rebuilt html docs for version 2.7.0-dev0 from branch develop with sph…

…inx at a952cb2

2.7.0-dev0/examples/constructing_universe.html

@@ -714,7 +714,7 @@ <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="e307874f10bf41429d69e16dcfde505e" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="3ef25a3a874d4a73a0d0aed23af64562" 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>

2.7.0-dev0/formats/auxiliary.html

@@ -260,7 +260,7 @@ <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 0x7f2741424f10&gt;</span>
+<span class="gh">Out[4]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f8a640f5400&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>
@@ -459,7 +459,7 @@ <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 0x7f27419e7e80&gt;</span>
+<span class="gh">Out[31]: </span><span class="go">&lt;MDAnalysis.auxiliary.XVG.XVGReader at 0x7f8a64095400&gt;</span>
 </pre></div>
 </div>
 <p>The ‘description’ of any or all the auxiliaries added to a trajectory can be
@@ -574,7 +574,7 @@ <h2>Standalone Usage<a class="headerlink" href="#standalone-usage" title="Permal
 <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 0x7f2740ee5a60&gt;]</span>
+<span class="gh">Out[46]: </span><span class="go">[&lt;matplotlib.lines.Line2D at 0x7f8a57b01b50&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>

2.7.0-dev0/index.html

@@ -189,7 +189,7 @@
   <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="Permalink to this heading"></a></h1>
 <p><strong>MDAnalysis version:</strong> 2.7.0-dev0</p>
-<p><strong>Last updated:</strong> Oct 20, 2023</p>
+<p><strong>Last updated:</strong> Oct 24, 2023</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>.

2.7.0-dev0/reading_and_writing.html

@@ -319,27 +319,27 @@ <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([[0.32915223, 0.20233008, 0.4655804 ],</span>
-<span class="go">       [0.02002795, 0.9595799 , 0.80808395],</span>
-<span class="go">       [0.19633448, 0.31359127, 0.8440003 ],</span>
+<span class="go">array([[0.4083164 , 0.8115714 , 0.26231602],</span>
+<span class="go">       [0.18446821, 0.2620959 , 0.04221888],</span>
+<span class="go">       [0.8351606 , 0.71731776, 0.09411266],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.88739234, 0.66383445, 0.9289024 ],</span>
-<span class="go">       [0.6425766 , 0.46775514, 0.15041722],</span>
-<span class="go">       [0.26307994, 0.77353156, 0.8702842 ]], dtype=float32)</span>
+<span class="go">       [0.47769526, 0.73662394, 0.06738218],</span>
+<span class="go">       [0.7096048 , 0.3611204 , 0.22876543],</span>
+<span class="go">       [0.6337315 , 0.65759605, 0.7659119 ]], 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([[0.32915223, 0.20233008, 0.4655804 ],</span>
-<span class="go">       [0.02002795, 0.9595799 , 0.80808395],</span>
-<span class="go">       [0.19633448, 0.31359127, 0.8440003 ],</span>
+<span class="go">array([[0.4083164 , 0.8115714 , 0.26231602],</span>
+<span class="go">       [0.18446821, 0.2620959 , 0.04221888],</span>
+<span class="go">       [0.8351606 , 0.71731776, 0.09411266],</span>
 <span class="go">       ...,</span>
-<span class="go">       [0.88739234, 0.66383445, 0.9289024 ],</span>
-<span class="go">       [0.6425766 , 0.46775514, 0.15041722],</span>
-<span class="go">       [0.26307994, 0.77353156, 0.8702842 ]], dtype=float32)</span>
+<span class="go">       [0.47769526, 0.73662394, 0.06738218],</span>
+<span class="go">       [0.7096048 , 0.3611204 , 0.22876543],</span>
+<span class="go">       [0.6337315 , 0.65759605, 0.7659119 ]], dtype=float32)</span>
 </pre></div>
 </div>
 </section>

