MesoHOPS v1.2.1

1. Corrected a bug in flux filters used for stable hierarchy and stable state errors
2. Corrected a bug in error_flux_down
3. Update filters to provide a stiffer error bound by providing an exact calculation of the boundary auxiliary error
4. Introduced a HopsFluxFilter class to provide easier access to flux filters.
5. Introduce HopsMode class and updated HopsSystem and HopsHierarchy to provide easier indexing
6. Introduce a new method to compare auxiliaries with a string hash that provides a speed-up to managing connections between auxiliaries
7. Improved implementation of eom_hops_ksuper for faster execution

Author: digbennett

docs/build/html/dynamics.html

@@ -1329,7 +1329,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dl class="class">
 <dt id="dynamics.hops_eom.HopsEOM">
 <em class="property">class </em><code class="sig-name descname">HopsEOM</code><span class="sig-paren">(</span><em class="sig-param">eom_params</em><span class="sig-paren">)</span><a class="headerlink" href="#dynamics.hops_eom.HopsEOM" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">pyhops.util.dynamic_dict.Dict_wDefaults</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">mesohops.util.dynamic_dict.Dict_wDefaults</span></code></p>
 <p>HopsEOM is the class that defines the equation of motion for time evolving
 the hops trajectory. Its primary responsibility is to define the derivative
 of the system state. It also contains the parameters that determine what
@@ -1361,7 +1361,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dl class="class">
 <dt id="dynamics.hops_hierarchy.HopsHierarchy">
 <em class="property">class </em><code class="sig-name descname">HopsHierarchy</code><span class="sig-paren">(</span><em class="sig-param">hierarchy_param</em>, <em class="sig-param">system_param</em><span class="sig-paren">)</span><a class="headerlink" href="#dynamics.hops_hierarchy.HopsHierarchy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">pyhops.util.dynamic_dict.Dict_wDefaults</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">mesohops.util.dynamic_dict.Dict_wDefaults</span></code></p>
 <p>HopsHierarchy defines the representation of the hierarchy in the HOPS
 calculation. It contains the user parameters, helper functions, and
 the list of all nodes contained in the hierarchy.</p>
@@ -1580,7 +1580,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dl class="class">
 <dt id="dynamics.hops_noise.HopsNoise">
 <em class="property">class </em><code class="sig-name descname">HopsNoise</code><span class="sig-paren">(</span><em class="sig-param">noise_param</em>, <em class="sig-param">noise_corr</em><span class="sig-paren">)</span><a class="headerlink" href="#dynamics.hops_noise.HopsNoise" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">pyhops.util.dynamic_dict.Dict_wDefaults</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">mesohops.util.dynamic_dict.Dict_wDefaults</span></code></p>
 <p>This is the BaseClass for defining a hops noise trajectory. All noise classes
 will inherit from here. Anything that defines the input-output structure of a
 noise trajectory should be controlled from this class - rather than any of the
@@ -2281,7 +2281,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dl class="class">
 <dt id="dynamics.noise_fft.FFTFilterNoise">
 <em class="property">class </em><code class="sig-name descname">FFTFilterNoise</code><span class="sig-paren">(</span><em class="sig-param">noise_param</em>, <em class="sig-param">noise_corr</em><span class="sig-paren">)</span><a class="headerlink" href="#dynamics.noise_fft.FFTFilterNoise" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">pyhops.dynamics.hops_noise.HopsNoise</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">mesohops.dynamics.hops_noise.HopsNoise</span></code></p>
 <p>This is a class that describes the noise function for a calculation.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Attributes</dt>
@@ -2455,7 +2455,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 <dl class="class">
 <dt id="dynamics.noise_zero.ZeroNoise">
 <em class="property">class </em><code class="sig-name descname">ZeroNoise</code><span class="sig-paren">(</span><em class="sig-param">noise_param</em>, <em class="sig-param">noise_corr</em><span class="sig-paren">)</span><a class="headerlink" href="#dynamics.noise_zero.ZeroNoise" title="Permalink to this definition">¶</a></dt>
-<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">pyhops.dynamics.hops_noise.HopsNoise</span></code></p>
+<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">mesohops.dynamics.hops_noise.HopsNoise</span></code></p>
 <p>This is a class that describes the noise function for a calculation.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Attributes</dt>