rebuilt html docs for version 2.11.0-dev0 from branch develop with sphinx at 1e7644f

Author: github-actions

2.11.0-dev0/_modules/MDAnalysis/lib/util.html

@@ -344,7 +344,7 @@ <h1>Source code for MDAnalysis.lib.util</h1><div class="highlight"><pre>
 <span class="kn">import</span><span class="w"> </span><span class="nn">errno</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">functools</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">gzip</span>
-<span class="kn">import</span><span class="w"> </span><span class="nn">importlib</span>
+<span class="kn">import</span><span class="w"> </span><span class="nn">importlib.util</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">inspect</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">io</span>
 <span class="kn">import</span><span class="w"> </span><span class="nn">itertools</span>

2.11.0-dev0/documentation_pages/analysis/align.html

@@ -520,7 +520,7 @@ <h2><span class="section-number">4.3.1.3. </span>Functions and Classes<a class="
 </div>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -535,7 +535,7 @@ <h2><span class="section-number">4.3.1.3. </span>Functions and Classes<a class="
 </div>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p>
 </dd>
 </dl>
 </dd></dl>

2.11.0-dev0/documentation_pages/analysis/atomicdistances.html

@@ -280,7 +280,7 @@ <h2><span class="section-number">4.3.4.1. </span>Basic usage<a class="headerlink
 the trajectory.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p>
 </dd>
 </dl>
 </dd></dl>

2.11.0-dev0/documentation_pages/analysis/base.html

@@ -321,7 +321,7 @@ <h2><span class="section-number">4.3.8.2. </span>Analysis classes<a class="heade
 <dt class="sig sig-object py" id="MDAnalysis.analysis.bat.BAT.results.bat">
 <span class="sig-prename descclassname"><span class="pre">results.</span></span><span class="sig-name descname"><span class="pre">bat</span></span><a class="headerlink" href="#MDAnalysis.analysis.bat.BAT.results.bat" title="Link to this definition"></a></dt>
 <dd><p>Contains the time series of the Bond-Angle-Torsion coordinates as a
-(nframes, 3N) <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a> array. Each row corresponds to
+(nframes, 3N) <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a> array. Each row corresponds to
 a frame in the trajectory. In each column, the first six elements
 describe external degrees of freedom. The first three are the center
 of mass of the initial atom. The next three specify the  external angles
@@ -344,7 +344,7 @@ <h2><span class="section-number">4.3.8.2. </span>Analysis classes<a class="heade
 Cartesian coordinates after modifying a specific torsion angle.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>bat_frame</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><em>numpy.ndarray</em></a>) – an array with dimensions (3N,) with external then internal
+<dd class="field-odd"><p><strong>bat_frame</strong> (<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)"><em>numpy.ndarray</em></a>) – an array with dimensions (3N,) with external then internal
 degrees of freedom based on the root atoms, followed by the bond,
 angle, and (proper and improper) torsion coordinates.</p>
 </dd>
@@ -355,7 +355,7 @@ <h2><span class="section-number">4.3.8.2. </span>Analysis classes<a class="heade
 periodic boundary.</p>
 </dd>
 <dt class="field-odd">Return type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>

2.11.0-dev0/documentation_pages/analysis/bat.html

@@ -325,7 +325,7 @@ <h2><span class="section-number">4.3.2.2. </span>Functions<a class="headerlink"
 <dt class="sig sig-object py" id="MDAnalysis.analysis.contacts.hard_cut_q">
 <span class="sig-prename descclassname"><span class="pre">MDAnalysis.analysis.contacts.</span></span><span class="sig-name descname"><span class="pre">hard_cut_q</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">r</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cutoff</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../../_modules/MDAnalysis/analysis/contacts.html#hard_cut_q"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#MDAnalysis.analysis.contacts.hard_cut_q" title="Link to this definition"></a></dt>
 <dd><p>Calculate fraction of native contacts <em>Q</em> for a hard cut off.</p>
-<p>The cutoff can either be a float or a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> of the same
+<p>The cutoff can either be a float or a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">ndarray</span></code></a> of the same
 shape as <cite>r</cite>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
@@ -467,7 +467,7 @@ <h2><span class="section-number">4.3.2.3. </span>Classes<a class="headerlink" hr
 <dd><p>2D array containing <em>Q</em> for all refgroup pairs and analyzed frames</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -482,7 +482,7 @@ <h2><span class="section-number">4.3.2.3. </span>Classes<a class="headerlink" hr
 </div>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -542,7 +542,7 @@ <h2><span class="section-number">4.3.2.3. </span>Classes<a class="headerlink" hr
 <dd><p>List of distance arrays between reference groups.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.14)">list</a>[<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a>]</p>
+<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.14)">list</a>[<a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a>]</p>
 </dd>
 </dl>
 </dd></dl>

