diff --git a/dist/kadmos-0.7.5-py2-none-any.whl b/dist/kadmos-0.7.5-py2-none-any.whl
deleted file mode 100644
index 8c1041f1b10835230a072841b98749ef974679ab..0000000000000000000000000000000000000000
Binary files a/dist/kadmos-0.7.5-py2-none-any.whl and /dev/null differ
diff --git a/dist/kadmos-0.7.5.tar.gz.REMOVED.git-id b/dist/kadmos-0.7.5.tar.gz.REMOVED.git-id
deleted file mode 100644
index 6f17cc52c95009295970a40aa31c7ee40d4db090..0000000000000000000000000000000000000000
--- a/dist/kadmos-0.7.5.tar.gz.REMOVED.git-id
+++ /dev/null
@@ -1 +0,0 @@
-f4a5fca5e2227152fb5f20756834785f44d96872
\ No newline at end of file
diff --git a/doc/.doctrees/KADMOS.doctree b/doc/.doctrees/KADMOS.doctree
index 6105ffae67e09e66489e5b51ea23c9580dfba2c4..6e6e585487db4508773862c451eb2739e2b10659 100644
Binary files a/doc/.doctrees/KADMOS.doctree and b/doc/.doctrees/KADMOS.doctree differ
diff --git a/doc/.doctrees/environment.pickle b/doc/.doctrees/environment.pickle
index 3935111c7626885fdebef17d60436d29a14bddca..cc0dbb03f6b04dbeff3aec78730487dc27f4d738 100644
Binary files a/doc/.doctrees/environment.pickle and b/doc/.doctrees/environment.pickle differ
diff --git a/doc/KADMOS.html b/doc/KADMOS.html
index 7402d5b8d6fe8295ccc93ad129aa3748a95fd2e8..eba02bdef00eb82cc9f677255b4eaddf60780e26 100644
--- a/doc/KADMOS.html
+++ b/doc/KADMOS.html
@@ -101,6 +101,47 @@
 </table>
 </dd></dl>
 
+<dl class="method">
+<dt id="kadmos.graph.graph_kadmos.KadmosGraph.add_edge">
+<code class="descname">add_edge</code><span class="sig-paren">(</span><em>u</em>, <em>v</em>, <em>**attr</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.add_edge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Add an edge between u and v.</p>
+<p>The nodes u and v will be automatically added if they are
+not already in the graph.</p>
+<p>Edge attributes can be specified with keywords or by directly
+accessing the edge’s attribute dictionary. See examples below.</p>
+<dl class="docutils">
+<dt>u, v <span class="classifier-delimiter">:</span> <span class="classifier">nodes</span></dt>
+<dd>Nodes can be, for example, strings or numbers.
+Nodes must be hashable (and not None) Python objects.</dd>
+<dt>attr <span class="classifier-delimiter">:</span> <span class="classifier">keyword arguments, optional</span></dt>
+<dd>Edge data (or labels or objects) can be assigned using
+keyword arguments.</dd>
+</dl>
+<p>add_edges_from : add a collection of edges</p>
+<p>Adding an edge that already exists updates the edge data.</p>
+<p>Many NetworkX algorithms designed for weighted graphs use
+an edge attribute (by default <cite>weight</cite>) to hold a numerical value.</p>
+<p>The following all add the edge e=(1, 2) to graph G:</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>   <span class="c1"># or DiGraph, MultiGraph, MultiDiGraph, etc</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">e</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>           <span class="c1"># explicit two-node form</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="o">*</span><span class="n">e</span><span class="p">)</span>             <span class="c1"># single edge as tuple of two nodes</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edges_from</span><span class="p">(</span> <span class="p">[(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span> <span class="p">)</span> <span class="c1"># add edges from iterable container</span>
+</pre></div>
+</div>
+<p>Associate data to edges using keywords:</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="mi">7</span><span class="p">,</span> <span class="n">capacity</span><span class="o">=</span><span class="mi">15</span><span class="p">,</span> <span class="n">length</span><span class="o">=</span><span class="mf">342.7</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>For non-string attribute keys, use subscript notation.</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="mi">0</span><span class="p">:</span> <span class="mi">5</span><span class="p">})</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="mi">0</span><span class="p">:</span> <span class="mi">5</span><span class="p">})</span>
+</pre></div>
+</div>
+</dd></dl>
+
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.add_edges_from">
 <code class="descname">add_edges_from</code><span class="sig-paren">(</span><em>ebunch</em>, <em>**attr</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.add_edges_from" title="Permalink to this definition">¶</a></dt>
@@ -154,7 +195,7 @@ attributes specified via keyword arguments.</p>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.add_equation_label">
-<code class="descname">add_equation_label</code><span class="sig-paren">(</span><em>edge</em>, <em>labeling_method='node_label'</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.add_equation_label" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_equation_label</code><span class="sig-paren">(</span><em>edge</em>, <em>label=None</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.add_equation_label" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to add an equation label to a edge that can (safely) be used as reference in an equation.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -162,7 +203,7 @@ attributes specified via keyword arguments.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>edge</strong> (<em>str</em>) – graph edge under consideration</li>
-<li><strong>labeling_method</strong> (<em>str</em>) – select method for automatic label string determination (node_id or node_label)</li>
+<li><strong>label</strong> (<em>str</em>) – label to be added (if not given it will be determined based on the node label or key)</li>
 <li><strong>language</strong> (<em>str</em>) – equation language used for the equation label</li>
 </ul>
 </td>
@@ -179,7 +220,7 @@ attributes specified via keyword arguments.</p>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.add_equation_labels">
-<code class="descname">add_equation_labels</code><span class="sig-paren">(</span><em>nodes</em>, <em>language='Python'</em>, <em>labeling_method='node_id'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.add_equation_labels" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_equation_labels</code><span class="sig-paren">(</span><em>nodes</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.add_equation_labels" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to add equation labels automatically to all input edges connected to the specified list of nodes</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -188,7 +229,6 @@ attributes specified via keyword arguments.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>nodes</strong> (<em>list</em>) – list of nodes</li>
 <li><strong>language</strong> (<em>str</em>) – equation language used for the equation label</li>
-<li><strong>labeling_method</strong> (<em>str</em>) – select method for automatic label string determination (node_id or node_label)</li>
 </ul>
 </td>
 </tr>
@@ -341,12 +381,6 @@ the graph.</dd>
 <dd><p>alias of <code class="xref py py-class docutils literal"><span class="pre">dict</span></code></p>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_kadmos.KadmosGraph.change_graph_class">
-<code class="descname">change_graph_class</code><span class="sig-paren">(</span><em>graph_class</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.change_graph_class" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to adjust the class of a graph.</p>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.check">
 <code class="descname">check</code><span class="sig-paren">(</span><em>raise_error=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.check" title="Permalink to this definition">¶</a></dt>
@@ -422,6 +456,24 @@ performed automatically when using the save method.</p>
 </table>
 </dd></dl>
 
