git and pip:
+ThermoParser can easily be installed with git and pip:
 
 .. code-block:: bash
 
-    git clone https://github.com/SMTG-UCL/ThermoPlotter.git
-    cd ThermoPlotter
+    git clone https://github.com/SMTG-UCL/ThermoParser.git
+    cd ThermoParser
     pip install .
 
-After installing, you may want to copy ``ThermoPlotter/tprc.yaml`` to
+After installing, you may want to copy ``ThermoParser/tprc.yaml`` to
 ``~/.config/tprc.yaml``, if you want to set your own default axis
 labels, unit conversions, default style sheets (two are provided),
 other aesthetic alterations and more!
@@ -66,22 +66,26 @@ longer process is required:
 2. ``python3 -m pip install cython numpy``
 3. ``brew info hdf5`` to retrieve the path to your hdf5 install
 4. ``HDF5_DIR=YOUR_HDF5_PATH --no-build-isolation h5py``
-5. ``git clone https://github.com/SMTG-UCL/ThermoPlotter.git``
-6. ``cd ThermoPlotter``
+5. ``git clone https://github.com/SMTG-UCL/ThermoParser.git``
+6. ``cd ThermoParser``
 7. ``pip install --user -e .``
 
 Using conda may circumvent this process.
 
-Command Line Usage
-------------------
+Command Line Interface (CLI)
+----------------------------
 
-ThermoPlotter uses `click`_, which has an easily navigable structure
+ThermoParser uses `click`_, which has an easily navigable structure
 from the command-line, detailed in the `tutorials`_.
+The most frequently useful commands are included in the CLI for maximum
+ease, including the ``tp get`` functions, which verbosely retrieve data
+from files which are normally tiresome and error-prone to navigate; and
+most of the simplest plot-types available through the Python interface.
 
-Python Usage
-------------
+Python Interface
+----------------
 
-ThermoPlotter is designed to have four main stages:
+ThermoParser is designed to have four main stages:
 
 #. *Axes*:
      Pick an axis layout from ``tp.axes``.
@@ -92,19 +96,19 @@ ThermoPlotter is designed to have four main stages:
 #. *Save*:
      Use ``plt.savefig`` or equivalent to produce the figure.
 
-As ThermoPlotter is dependent on matplotlib, each stage can be
+As ThermoParser is dependent on matplotlib, each stage can be
 substituted with bespoke code, e.g. using ``matplotlib.pyplot.subplots``
 or ``matplotlib.axes.Axes.scatter``. These can still be supplemented
-with ThermoPlotter helper functions, such as default labels which the
+with ThermoParser helper functions, such as default labels which the
 user can set in ``tp.settings``, colourmap generators in
 ``tp.plot.colour`` or legend helpers such as ``tp.axes.legend.alphabetise``.
 
-The best way to get a feel for ThermoPlotter is to see it in action:
+The best way to get a feel for ThermoParser is to see it in action:
 Take a look at our  `examples`_ and `tutorials`_. Currently supported
 codes are:
 
-.. _examples: https://github.com/smtg-ucl/ThermoPlotter/tree/master/examples
-.. _tutorials: https://smtg-ucl.github.io/ThermoPlotter/tutorials.html
+.. _examples: https://github.com/smtg-ucl/ThermoParser/tree/master/examples
+.. _tutorials: https://smtg-ucl.github.io/ThermoParser/tutorials.html
 
 * Phononic properties:
 
@@ -152,10 +156,10 @@ appropriate `examples`_, further `documentation`_ and `tests`_ are greatly
 appreciated. Documentation uses the `sphinx`_ package, and can be built from
 the ``docs`` directory with ``sphinx-build -b html src/ .``.
 
