Merge pull request #96 from SMTG-Bham/bug-fix

Bug fix

README.rst

@@ -13,7 +13,7 @@
  | | |___ ___ |___ |_____ ___ :|___/ ___ |___ ___ ___ |___ \
  | | | | / \ | \ | | | / \:| / | | \ / / \ | \/
  | | | | |___/ | | | | | |:| | | | \___ |___/ | \_____
- | | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.3\
+ | | | | \___ | | | | \___/:| \___|_ | \ \___ | :3.1.4\
  |____________________________________:_______________________/____________:_____/
 
 
@@ -197,6 +197,13 @@ Roughly chronologically, they are so far:
 * Katarina Brlec
 * Joe Willis
 
+Thanks also to the `JOSS`_ reviewers, Evan Walter Clarke
+Spotte-Smith, Enric Tomás Grau-Luque, and Francesco Nattino; and the
+editor Mojtaba Barzegari. An unintimidating and productive review
+process, which I would recommend if the opportunity arises!
+
+.. _JOSS: https://joss.theoj.org/
+
 License
 -------
 

docs/_modules/tp.html

@@ -83,6 +83,8 @@ <h1>Source code for tp</h1><div class="highlight"><pre>
 <span class="c1"># default values and metadata</span>
 <span class="c1">#&quot;&quot;&quot;</span>
 
+<span class="n">__version__</span> <span class="o">=</span> <span class="s1">&#39;3.1.4&#39;</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>

docs/_modules/tp/plot/frequency.html

@@ -968,7 +968,7 @@ <h1>Source code for tp.plot.frequency</h1><div class="highlight"><pre>
  <span class="n">cbar</span><span class="o">.</span><span class="n">set_alpha</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
  <span class="n">cbar</span><span class="o">.</span><span class="n">set_label</span><span class="p">(</span><span class="n">axlabels</span><span class="p">[</span><span class="n">projected</span><span class="p">])</span>
  <span class="n">tp</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">utilities</span><span class="o">.</span><span class="n">set_locators</span><span class="p">(</span><span class="n">cbar</span><span class="o">.</span><span class="n">ax</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">cbar</span><span class="o">.</span><span class="n">ax</span><span class="o">.</span><span class="n">yaxis</span><span class="o">.</span><span class="n">get_scale</span><span class="p">())</span>
- <span class="n">cbar</span><span class="o">.</span><span class="n">draw_all</span><span class="p">()</span>
+ <span class="n">cbar</span><span class="o">.</span><span class="n">_draw_all</span><span class="p">()</span>
 
  <span class="k">if</span> <span class="n">main</span><span class="p">:</span>
  <span class="n">data</span><span class="p">[</span><span class="n">xquantity</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span>

