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remove duplication of sections of the docs, minor editing
SMTG-Bham · Mar 18, 2024 · 0ea5463 · 0ea5463
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diff --git a/docs/.doctrees/contents.doctree b/docs/.doctrees/contents.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.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/_modules/index.html b/docs/_modules/index.html
@@ -44,7 +44,7 @@
 <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>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Python API</a></li>
 </ul>
 
  </div>

diff --git a/docs/_modules/tp.html b/docs/_modules/tp.html
@@ -44,7 +44,7 @@
 <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>
+<li class="toctree-l1"><a class="reference internal" href="../modules.html">Python API</a></li>
 </ul>
 
  </div>
@@ -72,16 +72,16 @@
  <div itemprop="articleBody">
 
  <h1>Source code for tp</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Everything.</span>
+<span></span><span class="sd">&quot;&quot;&quot;A package for postprocessings transport calculations.&quot;&quot;&quot;</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>
+<span class="c1">#Modules</span>
+<span class="c1">#-------</span>
+<span class="c1">#</span>
+<span class="c1"># calculate</span>
+<span class="c1"># tools for calculating derived properties and interpolating</span>
+<span class="c1"># settings</span>
+<span class="c1"># default values and metadata</span>
+<span class="c1">#&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>

diff --git a/docs/_modules/tp/axes/large.html b/docs/_modules/tp/axes/large.html
@@ -44,7 +44,7 @@
 <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>
+<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python API</a></li>
 </ul>
 
  </div>
@@ -79,39 +79,40 @@ <h1>Source code for tp.axes.large</h1><div class="highlight"><pre>
 <span class="sd">axes and an add_legend function. The legend function comes with a</span>
 <span class="sd">choice of positions and takes normal ax.legend arguments. Drawing large</span>
 <span class="sd">figures is significantly slower than small ones.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd"> one</span>
-
-<span class="sd"> one_colourbar</span>
-
-<span class="sd"> one_dos</span>
-<span class="sd"> </span>
-<span class="sd"> one_dos_colourbar</span>
-<span class="sd"> </span>
-<span class="sd"> two_h</span>
-<span class="sd"> </span>
-<span class="sd"> two_h_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> two_v</span>
-<span class="sd"> </span>
-<span class="sd"> two_v_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> three_h</span>
-<span class="sd"> </span>
-<span class="sd"> three_h_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> three_square</span>
-<span class="sd"> </span>
-<span class="sd"> three_square_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> four_square</span>
-<span class="sd"> </span>
-<span class="sd"> four_square_colourbars</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1"># one</span>
+<span class="c1">#</span>
+<span class="c1"># one_colourbar</span>
+<span class="c1">#</span>
+<span class="c1"># one_dos</span>
+<span class="c1"># </span>
+<span class="c1"># one_dos_colourbar</span>
+<span class="c1"># </span>
+<span class="c1"># two_h</span>
+<span class="c1"># </span>
+<span class="c1"># two_h_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># two_v</span>
+<span class="c1"># </span>
+<span class="c1"># two_v_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># three_h</span>
+<span class="c1"># </span>
+<span class="c1"># three_h_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># three_square</span>
+<span class="c1"># </span>
+<span class="c1"># three_square_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># four_square</span>
+<span class="c1"># </span>
+<span class="c1"># four_square_colourbars</span>
+<span class="c1">#&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">from</span> <span class="nn">matplotlib.gridspec</span> <span class="kn">import</span> <span class="n">GridSpec</span>
 <span class="kn">import</span> <span class="nn">tp</span>

diff --git a/docs/_modules/tp/axes/legend.html b/docs/_modules/tp/axes/legend.html
@@ -44,7 +44,7 @@
 <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>
+<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python API</a></li>
 </ul>
 
