Merge pull request #93 from SMTG-Bham/bug-fix

Rare installation fix and minor docs updates

Based on [issue 71](#71) in [this JOSS review](openjournals/joss-reviews#6340) by @enricgrau.

README.rst

@@ -13,7 +13,7 @@
     | |   |___   ___  |___  |_____   ___ :|___/  ___   |___   ___   ___  |___ \
     | |   |   | /   \ |   \ |  |  | /   \:|     /   |  |   \ /     /   \ |   \/
     | |   |   | |___/ |     |  |  | |   |:|     |   |  |     \___  |___/ |    \_____
-    | |   |   | \___  |     |  |  | \___/:|     \___|_ |         \ \___  |    :3.1.2\
+    | |   |   | \___  |     |  |  | \___/:|     \___|_ |         \ \___  |    :3.1.3\
     |____________________________________:_______________________/____________:_____/
 
 

docs/gallery.html

@@ -129,7 +129,7 @@ <h2>Note:<a class="headerlink" href="#note" title="Permalink to this headline">
 <code class="docutils literal notranslate"><span class="pre">ztmap</span></code> heatmap (the power factor <code class="docutils literal notranslate"><span class="pre">pfmap</span></code> is also available):</p>
 <a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/heatmaps.html"><img alt="A heatmap of ZT against carrier concentration and temperature" src="_images/ztmap1.png" /></a>
 <p>Click on the plot to see the script, or one could use</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x --discrete
 </pre></div>
 </div>
 <p>A related plot we hope people find useful for screening materials to

docs/heatmaps.html

@@ -89,7 +89,7 @@ <h1>Heatmaps<a class="headerlink" href="#heatmaps" title="Permalink to this head
 <img alt="ZT against carrier concentration and temperature." src="_images/ztmap1.png" />
 <p>This shows the classic ZT against carrier concentration and temperature
 heatmap. This can be plotted at the command line with:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="sb">`</span>tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c <span class="s1">&#39;#800080&#39;</span> -d x --discrete
 </pre></div>
 </div>
 <p>and in python with:</p>
@@ -118,7 +118,8 @@ <h1>Heatmaps<a class="headerlink" href="#heatmaps" title="Permalink to this head
 23
 24
 25
-26</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="ch">#!/usr/bin/env python3</span>
+26
+27</pre></div></td><td class="code"><div class="highlight"><pre><span></span><span class="ch">#!/usr/bin/env python3</span>
 
 <span class="kn">from</span> <span class="nn">os</span> <span class="kn">import</span> <span class="n">path</span>
 <span class="kn">import</span> <span class="nn">tp</span>
@@ -139,8 +140,9 @@ <h1>Heatmaps<a class="headerlink" href="#heatmaps" title="Permalink to this head
 <span class="n">kdata</span> <span class="o">=</span> <span class="n">tp</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">load</span><span class="o">.</span><span class="n">phono3py</span><span class="p">(</span><span class="n">kfile</span><span class="p">)</span>
 
 <span class="c1"># Add</span>
-<span class="hll"><span class="n">tp</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">heatmap</span><span class="o">.</span><span class="n">add_ztmap</span><span class="p">(</span><span class="n">ax</span><span class="p">,</span> <span class="n">adata</span><span class="p">,</span> <span class="n">kdata</span><span class="p">,</span> <span class="n">direction</span><span class="o">=</span><span class="n">direction</span><span class="p">,</span> <span class="n">colour</span><span class="o">=</span><span class="n">colour</span><span class="p">)</span>
-</span>
+<span class="hll"><span class="n">tp</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">heatmap</span><span class="o">.</span><span class="n">add_ztmap</span><span class="p">(</span><span class="n">ax</span><span class="p">,</span> <span class="n">adata</span><span class="p">,</span> <span class="n">kdata</span><span class="p">,</span> <span class="n">direction</span><span class="o">=</span><span class="n">direction</span><span class="p">,</span> <span class="n">colour</span><span class="o">=</span><span class="n">colour</span><span class="p">,</span>
+</span>                          <span class="n">discrete</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
 <span class="c1"># Save</span>
 <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;ztmap.pdf&#39;</span><span class="p">)</span>
 <span class="n">fig</span><span class="o">.</span><span class="n">savefig</span><span class="p">(</span><span class="s1">&#39;ztmap.png&#39;</span><span class="p">)</span>

