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2 changes: 1 addition & 1 deletion 2.8.0-dev0/examples/analysis/hydrogen_bonds/hbonds.html

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2 changes: 1 addition & 1 deletion 2.8.0-dev0/examples/constructing_universe.html
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Expand Up @@ -717,7 +717,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
<li><p>NMP: residues 30-59 (blue)</p></li>
<li><p>LID: residues 122-159 (yellow)</p></li>
</ul>
<p><img alt="4adf27c13f3642c1afb1dc989f1dfb68" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
<p><img alt="813f3c045dab4abe852f234784e358fb" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[26]:
</pre></div>
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6 changes: 3 additions & 3 deletions 2.8.0-dev0/formats/auxiliary.html
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Expand Up @@ -263,7 +263,7 @@ <h2>Reading data directly<a class="headerlink" href="#reading-data-directly" tit
<span class="gp">In [3]: </span><span class="n">aux</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="n">XVG_BZ2</span><span class="p">)</span>

<span class="gp">In [4]: </span><span class="n">aux</span>
<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44aeb1960&gt;</span>
<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3dfc1120&gt;</span>
</pre></div>
</div>
<p>In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.</p>
Expand Down Expand Up @@ -462,7 +462,7 @@ <h2>Recreating auxiliaries<a class="headerlink" href="#recreating-auxiliaries" t
<span class="gp">In [30]: </span><span class="k">del</span> <span class="n">aux</span>

<span class="gp">In [31]: </span><span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="o">**</span><span class="n">description</span><span class="p">)</span>
<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44bfef0d0&gt;</span>
<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3f38bf10&gt;</span>
</pre></div>
</div>
<p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
Expand Down Expand Up @@ -577,7 +577,7 @@ <h2>Standalone Usage<a class="headerlink" href="#standalone-usage" title="Link t
<div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [45]: </span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>

<span class="gp">In [46]: </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Time&quot;</span><span class="p">],</span> <span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Temperature&quot;</span><span class="p">])</span>
<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fe44a69edd0&gt;]</span>
<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f9f3d955180&gt;]</span>

<span class="gp">In [47]: </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Temperature [K]&quot;</span><span class="p">)</span>
<span class="gh">Out[47]: </span><span class="go">Text(0, 0.5, &#39;Temperature [K]&#39;)</span>
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2 changes: 1 addition & 1 deletion 2.8.0-dev0/index.html
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Expand Up @@ -194,7 +194,7 @@
<section id="welcome-to-mdanalysis-user-guide-s-documentation">
<h1>Welcome to MDAnalysis User Guide’s documentation!<a class="headerlink" href="#welcome-to-mdanalysis-user-guide-s-documentation" title="Link to this heading"></a></h1>
<p><strong>MDAnalysis version:</strong> 2.8.0-dev0</p>
<p><strong>Last updated:</strong> Oct 11, 2024</p>
<p><strong>Last updated:</strong> Oct 13, 2024</p>
<p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is a Python
toolkit to analyse molecular dynamics files and trajectories in <a class="reference internal" href="formats/index.html#formats"><span class="std std-ref">many popular formats</span></a>. MDAnalysis can write
most of these formats, too, together with atom selections for use in <a class="reference internal" href="formats/selection_exporters.html#selection-exporters"><span class="std std-ref">visualisation tools or other analysis programs</span></a>.
Expand Down
24 changes: 12 additions & 12 deletions 2.8.0-dev0/reading_and_writing.html
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Expand Up @@ -322,27 +322,27 @@ <h4>Building trajectories in memory<a class="headerlink" href="#building-traject

<span class="gp">In [16]: </span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
<span class="gh">Out[16]: </span>
<span class="go">array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01],</span>
<span class="go"> [4.0881673e-01, 9.6393579e-01, 3.1211577e-02],</span>
<span class="go"> [3.5682514e-01, 3.8312599e-01, 2.8178158e-01],</span>
<span class="go">array([[0.5946307 , 0.18919976, 0.44233742],</span>
<span class="go"> [0.5949025 , 0.9947764 , 0.6217801 ],</span>
<span class="go"> [0.9149371 , 0.6625653 , 0.798835 ],</span>
<span class="go"> ...,</span>
<span class="go"> [8.6615133e-01, 3.7646204e-01, 1.2250387e-02],</span>
<span class="go"> [1.4942519e-01, 9.2269385e-01, 8.5091987e-04],</span>
<span class="go"> [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32)</span>
<span class="go"> [0.7360544 , 0.5006215 , 0.67056286],</span>
<span class="go"> [0.7761591 , 0.55651474, 0.64369595],</span>
<span class="go"> [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)</span>
</pre></div>
</div>
<p>or they can be directly passed in when creating a Universe.</p>
<div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [17]: </span><span class="n">universe2</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PDB</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="n">MemoryReader</span><span class="p">)</span>