  </div>
@@ -73,18 +73,18 @@
  <div itemprop="articleBody">
 
  <h1>Source code for tp.axes.legend</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Functions for dealing with legends.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd"> consolidate</span>
-<span class="sd"> combine legends.</span>
-<span class="sd"> add_add_legend</span>
-<span class="sd"> add add_legend function.</span>
-<span class="sd"> alphabetise</span>
-<span class="sd"> alphabetises or enumerates axes.</span>
-<span class="sd">&quot;&quot;&quot;</span>
+<span></span><span class="sd">&quot;&quot;&quot;Functions for dealing with legends.&quot;&quot;&quot;</span>
+
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1"># consolidate</span>
+<span class="c1"># combine legends.</span>
+<span class="c1"># add_add_legend</span>
+<span class="c1"># add add_legend function.</span>
+<span class="c1"># alphabetise</span>
+<span class="c1"># alphabetises or enumerates axes.</span>
+<span class="c1">#&quot;&quot;&quot;</span>
 
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">tp</span>

diff --git a/docs/_modules/tp/axes/small.html b/docs/_modules/tp/axes/small.html
@@ -44,7 +44,7 @@
 <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>
+<li class="toctree-l1"><a class="reference internal" href="../../../modules.html">Python API</a></li>
 </ul>
 
  </div>
@@ -78,39 +78,40 @@ <h1>Source code for tp.axes.small</h1><div class="highlight"><pre>
 <span class="sd">Each function returns a figure, a set of axes or an array of sets of</span>
 <span class="sd">axes and an add_legend function. The legend function comes with a</span>
 <span class="sd">choice of positions and takes normal ax.legend arguments.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd"> one</span>
-<span class="sd"> </span>
-<span class="sd"> one_colourbar</span>
-<span class="sd"> </span>
-<span class="sd"> one_dos</span>
-<span class="sd"> </span>
-<span class="sd"> one_dos_colourbar</span>
-<span class="sd"> </span>
-<span class="sd"> two_h</span>
-<span class="sd"> </span>
-<span class="sd"> two_h_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> two_v</span>
-<span class="sd"> </span>
-<span class="sd"> two_v_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> three_h</span>
-<span class="sd"> </span>
-<span class="sd"> three_h_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> three_square</span>
-<span class="sd"> </span>
-<span class="sd"> three_square_colourbars</span>
-<span class="sd"> </span>
-<span class="sd"> four_square</span>
-<span class="sd"> </span>
-<span class="sd"> four_square_colourbars</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1"># one</span>
+<span class="c1"># </span>
+<span class="c1"># one_colourbar</span>
+<span class="c1"># </span>
+<span class="c1"># one_dos</span>
+<span class="c1"># </span>
+<span class="c1"># one_dos_colourbar</span>
+<span class="c1"># </span>
+<span class="c1"># two_h</span>
+<span class="c1"># </span>
+<span class="c1"># two_h_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># two_v</span>
+<span class="c1"># </span>
+<span class="c1"># two_v_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># three_h</span>
+<span class="c1"># </span>
+<span class="c1"># three_h_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># three_square</span>
+<span class="c1"># </span>
+<span class="c1"># three_square_colourbars</span>
+<span class="c1"># </span>
+<span class="c1"># four_square</span>
+<span class="c1"># </span>
+<span class="c1"># four_square_colourbars</span>
+<span class="c1">#&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>
 <span class="kn">from</span> <span class="nn">matplotlib.gridspec</span> <span class="kn">import</span> <span class="n">GridSpec</span>
 <span class="kn">import</span> <span class="nn">tp</span>

diff --git a/docs/_modules/tp/calculate.html b/docs/_modules/tp/calculate.html
@@ -44,7 +44,7 @@
 <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>
+<li class="toctree-l1"><a class="reference internal" href="../../modules.html">Python API</a></li>
 </ul>
 
  </div>
@@ -73,53 +73,54 @@
  <div itemprop="articleBody">
 
  <h1>Source code for tp.calculate</h1><div class="highlight"><pre>
-<span></span><span class="sd">&quot;&quot;&quot;Calculates stuff.</span>
+<span></span><span class="sd">&quot;&quot;&quot;Calculates quantities used in other modules.</span>
 