+<dl class="method">
+<dt id="kadmos.graph.graph_kadmos.KadmosGraph.cleancopy">
+<code class="descname">cleancopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.cleancopy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to make a clean copy of a graph.</p>
+<p>This method can be used to avoid deep-copy problems in graph manipulation algorithms.
+The graph class is kept.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">clean-copy of the graph</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.clear">
 <code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.clear" title="Permalink to this definition">¶</a></dt>
@@ -502,22 +554,6 @@ of the original graph without actually copying any data.</dd>
 </div>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_kadmos.KadmosGraph.copy_as">
-<code class="descname">copy_as</code><span class="sig-paren">(</span><em>graph_class</em>, <em>as_view=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.copy_as" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to make a copy of a graph and make it into another KADMOS graph class.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">copy of the graph</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.copy_node_with_suffix">
 <code class="descname">copy_node_with_suffix</code><span class="sig-paren">(</span><em>node</em>, <em>suffix</em>, <em>label_extension</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.copy_node_with_suffix" title="Permalink to this definition">¶</a></dt>
@@ -562,7 +598,7 @@ of the original graph without actually copying any data.</dd>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.create_dsm">
-<code class="descname">create_dsm</code><span class="sig-paren">(</span><em>file_name</em>, <em>destination_folder=None</em>, <em>open_pdf=False</em>, <em>mpg=None</em>, <em>include_system_vars=True</em>, <em>summarize_vars=False</em>, <em>function_order=None</em>, <em>keep_tex_file=False</em>, <em>abbreviate_keywords=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.create_dsm" title="Permalink to this definition">¶</a></dt>
+<code class="descname">create_dsm</code><span class="sig-paren">(</span><em>file_name</em>, <em>destination_folder=None</em>, <em>open_pdf=False</em>, <em>mpg=None</em>, <em>include_system_vars=True</em>, <em>summarize_vars=False</em>, <em>function_order=None</em>, <em>keep_tex_file=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.create_dsm" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to create a (X)DSM PDF file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -570,14 +606,13 @@ of the original graph without actually copying any data.</dd>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>file_name</strong> (<em>str</em>) – name of the file to be saved</li>
-<li><strong>destination_folder</strong> (<em>str</em>) – destination folder for the file to be saved</li>
 <li><strong>open_pdf</strong> (<em>bool</em>) – option for opening the created file directly</li>
+<li><strong>destination_folder</strong> (<em>str</em>) – destination folder for the file to be saved</li>
 <li><strong>mpg</strong> (<a class="reference internal" href="#kadmos.graph.graph_process.MdaoProcessGraph" title="kadmos.graph.graph_process.MdaoProcessGraph"><em>MdaoProcessGraph</em></a>) – optional MPG graph to be saved with MDG as XDSM (if None a DSM is created)</li>
 <li><strong>include_system_vars</strong> (<em>bool</em>) – option for including system variables (only applicable for DSMs)</li>
 <li><strong>summarize_vars</strong> (<em>bool</em>) – option for summarizing label</li>
 <li><strong>function_order</strong> (<em>list</em>) – optional function order for the diagonal of the graph (only applicable for DSMs)</li>
 <li><strong>keep_tex_file</strong> (<em>bool</em>) – optional argument to keep the tex file of the PDF</li>
-<li><strong>abbreviate_keywords</strong> (<em>bool</em>) – optional argument to keep make keywords shorter (input -&gt; inp., output -&gt; outp.)</li>
 </ul>
 </td>
 </tr>
@@ -585,38 +620,6 @@ of the original graph without actually copying any data.</dd>
 </table>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_kadmos.KadmosGraph.deepcopy">
-<code class="descname">deepcopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.deepcopy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to make a deep copy of a graph.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">deepcopy of the graph</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_kadmos.KadmosGraph.deepcopy_as">
-<code class="descname">deepcopy_as</code><span class="sig-paren">(</span><em>graph_class</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.deepcopy_as" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to make a deep copy of a graph and make it into another KADMOS graph class.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">deepcopy of the graph</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="attribute">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.degree">
 <code class="descname">degree</code><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.degree" title="Permalink to this definition">¶</a></dt>
@@ -655,7 +658,7 @@ nd_iter : iterator</p>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.disconnect_problematic_variables_from">
-<code class="descname">disconnect_problematic_variables_from</code><span class="sig-paren">(</span><em>function</em>, <em>disconnect_collided_targets=True</em>, <em>disconnect_shared_sources=True</em>, <em>ignore_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.disconnect_problematic_variables_from" title="Permalink to this definition">¶</a></dt>
+<code class="descname">disconnect_problematic_variables_from</code><span class="sig-paren">(</span><em>function</em>, <em>disconnect_collided_targets=True</em>, <em>disconnect_shared_sources=True</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.disconnect_problematic_variables_from" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to automatically disconnect certain problematic variables with respect to a given function.</p>
 <p>If given as setting (disconnect_collided_targets=True) then the collided targets will be disconnected from this
 function. Also, if given as setting (disconnect_shared_sources=True), shared sources are also disconnected.</p>
@@ -666,8 +669,7 @@ function. Also, if given as setting (disconnect_shared_sources=True), shared sou
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>function</strong> (<em>basestring</em>) – function around which problematic variables are disconnected</li>
 <li><strong>disconnect_collided_targets</strong> (<em>bool</em>) – setting to disconnect collided targets</li>
-<li><strong>disconnect_shared_sources</strong> (<em>list</em>) – setting to disconnect shared sources</li>
-<li><strong>disconnect_shared_sources</strong> – setting to ignore certain nodes</li>
+<li><strong>disconnect_shared_sources</strong> (<em>bool</em>) – setting to disconnect shared sources</li>
 </ul>
 </td>
 </tr>
@@ -1357,30 +1359,6 @@ into an undirected graph.</p>
 </table>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_kadmos.KadmosGraph.get_same_graph_class">
-<code class="descname">get_same_graph_class</code><span class="sig-paren">(</span><em>graph</em>, <em>copy_type='deep'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.get_same_graph_class" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to reinstantiate a given graph according to the same graph class as the self.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>graph</strong> (<em>DiGraph</em>) – graph object to be reinstantiated</li>
-<li><strong>copy_type</strong> (<em>basestring</em>) – setting to have a deep or shallow copy of the graph</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">reinstantiated graph</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="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.get_sources">
 <code class="descname">get_sources</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.get_sources" title="Permalink to this definition">¶</a></dt>
@@ -1665,8 +1643,8 @@ attribute lookup as <cite>edges[u, v][‘foo’]</cite>.</dd>
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>args</strong> (<em>str</em>) – function (first arg) and then followed by modes to be contracted.</li>
-<li><strong>kwargs</strong> (<em>dict</em><em> or </em><em>str</em>) – new_label to specify new node label manually (optional)</li>
+<li><strong>args</strong> (<em>list</em>) – function (first arg) and then followed by modes to be contracted.</li>
+<li><strong>kwargs</strong> (<em>dict</em>) – new_label to specify new node label manually (optional)</li>
 </ul>
 </td>
 </tr>
@@ -2363,7 +2341,7 @@ remove_node of a function node might lead to unconnected variables in the graph.
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<em>str</em><em> or </em><em>list</em>) – function node id(s)</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<em>str</em>) – function node id(s)</td>
 </tr>
 </tbody>
 </table>
@@ -2431,7 +2409,7 @@ the original graph.</dd>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_kadmos.KadmosGraph.save">
-<code class="descname">save</code><span class="sig-paren">(</span><em>file_name</em>, <em>file_type='kdms'</em>, <em>graph_check_critical=True</em>, <em>destination_folder=None</em>, <em>mpg=None</em>, <em>description=''</em>, <em>creator=''</em>, <em>version='1.0'</em>, <em>timestamp=datetime.datetime(2017</em>, <em>12</em>, <em>21</em>, <em>12</em>, <em>29</em>, <em>13</em>, <em>797157)</em>, <em>keep_empty_elements=False</em>, <em>pretty_print=False</em>, <em>convention=True</em>, <em>integrity=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save</code><span class="sig-paren">(</span><em>file_name</em>, <em>file_type='kdms'</em>, <em>graph_check_critical=True</em>, <em>destination_folder=None</em>, <em>mpg=None</em>, <em>description=''</em>, <em>creator=''</em>, <em>version='1.0'</em>, <em>timestamp=datetime.datetime(2017</em>, <em>12</em>, <em>21</em>, <em>14</em>, <em>2</em>, <em>22</em>, <em>819074)</em>, <em>keep_empty_elements=False</em>, <em>pretty_print=False</em>, <em>convention=True</em>, <em>integrity=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_kadmos.KadmosGraph.save" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to save the graph.</p>
 <p>Different output file types are implemented for saving graphs. They are listed in the following.
 kdms: the most simple file type which makes use of pickling
@@ -2808,6 +2786,47 @@ architectures for the same problem in one VISTOMS instance.</p>
 </table>
 </dd></dl>
 
+<dl class="method">
+<dt id="kadmos.graph.graph_data.DataGraph.add_edge">
+<code class="descname">add_edge</code><span class="sig-paren">(</span><em>u</em>, <em>v</em>, <em>**attr</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.add_edge" title="Permalink to this definition">¶</a></dt>
+<dd><p>Add an edge between u and v.</p>
+<p>The nodes u and v will be automatically added if they are
+not already in the graph.</p>
+<p>Edge attributes can be specified with keywords or by directly
+accessing the edge’s attribute dictionary. See examples below.</p>
+<dl class="docutils">
+<dt>u, v <span class="classifier-delimiter">:</span> <span class="classifier">nodes</span></dt>
+<dd>Nodes can be, for example, strings or numbers.
+Nodes must be hashable (and not None) Python objects.</dd>
+<dt>attr <span class="classifier-delimiter">:</span> <span class="classifier">keyword arguments, optional</span></dt>
+<dd>Edge data (or labels or objects) can be assigned using
+keyword arguments.</dd>
+</dl>
+<p>add_edges_from : add a collection of edges</p>
+<p>Adding an edge that already exists updates the edge data.</p>
+<p>Many NetworkX algorithms designed for weighted graphs use
+an edge attribute (by default <cite>weight</cite>) to hold a numerical value.</p>
+<p>The following all add the edge e=(1, 2) to graph G:</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">G</span> <span class="o">=</span> <span class="n">nx</span><span class="o">.</span><span class="n">Graph</span><span class="p">()</span>   <span class="c1"># or DiGraph, MultiGraph, MultiDiGraph, etc</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">e</span> <span class="o">=</span> <span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>           <span class="c1"># explicit two-node form</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="o">*</span><span class="n">e</span><span class="p">)</span>             <span class="c1"># single edge as tuple of two nodes</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edges_from</span><span class="p">(</span> <span class="p">[(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)]</span> <span class="p">)</span> <span class="c1"># add edges from iterable container</span>
+</pre></div>
+</div>
+<p>Associate data to edges using keywords:</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="mi">3</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="n">weight</span><span class="o">=</span><span class="mi">7</span><span class="p">,</span> <span class="n">capacity</span><span class="o">=</span><span class="mi">15</span><span class="p">,</span> <span class="n">length</span><span class="o">=</span><span class="mf">342.7</span><span class="p">)</span>
+</pre></div>
+</div>
+<p>For non-string attribute keys, use subscript notation.</p>
+<div class="highlight-default"><div class="highlight"><pre><span></span><span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">add_edge</span><span class="p">(</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">)</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="p">[</span><span class="mi">1</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="mi">0</span><span class="p">:</span> <span class="mi">5</span><span class="p">})</span>
+<span class="gp">&gt;&gt;&gt; </span><span class="n">G</span><span class="o">.</span><span class="n">edges</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span> <span class="mi">2</span><span class="p">]</span><span class="o">.</span><span class="n">update</span><span class="p">({</span><span class="mi">0</span><span class="p">:</span> <span class="mi">5</span><span class="p">})</span>
+</pre></div>
+</div>
+</dd></dl>
+
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.add_edges_from">
 <code class="descname">add_edges_from</code><span class="sig-paren">(</span><em>ebunch</em>, <em>**attr</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.add_edges_from" title="Permalink to this definition">¶</a></dt>
@@ -2861,7 +2880,7 @@ attributes specified via keyword arguments.</p>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.add_equation_label">
-<code class="descname">add_equation_label</code><span class="sig-paren">(</span><em>edge</em>, <em>labeling_method='node_label'</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.add_equation_label" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_equation_label</code><span class="sig-paren">(</span><em>edge</em>, <em>label=None</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.add_equation_label" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to add an equation label to a edge that can (safely) be used as reference in an equation.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -2869,7 +2888,7 @@ attributes specified via keyword arguments.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>edge</strong> (<em>str</em>) – graph edge under consideration</li>
-<li><strong>labeling_method</strong> (<em>str</em>) – select method for automatic label string determination (node_id or node_label)</li>
+<li><strong>label</strong> (<em>str</em>) – label to be added (if not given it will be determined based on the node label or key)</li>
 <li><strong>language</strong> (<em>str</em>) – equation language used for the equation label</li>
 </ul>
 </td>
@@ -2886,7 +2905,7 @@ attributes specified via keyword arguments.</p>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.add_equation_labels">
-<code class="descname">add_equation_labels</code><span class="sig-paren">(</span><em>nodes</em>, <em>language='Python'</em>, <em>labeling_method='node_id'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.add_equation_labels" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_equation_labels</code><span class="sig-paren">(</span><em>nodes</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.add_equation_labels" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to add equation labels automatically to all input edges connected to the specified list of nodes</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -2895,7 +2914,6 @@ attributes specified via keyword arguments.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>nodes</strong> (<em>list</em>) – list of nodes</li>
 <li><strong>language</strong> (<em>str</em>) – equation language used for the equation label</li>
-<li><strong>labeling_method</strong> (<em>str</em>) – select method for automatic label string determination (node_id or node_label)</li>
 </ul>
 </td>
 </tr>
@@ -3048,12 +3066,6 @@ the graph.</dd>
 <dd><p>alias of <code class="xref py py-class docutils literal"><span class="pre">dict</span></code></p>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.change_graph_class">
-<code class="descname">change_graph_class</code><span class="sig-paren">(</span><em>graph_class</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.change_graph_class" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to adjust the class of a graph.</p>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.check">
 <code class="descname">check</code><span class="sig-paren">(</span><em>raise_error=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.check" title="Permalink to this definition">¶</a></dt>
@@ -3129,6 +3141,24 @@ performed automatically when using the save method.</p>
 </table>
 </dd></dl>
 
