More renaming and update pgm pyi

docs/build/html/genindex.html

@@ -218,7 +218,7 @@ <h2 id="D">D</h2>
 </li>
       <li><a href="phylojunction.calculation.html#phylojunction.calculation.discrete_sse.DiscreteStateDependentRate">DiscreteStateDependentRate (class in phylojunction.calculation.discrete_sse)</a>
 </li>
-      <li><a href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistributionPGM">DistributionPGM (class in phylojunction.pgm.pgm)</a>
+      <li><a href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistrForSampling">DistrForSampling (class in phylojunction.pgm.pgm)</a>
 </li>
       <li><a href="phylojunction.interface.grammar.html#phylojunction.interface.grammar.dn_grammar.PJDnGrammar.dn_grammar_dict">dn_grammar_dict (phylojunction.interface.grammar.dn_grammar.PJDnGrammar attribute)</a>
 </li>
@@ -235,7 +235,7 @@ <h2 id="D">D</h2>
 </li>
         <li><a href="phylojunction.distribution.html#phylojunction.distribution.dn_parametric.DnUnif.DN_NAME">(phylojunction.distribution.dn_parametric.DnUnif attribute)</a>
 </li>
-        <li><a href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistributionPGM.DN_NAME">(phylojunction.pgm.pgm.DistributionPGM property)</a>
+        <li><a href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistrForSampling.DN_NAME">(phylojunction.pgm.pgm.DistrForSampling property)</a>
 </li>
       </ul></li>
   </ul></td>

docs/build/html/phylojunction.inference.revbayes.html

@@ -96,7 +96,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="py function">
 <dt class="sig sig-object py" id="phylojunction.inference.revbayes.rb_dn_parametric.get_rev_str_from_dn_parametric_obj">
-<code class="sig-prename descclassname"><span class="pre">phylojunction.inference.revbayes.rb_dn_parametric.</span></code><code class="sig-name descname"><span class="pre">get_rev_str_from_dn_parametric_obj</span></code><span class="sig-paren">(</span><em><span class="n"><span class="pre">dn_obj</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistributionPGM" title="phylojunction.pgm.pgm.DistributionPGM"><span class="pre">DistributionPGM</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#phylojunction.inference.revbayes.rb_dn_parametric.get_rev_str_from_dn_parametric_obj" title="Permalink to this definition"></a></dt>
+<code class="sig-prename descclassname"><span class="pre">phylojunction.inference.revbayes.rb_dn_parametric.</span></code><code class="sig-name descname"><span class="pre">get_rev_str_from_dn_parametric_obj</span></code><span class="sig-paren">(</span><em><span class="n"><span class="pre">dn_obj</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistrForSampling" title="phylojunction.pgm.pgm.DistrForSampling"><span class="pre">DistrForSampling</span></a></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><span class="pre">Tuple</span><span class="p"><span class="pre">[</span></span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">int</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></span><a class="headerlink" href="#phylojunction.inference.revbayes.rb_dn_parametric.get_rev_str_from_dn_parametric_obj" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
 <dl class="py function">

docs/build/html/phylojunction.interface.grammar.html

@@ -147,7 +147,7 @@ <h2>phylojunction.interface.grammar.det_fn_discrete_sse module<a class="headerli
 <dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
 <dl class="py method">
 <dt class="sig sig-object py" id="phylojunction.interface.grammar.dn_grammar.PJDnGrammar.create_dn_obj">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><code class="sig-name descname"><span class="pre">create_dn_obj</span></code><span class="sig-paren">(</span><em><span class="n"><span class="pre">dn_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em><span class="n"><span class="pre">dn_param_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.NodePGM" title="phylojunction.pgm.pgm.NodePGM"><span class="pre">NodePGM</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistributionPGM" title="phylojunction.pgm.pgm.DistributionPGM"><span class="pre">DistributionPGM</span></a></span></span><a class="headerlink" href="#phylojunction.interface.grammar.dn_grammar.PJDnGrammar.create_dn_obj" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><code class="sig-name descname"><span class="pre">create_dn_obj</span></code><span class="sig-paren">(</span><em><span class="n"><span class="pre">dn_id</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">str</span></span></em>, <em><span class="n"><span class="pre">dn_param_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.NodePGM" title="phylojunction.pgm.pgm.NodePGM"><span class="pre">NodePGM</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistrForSampling" title="phylojunction.pgm.pgm.DistrForSampling"><span class="pre">DistrForSampling</span></a></span></span><a class="headerlink" href="#phylojunction.interface.grammar.dn_grammar.PJDnGrammar.create_dn_obj" title="Permalink to this definition"></a></dt>
 <dd><p>Build and return sampling distribution object</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -161,10 +161,10 @@ <h2>phylojunction.interface.grammar.det_fn_discrete_sse module<a class="headerli
 </ul>
 </td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">a DistributionPGM instance</p>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">a DistrForSampling instance</p>
 </td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistributionPGM" title="phylojunction.pgm.pgm.DistributionPGM">DistributionPGM</a></p>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistrForSampling" title="phylojunction.pgm.pgm.DistrForSampling">DistrForSampling</a></p>
 </td>
 </tr>
 </tbody>
@@ -183,7 +183,7 @@ <h2>phylojunction.interface.grammar.det_fn_discrete_sse module<a class="headerli
 
 <dl class="py method">
 <dt class="sig sig-object py" id="phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_discrete_SSE_dn">
-<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><code class="sig-name descname"><span class="pre">init_return_discrete_SSE_dn</span></code><span class="sig-paren">(</span><em><span class="n"><span class="pre">dn_param_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.NodePGM" title="phylojunction.pgm.pgm.NodePGM"><span class="pre">NodePGM</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistributionPGM" title="phylojunction.pgm.pgm.DistributionPGM"><span class="pre">DistributionPGM</span></a></span></span><a class="headerlink" href="#phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_discrete_SSE_dn" title="Permalink to this definition"></a></dt>
+<em class="property"><span class="pre">classmethod</span><span class="w"> </span></em><code class="sig-name descname"><span class="pre">init_return_discrete_SSE_dn</span></code><span class="sig-paren">(</span><em><span class="n"><span class="pre">dn_param_dict</span></span><span class="p"><span class="pre">:</span></span><span class="w"> </span><span class="n"><span class="pre">Dict</span><span class="p"><span class="pre">[</span></span><span class="pre">str</span><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">List</span><span class="p"><span class="pre">[</span></span><span class="pre">Union</span><span class="p"><span class="pre">[</span></span><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.NodePGM" title="phylojunction.pgm.pgm.NodePGM"><span class="pre">NodePGM</span></a><span class="p"><span class="pre">,</span></span><span class="w"> </span><span class="pre">str</span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span><span class="p"><span class="pre">]</span></span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="phylojunction.pgm.html#phylojunction.pgm.pgm.DistrForSampling" title="phylojunction.pgm.pgm.DistrForSampling"><span class="pre">DistrForSampling</span></a></span></span><a class="headerlink" href="#phylojunction.interface.grammar.dn_grammar.PJDnGrammar.init_return_discrete_SSE_dn" title="Permalink to this definition"></a></dt>
 <dd></dd></dl>
 
 </dd></dl>