 <span class="sd">Uses tp units by default, but can read the tprc.yaml to customise.</span>
-
-<span class="sd">Functions</span>
-<span class="sd">---------</span>
-
-<span class="sd"> cumulate:</span>
-<span class="sd"> sorts and cumulates.</span>
-<span class="sd"> gaussian:</span>
-<span class="sd"> gaussian distribution of height 1.</span>
-<span class="sd"> lorentzian:</span>
-<span class="sd"> area conserved lorentzian distribution.</span>
-<span class="sd"> lifetime:</span>
-<span class="sd"> particle lifetime.</span>
-<span class="sd"> mfp:</span>
-<span class="sd"> particle mean free path.</span>
-<span class="sd"> fd_occupation:</span>
-<span class="sd"> fermion occupation.</span>
-<span class="sd"> be_occupation:</span>
-<span class="sd"> boson occupation.</span>
-<span class="sd"> dfdde:</span>
-<span class="sd"> derivative of the Fermi-Dirac distribution.</span>
-<span class="sd"> thermal_conductivity:</span>
-<span class="sd"> total thermal conductivity.</span>
-<span class="sd"> power_factor:</span>
-<span class="sd"> power factor.</span>
-<span class="sd"> zt:</span>
-<span class="sd"> ZT.</span>
-<span class="sd"> kl:</span>
-<span class="sd"> lattice thermal conductivity for target ZT.</span>
-
-<span class="sd"> power_factor_fromdict:</span>
-<span class="sd"> adds power factor to dictionary.</span>
-<span class="sd"> zt_fromdict:</span>
-<span class="sd"> adds zt to dictionary.</span>
-<span class="sd"> kl_fromdict:</span>
-<span class="sd"> adds lattice thermal conductivity for target ZT to dictionary.</span>
-
-<span class="sd"> to_tp:</span>
-<span class="sd"> converts quantities to tp defaults from tprc.yaml.</span>
-<span class="sd"> from_tp:</span>
-<span class="sd"> converts quantities from tp defaults from tprc.yaml.</span>
-<span class="sd"> interpolate:</span>
-<span class="sd"> shrinks to smallest data size and interpolates.</span>
 <span class="sd">&quot;&quot;&quot;</span>
 
+<span class="c1">#Functions</span>
+<span class="c1">#---------</span>
+<span class="c1">#</span>
+<span class="c1"># cumulate:</span>
+<span class="c1"># sorts and cumulates.</span>
+<span class="c1"># gaussian:</span>
+<span class="c1"># gaussian distribution of height 1.</span>
+<span class="c1"># lorentzian:</span>
+<span class="c1"># area conserved lorentzian distribution.</span>
+<span class="c1"># lifetime:</span>
+<span class="c1"># particle lifetime.</span>
+<span class="c1"># mfp:</span>
+<span class="c1"># particle mean free path.</span>
+<span class="c1"># fd_occupation:</span>
+<span class="c1"># fermion occupation.</span>
+<span class="c1"># be_occupation:</span>
+<span class="c1"># boson occupation.</span>
+<span class="c1"># dfdde:</span>
+<span class="c1"># derivative of the Fermi-Dirac distribution.</span>
+<span class="c1"># thermal_conductivity:</span>
+<span class="c1"># total thermal conductivity.</span>
+<span class="c1"># power_factor:</span>
+<span class="c1"># power factor.</span>
+<span class="c1"># zt:</span>
+<span class="c1"># ZT.</span>
+<span class="c1"># kl:</span>
+<span class="c1"># lattice thermal conductivity for target ZT.</span>
+<span class="c1">#</span>
+<span class="c1"># power_factor_fromdict:</span>
+<span class="c1"># adds power factor to dictionary.</span>
+<span class="c1"># zt_fromdict:</span>
+<span class="c1"># adds zt to dictionary.</span>
+<span class="c1"># kl_fromdict:</span>
+<span class="c1"># adds lattice thermal conductivity for target ZT to dictionary.</span>
+<span class="c1">#</span>
+<span class="c1"># to_tp:</span>
+<span class="c1"># converts quantities to tp defaults from tprc.yaml.</span>
+<span class="c1"># from_tp:</span>
+<span class="c1"># converts quantities from tp defaults from tprc.yaml.</span>
+<span class="c1"># interpolate:</span>
+<span class="c1"># shrinks to smallest data size and interpolates.</span>
+<span class="c1">#&quot;&quot;&quot;</span>
+
 <span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="kn">import</span> <span class="nn">tp</span>
 <span class="kn">from</span> <span class="nn">scipy.constants</span> <span class="kn">import</span> <span class="n">physical_constants</span>