2.7.0-dev0/standard_selections.html

@@ -346,44 +346,44 @@ <h3>Protein backbone<a class="headerlink" href="#protein-backbone" title="Permal
 <p>The below names are drawn from largely from the CHARMM force field.</p>
 <table class="docutils align-default">
 <tbody>
-<tr class="row-odd"><td><p>RC</p></td>
-<td><p>A</p></td>
-<td><p>DC3</p></td>
-<td><p>GUA</p></td>
-<td><p>RU3</p></td>
-<td><p>CYT</p></td>
-<td><p>RA</p></td>
+<tr class="row-odd"><td><p>DA3</p></td>
+<td><p>DT3</p></td>
 <td><p>DT</p></td>
+<td><p>DG3</p></td>
+<td><p>RA5</p></td>
+<td><p>RG3</p></td>
+<td><p>DT5</p></td>
+<td><p>DC3</p></td>
 </tr>
-<tr class="row-even"><td><p>DT3</p></td>
-<td><p>THY</p></td>
+<tr class="row-even"><td><p>RU5</p></td>
 <td><p>G</p></td>
-<td><p>ADE</p></td>
-<td><p>DC</p></td>
-<td><p>DT5</p></td>
+<td><p>THY</p></td>
+<td><p>RA</p></td>
+<td><p>U</p></td>
 <td><p>RU</p></td>
-<td><p>DC5</p></td>
+<td><p>RC5</p></td>
+<td><p>ADE</p></td>
 </tr>
-<tr class="row-odd"><td><p>RG3</p></td>
-<td><p>DG3</p></td>
-<td><p>URA</p></td>
-<td><p>RA3</p></td>
-<td><p>RG</p></td>
-<td><p>RU5</p></td>
-<td><p>DA3</p></td>
+<tr class="row-odd"><td><p>RA3</p></td>
+<td><p>A</p></td>
+<td><p>RU3</p></td>
+<td><p>DA</p></td>
+<td><p>DC</p></td>
 <td><p>RC3</p></td>
-</tr>
-<tr class="row-even"><td><p>U</p></td>
-<td><p>RC5</p></td>
-<td><p>DG5</p></td>
+<td><p>URA</p></td>
 <td><p>DG</p></td>
-<td><p>RG5</p></td>
-<td><p>T</p></td>
+</tr>
+<tr class="row-even"><td><p>T</p></td>
 <td><p>C</p></td>
 <td><p>DA5</p></td>
+<td><p>DC5</p></td>
+<td><p>GUA</p></td>
+<td><p>DG5</p></td>
+<td><p>RG</p></td>
+<td><p>CYT</p></td>
 </tr>
-<tr class="row-odd"><td><p>DA</p></td>
-<td><p>RA5</p></td>
+<tr class="row-odd"><td><p>RC</p></td>
+<td><p>RG5</p></td>
 <td></td>
 <td></td>
 <td></td>
@@ -398,11 +398,11 @@ <h3>Nucleic backbone<a class="headerlink" href="#nucleic-backbone" title="Permal
 <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>C3’</p></td>
-<td><p>C5’</p></td>
-<td><p>O3’</p></td>
-<td><p>P</p></td>
+<tr class="row-odd"><td><p>O3’</p></td>
+<td><p>C3’</p></td>
 <td><p>O5’</p></td>
+<td><p>P</p></td>
+<td><p>C5’</p></td>
 </tr>
 </tbody>
 </table>
@@ -412,24 +412,24 @@ <h3>Nucleic backbone<a class="headerlink" href="#nucleic-backbone" title="Permal
 <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>N9</p></td>
-<td><p>O6</p></td>
-<td><p>O2</p></td>
+<tr class="row-odd"><td><p>C2</p></td>
 <td><p>C5</p></td>
-<td><p>N3</p></td>
-<td><p>C2</p></td>
-<td><p>C8</p></td>
-<td><p>C5M</p></td>
-</tr>
-<tr class="row-even"><td><p>C6</p></td>
+<td><p>O2</p></td>
+<td><p>N9</p></td>
 <td><p>N6</p></td>
-<td><p>O4</p></td>
-<td><p>N7</p></td>
-<td><p>C4</p></td>
+<td><p>O6</p></td>
 <td><p>N2</p></td>
-<td><p>N1</p></td>
 <td><p>N4</p></td>
 </tr>
+<tr class="row-even"><td><p>N1</p></td>
+<td><p>C6</p></td>
+<td><p>C4</p></td>
+<td><p>C8</p></td>
+<td><p>N7</p></td>
+<td><p>O4</p></td>
+<td><p>C5M</p></td>
+<td><p>N3</p></td>
+</tr>
 </tbody>
 </table>
 </section>
@@ -439,10 +439,10 @@ <h3>Nucleic sugars<a class="headerlink" href="#nucleic-sugars" title="Permalink
 <table class="docutils align-default">
 <tbody>
 <tr class="row-odd"><td><p>C3’</p></td>
-<td><p>C1’</p></td>
+<td><p>C2’</p></td>
 <td><p>O4’</p></td>
+<td><p>C1’</p></td>
 <td><p>C4’</p></td>
-<td><p>C2’</p></td>
 </tr>
 </tbody>
 </table>