-.. _issue tracker: https://github.com/smtg-ucl/ThermoPlotter/issues
+.. _issue tracker: https://github.com/smtg-ucl/ThermoParser/issues
 .. _fork and pull: https://guides.github.com/activities/forking
-.. _documentation: https://smtg-ucl.github.io/ThermoPlotter/
-.. _tests: https://github.com/smtg-ucl/ThermoPlotter/tree/master/tests
+.. _documentation: https://smtg-ucl.github.io/ThermoParser/
+.. _tests: https://github.com/smtg-ucl/ThermoParser/tree/master/tests
 
 Testing
 -------
@@ -168,7 +172,7 @@ with ``python3 -m unittest``.
 Contributors
 ------------
 
-Many thanks to all those who contributed code or ideas to ThermoPlotter!
+Many thanks to all those who contributed code or ideas to ThermoParser!
 Roughly chronologically, they are so far:
 
 * Kieran B. Spooner
@@ -184,13 +188,13 @@ Roughly chronologically, they are so far:
 License
 -------
 
-ThermoPlotter is licensed under the GNU Affero General Public License v3
+ThermoParser is licensed under the GNU Affero General Public License v3
 (AGPLv3).
 
 Requirements
 ------------
 
-ThermoPlotter uses the following open-source packages:
+ThermoParser uses the following open-source packages:
 
 * `click <https://click.palletsprojects.com/en/8.0.x/>`_
 * `h5py <http://docs.h5py.org/>`_

