Updated from JOSS review 2 (mostly)

Added context to the examples
Corrected some bugs in the examples
Updated ztdiff example
updated \mathregular strings to agree with modern python
expanded tests
stopped load tests reacting to tprc.yaml
improved docs typography
miscellaneous bug fixes
paper refining

Thanks to @enricgrau
This update is mostly based on #71 and relevant to openjournals/joss-reviews#6340

docs/_sources/gallery.rst.txt

@@ -18,7 +18,7 @@ explanations. More details on each of the plots, including the scripts
 and specific commands used are available by clicking on the figures, and we
 also have `tutorials`_!
 
-.. _tutorials: https://smtg-ucl.github.io/ThermoParser/tutorials.html
+.. _tutorials: https://smtg-bham.github.io/ThermoParser/tutorials.html
 
 .. hint::
     Click on the images to see the script which generated them.
@@ -29,7 +29,7 @@ from either a python script or the command line, such as the classic
 
 .. image:: figures/ztmap.png
    :alt: A heatmap of ZT against carrier concentration and temperature
-   :target: https://smtg-ucl.github.io/ThermoParser/heatmaps.html
+   :target: https://smtg-bham.github.io/ThermoParser/heatmaps.html
 
 Click on the plot to see the script, or one could use
 
@@ -44,7 +44,7 @@ ZT, in this case 2.
 
 .. image:: figures/kappa-target.png
    :alt: A heatmap of target lattice thermal conductivity against carrier concentration and temperature
-   :target: https://smtg-ucl.github.io/ThermoParser/heatmaps.html
+   :target: https://smtg-bham.github.io/ThermoParser/heatmaps.html
 
 .. code-block:: bash
 
@@ -55,7 +55,7 @@ comparison among different datasets.
 
 .. image:: figures/ztdiff.png
    :alt: A heatmap of differentce in ZT against carrier concentration and temperature
-   :target: https://smtg-ucl.github.io/ThermoParser/heatmaps.html
+   :target: https://smtg-bham.github.io/ThermoParser/heatmaps.html
 
 .. code-block:: bash
 
@@ -66,15 +66,15 @@ phonon dispersions, which can be overlayed and plotted with DoSs.
 
 .. image:: figures/multiphon.png
    :alt: A plot converging phonon dispersions against supercell size
-   :target: https://smtg-ucl.github.io/ThermoParser/phonons.html
+   :target: https://smtg-bham.github.io/ThermoParser/phonons.html
 
 .. code-block:: bash
 
    tp plot phonons <list of band.yamls> -l <list of labels> -t 'Supercell\ Size'
 
 .. image:: figures/phonons.png
    :alt: A phonon dispersion and DoS
-   :target: https://smtg-ucl.github.io/ThermoParser/phonons.html
+   :target: https://smtg-bham.github.io/ThermoParser/phonons.html
 
 .. code-block:: bash
 
@@ -88,7 +88,7 @@ e.g. Phonopy or maintain multiple data files.
 
 .. image:: figures/dos.png
    :alt: A DoS plot without and with gaussian smearing (sigma=0.2)
-   :target: https://smtg-ucl.github.io/ThermoParser/dos.html
+   :target: https://smtg-bham.github.io/ThermoParser/dos.html
 
 The right-hand plot can be plotted with:
 
@@ -102,13 +102,13 @@ plotting, to enable nicely formatted multi-axes plots...
 
 .. image:: figures/cumkappa.png
    :alt: Cumulative kappa against frequency and mean free path, broken down by direction
-   :target: https://smtg-ucl.github.io/ThermoParser/cumkappa.html
+   :target: https://smtg-bham.github.io/ThermoParser/cumkappa.html
 
 \...and multi-plot axes, to highlight particular interactions.
 