+<dl class="method">
+<dt id="kadmos.graph.graph_data.DataGraph.cleancopy">
+<code class="descname">cleancopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.cleancopy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to make a clean copy of a graph.</p>
+<p>This method can be used to avoid deep-copy problems in graph manipulation algorithms.
+The graph class is kept.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">clean-copy of the graph</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_data.DataGraph" title="kadmos.graph.graph_data.DataGraph">DataGraph</a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.clear">
 <code class="descname">clear</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.clear" title="Permalink to this definition">¶</a></dt>
@@ -3209,22 +3239,6 @@ of the original graph without actually copying any data.</dd>
 </div>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.copy_as">
-<code class="descname">copy_as</code><span class="sig-paren">(</span><em>graph_class</em>, <em>as_view=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.copy_as" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to make a copy of a graph and make it into another KADMOS graph class.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">copy of the graph</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.copy_node_with_suffix">
 <code class="descname">copy_node_with_suffix</code><span class="sig-paren">(</span><em>node</em>, <em>suffix</em>, <em>label_extension</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.copy_node_with_suffix" title="Permalink to this definition">¶</a></dt>
@@ -3269,7 +3283,7 @@ of the original graph without actually copying any data.</dd>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.create_dsm">
-<code class="descname">create_dsm</code><span class="sig-paren">(</span><em>file_name</em>, <em>destination_folder=None</em>, <em>open_pdf=False</em>, <em>mpg=None</em>, <em>include_system_vars=True</em>, <em>summarize_vars=False</em>, <em>function_order=None</em>, <em>keep_tex_file=False</em>, <em>abbreviate_keywords=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.create_dsm" title="Permalink to this definition">¶</a></dt>
+<code class="descname">create_dsm</code><span class="sig-paren">(</span><em>file_name</em>, <em>destination_folder=None</em>, <em>open_pdf=False</em>, <em>mpg=None</em>, <em>include_system_vars=True</em>, <em>summarize_vars=False</em>, <em>function_order=None</em>, <em>keep_tex_file=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.create_dsm" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to create a (X)DSM PDF file</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -3277,14 +3291,13 @@ of the original graph without actually copying any data.</dd>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>file_name</strong> (<em>str</em>) – name of the file to be saved</li>
-<li><strong>destination_folder</strong> (<em>str</em>) – destination folder for the file to be saved</li>
 <li><strong>open_pdf</strong> (<em>bool</em>) – option for opening the created file directly</li>
+<li><strong>destination_folder</strong> (<em>str</em>) – destination folder for the file to be saved</li>
 <li><strong>mpg</strong> (<a class="reference internal" href="#kadmos.graph.graph_process.MdaoProcessGraph" title="kadmos.graph.graph_process.MdaoProcessGraph"><em>MdaoProcessGraph</em></a>) – optional MPG graph to be saved with MDG as XDSM (if None a DSM is created)</li>
 <li><strong>include_system_vars</strong> (<em>bool</em>) – option for including system variables (only applicable for DSMs)</li>
 <li><strong>summarize_vars</strong> (<em>bool</em>) – option for summarizing label</li>
 <li><strong>function_order</strong> (<em>list</em>) – optional function order for the diagonal of the graph (only applicable for DSMs)</li>
 <li><strong>keep_tex_file</strong> (<em>bool</em>) – optional argument to keep the tex file of the PDF</li>
-<li><strong>abbreviate_keywords</strong> (<em>bool</em>) – optional argument to keep make keywords shorter (input -&gt; inp., output -&gt; outp.)</li>
 </ul>
 </td>
 </tr>
@@ -3292,38 +3305,6 @@ of the original graph without actually copying any data.</dd>
 </table>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.deepcopy">
-<code class="descname">deepcopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.deepcopy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to make a deep copy of a graph.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">deepcopy of the graph</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.deepcopy_as">
-<code class="descname">deepcopy_as</code><span class="sig-paren">(</span><em>graph_class</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.deepcopy_as" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to make a deep copy of a graph and make it into another KADMOS graph class.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">deepcopy of the graph</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="attribute">
 <dt id="kadmos.graph.graph_data.DataGraph.degree">
 <code class="descname">degree</code><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.degree" title="Permalink to this definition">¶</a></dt>
@@ -3362,7 +3343,7 @@ nd_iter : iterator</p>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.disconnect_problematic_variables_from">
-<code class="descname">disconnect_problematic_variables_from</code><span class="sig-paren">(</span><em>function</em>, <em>disconnect_collided_targets=True</em>, <em>disconnect_shared_sources=True</em>, <em>ignore_list=[]</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.disconnect_problematic_variables_from" title="Permalink to this definition">¶</a></dt>
+<code class="descname">disconnect_problematic_variables_from</code><span class="sig-paren">(</span><em>function</em>, <em>disconnect_collided_targets=True</em>, <em>disconnect_shared_sources=True</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.disconnect_problematic_variables_from" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to automatically disconnect certain problematic variables with respect to a given function.</p>
 <p>If given as setting (disconnect_collided_targets=True) then the collided targets will be disconnected from this
 function. Also, if given as setting (disconnect_shared_sources=True), shared sources are also disconnected.</p>
@@ -3373,8 +3354,7 @@ function. Also, if given as setting (disconnect_shared_sources=True), shared sou
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>function</strong> (<em>basestring</em>) – function around which problematic variables are disconnected</li>
 <li><strong>disconnect_collided_targets</strong> (<em>bool</em>) – setting to disconnect collided targets</li>
-<li><strong>disconnect_shared_sources</strong> (<em>list</em>) – setting to disconnect shared sources</li>
-<li><strong>disconnect_shared_sources</strong> – setting to ignore certain nodes</li>
+<li><strong>disconnect_shared_sources</strong> (<em>bool</em>) – setting to disconnect shared sources</li>
 </ul>
 </td>
 </tr>
@@ -3677,30 +3657,6 @@ the graph connections still being represented.</p>
 </table>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.get_coupling_matrix">
-<code class="descname">get_coupling_matrix</code><span class="sig-paren">(</span><em>function_order_method='manual'</em>, <em>node_selection=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.get_coupling_matrix" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to determine the role of the different functions in the FPG.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>function_order_method</strong> (<em>basestring</em>) – algorithm to be used for the order in which the functions are executed.</li>
-<li><strong>node_selection</strong> (<em>list</em>) – selection of nodes for which the coupling matrix will be calculated only</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">graph with enriched function node attributes and function problem role dictionary</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="#kadmos.graph.graph_data.FundamentalProblemGraph" title="kadmos.graph.graph_data.FundamentalProblemGraph">FundamentalProblemGraph</a></p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.get_direct_coupling_nodes">
 <code class="descname">get_direct_coupling_nodes</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.get_direct_coupling_nodes" title="Permalink to this definition">¶</a></dt>
@@ -3777,22 +3733,6 @@ But it is safe to assign attributes <cite>G[u][v][‘foo’]</cite></p>
 </div>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.get_feedback_info">
-<code class="descname">get_feedback_info</code><span class="sig-paren">(</span><em>function_order</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.get_feedback_info" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to determine the number of feedback loops for a given function order</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>function_order</strong> (<em>list</em>) – function order of the nodes</td>
-</tr>
-</tbody>
-</table>
-<p>:return number of feedback loops
-:rtype int</p>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.get_function_graph">
 <code class="descname">get_function_graph</code><span class="sig-paren">(</span><em>keep_objective_variables=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.get_function_graph" title="Permalink to this definition">¶</a></dt>
@@ -4104,51 +4044,6 @@ into an undirected graph.</p>
 </table>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.get_possible_function_order">
-<code class="descname">get_possible_function_order</code><span class="sig-paren">(</span><em>method</em>, <em>multi_start=None</em>, <em>check_graph=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.get_possible_function_order" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to find a possible function order, in the order: pre-coupled, coupled, post-coupled functions</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>method</strong> (<em>str</em>) – algorithm which will be used to minimize the feedback loops</li>
-<li><strong>multi_start</strong> (<em>int</em>) – start the algorithm from multiple starting points</li>
-<li><strong>check_graph</strong> (<em>bool</em>) – check whether graph has problematic variables</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-<p>:return Possible function order
-:rtype list</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.get_same_graph_class">
-<code class="descname">get_same_graph_class</code><span class="sig-paren">(</span><em>graph</em>, <em>copy_type='deep'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.get_same_graph_class" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to reinstantiate a given graph according to the same graph class as the self.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>graph</strong> (<em>DiGraph</em>) – graph object to be reinstantiated</li>
-<li><strong>copy_type</strong> (<em>basestring</em>) – setting to have a deep or shallow copy of the graph</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">reinstantiated graph</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="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.get_sources">
 <code class="descname">get_sources</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.get_sources" title="Permalink to this definition">¶</a></dt>
@@ -4425,171 +4320,58 @@ attribute lookup as <cite>edges[u, v][‘foo’]</cite>.</dd>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.mark_as_constraint">
-<code class="descname">mark_as_constraint</code><span class="sig-paren">(</span><em>node</em>, <em>operator</em>, <em>reference_value</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.mark_as_constraint" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to mark a node as a constraint.</p>
+<dt id="kadmos.graph.graph_data.DataGraph.merge_function_modes">
+<code class="descname">merge_function_modes</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.merge_function_modes" title="Permalink to this definition">¶</a></dt>
+<dd><p>Function to contract certain modes of the same function.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>node</strong> – node to be marked (on the left side of the operator</li>
-<li><strong>operator</strong> (<em>str</em>) – constraint operator</li>
-<li><strong>reference_value</strong> (<em>numbers.Number</em>) – value on the right side of the operator</li>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>args</strong> (<em>list</em>) – function (first arg) and then followed by modes to be contracted.</li>
+<li><strong>kwargs</strong> (<em>dict</em>) – new_label to specify new node label manually (optional)</li>
 </ul>
 </td>
 </tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">contracted graph</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="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></p>
+</td>
+</tr>
 </tbody>
 </table>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.mark_as_constraints">
-<code class="descname">mark_as_constraints</code><span class="sig-paren">(</span><em>nodes</em>, <em>operators</em>, <em>reference_values</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.mark_as_constraints" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to mark multiple nodes as constraints.</p>
+<dt id="kadmos.graph.graph_data.DataGraph.merge_function_nodes_based_on_modes">
+<code class="descname">merge_function_nodes_based_on_modes</code><span class="sig-paren">(</span><em>merge_funcs=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.merge_function_nodes_based_on_modes" title="Permalink to this definition">¶</a></dt>
+<dd><p>This class method merges all execution modes of the same function into a single node.</p>
+<p>Mainly used for illustration purposes since information on the execution modes gets lost.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>nodes</strong> – list of nodes to be marked.</li>
-<li><strong>operators</strong> – operators to be implemented (as list per node or as single operator for all)</li>
-<li><strong>reference_values</strong> – reference values to be used (as list of values per node or as single value for all)</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">graph with enriched constraint nodes</p>
-</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>merge_funcs</strong> – List of tuple of functions to merge. If empty (default), all functions are merged.</td>
 </tr>
 </tbody>
 </table>
+<p>Functions must be present in graph.
+:type merge_funcs: list, tuple
+:return: merged graph</p>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.mark_as_design_variable">
-<code class="descname">mark_as_design_variable</code><span class="sig-paren">(</span><em>node</em>, <em>lower_bound=None</em>, <em>upper_bound=None</em>, <em>samples=None</em>, <em>nominal_value=0.0</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.mark_as_design_variable" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to mark a single node as a design variable and add the required metadata for its definition.</p>
+<dt id="kadmos.graph.graph_data.DataGraph.merge_parallel_functions">
+<code class="descname">merge_parallel_functions</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.merge_parallel_functions" title="Permalink to this definition">¶</a></dt>
+<dd><p>Function to merge a list of functions</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>node</strong> – </li>
-<li><strong>lower_bound</strong> – </li>
-<li><strong>upper_bound</strong> – </li>
-<li><strong>samples</strong> – </li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last"></p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.mark_as_design_variables">
-<code class="descname">mark_as_design_variables</code><span class="sig-paren">(</span><em>nodes</em>, <em>lower_bounds=None</em>, <em>upper_bounds=None</em>, <em>samples=None</em>, <em>nominal_values=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.mark_as_design_variables" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to mark a list of nodes as design variable and add metadata.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>nodes</strong> (<em>list</em><em> or </em><em>str</em>) – list of nodes present in the graph</li>
-<li><strong>lower_bounds</strong> (<em>list</em><em> or </em><em>numbers.Number</em>) – list of lower bound values</li>
-<li><strong>upper_bounds</strong> (<em>list</em><em> or </em><em>numbers.Number</em>) – list of upper bounds</li>
-<li><strong>samples</strong> (<em>list</em>) – nested list of kadmos values</li>
-<li><strong>nominal_values</strong> (<em>list</em><em> or </em><em>numbers.Number</em>) – list of nominal values</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.mark_as_objective">
-<code class="descname">mark_as_objective</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.mark_as_objective" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to mark a single node as objective.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>node</strong> (<em>basestring</em>) – variable node</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.mark_as_qois">
-<code class="descname">mark_as_qois</code><span class="sig-paren">(</span><em>nodes</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.mark_as_qois" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to mark a list of nodes as quantity of interest.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>nodes</strong> (<em>list</em>) – list of nodes present in the graph</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.merge_function_modes">
-<code class="descname">merge_function_modes</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.merge_function_modes" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to contract certain modes of the same function.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>args</strong> (<em>str</em>) – function (first arg) and then followed by modes to be contracted.</li>
-<li><strong>kwargs</strong> (<em>dict</em><em> or </em><em>str</em>) – new_label to specify new node label manually (optional)</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">contracted graph</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="#kadmos.graph.graph_kadmos.KadmosGraph" title="kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph</a></p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.merge_function_nodes_based_on_modes">
-<code class="descname">merge_function_nodes_based_on_modes</code><span class="sig-paren">(</span><em>merge_funcs=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.merge_function_nodes_based_on_modes" title="Permalink to this definition">¶</a></dt>
-<dd><p>This class method merges all execution modes of the same function into a single node.</p>
-<p>Mainly used for illustration purposes since information on the execution modes gets lost.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>merge_funcs</strong> – List of tuple of functions to merge. If empty (default), all functions are merged.</td>
-</tr>
-</tbody>
-</table>
-<p>Functions must be present in graph.
-:type merge_funcs: list, tuple
-:return: merged graph</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.merge_parallel_functions">
-<code class="descname">merge_parallel_functions</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.merge_parallel_functions" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to merge a list of functions</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>args</strong> (<em>node_ids</em>) – functions to be merged</li>
-<li><strong>kwargs</strong> (<em>dict</em>) – new_label to specify new node label manually (optional)</li>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>args</strong> (<em>node_ids</em>) – functions to be merged</li>
+<li><strong>kwargs</strong> (<em>dict</em>) – new_label to specify new node label manually (optional)</li>
 </ul>
 </td>
 </tr>
@@ -4617,27 +4399,6 @@ function.</p>
 </table>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.minimize_feedback">
-<code class="descname">minimize_feedback</code><span class="sig-paren">(</span><em>nodes</em>, <em>method</em>, <em>multi_start=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.minimize_feedback" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to find the function order with minimum feedback</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>nodes</strong> (<em>list</em>) – nodes for which the feedback needs to be minimized</li>
-<li><strong>method</strong> (<em>str</em>) – algorithm used to find optimal function order</li>
-<li><strong>multi_start</strong> (<em>int</em>) – start the algorithm from multiple starting points</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-<p>:return function order
-:rtype list</p>
-</dd></dl>
-
 <dl class="attribute">
 <dt id="kadmos.graph.graph_data.DataGraph.name">
 <code class="descname">name</code><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.name" title="Permalink to this definition">¶</a></dt>
@@ -5265,7 +5026,7 @@ remove_node of a function node might lead to unconnected variables in the graph.
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<em>str</em><em> or </em><em>list</em>) – function node id(s)</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>args</strong> (<em>str</em>) – function node id(s)</td>
 </tr>
 </tbody>
 </table>
@@ -5333,7 +5094,7 @@ the original graph.</dd>
 