<span class="gp">In [18]: </span><span class="n">universe2</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
<span class="gh">Out[18]: </span>
<span class="go">array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01],</span>
<span class="go"> [4.0881673e-01, 9.6393579e-01, 3.1211577e-02],</span>
<span class="go"> [3.5682514e-01, 3.8312599e-01, 2.8178158e-01],</span>
<span class="go">array([[0.5946307 , 0.18919976, 0.44233742],</span>
<span class="go"> [0.5949025 , 0.9947764 , 0.6217801 ],</span>
<span class="go"> [0.9149371 , 0.6625653 , 0.798835 ],</span>
<span class="go"> ...,</span>
<span class="go"> [8.6615133e-01, 3.7646204e-01, 1.2250387e-02],</span>
<span class="go"> [1.4942519e-01, 9.2269385e-01, 8.5091987e-04],</span>
<span class="go"> [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32)</span>
<span class="go"> [0.7360544 , 0.5006215 , 0.67056286],</span>
<span class="go"> [0.7761591 , 0.55651474, 0.64369595],</span>
<span class="go"> [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)</span>
</pre></div>
</div>
</section>
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2 changes: 1 addition & 1 deletion 2.8.0-dev0/searchindex.js

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88 changes: 44 additions & 44 deletions 2.8.0-dev0/standard_selections.html
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Expand Up @@ -334,10 +334,10 @@ <h3>Protein backbone<a class="headerlink" href="#protein-backbone" title="Link t
<p>Protein backbone atoms in MDAnalysis belong to a recognised protein residue and have the atom names:</p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>N</p></td>
<td><p>CA</p></td>
<tr class="row-odd"><td><p>CA</p></td>
<td><p>C</p></td>
<td><p>O</p></td>
<td><p>N</p></td>
</tr>
</tbody>
</table>
Expand All @@ -351,42 +351,42 @@ <h3>Protein backbone<a class="headerlink" href="#protein-backbone" title="Link t
<tbody>
<tr class="row-odd"><td><p>RU</p></td>
<td><p>RG3</p></td>
<td><p>GUA</p></td>
<td><p>RC5</p></td>
<td><p>RG</p></td>
<td><p>RA</p></td>
<td><p>THY</p></td>
<td><p>DA5</p></td>
<td><p>DC5</p></td>
<td><p>RC</p></td>
</tr>
<tr class="row-even"><td><p>DC3</p></td>
<td><p>ADE</p></td>
<td><p>A</p></td>
<td><p>DT3</p></td>
<td><p>DA</p></td>
<td><p>C</p></td>
<td><p>CYT</p></td>
<td><p>DG5</p></td>
<td><p>URA</p></td>
</tr>
<tr class="row-odd"><td><p>DC</p></td>
<td><p>CYT</p></td>
<tr class="row-even"><td><p>RA5</p></td>
<td><p>RC3</p></td>
<td><p>RA3</p></td>
<td><p>T</p></td>
<td><p>RG</p></td>
<td><p>RC</p></td>
<td><p>DA3</p></td>
<td><p>U</p></td>
</tr>
<tr class="row-even"><td><p>RG5</p></td>
<td><p>RU5</p></td>
<td><p>DG3</p></td>
<td><p>DT</p></td>
<td><p>DG</p></td>
<td><p>RC5</p></td>
<td><p>RA5</p></td>
<td><p>DT5</p></td>
<td><p>URA</p></td>
<td><p>DT</p></td>
<td><p>RG5</p></td>
</tr>
<tr class="row-odd"><td><p>G</p></td>
<tr class="row-odd"><td><p>DG3</p></td>
<td><p>DT3</p></td>
<td><p>RA3</p></td>
<td><p>DC3</p></td>
<td><p>RU3</p></td>
<td><p>DT5</p></td>
<td><p>A</p></td>
<td><p>DC</p></td>
</tr>
<tr class="row-even"><td><p>DA5</p></td>
<td><p>ADE</p></td>
<td><p>DA</p></td>
<td><p>G</p></td>
<td><p>U</p></td>
<td><p>GUA</p></td>
<td><p>T</p></td>
<td><p>RU5</p></td>
</tr>
<tr class="row-odd"><td><p>C</p></td>
<td><p>THY</p></td>
<td></td>
<td></td>
<td></td>
Expand All @@ -401,11 +401,11 @@ <h3>Nucleic backbone<a class="headerlink" href="#nucleic-backbone" title="Link t
<p>Nucleic backbone atoms in MDAnalysis belong to a recognised nucleic acid residue and have the atom names:</p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>O3</p></td>
<tr class="row-odd"><td><p>O5</p></td>
<td><p>C5’</p></td>
<td><p>C3’</p></td>
<td><p>P</p></td>
<td><p>O5</p></td>
<td><p>O3</p></td>
</tr>
</tbody>
</table>
Expand All @@ -415,23 +415,23 @@ <h3>Nucleic backbone<a class="headerlink" href="#nucleic-backbone" title="Link t
<p>Nucleobase atoms from nucleic acid residues are recognised based on their names in CHARMM.</p>
<table class="docutils align-default">
<tbody>
<tr class="row-odd"><td><p>N4</p></td>
<tr class="row-odd"><td><p>N1</p></td>
<td><p>O2</p></td>
<td><p>N9</p></td>
<td><p>N3</p></td>
<td><p>C8</p></td>
<td><p>N6</p></td>
<td><p>N7</p></td>
<td><p>N1</p></td>
<td><p>O2</p></td>
<td><p>C5</p></td>
</tr>
<tr class="row-even"><td><p>C6</p></td>
<td><p>N2</p></td>
<td><p>N6</p></td>
<td><p>O4</p></td>
<td><p>C4</p></td>
<td><p>O6</p></td>
<td><p>C2</p></td>
</tr>
<tr class="row-even"><td><p>N4</p></td>
<td><p>C8</p></td>
<td><p>O4</p></td>
<td><p>C5M</p></td>
<td><p>C6</p></td>
<td><p>C5</p></td>
<td><p>N3</p></td>
<td><p>C4</p></td>
</tr>
</tbody>
</table>
Expand All @@ -443,9 +443,9 @@ <h3>Nucleic sugars<a class="headerlink" href="#nucleic-sugars" title="Link to th
<tbody>
<tr class="row-odd"><td><p>O4’</p></td>
<td><p>C1’</p></td>
<td><p>C4’</p></td>
<td><p>C3’</p></td>
<td><p>C2’</p></td>
<td><p>C3’</p></td>
<td><p>C4’</p></td>
</tr>
</tbody>
</table>
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2 changes: 1 addition & 1 deletion dev/examples/analysis/hydrogen_bonds/hbonds.html