diff --git a/citation.cff b/citation.cff
@@ -0,0 +1,19 @@
+cff-version: 1.2.0
+message: "If you use ThermoParser, please cite it as below:"
+authors:
+- family-names: "Spooner"
+  given-names: "Kieran B."
+  orcid: "https://orcid.org/0000-0002-4078-3148"
+- family-names: "Einhorn"
+  given-names: "Maud"
+  orcid: "https://orcid.org/0000-0003-0371-0262"
+- family-names: "Davies"
+  given-names: "Daniel W."
+  orcid: "https://orcid.org/0000-0003-4094-5992"
+- family-names: "Scanlon"
+  given-names: "David O."
+  orcid: "https://orcid.org/0000-0001-9174-8601"
+title: "ThermoParser: Streamlined Analysis of Thermoelectric Properties"
+version: 3.0.0
+date-released: 2023-08-16
+url: "https://github.com/SMTG-UCL/ThermoParser"
diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 8763cfb3d8fdbb00210c4d226bd71e51
+config: 0941f3fdcba972ea838af7d173568d7a
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/avg-rates.doctree b/docs/.doctrees/avg-rates.doctree
diff --git a/docs/.doctrees/contents.doctree b/docs/.doctrees/contents.doctree
diff --git a/docs/.doctrees/cumkappa.doctree b/docs/.doctrees/cumkappa.doctree
diff --git a/docs/.doctrees/dos.doctree b/docs/.doctrees/dos.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/gallery.doctree b/docs/.doctrees/gallery.doctree
diff --git a/docs/.doctrees/heatmaps.doctree b/docs/.doctrees/heatmaps.doctree
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/phonons.doctree b/docs/.doctrees/phonons.doctree
diff --git a/docs/.doctrees/prophon.doctree b/docs/.doctrees/prophon.doctree
diff --git a/docs/.doctrees/tp.axes.doctree b/docs/.doctrees/tp.axes.doctree
diff --git a/docs/.doctrees/tp.cli.doctree b/docs/.doctrees/tp.cli.doctree
diff --git a/docs/.doctrees/tp.data.doctree b/docs/.doctrees/tp.data.doctree
diff --git a/docs/.doctrees/tp.doctree b/docs/.doctrees/tp.doctree
diff --git a/docs/.doctrees/tp.plot.doctree b/docs/.doctrees/tp.plot.doctree
diff --git a/docs/.doctrees/tp.setup.doctree b/docs/.doctrees/tp.setup.doctree
diff --git a/docs/.doctrees/tutorial-00.doctree b/docs/.doctrees/tutorial-00.doctree
diff --git a/docs/.doctrees/tutorial-01.doctree b/docs/.doctrees/tutorial-01.doctree
diff --git a/docs/.doctrees/tutorial-02.doctree b/docs/.doctrees/tutorial-02.doctree
diff --git a/docs/.doctrees/tutorial-03.doctree b/docs/.doctrees/tutorial-03.doctree
diff --git a/docs/.doctrees/tutorial-04.doctree b/docs/.doctrees/tutorial-04.doctree
diff --git a/docs/.doctrees/tutorial-05.doctree b/docs/.doctrees/tutorial-05.doctree
diff --git a/docs/.doctrees/tutorial-06.doctree b/docs/.doctrees/tutorial-06.doctree
diff --git a/docs/.doctrees/tutorials.doctree b/docs/.doctrees/tutorials.doctree
diff --git a/docs/.doctrees/waterfalls.doctree b/docs/.doctrees/waterfalls.doctree
diff --git a/docs/_images/avg-rates.png b/docs/_images/avg-rates.png
diff --git a/docs/_images/cumkappa1.png b/docs/_images/cumkappa1.png
diff --git a/docs/_images/density.png b/docs/_images/density.png
diff --git a/docs/_images/dos1.png b/docs/_images/dos1.png
diff --git a/docs/_images/kappa-target1.png b/docs/_images/kappa-target1.png
diff --git a/docs/_images/multiphon1.png b/docs/_images/multiphon1.png
diff --git a/docs/_images/phonons1.png b/docs/_images/phonons1.png
diff --git a/docs/_images/prophon1.png b/docs/_images/prophon1.png
diff --git a/docs/_images/waterfall1.png b/docs/_images/waterfall1.png
diff --git a/docs/_images/wideband1.png b/docs/_images/wideband1.png
diff --git a/docs/_images/ztdiff1.png b/docs/_images/ztdiff1.png
diff --git a/docs/_images/ztmap1.png b/docs/_images/ztmap1.png
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>Overview: module code &mdash; ThermoPlotter 2.0.0 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+  <title>Overview: module code &mdash; ThermoParser 3.0.0 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
   <!--[if lt IE 9]>
     <script src="../_static/js/html5shiv.min.js"></script>
@@ -23,7 +23,7 @@
     <nav data-toggle="wy-nav-shift" class="wy-nav-side">
       <div class="wy-side-scroll">
         <div class="wy-side-nav-search" >
-            <a href="../contents.html" class="icon icon-home"> ThermoPlotter<img src="../_static/tp-logo.png" class="logo" alt="Logo"/>
+            <a href="../contents.html" class="icon icon-home"> ThermoParser<img src="../_static/tp-logo.png" class="logo" alt="Logo"/>
           </a>
 <div role="search">
   <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
@@ -37,8 +37,8 @@
 <li class="toctree-l1"><a class="reference internal" href="../gallery.html">Gallery</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../tutorials.html">Tutorials</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html">Installation</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../index.html#command-line-usage">Command Line Usage</a></li>
-<li class="toctree-l1"><a class="reference internal" href="../index.html#python-usage">Python Usage</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#command-line-interface-cli">Command Line Interface (CLI)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#python-interface">Python Interface</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#contributing">Contributing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#testing">Testing</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../index.html#contributors">Contributors</a></li>
@@ -53,7 +53,7 @@
 
     <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
           <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
-          <a href="../contents.html">ThermoPlotter</a>
+          <a href="../contents.html">ThermoParser</a>
       </nav>
 
       <div class="wy-nav-content">
@@ -71,6 +71,7 @@
            <div itemprop="articleBody">
 