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.save">
-<code class="descname">save</code><span class="sig-paren">(</span><em>file_name</em>, <em>file_type='kdms'</em>, <em>graph_check_critical=True</em>, <em>destination_folder=None</em>, <em>mpg=None</em>, <em>description=''</em>, <em>creator=''</em>, <em>version='1.0'</em>, <em>timestamp=datetime.datetime(2017</em>, <em>12</em>, <em>21</em>, <em>12</em>, <em>29</em>, <em>13</em>, <em>797157)</em>, <em>keep_empty_elements=False</em>, <em>pretty_print=False</em>, <em>convention=True</em>, <em>integrity=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.save" title="Permalink to this definition">¶</a></dt>
+<code class="descname">save</code><span class="sig-paren">(</span><em>file_name</em>, <em>file_type='kdms'</em>, <em>graph_check_critical=True</em>, <em>destination_folder=None</em>, <em>mpg=None</em>, <em>description=''</em>, <em>creator=''</em>, <em>version='1.0'</em>, <em>timestamp=datetime.datetime(2017</em>, <em>12</em>, <em>21</em>, <em>14</em>, <em>2</em>, <em>22</em>, <em>819074)</em>, <em>keep_empty_elements=False</em>, <em>pretty_print=False</em>, <em>convention=True</em>, <em>integrity=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.save" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to save the graph.</p>
 <p>Different output file types are implemented for saving graphs. They are listed in the following.
 kdms: the most simple file type which makes use of pickling
@@ -5416,22 +5177,6 @@ as a weight. If None, then each edge has weight 1.</dd>
 </div>
 </dd></dl>
 