 .. image:: figures/waterfall.png
    :alt: A plot of mean free path and lattice thermal conductivity against frequency overlaid on a DoS
-   :target: https://smtg-ucl.github.io/ThermoParser/waterfall.html
+   :target: https://smtg-bham.github.io/ThermoParser/waterfall.html
 
 As well as projecting third-order phonon properties onto each other as
 above, so below we see there are also a number of functions for
@@ -118,15 +118,15 @@ latter shows the same data, but in a more quantitative way.
 
 .. image:: figures/wideband.png
    :alt: A phonon dispersion where widened bands show phonon scattering
-   :target: https://smtg-ucl.github.io/ThermoParser/prophon.html
+   :target: https://smtg-bham.github.io/ThermoParser/prophon.html
 
 .. code-block:: bash
 
    tp plot wideband band.yaml kappa-m<xxx>.hdf5 -c '#000000' '#ff0000' -s dark_background
 
 .. image:: figures/prophon.png
    :alt: A phonon dispersion where dark colours show phonn scattering
-   :target: https://smtg-ucl.github.io/ThermoParser/prophon.html
+   :target: https://smtg-bham.github.io/ThermoParser/prophon.html
 
 Besides plotting, ThermoParser offers a number of ways to streamline
 transport property workflows, from generating more efficent input files
@@ -138,7 +138,7 @@ but is easily scripted or plotted at the command line:
 
 .. image:: avg-rates.png
    :alt: A plot of weighted average scattering rates against temperature and carrier concnetration.
-   :target: https://smtg-ucl.github.io/ThermoParser/avg-rates.html
+   :target: https://smtg-bham.github.io/ThermoParser/avg-rates.html
 
 .. code-block::
 

docs/_sources/tutorials.rst.txt

@@ -54,12 +54,12 @@ types in the `gallery`_.
  * A selection of scripts to help get the most out of VASP calculations,
    and some extras.
 
-.. _gallery: https://smtg-ucl.github.io/ThermoParser/gallery.html
-.. _Tutorial-00: https://smtg-ucl.github.io/ThermoParser/tutorial-00.html
-.. _Tutorial-01: https://smtg-ucl.github.io/ThermoParser/tutorial-01.html
-.. _Tutorial-02: https://smtg-ucl.github.io/ThermoParser/tutorial-02.html
-.. _Tutorial-03: https://smtg-ucl.github.io/ThermoParser/tutorial-03.html
-.. _Tutorial-04: https://smtg-ucl.github.io/ThermoParser/tutorial-04.html
-.. _Tutorial-05: https://smtg-ucl.github.io/ThermoParser/tutorial-05.html
-.. _Tutorial-06: https://smtg-ucl.github.io/ThermoParser/tutorial-06.html
-.. _Tutorial-0X: https://smtg-ucl.github.io/ThermoParser/tutorial-0X.html
+.. _gallery: https://smtg-bham.github.io/ThermoParser/gallery.html
+.. _Tutorial-00: https://smtg-bham.github.io/ThermoParser/tutorial-00.html
+.. _Tutorial-01: https://smtg-bham.github.io/ThermoParser/tutorial-01.html
+.. _Tutorial-02: https://smtg-bham.github.io/ThermoParser/tutorial-02.html
+.. _Tutorial-03: https://smtg-bham.github.io/ThermoParser/tutorial-03.html
+.. _Tutorial-04: https://smtg-bham.github.io/ThermoParser/tutorial-04.html
+.. _Tutorial-05: https://smtg-bham.github.io/ThermoParser/tutorial-05.html
+.. _Tutorial-06: https://smtg-bham.github.io/ThermoParser/tutorial-06.html
+.. _Tutorial-0X: https://smtg-bham.github.io/ThermoParser/tutorial-0X.html

docs/avg-rates.html

@@ -161,7 +161,7 @@ <h1>Average Rates<a class="headerlink" href="#average-rates" title="Permalink to
 <span class="c1"># Example only shenanegans</span>
 <span class="kn">from</span> <span class="nn">os</span> <span class="kn">import</span> <span class="n">path</span>
 <span class="k">if</span> <span class="ow">not</span> <span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="ow">or</span> <span class="n">path</span><span class="o">.</span><span class="n">getsize</span><span class="p">(</span><span class="n">f</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">1024</span><span class="o">*</span><span class="mi">1024</span><span class="o">*</span><span class="mi">10</span><span class="p">:</span>
-    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;File not found, please use get-data.sh&#39;</span><span class="p">)</span>
+    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;File not found, please use get-data.sh in the folder above.&#39;</span><span class="p">)</span>
 <span class="c1"># End of example only shenanegans</span>
 