2.7.0-dev0/testing.html

@@ -432,13 +432,13 @@ <h4>Testing exceptions and warnings<a class="headerlink" href="#testing-exceptio
 </section>
 <section id="failing-tests">
 <h4>Failing tests<a class="headerlink" href="#failing-tests" title="Permalink to this heading"></a></h4>
-<p>To mark an expected failure, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.xfail" title="(in pytest v0.1.dev131+gcdddd6d)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.xfail()</span></code></a> decorator:</p>
+<p>To mark an expected failure, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.xfail" title="(in pytest v0.1.dev109+g667b9fd)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.xfail()</span></code></a> decorator:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@pytest</span><span class="o">.</span><span class="n">mark</span><span class="o">.</span><span class="n">xfail</span>
 <span class="k">def</span> <span class="nf">tested_expected_failure</span><span class="p">():</span>
     <span class="k">assert</span> <span class="mi">1</span> <span class="o">==</span> <span class="mi">2</span>
 </pre></div>
 </div>
-<p>To manually fail a test, make a call to <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fail" title="(in pytest v0.1.dev131+gcdddd6d)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fail()</span></code></a>:</p>
+<p>To manually fail a test, make a call to <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fail" title="(in pytest v0.1.dev109+g667b9fd)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fail()</span></code></a>:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">test_open</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">tmpdir</span><span class="p">):</span>
     <span class="n">outfile</span> <span class="o">=</span> <span class="nb">str</span><span class="p">(</span><span class="n">tmpdir</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="s1">&#39;lammps-writer-test.dcd&#39;</span><span class="p">))</span>
     <span class="k">try</span><span class="p">:</span>
@@ -451,7 +451,7 @@ <h4>Failing tests<a class="headerlink" href="#failing-tests" title="Permalink to
 </section>
 <section id="skipping-tests">
 <h4>Skipping tests<a class="headerlink" href="#skipping-tests" title="Permalink to this heading"></a></h4>
-<p>To skip tests based on a condition, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.skipif" title="(in pytest v0.1.dev131+gcdddd6d)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.skipif(condition)</span></code></a> decorator:</p>
+<p>To skip tests based on a condition, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.mark.skipif" title="(in pytest v0.1.dev109+g667b9fd)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.mark.skipif(condition)</span></code></a> decorator:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>
 <span class="k">try</span><span class="p">:</span>
     <span class="kn">from</span> <span class="nn">numpy</span> <span class="kn">import</span> <span class="n">shares_memory</span>
@@ -466,7 +466,7 @@ <h4>Skipping tests<a class="headerlink" href="#skipping-tests" title="Permalink
     <span class="k">assert</span> <span class="ow">not</span> <span class="n">np</span><span class="o">.</span><span class="n">shares_memory</span><span class="p">(</span><span class="n">original</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">positions</span><span class="p">,</span> <span class="n">copy</span><span class="o">.</span><span class="n">ts</span><span class="o">.</span><span class="n">positions</span><span class="p">)</span>
 </pre></div>
 </div>
-<p>To skip a test if a module is not available for importing, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.importorskip" title="(in pytest v0.1.dev131+gcdddd6d)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.importorskip('module_name')</span></code></a></p>
+<p>To skip a test if a module is not available for importing, use <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.importorskip" title="(in pytest v0.1.dev109+g667b9fd)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.importorskip('module_name')</span></code></a></p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="k">def</span> <span class="nf">test_write_trajectory_netCDF4</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">universe</span><span class="p">,</span> <span class="n">outfile</span><span class="p">):</span>
     <span class="n">pytest</span><span class="o">.</span><span class="n">importorskip</span><span class="p">(</span><span class="s2">&quot;netCDF4&quot;</span><span class="p">)</span>
     <span class="k">return</span> <span class="bp">self</span><span class="o">.</span><span class="n">_test_write_trajectory</span><span class="p">(</span><span class="n">universe</span><span class="p">,</span> <span class="n">outfile</span><span class="p">)</span>
@@ -476,7 +476,7 @@ <h4>Skipping tests<a class="headerlink" href="#skipping-tests" title="Permalink
 </section>
 <section id="fixtures">
 <h3>Fixtures<a class="headerlink" href="#fixtures" title="Permalink to this heading"></a></h3>
-<p>Use <a class="reference external" href="https://docs.pytest.org/en/latest/fixture.html">fixtures</a> as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fixture" title="(in pytest v0.1.dev131+gcdddd6d)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fixture()</span></code></a> decorator, over a function that returns the object you need:</p>
+<p>Use <a class="reference external" href="https://docs.pytest.org/en/latest/fixture.html">fixtures</a> as much as possible to reuse “resources” between test methods/functions. Pytest fixtures are functions that run before each test function that uses that fixture. A fixture is typically set up with the <a class="reference external" href="https://docs.pytest.org/en/latest/reference/reference.html#pytest.fixture" title="(in pytest v0.1.dev109+g667b9fd)"><code class="xref py py-func docutils literal notranslate"><span class="pre">pytest.fixture()</span></code></a> decorator, over a function that returns the object you need:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="nd">@pytest</span><span class="o">.</span><span class="n">fixture</span>
 <span class="k">def</span> <span class="nf">universe</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
     <span class="k">return</span> <span class="n">mda</span><span class="o">.</span><span class="n">Universe</span><span class="p">(</span><span class="bp">self</span><span class="o">.</span><span class="n">ref_filename</span><span class="p">)</span>

dev/examples/constructing_universe.html

@@ -714,7 +714,7 @@ <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="e307874f10bf41429d69e16dcfde505e" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
+<p><img alt="3ef25a3a874d4a73a0d0aed23af64562" src="https://github.com/MDAnalysis/MDAnalysisTutorial/blob/master/doc/sphinx/figs/angle_defs.png?raw=true" /></p>
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