-<dl class="method">
-<dt id="kadmos.graph.graph_data.DataGraph.sort_non_coupled_nodes">
-<code class="descname">sort_non_coupled_nodes</code><span class="sig-paren">(</span><em>nodes</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.sort_non_coupled_nodes" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to sort the pre and post coupling nodes</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>nodes</strong> (<em>list</em>) – nodes that need to be sorted</td>
-</tr>
-</tbody>
-</table>
-<p>:return nodes in sorted order
-:rtype list</p>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.graph.graph_data.DataGraph.split_variables">
 <code class="descname">split_variables</code><span class="sig-paren">(</span><em>*args</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.DataGraph.split_variables" title="Permalink to this definition">¶</a></dt>
@@ -5695,32 +5440,18 @@ architectures for the same problem in one VISTOMS instance.</p>
 <dt id="kadmos.graph.graph_data.RepositoryConnectivityGraph">
 <em class="property">class </em><code class="descclassname">kadmos.graph.graph_data.</code><code class="descname">RepositoryConnectivityGraph</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.RepositoryConnectivityGraph" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="method">
-<dt id="kadmos.graph.graph_data.RepositoryConnectivityGraph.create_mathematical_problem">
-<code class="descname">create_mathematical_problem</code><span class="sig-paren">(</span><em>n_disciplines</em>, <em>coupling_strength</em>, <em>n_global_var=None</em>, <em>n_local_var=None</em>, <em>n_coupling_var=None</em>, <em>n_global_constraints=None</em>, <em>B=None</em>, <em>C=None</em>, <em>D=None</em>, <em>H=None</em>, <em>I=None</em>, <em>J=None</em>, <em>s=None</em>, <em>write_problem_to_textfile=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.RepositoryConnectivityGraph.create_mathematical_problem" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to get a mathematical problem according to the variable complexity problem as described in:
-Zhang D., Song B., Wang P. and He Y. ‘Performance Evaluation of MDO Architectures within a Variable
-Complexity Problem’, Mathematical Problems in Engineering, 2017.</p>
+<dt id="kadmos.graph.graph_data.RepositoryConnectivityGraph.cleancopy">
+<code class="descname">cleancopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.RepositoryConnectivityGraph.cleancopy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to make a clean copy of a graph.</p>
+<p>This method can be used to avoid deep-copy problems in graph manipulation algorithms.
+The graph class is kept.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>n_disciplines</strong> – Number of disciplines</li>
-<li><strong>coupling_strength</strong> – percentage of couplings, 0 no couplings, 1 all possible couplings</li>
-<li><strong>n_global_var</strong> – Number of global design variables</li>
-<li><strong>n_local_var</strong> – Number of local design variables for each discipline</li>
-<li><strong>n_coupling_var</strong> – Number of output variables for each discipline</li>
-<li><strong>n_global_constraints</strong> – Number of global constraints</li>
-<li><strong>B</strong> – relation between the coupling variables</li>
-<li><strong>C</strong> – relation between the global design variables and coupling variables</li>
-<li><strong>D</strong> – relation between the local design variables and coupling variables</li>
-<li><strong>H</strong> – relation between the global design variables and global constraints</li>
-<li><strong>I</strong> – relation between the local design variables and global constraints</li>
-<li><strong>J</strong> – relation between the coupling variables and global constraints</li>
-<li><strong>s</strong> – positive scalars to be used for the global constraints</li>
-<li><strong>write_problem_to_textfile</strong> – option to write generated problem to a textfile</li>
-</ul>
-</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">clean-copy of the graph</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_data.RepositoryConnectivityGraph" title="kadmos.graph.graph_data.RepositoryConnectivityGraph">RepositoryConnectivityGraph</a></td>
 </tr>
 </tbody>
 </table>
@@ -5899,6 +5630,24 @@ sort_by must be one of [“couplings”, “system_inputs”, “edges”, “no
 </table>
 </dd></dl>
 
+<dl class="method">
+<dt id="kadmos.graph.graph_data.FundamentalProblemGraph.cleancopy">
+<code class="descname">cleancopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.cleancopy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to make a clean copy of a graph.</p>
+<p>This method can be used to avoid deep-copy problems in graph manipulation algorithms.
+The graph class is kept.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">clean-copy of the graph</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_data.FundamentalProblemGraph" title="kadmos.graph.graph_data.FundamentalProblemGraph">FundamentalProblemGraph</a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 <dl class="method">
 <dt id="kadmos.graph.graph_data.FundamentalProblemGraph.create_mdg">
 <code class="descname">create_mdg</code><span class="sig-paren">(</span><em>mg_function_ordering</em>, <em>name='MDG'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.create_mdg" title="Permalink to this definition">¶</a></dt>
@@ -5947,6 +5696,24 @@ sort_by must be one of [“couplings”, “system_inputs”, “edges”, “no
 </table>
 </dd></dl>
 
+<dl class="method">
+<dt id="kadmos.graph.graph_data.FundamentalProblemGraph.get_coupling_matrix">
+<code class="descname">get_coupling_matrix</code><span class="sig-paren">(</span><em>function_order_method='manual'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.get_coupling_matrix" title="Permalink to this definition">¶</a></dt>
+<dd><p>Function to determine the role of the different functions in the FPG.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>function_order_method</strong> (<em>basestring</em>) – algorithm to be used for the order in which the functions are executed.</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">graph with enriched function node attributes and function problem role dictionary</td>
+</tr>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_data.FundamentalProblemGraph" title="kadmos.graph.graph_data.FundamentalProblemGraph">FundamentalProblemGraph</a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 <dl class="method">
 <dt id="kadmos.graph.graph_data.FundamentalProblemGraph.get_mdg">
 <code class="descname">get_mdg</code><span class="sig-paren">(</span><em>name='MDG'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.get_mdg" title="Permalink to this definition">¶</a></dt>
@@ -6007,6 +5774,74 @@ have to be divided in  two parts: the first part does not use the design variabl
 </table>
 </dd></dl>
 
+<dl class="method">
+<dt id="kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_constraint">
+<code class="descname">mark_as_constraint</code><span class="sig-paren">(</span><em>nodes</em>, <em>lower_bounds=None</em>, <em>upper_bounds=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_constraint" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to mark a list of nodes as constraint.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>nodes</strong> (<em>list</em>) – list of nodes present in the graph</li>
+<li><strong>lower_bounds</strong> (<em>list</em>) – list of lower bound values</li>
+<li><strong>upper_bounds</strong> (<em>list</em>) – list of upper bound values</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_design_variable">
+<code class="descname">mark_as_design_variable</code><span class="sig-paren">(</span><em>nodes</em>, <em>lower_bounds=None</em>, <em>nominal_values=None</em>, <em>upper_bounds=None</em>, <em>samples=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_design_variable" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to mark a list of nodes as design variable and add metadata.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>nodes</strong> (<em>list</em>) – list of nodes present in the graph</li>
+<li><strong>lower_bounds</strong> (<em>list</em>) – list of lower bound values</li>
+<li><strong>nominal_values</strong> (<em>list</em>) – list of nominal values</li>
+<li><strong>upper_bounds</strong> (<em>list</em>) – list of upper bounds</li>
+<li><strong>samples</strong> (<em>list</em>) – nested list of kadmos values</li>
+</ul>
+</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_objective">
+<code class="descname">mark_as_objective</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_objective" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to mark a single node as objective.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>node</strong> (<em>basestring</em>) – variable node</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+<dl class="method">
+<dt id="kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_qoi">
+<code class="descname">mark_as_qoi</code><span class="sig-paren">(</span><em>nodes</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_qoi" title="Permalink to this definition">¶</a></dt>
+<dd><p>Function to mark a list of nodes as quantity of interest.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>nodes</strong> (<em>list</em>) – list of nodes present in the graph</td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
 </dd></dl>
 
 </div>
@@ -6015,7 +5850,25 @@ have to be divided in  two parts: the first part does not use the design variabl
 <dl class="class">
 <dt id="kadmos.graph.graph_process.ProcessGraph">
 <em class="property">class </em><code class="descclassname">kadmos.graph.graph_process.</code><code class="descname">ProcessGraph</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.ProcessGraph" title="Permalink to this definition">¶</a></dt>
-<dd></dd></dl>
+<dd><dl class="method">
+<dt id="kadmos.graph.graph_process.ProcessGraph.cleancopy">
+<code class="descname">cleancopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.ProcessGraph.cleancopy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to make a clean copy of a graph.</p>
+<p>This method can be used to avoid deep-copy problems in graph manipulation algorithms.
+The graph class is kept.</p>
+<table class="docutils field-list" frame="void" rules="none">
+<col class="field-name" />
+<col class="field-body" />
+<tbody valign="top">
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">clean-copy of the graph</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_process.ProcessGraph" title="kadmos.graph.graph_process.ProcessGraph">ProcessGraph</a></td>
+</tr>
+</tbody>
+</table>
+</dd></dl>
+
+</dd></dl>
 