 <span class="c1"># Axes</span>
@@ -199,7 +199,7 @@ <h1>Average Rates<a class="headerlink" href="#average-rates" title="Permalink to
 as simple as using the resolve function (lines 26/27). To plot the
 graph matplotlib’s normal <code class="docutils literal notranslate"><span class="pre">plot</span></code> function is used, and the axes,
 labels, ticks and legend are all sorted out by tp functions (lines 21,
-34-38. 39/40 and 42 respectively, see also <a class="reference external" href="https://smtg-ucl.github.io/ThermoParser/tutorial-05.html">Tutorial-05</a>).</p>
+34-38. 39/40 and 42 respectively, see also <a class="reference external" href="https://smtg-bham.github.io/ThermoParser/tutorial-05.html">Tutorial-05</a>).</p>
 <p>This graph can instead show weighted mean free paths, by adding the
 <code class="docutils literal notranslate"><span class="pre">--mfp</span></code> tag at the command line or changing <code class="docutils literal notranslate"><span class="pre">q</span></code> to equal
 <code class="docutils literal notranslate"><span class="pre">weighted_mfp</span></code> in python.</p>

docs/cumkappa.html

@@ -89,7 +89,7 @@ <h1>Cumulative Lattice Thermal Conductivity<a class="headerlink" href="#cumulati
 <img alt="Cumulative lattice thermal conductivity against frequency and mean free path." src="_images/cumkappa1.png" />
 <p>This shows two plots of cumulative lattice thermal conductivity. The
 first one is against frequency, and particularly in conjunction with a
-<a class="reference external" href="https://github.com/SMTG-UCL/ThermoParser/blob/master/examples/dos/">density of states</a> (DoS) or a phonon band structure, this can show the
+<a class="reference external" href="https://github.com/smtg-bham/ThermoParser/blob/master/examples/dos/">density of states</a> (DoS) or a phonon band structure, this can show the
 relative contributions of the constituent atoms to the lattice thermal
 conductivity. The second is against mean free path, and can be used to
 approximate the effect of nanostructuring, for which reason the ability
@@ -157,7 +157,7 @@ <h1>Cumulative Lattice Thermal Conductivity<a class="headerlink" href="#cumulati
 <span class="c1"># You can ignore this section</span>
 <span class="kn">from</span> <span class="nn">os</span> <span class="kn">import</span> <span class="n">path</span>
 <span class="k">if</span> <span class="ow">not</span> <span class="n">path</span><span class="o">.</span><span class="n">isfile</span><span class="p">(</span><span class="n">kappafile</span><span class="p">)</span> <span class="ow">or</span> <span class="p">(</span><span class="n">path</span><span class="o">.</span><span class="n">getsize</span><span class="p">(</span><span class="n">kappafile</span><span class="p">)</span> <span class="o">&lt;</span> <span class="mi">1024</span><span class="o">*</span><span class="mi">1024</span><span class="o">*</span><span class="mi">100</span><span class="p">):</span>
-    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;File not found, please use get-data.sh&#39;</span><span class="p">)</span>
+    <span class="k">raise</span> <span class="ne">Exception</span><span class="p">(</span><span class="s1">&#39;File not found, please use get-data.sh in the folder above.&#39;</span><span class="p">)</span>
 <span class="c1"># End ignore</span>
 
 <span class="n">dosfile</span> <span class="o">=</span> <span class="s1">&#39;../data/zno/projected_dos.dat&#39;</span>