docs/_modules/tp/plot/heatmap.html

@@ -321,17 +321,16 @@ <h1>Source code for tp.plot.heatmap</h1><div class="highlight"><pre>
  <span class="c1"># plotting</span>
  <span class="k">if</span> <span class="n">discrete</span><span class="p">:</span>
  <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">&#39;rasterized&#39;</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">levels</span> <span class="ow">is</span> <span class="kc">None</span> <span class="ow">or</span> <span class="n">levels</span> <span class="o">==</span> <span class="p">():</span>
- <span class="n">heat</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">contourf</span><span class="p">(</span><span class="n">x</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">y</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">c</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">colours</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">cnorm</span><span class="p">,</span>
- <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="k">if</span> <span class="n">levels</span> <span class="ow">in</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="p">(),</span> <span class="p">[</span><span class="kc">None</span><span class="p">],</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)]:</span>
+ <span class="n">levels</span> <span class="o">=</span> <span class="mi">10</span>
  <span class="k">else</span><span class="p">:</span>
  <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">levels</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">,</span> <span class="nb">tuple</span><span class="p">))</span> <span class="ow">and</span> <span class="nb">len</span><span class="p">(</span><span class="n">levels</span><span class="p">)</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
  <span class="n">levels</span> <span class="o">=</span> <span class="nb">int</span><span class="p">(</span><span class="n">levels</span><span class="p">[</span><span class="mi">0</span><span class="p">])</span>
  <span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">levels</span><span class="p">,</span> <span class="nb">float</span><span class="p">):</span>
- <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span><span class="s1">&#39;levels must be an int or array-like, not float&#39;</span><span class="p">)</span>
- <span class="k">if</span> <span class="n">levels</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">levels</span> <span class="o">!=</span> <span class="p">():</span>
-  <span class="n">heat</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">contourf</span><span class="p">(</span><span class="n">x</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">y</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">c</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">colours</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">cnorm</span><span class="p">,</span>
-  <span class="n">levels</span><span class="o">=</span><span class="n">levels</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+ <span class="k">raise</span> <span class="ne">TypeError</span><span class="p">(</span>
+  <span class="s1">&#39;levels must be an int or array-like, not float&#39;</span><span class="p">)</span>
+ <span class="n">heat</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">contourf</span><span class="p">(</span><span class="n">x</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">y</span><span class="p">[:</span><span class="o">-</span><span class="mi">1</span><span class="p">],</span> <span class="n">c</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">colours</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">cnorm</span><span class="p">,</span>
+ <span class="n">levels</span><span class="o">=</span><span class="n">levels</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
  <span class="k">else</span><span class="p">:</span>
  <span class="n">heat</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">pcolormesh</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">c</span><span class="p">,</span> <span class="n">cmap</span><span class="o">=</span><span class="n">colours</span><span class="p">,</span> <span class="n">norm</span><span class="o">=</span><span class="n">cnorm</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
  <span class="n">fig</span> <span class="o">=</span> <span class="n">ax</span><span class="o">.</span><span class="n">get_figure</span><span class="p">()</span>
@@ -342,7 +341,7 @@ <h1>Source code for tp.plot.heatmap</h1><div class="highlight"><pre>
  <span class="n">cbar</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">colorbar</span><span class="p">(</span><span class="n">heat</span><span class="p">,</span> <span class="n">ax</span><span class="o">=</span><span class="n">ax</span><span class="p">,</span> <span class="n">extend</span><span class="o">=</span><span class="n">extend</span><span class="p">)</span>
 
  <span class="c1"># contours</span>
- <span class="k">if</span> <span class="n">contours</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span> <span class="ow">and</span> <span class="n">contours</span> <span class="o">!=</span> <span class="p">():</span>
+ <span class="k">if</span> <span class="n">contours</span> <span class="ow">not</span> <span class="ow">in</span> <span class="p">[</span><span class="kc">None</span><span class="p">,</span> <span class="p">[</span><span class="kc">None</span><span class="p">],</span> <span class="p">(),</span> <span class="p">(</span><span class="kc">None</span><span class="p">,)]:</span>
  <span class="k">if</span> <span class="n">contourkwargs</span> <span class="o">==</span> <span class="kc">None</span><span class="p">:</span>
  <span class="n">contourkwargs</span> <span class="o">=</span> <span class="p">{}</span>
  <span class="k">if</span> <span class="ow">not</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">contours</span><span class="p">,</span> <span class="p">(</span><span class="nb">list</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">ndarray</span><span class="p">)):</span>

docs/_modules/tp/plot/phonons.html

@@ -878,7 +878,7 @@ <h1>Source code for tp.plot.phonons</h1><div class="highlight"><pre>
  <span class="n">cbar</span><span class="o">.</span><span class="n">set_alpha</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
  <span class="n">cbar</span><span class="o">.</span><span class="n">set_label</span><span class="p">(</span><span class="n">axlabels</span><span class="p">[</span><span class="n">quantity</span><span class="p">])</span>
  <span class="n">tp</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">utilities</span><span class="o">.</span><span class="n">set_locators</span><span class="p">(</span><span class="n">cbar</span><span class="o">.</span><span class="n">ax</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">cbar</span><span class="o">.</span><span class="n">ax</span><span class="o">.</span><span class="n">yaxis</span><span class="o">.</span><span class="n">get_scale</span><span class="p">())</span>
- <span class="n">cbar</span><span class="o">.</span><span class="n">draw_all</span><span class="p">()</span>
+ <span class="n">cbar</span><span class="o">.</span><span class="n">_draw_all</span><span class="p">()</span>
 