 </div>
 <div class="section" id="mdaoprocessgraph">
@@ -6024,20 +5877,20 @@ have to be divided in  two parts: the first part does not use the design variabl
 <dt id="kadmos.graph.graph_process.MdaoProcessGraph">
 <em class="property">class </em><code class="descclassname">kadmos.graph.graph_process.</code><code class="descname">MdaoProcessGraph</code><span class="sig-paren">(</span><em>*args</em>, <em>**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph" title="Permalink to this definition">¶</a></dt>
 <dd><dl class="method">
-<dt id="kadmos.graph.graph_process.MdaoProcessGraph.add_process">
-<code class="descname">add_process</code><span class="sig-paren">(</span><em>sequence</em>, <em>start_step</em>, <em>mdg</em>, <em>end_in_iterative_node=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.add_process" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to add a process to a list of functions.</p>
-<p>The sequence is assumed to be the order of the functions in the input list. The sequence is considered simple,
-since it is not analyzed for the possibility to run functions in parallel.</p>
+<dt id="kadmos.graph.graph_process.MdaoProcessGraph.add_parallel_process">
+<code class="descname">add_parallel_process</code><span class="sig-paren">(</span><em>start_nodes</em>, <em>parallel_functions</em>, <em>start_step</em>, <em>end_node=None</em>, <em>end_in_converger=False</em>, <em>use_data_graph=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.add_parallel_process" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to add a process to run multiple functions in parallel from a single start node.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>sequence</strong> (<em>list</em>) – list of functions in the required sequence</li>
-<li><strong>start_step</strong> (<em>int</em>) – process step number for the first element in the sequence</li>
-<li><strong>mdg</strong> (<em>MdaoDataGraph</em>) – data graph to be used for execution dependencies</li>
-<li><strong>end_in_iterative_node</strong> (<em>basestring</em>) – (optional) iterative node to which the last function should go</li>
+<li><strong>start_nodes</strong> (<em>basestring</em><em> or </em><em>list</em>) – node or list of nodes from which all the functions are executed in parallel</li>
+<li><strong>parallel_functions</strong> (<em>list</em>) – list of function to be run in parallel from the start node</li>
+<li><strong>start_step</strong> (<em>int</em>) – process step number of the start_node</li>
+<li><strong>end_node</strong> (<em>basestring</em>) – (optional) node to which all the parallel functions go after execution</li>
+<li><strong>end_in_converger</strong> (<em>bool</em>) – (optional) indicate whether the end node finishes a convergence loop</li>
+<li><strong>use_data_graph</strong> (<em>MdaoDataGraph</em><em> or </em><em>None</em>) – (optional) use data graph to assess whether nodes are actually coupled</li>
 </ul>
 </td>
 </tr>
@@ -6046,17 +5899,19 @@ since it is not analyzed for the possibility to run functions in parallel.</p>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_process.MdaoProcessGraph.connect_nested_iterators">
-<code class="descname">connect_nested_iterators</code><span class="sig-paren">(</span><em>master</em>, <em>slave</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.connect_nested_iterators" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to connect a slave iterator to a master iterator in a nested configuration.</p>
-<p>An example is if a converger inside an optimizer in MDF needs to be linked back.</p>
+<dt id="kadmos.graph.graph_process.MdaoProcessGraph.add_simple_sequential_process">
+<code class="descname">add_simple_sequential_process</code><span class="sig-paren">(</span><em>functions</em>, <em>start_step</em>, <em>end_in_iterative_node=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.add_simple_sequential_process" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to add a simple sequential process to a list of functions.</p>
+<p>The sequence is assumed to be the order of the functions in the input list. The sequence is considered simple,
+since it is not analyzed for the possibility to run functions in parallel.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>master</strong> (<em>basestring</em>) – upper iterator node in the nested configuration</li>
-<li><strong>slave</strong> (<em>basestring</em>) – lower iterator node in the nested configuration</li>
+<li><strong>functions</strong> (<em>list</em>) – list of functions in the required sequence</li>
+<li><strong>start_step</strong> – </li>
+<li><strong>end_in_iterative_node</strong> (<em>basestring</em>) – (optional) iterative node to which the last function should go</li>
 </ul>
 </td>
 </tr>
@@ -6065,68 +5920,71 @@ since it is not analyzed for the possibility to run functions in parallel.</p>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_process.MdaoProcessGraph.get_lowest_psn">
-<code class="descname">get_lowest_psn</code><span class="sig-paren">(</span><em>cycle</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.get_lowest_psn" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to retrieve the lowest process step number (PSN) of a list of nodes in a cycle.</p>
+<dt id="kadmos.graph.graph_process.MdaoProcessGraph.cleancopy">
+<code class="descname">cleancopy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.cleancopy" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to make a clean copy of a graph.</p>
+<p>This method can be used to avoid deep-copy problems in graph manipulation algorithms.
+The graph class is kept.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>cycle</strong> (<em>list</em>) – list with nodes on a cycle</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">clean-copy of the graph</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">the minimal PSN and the index of the first element having this PSN</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">tuple</td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body"><a class="reference internal" href="#kadmos.graph.graph_process.MdaoProcessGraph" title="kadmos.graph.graph_process.MdaoProcessGraph">MdaoProcessGraph</a></td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_process.MdaoProcessGraph.get_node_text">
-<code class="descname">get_node_text</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.get_node_text" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to determine the text of a function node (for use in a XDSM diagram).</p>
+<dt id="kadmos.graph.graph_process.MdaoProcessGraph.connect_nested_iterators">
+<code class="descname">connect_nested_iterators</code><span class="sig-paren">(</span><em>master</em>, <em>slave</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.connect_nested_iterators" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to connect a slave iterator to a master iterator in a nested configuration.</p>
+<p>An example is if a converger inside an optimizer in MDF needs to be linked back.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>node</strong> (<em>basestring</em>) – node</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">node text for in the XDSM function box</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">basestring</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
+<li><strong>master</strong> (<em>basestring</em>) – upper iterator node in the nested configuration</li>
+<li><strong>slave</strong> (<em>basestring</em>) – lower iterator node in the nested configuration</li>
+</ul>
+</td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_process.MdaoProcessGraph.get_ordered_cycles">
-<code class="descname">get_ordered_cycles</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.get_ordered_cycles" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get the cycles of a process graph ordered according to process step number.</p>
+<dt id="kadmos.graph.graph_process.MdaoProcessGraph.get_nested_process_ordering">
+<code class="descname">get_nested_process_ordering</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.get_nested_process_ordering" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to determine the nesting of iterative elements in the process graph.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">list with the cycles of a graph ordered based on PSN</td>
+<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">tuple with iterative_nodes, process_info dictionary, and nested_functions list</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">list</td>
+<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">tuple</td>
 </tr>
 </tbody>
 </table>
 </dd></dl>
 
 <dl class="method">
-<dt id="kadmos.graph.graph_process.MdaoProcessGraph.get_process_hierarchy">
-<code class="descname">get_process_hierarchy</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.get_process_hierarchy" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to assess the hierarchy of the process based on the process lines in a ProcessGraph.</p>
+<dt id="kadmos.graph.graph_process.MdaoProcessGraph.get_node_text">
+<code class="descname">get_node_text</code><span class="sig-paren">(</span><em>node</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.graph_process.MdaoProcessGraph.get_node_text" title="Permalink to this definition">¶</a></dt>
+<dd><p>Method to determine the text of a function node (for use in a XDSM diagram).</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">nested list with process hierarchy, e.g. [COOR, A, [OPT, [CONV, D1, D2], F1, G1, G2]]</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>node</strong> (<em>basestring</em>) – node</td>
+</tr>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">node text for in the XDSM function box</td>
 </tr>
-<tr class="field-even field"><th class="field-name">Return type:</th><td class="field-body">list</td>
+<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">basestring</td>
 </tr>
 </tbody>
 </table>
@@ -6226,7 +6084,7 @@ since it is not analyzed for the possibility to run functions in parallel.</p>
 
 <dl class="method">
 <dt id="kadmos.graph.mixin_equation.EquationMixin.add_equation_label">
-<code class="descname">add_equation_label</code><span class="sig-paren">(</span><em>edge</em>, <em>labeling_method='node_label'</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.mixin_equation.EquationMixin.add_equation_label" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_equation_label</code><span class="sig-paren">(</span><em>edge</em>, <em>label=None</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.mixin_equation.EquationMixin.add_equation_label" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to add an equation label to a edge that can (safely) be used as reference in an equation.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -6234,7 +6092,7 @@ since it is not analyzed for the possibility to run functions in parallel.</p>
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>edge</strong> (<em>str</em>) – graph edge under consideration</li>
-<li><strong>labeling_method</strong> (<em>str</em>) – select method for automatic label string determination (node_id or node_label)</li>
+<li><strong>label</strong> (<em>str</em>) – label to be added (if not given it will be determined based on the node label or key)</li>
 <li><strong>language</strong> (<em>str</em>) – equation language used for the equation label</li>
 </ul>
 </td>
@@ -6251,7 +6109,7 @@ since it is not analyzed for the possibility to run functions in parallel.</p>
 