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2 changes: 1 addition & 1 deletion dev/examples/constructing_universe.html
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Expand Up @@ -717,7 +717,7 @@ <h2>Adding a new segment<a class="headerlink" href="#Adding-a-new-segment" title
<li><p>NMP: residues 30-59 (blue)</p></li>
<li><p>LID: residues 122-159 (yellow)</p></li>
</ul>
<p><img alt="4adf27c13f3642c1afb1dc989f1dfb68" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
<p><img alt="813f3c045dab4abe852f234784e358fb" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
<div class="nbinput docutils container">
<div class="prompt highlight-none notranslate"><div class="highlight"><pre><span></span>[26]:
</pre></div>
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6 changes: 3 additions & 3 deletions dev/formats/auxiliary.html
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Expand Up @@ -263,7 +263,7 @@ <h2>Reading data directly<a class="headerlink" href="#reading-data-directly" tit
<span class="gp">In [3]: </span><span class="n">aux</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="n">XVG_BZ2</span><span class="p">)</span>

<span class="gp">In [4]: </span><span class="n">aux</span>
<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44aeb1960&gt;</span>
<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3dfc1120&gt;</span>
</pre></div>
</div>
<p>In stand-alone use, an auxiliary reader allows you to iterate over each step in a set of auxiliary data.</p>
Expand Down Expand Up @@ -462,7 +462,7 @@ <h2>Recreating auxiliaries<a class="headerlink" href="#recreating-auxiliaries" t
<span class="gp">In [30]: </span><span class="k">del</span> <span class="n">aux</span>

<span class="gp">In [31]: </span><span class="n">mda</span><span class="o">.</span><span class="n">auxiliary</span><span class="o">.</span><span class="n">core</span><span class="o">.</span><span class="n">auxreader</span><span class="p">(</span><span class="o">**</span><span class="n">description</span><span class="p">)</span>
<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7fe44bfef0d0&gt;</span>
<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f9f3f38bf10&gt;</span>
</pre></div>
</div>
<p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
Expand Down Expand Up @@ -577,7 +577,7 @@ <h2>Standalone Usage<a class="headerlink" href="#standalone-usage" title="Link t
<div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [45]: </span><span class="kn">import</span> <span class="nn">matplotlib.pyplot</span> <span class="k">as</span> <span class="nn">plt</span>

<span class="gp">In [46]: </span><span class="n">plt</span><span class="o">.</span><span class="n">plot</span><span class="p">(</span><span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Time&quot;</span><span class="p">],</span> <span class="n">temp</span><span class="p">[</span><span class="s2">&quot;Temperature&quot;</span><span class="p">])</span>
<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7fe44a69edd0&gt;]</span>
<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f9f3d955180&gt;]</span>