  <span class="k">if</span> <span class="n">main</span><span class="p">:</span>
  <span class="k">if</span> <span class="nb">round</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">amin</span><span class="p">(</span><span class="n">f</span><span class="p">),</span> <span class="mi">1</span><span class="p">)</span> <span class="o">==</span> <span class="mi">0</span><span class="p">:</span>
@@ -1120,7 +1120,7 @@ <h1>Source code for tp.plot.phonons</h1><div class="highlight"><pre>
  <span class="n">cbar</span><span class="o">.</span><span class="n">set_alpha</span><span class="p">(</span><span class="mi">1</span><span class="p">)</span>
  <span class="n">cbar</span><span class="o">.</span><span class="n">set_label</span><span class="p">(</span><span class="n">axlabels</span><span class="p">[</span><span class="n">projected</span><span class="p">])</span>
  <span class="n">tp</span><span class="o">.</span><span class="n">plot</span><span class="o">.</span><span class="n">utilities</span><span class="o">.</span><span class="n">set_locators</span><span class="p">(</span><span class="n">cbar</span><span class="o">.</span><span class="n">ax</span><span class="p">,</span> <span class="n">y</span><span class="o">=</span><span class="n">cbar</span><span class="o">.</span><span class="n">ax</span><span class="o">.</span><span class="n">yaxis</span><span class="o">.</span><span class="n">get_scale</span><span class="p">())</span>
- <span class="n">cbar</span><span class="o">.</span><span class="n">draw_all</span><span class="p">()</span>
+ <span class="n">cbar</span><span class="o">.</span><span class="n">_draw_all</span><span class="p">()</span>
 
  <span class="k">if</span> <span class="n">main</span><span class="p">:</span>
  <span class="n">ax</span><span class="o">.</span><span class="n">set_ylim</span><span class="p">(</span><span class="n">ymin</span><span class="p">,</span> <span class="n">ymax</span><span class="p">)</span>

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 --discrete
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></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
@@ -153,7 +153,7 @@ <h2>Note:<a class="headerlink" href="#note" title="Permalink to this headline">
 </pre></div>
 </div>
 <a class="reference external image-reference" href="https://smtg-bham.github.io/ThermoParser/phonons.html"><img alt="A phonon dispersion and DoS" src="_images/phonons1.png" /></a>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR -doscolour <span class="s1">&#39;#d46ef9&#39;</span> --doscolour <span class="s1">&#39;#7b8eff&#39;</span> -c <span class="s1">&#39;#f0901f&#39;</span>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>tp plot phonons ../data/zno/band.yaml --dos ../data/zno/projected_dos.dat --poscar ../data/zno/POSCAR --doscolour <span class="s1">&#39;#d46ef9&#39;</span> --doscolour <span class="s1">&#39;#7b8eff&#39;</span> -c <span class="s1">&#39;#f0901f&#39;</span>
 </pre></div>
 </div>
 <p>This is where some of the more useful functions of <code class="docutils literal notranslate"><span class="pre">ThermoParser</span></code>

docs/genindex.html

@@ -125,10 +125,10 @@ <h2 id="A">A</h2>
 </li>
  <li><a href="tp.plot.html#tp.plot.phonons.add_multi">add_multi() (in module tp.plot.phonons)</a>
 </li>
- </ul></td>
- <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="tp.plot.html#tp.plot.heatmap.add_pfdiff">add_pfdiff() (in module tp.plot.heatmap)</a>
 </li>
+ </ul></td>
+ <td style="width: 33%; vertical-align: top;"><ul>
  <li><a href="tp.plot.html#tp.plot.heatmap.add_pfmap">add_pfmap() (in module tp.plot.heatmap)</a>
 </li>
  <li><a href="tp.plot.html#tp.plot.phonons.add_projected_dispersion">add_projected_dispersion() (in module tp.plot.phonons)</a>
@@ -142,6 +142,8 @@ <h2 id="A">A</h2>
  <li><a href="tp.plot.html#tp.plot.heatmap.add_ztdiff">add_ztdiff() (in module tp.plot.heatmap)</a>
 </li>
  <li><a href="tp.plot.html#tp.plot.heatmap.add_ztmap">add_ztmap() (in module tp.plot.heatmap)</a>
+</li>
+ <li><a href="tp.cli.html#tp.cli.options.adminsitrative_options">adminsitrative_options() (in module tp.cli.options)</a>
 </li>
  <li><a href="tp.axes.html#tp.axes.legend.alphabetise">alphabetise() (in module tp.axes.legend)</a>
 </li>

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 --discrete
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></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>