 <dl class="method">
 <dt id="kadmos.graph.mixin_equation.EquationMixin.add_equation_labels">
-<code class="descname">add_equation_labels</code><span class="sig-paren">(</span><em>nodes</em>, <em>language='Python'</em>, <em>labeling_method='node_id'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.mixin_equation.EquationMixin.add_equation_labels" title="Permalink to this definition">¶</a></dt>
+<code class="descname">add_equation_labels</code><span class="sig-paren">(</span><em>nodes</em>, <em>language='Python'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.mixin_equation.EquationMixin.add_equation_labels" title="Permalink to this definition">¶</a></dt>
 <dd><p>Method to add equation labels automatically to all input edges connected to the specified list of nodes</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -6260,7 +6118,6 @@ since it is not analyzed for the possibility to run functions in parallel.</p>
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
 <li><strong>nodes</strong> (<em>list</em>) – list of nodes</li>
 <li><strong>language</strong> (<em>str</em>) – equation language used for the equation label</li>
-<li><strong>labeling_method</strong> (<em>str</em>) – select method for automatic label string determination (node_id or node_label)</li>
 </ul>
 </td>
 </tr>
@@ -6273,63 +6130,6 @@ since it is not analyzed for the possibility to run functions in parallel.</p>
 </div>
 <div class="section" id="vistomsmixin">
 <h3>VistomsMixin<a class="headerlink" href="#vistomsmixin" title="Permalink to this headline">¶</a></h3>
-<dl class="class">
-<dt id="kadmos.graph.mixin_vistoms.VistomsMixin">
-<em class="property">class </em><code class="descclassname">kadmos.graph.mixin_vistoms.</code><code class="descname">VistomsMixin</code><a class="headerlink" href="#kadmos.graph.mixin_vistoms.VistomsMixin" title="Permalink to this definition">¶</a></dt>
-<dd><dl class="method">
-<dt id="kadmos.graph.mixin_vistoms.VistomsMixin.vistoms_add">
-<code class="descname">vistoms_add</code><span class="sig-paren">(</span><em>vistoms_dir</em>, <em>mpg=None</em>, <em>function_order=None</em>, <em>reference_file=None</em>, <em>compress=False</em>, <em>remove_after_compress=True</em>, <em>graph_id=None</em>, <em>replacement_id=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.mixin_vistoms.VistomsMixin.vistoms_add" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to add a graph to a existing VISTOMS instance.</p>
-<p>In one VISTOMS instance different graphs can be shown. For example it is possible to include different
-architectures for the same problem in one VISTOMS instance.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>vistoms_dir</strong> (<em>str</em>) – directory of the VISTOMS directory to be used for addition</li>
-<li><strong>mpg</strong> (<a class="reference internal" href="#kadmos.graph.graph_process.MdaoProcessGraph" title="kadmos.graph.graph_process.MdaoProcessGraph"><em>MdaoProcessGraph</em></a>) – optional MPG graph to be saved with MDG as XDSM (if None a DSM is created)</li>
-<li><strong>function_order</strong> (<em>list</em>) – optional function order for the diagonal of the graph (only applicable for DSMs)</li>
-<li><strong>reference_file</strong> (<em>str</em>) – file from which reference values are extracted (either full path or file in same folder)</li>
-<li><strong>compress</strong> (<em>bool</em>) – setting whether to compress the final VISTOMS instance folder to a zip file</li>
-<li><strong>remove_after_compress</strong> (<em>bool</em>) – setting whether to remove the original folder after compression</li>
-<li><strong>replacement_id</strong> (<em>basestr</em>) – indentifier of the graph to be replaced</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.graph.mixin_vistoms.VistomsMixin.vistoms_create">
-<code class="descname">vistoms_create</code><span class="sig-paren">(</span><em>vistoms_dir</em>, <em>vistoms_version=None</em>, <em>mpg=None</em>, <em>function_order=None</em>, <em>reference_file=None</em>, <em>compress=False</em>, <em>remove_after_compress=True</em>, <em>graph_id=None</em>, <em>use_png_figs=False</em>, <em>file_refs=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.graph.mixin_vistoms.VistomsMixin.vistoms_create" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to create a new VISTOMS instance from a graph.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first last simple">
-<li><strong>vistoms_dir</strong> (<em>str</em>) – directory of the VISTOMS directory to be created</li>
-<li><strong>vistoms_version</strong> – version of the VISTOMS instance to be used (as stored in the package itself)</li>
-<li><strong>vispack_version</strong> – str</li>
-<li><strong>mpg</strong> (<a class="reference internal" href="#kadmos.graph.graph_process.MdaoProcessGraph" title="kadmos.graph.graph_process.MdaoProcessGraph"><em>MdaoProcessGraph</em></a>) – optional MPG graph to be saved with MDG as XDSM (if None a DSM is created)</li>
-<li><strong>function_order</strong> (<em>list</em>) – optional function order for the diagonal of the graph (only applicable for DSMs)</li>
-<li><strong>reference_file</strong> (<em>str</em>) – file from which reference values are extracted (either full path or file in same folder)</li>
-<li><strong>compress</strong> (<em>bool</em>) – setting whether to compress the final VISTOMS instance folder to a zip file</li>
-<li><strong>remove_after_compress</strong> (<em>bool</em>) – setting whether to remove the original folder after compression</li>
-<li><strong>graph_id</strong> (<em>basestring</em>) – identifier of the new graph</li>
-<li><strong>use_png_figs</strong> (<em>bool</em>) – setting whether to use the PNG figures instead of the SVG figures for local execution</li>
-<li><strong>file_refs</strong> (<em>dict</em>) – setting to provide file references manually (to use VISTOMS on a server)</li>
-</ul>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-</dd></dl>
-
 </div>
 </div>
 <div class="section" id="cmdows">
@@ -6339,48 +6139,6 @@ architectures for the same problem in one VISTOMS instance.</p>
 <dt id="kadmos.cmdows.cmdows.CMDOWS">
 <em class="property">class </em><code class="descclassname">kadmos.cmdows.cmdows.</code><code class="descname">CMDOWS</code><span class="sig-paren">(</span><em>file_path=None</em>, <em>element=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class for with various methods for checking and manipulating CMDOWS files</p>
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.add_actor">
-<code class="descname">add_actor</code><span class="sig-paren">(</span><em>contact_uid</em>, <em>role</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.add_actor" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to add a role element to the organization branch.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.add_contact">
-<code class="descname">add_contact</code><span class="sig-paren">(</span><em>name</em>, <em>email</em>, <em>uid</em>, <em>company=None</em>, <em>department=None</em>, <em>function=None</em>, <em>address=None</em>, <em>telephone=None</em>, <em>country=None</em>, <em>roles=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.add_contact" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to add a contact element to the organization branch.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.add_dc_general_info">
-<code class="descname">add_dc_general_info</code><span class="sig-paren">(</span><em>dc_uid</em>, <em>description</em>, <em>status=None</em>, <em>creation_date=None</em>, <em>owner_uid=None</em>, <em>creator_uid=None</em>, <em>operator_uid=None</em>, <em>model_definition=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.add_dc_general_info" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to add a general info element to a dc branch.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.add_dc_performance_info">
-<code class="descname">add_dc_performance_info</code><span class="sig-paren">(</span><em>dc_uid</em>, <em>precision=None</em>, <em>fidelity_level=None</em>, <em>run_time=None</em>, <em>verification=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.add_dc_performance_info" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to add a performance info element to a DC branch.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.add_dc_remote_component_info">
-<code class="descname">add_dc_remote_component_info</code><span class="sig-paren">(</span><em>dc_uid</em>, <em>single_or_multi_execution</em>, <em>job_name</em>, <em>remote_engineer</em>, <em>notification_message</em>, <em>data_exchange_dict=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.add_dc_remote_component_info" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to add a remote execution info element to a dc branch.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.add_dc_verification">
-<code class="descname">add_dc_verification</code><span class="sig-paren">(</span><em>dc_uid</em>, <em>method</em>, <em>verifier</em>, <em>result</em>, <em>date</em>, <em>version</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.add_dc_verification" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to add a verification to a DC</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.assert_element_tag">
-<code class="descname">assert_element_tag</code><span class="sig-paren">(</span><em>el</em>, <em>expected_tag</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.assert_element_tag" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to assert that the tag of an element is as expected.</p>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.cmdows.cmdows.CMDOWS.check">
 <code class="descname">check</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.check" title="Permalink to this definition">¶</a></dt>
@@ -6402,145 +6160,7 @@ architectures for the same problem in one VISTOMS instance.</p>
 <dl class="method">
 <dt id="kadmos.cmdows.cmdows.CMDOWS.check_uids">
 <code class="descname">check_uids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.check_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to check if all uIDs are actually unique in a CMDOWS file</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.ensure_abs_xpath">
-<code class="descname">ensure_abs_xpath</code><span class="sig-paren">(</span><em>xpath</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.ensure_abs_xpath" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to ensure that the elements given by an absolute XPath exist.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_design_competences_uids">
-<code class="descname">get_design_competences_uids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_design_competences_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get a list of all the design competences UIDs present in the file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_element_of_uid">
-<code class="descname">get_element_of_uid</code><span class="sig-paren">(</span><em>uid</em>, <em>expected_tag=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_element_of_uid" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get the element based on a UID value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_executable_blocks_uids">
-<code class="descname">get_executable_blocks_uids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_executable_blocks_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get a list of all the executable block UIDs present in the file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_inputs_uids">
-<code class="descname">get_inputs_uids</code><span class="sig-paren">(</span><em>exblock_uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_inputs_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to collect the inputs of a CMDOWS file executableBlock entry</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_mathematical_functions_uids">
-<code class="descname">get_mathematical_functions_uids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_mathematical_functions_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get a list of all the mathematical functions UIDs present in the file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_outputs_uids">
-<code class="descname">get_outputs_uids</code><span class="sig-paren">(</span><em>exblock_uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_outputs_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to collect the outputs of a CMDOWS file executableBlock entry</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_parameters_uids">
-<code class="descname">get_parameters_uids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_parameters_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get a list of all the parameter UIDs present in the file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_used_parameter_uids">
-<code class="descname">get_used_parameter_uids</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_used_parameter_uids" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get a list of all the parameter UIDs used in the file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.get_xpath_of_uid">
-<code class="descname">get_xpath_of_uid</code><span class="sig-paren">(</span><em>uid</em>, <em>expected_tag=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.get_xpath_of_uid" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get the xpath based on a UID value.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_children_of">
-<code class="descname">remove_children_of</code><span class="sig-paren">(</span><em>uid</em>, <em>children_to_remove='all'</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_children_of" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove the children of a CMDOWS file element.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_contact">
-<code class="descname">remove_contact</code><span class="sig-paren">(</span><em>contact_uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_contact" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove a contact based on its UID.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_data_graph_element">
-<code class="descname">remove_data_graph_element</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_data_graph_element" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove a dataGraph element from a CMDOWS file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_element_based_on_uid">
-<code class="descname">remove_element_based_on_uid</code><span class="sig-paren">(</span><em>uid</em>, <em>expected_tag=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_element_based_on_uid" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove an element based on its UID.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_element_based_on_xpath">
-<code class="descname">remove_element_based_on_xpath</code><span class="sig-paren">(</span><em>xpath</em>, <em>expected_amount=None</em>, <em>expected_text=None</em>, <em>higher_level_removal=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_element_based_on_xpath" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove an element based on its XPath.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_in_and_outputs">
-<code class="descname">remove_in_and_outputs</code><span class="sig-paren">(</span><em>exblock_uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_in_and_outputs" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove the in- and outputs of a CMDOWS file executableBlock entry</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_inputs">
-<code class="descname">remove_inputs</code><span class="sig-paren">(</span><em>exblock_uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_inputs" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove the inputs of a CMDOWS file executableBlock entry</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_outputs">
-<code class="descname">remove_outputs</code><span class="sig-paren">(</span><em>exblock_uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_outputs" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove the outputs of a CMDOWS file executableBlock entry</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_parameter">
-<code class="descname">remove_parameter</code><span class="sig-paren">(</span><em>param_uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_parameter" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove a parameter based on its UID.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_parameters">
-<code class="descname">remove_parameters</code><span class="sig-paren">(</span><em>params_uids</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_parameters" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove a list of parameters based on their UID.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_parameters_element">
-<code class="descname">remove_parameters_element</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_parameters_element" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove a parameters element from a CMDOWS file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_process_graph_element">
-<code class="descname">remove_process_graph_element</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_process_graph_element" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove a processGraph element from a CMDOWS file.</p>
-</dd></dl>
-
-<dl class="method">
-<dt id="kadmos.cmdows.cmdows.CMDOWS.remove_workflow_element">
-<code class="descname">remove_workflow_element</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.cmdows.cmdows.CMDOWS.remove_workflow_element" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to remove a workflow element from a CMDOWS file.</p>
+<dd><p>Method so check if all uIDs are actually unique in a CMDOWS file</p>
 </dd></dl>
 