<span class="gp">In [47]: </span><span class="n">plt</span><span class="o">.</span><span class="n">ylabel</span><span class="p">(</span><span class="s2">&quot;Temperature [K]&quot;</span><span class="p">)</span>
<span class="gh">Out[47]: </span><span class="go">Text(0, 0.5, &#39;Temperature [K]&#39;)</span>
Expand Down
2 changes: 1 addition & 1 deletion dev/index.html
Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,7 @@
<section id="welcome-to-mdanalysis-user-guide-s-documentation">
<h1>Welcome to MDAnalysis User Guide’s documentation!<a class="headerlink" href="#welcome-to-mdanalysis-user-guide-s-documentation" title="Link to this heading"></a></h1>
<p><strong>MDAnalysis version:</strong> 2.8.0-dev0</p>
<p><strong>Last updated:</strong> Oct 11, 2024</p>
<p><strong>Last updated:</strong> Oct 13, 2024</p>
<p><strong>MDAnalysis</strong> (<a class="reference external" href="https://www.mdanalysis.org">www.mdanalysis.org</a>) is a Python
toolkit to analyse molecular dynamics files and trajectories in <a class="reference internal" href="formats/index.html#formats"><span class="std std-ref">many popular formats</span></a>. MDAnalysis can write
most of these formats, too, together with atom selections for use in <a class="reference internal" href="formats/selection_exporters.html#selection-exporters"><span class="std std-ref">visualisation tools or other analysis programs</span></a>.
Expand Down
24 changes: 12 additions & 12 deletions dev/reading_and_writing.html
Original file line number Diff line number Diff line change
Expand Up @@ -322,27 +322,27 @@ <h4>Building trajectories in memory<a class="headerlink" href="#building-traject

<span class="gp">In [16]: </span><span class="n">universe</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
<span class="gh">Out[16]: </span>
<span class="go">array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01],</span>
<span class="go"> [4.0881673e-01, 9.6393579e-01, 3.1211577e-02],</span>
<span class="go"> [3.5682514e-01, 3.8312599e-01, 2.8178158e-01],</span>
<span class="go">array([[0.5946307 , 0.18919976, 0.44233742],</span>
<span class="go"> [0.5949025 , 0.9947764 , 0.6217801 ],</span>
<span class="go"> [0.9149371 , 0.6625653 , 0.798835 ],</span>
<span class="go"> ...,</span>
<span class="go"> [8.6615133e-01, 3.7646204e-01, 1.2250387e-02],</span>
<span class="go"> [1.4942519e-01, 9.2269385e-01, 8.5091987e-04],</span>
<span class="go"> [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32)</span>
<span class="go"> [0.7360544 , 0.5006215 , 0.67056286],</span>
<span class="go"> [0.7761591 , 0.55651474, 0.64369595],</span>
<span class="go"> [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)</span>
</pre></div>
</div>
<p>or they can be directly passed in when creating a Universe.</p>
<div class="highlight-ipython notranslate"><div class="highlight"><pre><span></span><span class="gp">In [17]: </span><span class="n">universe2</span> <span class="o">=</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="n">PDB</span><span class="p">,</span> <span class="n">coordinates</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="n">MemoryReader</span><span class="p">)</span>

<span class="gp">In [18]: </span><span class="n">universe2</span><span class="o">.</span><span class="n">atoms</span><span class="o">.</span><span class="n">positions</span>
<span class="gh">Out[18]: </span>
<span class="go">array([[9.1805226e-01, 7.9359460e-01, 1.5382159e-01],</span>
<span class="go"> [4.0881673e-01, 9.6393579e-01, 3.1211577e-02],</span>
<span class="go"> [3.5682514e-01, 3.8312599e-01, 2.8178158e-01],</span>
<span class="go">array([[0.5946307 , 0.18919976, 0.44233742],</span>
<span class="go"> [0.5949025 , 0.9947764 , 0.6217801 ],</span>
<span class="go"> [0.9149371 , 0.6625653 , 0.798835 ],</span>
<span class="go"> ...,</span>
<span class="go"> [8.6615133e-01, 3.7646204e-01, 1.2250387e-02],</span>
<span class="go"> [1.4942519e-01, 9.2269385e-01, 8.5091987e-04],</span>
<span class="go"> [1.4744800e-01, 2.0260128e-01, 2.9822797e-01]], dtype=float32)</span>
<span class="go"> [0.7360544 , 0.5006215 , 0.67056286],</span>
<span class="go"> [0.7761591 , 0.55651474, 0.64369595],</span>
<span class="go"> [0.45982844, 0.9889626 , 0.06811332]], dtype=float32)</span>
</pre></div>
</div>
</section>
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2 changes: 1 addition & 1 deletion dev/searchindex.js

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