   <h1>All modules for which code is available</h1>
+<ul><li><a href="tp.html">tp</a></li>
 <ul><li><a href="tp/axes/large.html">tp.axes.large</a></li>
 <li><a href="tp/axes/legend.html">tp.axes.legend</a></li>
 <li><a href="tp/axes/small.html">tp.axes.small</a></li>
@@ -89,7 +90,7 @@ <h1>All modules for which code is available</h1>
 <li><a href="tp/plot/utilities.html">tp.plot.utilities</a></li>
 <li><a href="tp/settings.html">tp.settings</a></li>
 <li><a href="tp/setup/vasp.html">tp.setup.vasp</a></li>
-</ul>
+</ul></ul>
 
            </div>
           </div>
@@ -98,7 +99,7 @@ <h1>All modules for which code is available</h1>
   <hr/>
 
   <div role="contentinfo">
-    <p>&#169; Copyright 2021, Scanlon Materials Theory Group.</p>
+    <p>&#169; Copyright 2023, Scanlon Materials Theory Group.</p>
   </div>
 
   Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a

diff --git a/docs/_modules/tp.html b/docs/_modules/tp.html
@@ -0,0 +1,123 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" >
+<head>
+  <meta charset="utf-8" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>tp &mdash; ThermoParser 3.0.0 documentation</title><link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
+    <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
+        <script src="../_static/jquery.js"></script>
+        <script src="../_static/underscore.js"></script>
+        <script src="../_static/doctools.js"></script>
+        <script src="../_static/language_data.js"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+            <a href="../contents.html" class="icon icon-home"> ThermoParser<img src="../_static/tp-logo.png" class="logo" alt="Logo"/>
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <ul>
+<li class="toctree-l1"><a class="reference internal" href="../gallery.html">Gallery</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../tutorials.html">Tutorials</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#command-line-interface-cli">Command Line Interface (CLI)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#python-interface">Python Interface</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#contributing">Contributing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#testing">Testing</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#contributors">Contributors</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#license">License</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../index.html#requirements">Requirements</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Python Package</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../contents.html">ThermoParser</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../contents.html" class="icon icon-home"></a> &raquo;</li>
+          <li><a href="index.html">Module code</a> &raquo;</li>
+      <li>tp</li>
+      <li class="wy-breadcrumbs-aside">
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+
+  <h1>Source code for tp</h1><div class="highlight"><pre>
+<span></span><span class="sd">&quot;&quot;&quot;Everything.</span>
+
+<span class="sd">Modules</span>
+<span class="sd">-------</span>
+
+<span class="sd">    calculate</span>
+<span class="sd">        tools for calculating derived properties and interpolating</span>
+<span class="sd">    settings</span>
+<span class="sd">        default values and metadata</span>
+<span class="sd">&quot;&quot;&quot;</span>
+
+<div class="viewcode-block" id="docstring_replace"><a class="viewcode-back" href="../tp.html#tp.docstring_replace">[docs]</a><span class="k">def</span> <span class="nf">docstring_replace</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
+    <span class="k">def</span> <span class="nf">d</span><span class="p">(</span><span class="n">f</span><span class="p">):</span>
+        <span class="n">f</span><span class="o">.</span><span class="vm">__doc__</span> <span class="o">=</span> <span class="n">f</span><span class="o">.</span><span class="vm">__doc__</span><span class="o">.</span><span class="n">format</span><span class="p">(</span><span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+        <span class="k">return</span> <span class="n">f</span>
+    <span class="k">return</span> <span class="n">d</span></div>
+
+<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">settings</span> <span class="c1"># required for other imports, prevents circularity</span>
+<span class="kn">from</span> <span class="nn">.</span> <span class="kn">import</span> <span class="n">axes</span><span class="p">,</span> <span class="n">calculate</span><span class="p">,</span> <span class="n">data</span><span class="p">,</span> <span class="n">plot</span><span class="p">,</span> <span class="n">setup</span><span class="p">,</span> <span class="n">cli</span>
+</pre></div>
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
+  <div role="contentinfo">
+    <p>&#169; Copyright 2023, Scanlon Materials Theory Group.</p>
+  </div>
+
+  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
+    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
+    provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
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