2.11.0-dev0/documentation_pages/analysis/contacts.html

@@ -626,7 +626,7 @@ <h2><span class="section-number">4.9.1.3. </span>Density object<a class="headerl
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>grid</strong> (<em>array_like</em>) – histogram or density, typically a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p></li>
+<li><p><strong>grid</strong> (<em>array_like</em>) – histogram or density, typically a <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)"><code class="xref py py-class docutils literal notranslate"><span class="pre">numpy.ndarray</span></code></a></p></li>
 <li><p><strong>edges</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.14)"><em>list</em></a>) – list of arrays, the lower and upper bin edges along the axes</p></li>
 <li><p><strong>parameters</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#dict" title="(in Python v3.14)"><em>dict</em></a>) – <p>dictionary of class parameters; saved with
 <a class="reference internal" href="#MDAnalysis.analysis.density.Density.save" title="MDAnalysis.analysis.density.Density.save"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Density.save()</span></code></a>. The following keys are meaningful to
@@ -671,7 +671,7 @@ <h2><span class="section-number">4.9.1.3. </span>Density object<a class="headerl
 <dt class="sig sig-object py" id="MDAnalysis.analysis.density.Density.edges">
 <span class="sig-name descname"><span class="pre">edges</span></span><a class="headerlink" href="#MDAnalysis.analysis.density.Density.edges" title="Link to this definition"></a></dt>
 <dd><p>The boundaries of each cell in <cite>grid</cite> along all axes (equivalent
-to what <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.histogramdd.html#numpy.histogramdd" title="(in NumPy v2.3)"><code class="xref py py-func docutils literal notranslate"><span class="pre">numpy.histogramdd()</span></code></a> returns).</p>
+to what <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.histogramdd.html#numpy.histogramdd" title="(in NumPy v2.4)"><code class="xref py py-func docutils literal notranslate"><span class="pre">numpy.histogramdd()</span></code></a> returns).</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
 <dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.14)">list</a> of 1d-arrays</p>
@@ -732,7 +732,7 @@ <h2><span class="section-number">4.9.1.3. </span>Density object<a class="headerl
 <p>If the input histogram consists of counts per cell then the
 <a class="reference internal" href="#MDAnalysis.analysis.density.Density.make_density" title="MDAnalysis.analysis.density.Density.make_density"><code class="xref py py-meth docutils literal notranslate"><span class="pre">Density.make_density()</span></code></a> method converts the grid to a physical density. For
 a probability density, divide it by <code class="xref py py-meth docutils literal notranslate"><span class="pre">Density.grid.sum()</span></code> or use <code class="docutils literal notranslate"><span class="pre">density=True</span></code>
-right away in <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.histogramdd.html#numpy.histogramdd" title="(in NumPy v2.3)"><code class="xref py py-func docutils literal notranslate"><span class="pre">histogramdd()</span></code></a>.</p>
+right away in <a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.histogramdd.html#numpy.histogramdd" title="(in NumPy v2.4)"><code class="xref py py-func docutils literal notranslate"><span class="pre">histogramdd()</span></code></a>.</p>
 <p>The user <em>should</em> set the <em>parameters</em> keyword (see docs for the
 constructor); in particular, if the data are already a density, one must
 set <code class="docutils literal notranslate"><span class="pre">isDensity=True</span></code> because there is no reliable way to detect if

2.11.0-dev0/documentation_pages/analysis/density.html

@@ -216,7 +216,7 @@
 <span class="math notranslate nohighlight">\(\langle \boldsymbol M \rangle\)</span> in <span class="math notranslate nohighlight">\(eÅ\)</span>.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -228,7 +228,7 @@
 <span class="math notranslate nohighlight">\(\langle \boldsymbol M^2 \rangle\)</span> in <span class="math notranslate nohighlight">\((eÅ)^2\)</span></p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>
@@ -252,7 +252,7 @@
 <dd><p>Directional dependant static dielectric constant</p>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a></p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a></p>
 </dd>
 </dl>
 </dd></dl>

2.11.0-dev0/documentation_pages/analysis/dielectric.html

@@ -355,7 +355,7 @@ <h2><span class="section-number">4.10.1.2. </span>Classes<a class="headerlink" h
 </div>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a>, (n_frames, n_frames)</p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a>, (n_frames, n_frames)</p>
 </dd>
 </dl>
 </dd></dl>
@@ -369,7 +369,7 @@ <h2><span class="section-number">4.10.1.2. </span>Classes<a class="headerlink" h
 </div>
 <dl class="field-list simple">
 <dt class="field-odd">Type<span class="colon">:</span></dt>
-<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.3)">numpy.ndarray</a>, (n_frames, n_frames)</p>
+<dd class="field-odd"><p><a class="reference external" href="https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html#numpy.ndarray" title="(in NumPy v2.4)">numpy.ndarray</a>, (n_frames, n_frames)</p>
 </dd>
 </dl>
 </dd></dl>