docs/index.html

@@ -76,7 +76,7 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/"><img alt="The ThermoParser logo, which looks like &quot;TP&quot;" class="align-center" src="figures/tp-logo-header.png" /></a>
+  <a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/"><img alt="The ThermoParser logo, which looks like &quot;TP&quot;" class="align-center" src="_images/tp-logo-header.png" /></a>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span> <span class="n">________</span>
 <span class="o">/////</span> \\\\
 \<span class="n">________</span><span class="o">/</span><span class="n">________________________________________________________________</span>
@@ -85,7 +85,7 @@
 <span class="o">|</span> <span class="o">|</span>   <span class="o">|</span><span class="n">___</span>   <span class="n">___</span>  <span class="o">|</span><span class="n">___</span>  <span class="o">|</span><span class="n">_____</span>   <span class="n">___</span> <span class="p">:</span><span class="o">|</span><span class="n">___</span><span class="o">/</span>  <span class="n">___</span>   <span class="o">|</span><span class="n">___</span>   <span class="n">___</span>   <span class="n">___</span>  <span class="o">|</span><span class="n">___</span> \
 <span class="o">|</span> <span class="o">|</span>   <span class="o">|</span>   <span class="o">|</span> <span class="o">/</span>   \ <span class="o">|</span>   \ <span class="o">|</span>  <span class="o">|</span>  <span class="o">|</span> <span class="o">/</span>   \<span class="p">:</span><span class="o">|</span>     <span class="o">/</span>   <span class="o">|</span>  <span class="o">|</span>   \ <span class="o">/</span>     <span class="o">/</span>   \ <span class="o">|</span>   \<span class="o">/</span>
 <span class="o">|</span> <span class="o">|</span>   <span class="o">|</span>   <span class="o">|</span> <span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="o">|</span>     <span class="o">|</span>  <span class="o">|</span>  <span class="o">|</span> <span class="o">|</span>   <span class="o">|</span><span class="p">:</span><span class="o">|</span>     <span class="o">|</span>   <span class="o">|</span>  <span class="o">|</span>     \<span class="n">___</span>  <span class="o">|</span><span class="n">___</span><span class="o">/</span> <span class="o">|</span>    \<span class="n">_____</span>
-<span class="o">|</span> <span class="o">|</span>   <span class="o">|</span>   <span class="o">|</span> \<span class="n">___</span>  <span class="o">|</span>     <span class="o">|</span>  <span class="o">|</span>  <span class="o">|</span> \<span class="n">___</span><span class="o">/</span><span class="p">:</span><span class="o">|</span>     \<span class="n">___</span><span class="o">|</span><span class="n">_</span> <span class="o">|</span>         \ \<span class="n">___</span>  <span class="o">|</span>    <span class="p">:</span><span class="mf">3.1</span><span class="o">.</span><span class="mi">2</span>\
+<span class="o">|</span> <span class="o">|</span>   <span class="o">|</span>   <span class="o">|</span> \<span class="n">___</span>  <span class="o">|</span>     <span class="o">|</span>  <span class="o">|</span>  <span class="o">|</span> \<span class="n">___</span><span class="o">/</span><span class="p">:</span><span class="o">|</span>     \<span class="n">___</span><span class="o">|</span><span class="n">_</span> <span class="o">|</span>         \ \<span class="n">___</span>  <span class="o">|</span>    <span class="p">:</span><span class="mf">3.1</span><span class="o">.</span><span class="mi">3</span>\
 <span class="o">|</span><span class="n">____________________________________</span><span class="p">:</span><span class="n">_______________________</span><span class="o">/</span><span class="n">____________</span><span class="p">:</span><span class="n">_____</span><span class="o">/</span>
 </pre></div>
 </div>
@@ -102,7 +102,7 @@
 also contains a suite of command-line tools which can retrieve specific
 data, save derived properties and plot graphs in a single command.</p>
 <p>Click on the image to go to the <a class="reference external" href="https://smtg-bham.github.io/ThermoParser/gallery.html">gallery</a>!</p>
-<a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/gallery.html"><img alt="A phonon dispersion where widened bands show phonon scattering" src="figures/wideband.png" /></a>
+<a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/gallery.html"><img alt="A phonon dispersion where widened bands show phonon scattering" src="_images/wideband.png" /></a>
 <div class="section" id="installation">
 <h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
 <p>ThermoParser can easily be installed with git and pip:</p>

examples/heatmaps/plot-zt.py

@@ -19,7 +19,8 @@
 kdata = tp.data.load.phono3py(kfile)
 
 # Add
-tp.plot.heatmap.add_ztmap(ax, adata, kdata, direction=direction, colour=colour)
+tp.plot.heatmap.add_ztmap(ax, adata, kdata, direction=direction, colour=colour,
+                          discrete=True)
 
 # Save
 fig.savefig('ztmap.pdf')

examples/heatmaps/plot-zt.sh

@@ -1 +1 @@
-`tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x
+`tp plot ztmap ../data/zno/boltztrap.hdf5 -k ../data/zno/kappa-m404021.hdf5 -c '#800080' -d x --discrete

requirements.txt

@@ -4,4 +4,6 @@ matplotlib
 numpy >=1.14.3
 pymatgen >=2020.1.28
 pyyaml
-scipy
+scipy
+setuptools
+wheel

setup.py

@@ -3,10 +3,10 @@
 __name__ =       'ThermoParser'
 __author__ =     'Kieran B. Spooner'
 __copyright__ =  'Copyright Scanlon Materials Theory Group (2024)'
-__version__ =    '3.1.2'
+__version__ =    '3.1.3'
 __maintainer__ = 'Kieran B. Spooner'
 __email__ =      'k.b.spooner@bham.ac.uk'
-__date__ =       'March 5th 2024'
+__date__ =       'March 21st 2024'
 
 import os
 import setuptools
@@ -61,7 +61,7 @@ def __init__(self, *args, **kwargs):
              'amset boltztrap tp te matplotlib vasp transport',
     test_suite='setup.load_test_suite',
     install_requires=['click', 'h5py', 'matplotlib', 'numpy', 'pymatgen',
-                      'pyyaml', 'scipy'],
+                      'pyyaml', 'scipy', 'setuptools', 'wheel'],
     extras_require={'docs':  ['sphinx', 'sphinx_rtd_theme'],
                     'tests': ['unitest']},
     python_requires='>=3.6',