 <dl class="method">
@@ -6587,12 +6207,6 @@ architectures for the same problem in one VISTOMS instance.</p>
 <p>Below the utilities used by KADMOS are listed.</p>
 <div class="section" id="module-kadmos.utilities.general">
 <span id="general"></span><h3>General<a class="headerlink" href="#module-kadmos.utilities.general" title="Permalink to this headline">¶</a></h3>
-<dl class="function">
-<dt id="kadmos.utilities.general.assert_dict_keys">
-<code class="descclassname">kadmos.utilities.general.</code><code class="descname">assert_dict_keys</code><span class="sig-paren">(</span><em>dic</em>, <em>expected_keys</em>, <em>all_keys_required=False</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.general.assert_dict_keys" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to assert that a dictionary has the expected keys and (optionally) to check if is has all the keys.</p>
-</dd></dl>
-
 <dl class="function">
 <dt id="kadmos.utilities.general.color_list">
 <code class="descclassname">kadmos.utilities.general.</code><code class="descname">color_list</code><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.general.color_list" title="Permalink to this definition">¶</a></dt>
@@ -6607,13 +6221,6 @@ architectures for the same problem in one VISTOMS instance.</p>
 </table>
 </dd></dl>
 
-<dl class="function">
-<dt id="kadmos.utilities.general.dict_to_ord_dict">
-<code class="descclassname">kadmos.utilities.general.</code><code class="descname">dict_to_ord_dict</code><span class="sig-paren">(</span><em>dic</em>, <em>key_order</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.general.dict_to_ord_dict" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to transform a Python dictionary into a Python ordered dictionary. Note that the key_order list can have
-items that are not present in the given dictionary. All keys of the dictionary should be in the order though.</p>
-</dd></dl>
-
 <dl class="function">
 <dt id="kadmos.utilities.general.export_as_json">
 <code class="descclassname">kadmos.utilities.general.</code><code class="descname">export_as_json</code><span class="sig-paren">(</span><em>data</em>, <em>filename</em>, <em>indent=None</em>, <em>sort_keys=True</em>, <em>cwd=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.general.export_as_json" title="Permalink to this definition">¶</a></dt>
@@ -6642,34 +6249,9 @@ items that are not present in the given dictionary. All keys of the dictionary s
 </dd></dl>
 
 <dl class="function">
-<dt id="kadmos.utilities.general.format_string_for_latex">
-<code class="descclassname">kadmos.utilities.general.</code><code class="descname">format_string_for_latex</code><span class="sig-paren">(</span><em>string</em>, <em>prefix=''</em>, <em>suffix=''</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.general.format_string_for_latex" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to format a string such that it can be used in LaTeX.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
-<li><strong>string</strong> (<em>str</em>) – string to be formatted</li>
-<li><strong>prefix</strong> (<em>basestring</em>) – prefix to be placed in front of the string</li>
-<li><strong>suffix</strong> (<em>basestring</em>) – suffix to be appended to the string</li>
-</ul>
-</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first">formatted string</p>
-</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body"><p class="first last">basestring</p>
-</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
-<dl class="function">
-<dt id="kadmos.utilities.general.format_string_for_vistoms">
-<code class="descclassname">kadmos.utilities.general.</code><code class="descname">format_string_for_vistoms</code><span class="sig-paren">(</span><em>string</em>, <em>prefix=''</em>, <em>suffix=''</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.general.format_string_for_vistoms" title="Permalink to this definition">¶</a></dt>
-<dd><p>Function to format a string such that it can be used in VISTOMS.</p>
+<dt id="kadmos.utilities.general.format_string_for_d3js">
+<code class="descclassname">kadmos.utilities.general.</code><code class="descname">format_string_for_d3js</code><span class="sig-paren">(</span><em>string</em>, <em>prefix=''</em>, <em>suffix=''</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.general.format_string_for_d3js" title="Permalink to this definition">¶</a></dt>
+<dd><p>Function to format a string such that it can be used in the dynamic visualization package.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
@@ -7056,7 +6638,7 @@ items that are not present in the given dictionary. All keys of the dictionary s
 
 <dl class="function">
 <dt id="kadmos.utilities.xml.get_element_details">
-<code class="descclassname">kadmos.utilities.xml.</code><code class="descname">get_element_details</code><span class="sig-paren">(</span><em>tree</em>, <em>xpath</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.xml.get_element_details" title="Permalink to this definition">¶</a></dt>
+<code class="descclassname">kadmos.utilities.xml.</code><code class="descname">get_element_details</code><span class="sig-paren">(</span><em>tree</em>, <em>uxpath</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.xml.get_element_details" title="Permalink to this definition">¶</a></dt>
 <dd><p>Function to determine the value and dimension of an UXPath element in a reference file.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
@@ -7064,7 +6646,7 @@ items that are not present in the given dictionary. All keys of the dictionary s
 <tbody valign="top">
 <tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
 <li><strong>tree</strong> – ElementTree object used for finding the XPath</li>
-<li><strong>xpath</strong> – XPath</li>
+<li><strong>uxpath</strong> – UXPath</li>
 </ul>
 </td>
 </tr>
@@ -7076,18 +6658,21 @@ items that are not present in the given dictionary. All keys of the dictionary s
 </dd></dl>
 
 <dl class="function">
-<dt id="kadmos.utilities.xml.get_uid_search_xpath">
-<code class="descclassname">kadmos.utilities.xml.</code><code class="descname">get_uid_search_xpath</code><span class="sig-paren">(</span><em>uid</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.xml.get_uid_search_xpath" title="Permalink to this definition">¶</a></dt>
-<dd><p>Method to get the XPath expression for a UID which might contain quote characters.</p>
+<dt id="kadmos.utilities.xml.get_xpath_from_uxpath">
+<code class="descclassname">kadmos.utilities.xml.</code><code class="descname">get_xpath_from_uxpath</code><span class="sig-paren">(</span><em>tree</em>, <em>uxpath</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.utilities.xml.get_xpath_from_uxpath" title="Permalink to this definition">¶</a></dt>
+<dd><p>Utility function to determine the XPath belonging to a UXPath for a given ElementTree object.</p>
 <table class="docutils field-list" frame="void" rules="none">
 <col class="field-name" />
 <col class="field-body" />
 <tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><strong>uid</strong> (<em>str</em>) – uID string</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body">XPath expression</td>
+<tr class="field-odd field"><th class="field-name">Parameters:</th><td class="field-body"><ul class="first simple">
+<li><strong>tree</strong> – ElementTree object used for finding the XPath</li>
+<li><strong>uxpath</strong> – UXPath</li>
+</ul>
+</td>
 </tr>
-<tr class="field-odd field"><th class="field-name">Return type:</th><td class="field-body">str</td>
+<tr class="field-even field"><th class="field-name">Returns:</th><td class="field-body"><p class="first last">XPath</p>
+</td>
 </tr>
 </tbody>
 </table>
@@ -7171,8 +6756,8 @@ items that are not present in the given dictionary. All keys of the dictionary s
 </dd></dl>
 
 </div>
-<div class="section" id="module-kadmos.utilities.strings">
-<span id="strings"></span><h3>Strings<a class="headerlink" href="#module-kadmos.utilities.strings" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="strings">
+<h3>Strings<a class="headerlink" href="#strings" title="Permalink to this headline">¶</a></h3>
 </div>
 <div class="section" id="module-kadmos.utilities.printing">
 <span id="printing"></span><h3>Printing<a class="headerlink" href="#module-kadmos.utilities.printing" title="Permalink to this headline">¶</a></h3>
@@ -7226,25 +6811,6 @@ print_indexed_list(message = “These are the tools: “, index_bracket = “rou
 <dt id="kadmos.knowledgebase.knowledgebase.KnowledgeBase">
 <em class="property">class </em><code class="descclassname">kadmos.knowledgebase.knowledgebase.</code><code class="descname">KnowledgeBase</code><span class="sig-paren">(</span><em>kb_dir_path</em>, <em>knowledge_base</em>, <em>ignoreFunctions=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.knowledgebase.knowledgebase.KnowledgeBase" title="Permalink to this definition">¶</a></dt>
 <dd><p>Class that imports the data stored in a knowledge base. This is a start point for graph visualizations.</p>
-<dl class="method">
-<dt id="kadmos.knowledgebase.knowledgebase.KnowledgeBase.get_function_dependencies">
-<code class="descname">get_function_dependencies</code><span class="sig-paren">(</span><em>funcName</em>, <em>mode</em>, <em>inOut=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.knowledgebase.knowledgebase.KnowledgeBase.get_function_dependencies" title="Permalink to this definition">¶</a></dt>
-<dd><p>This function builds a directed graph (KadmosGraph object) for the specified function using the “networkx” package. If inOut
-argument is specified, only the input or output of the function will be included in the graph, otherwise both.</p>
-<table class="docutils field-list" frame="void" rules="none">
-<col class="field-name" />
-<col class="field-body" />
-<tbody valign="top">
-<tr class="field-odd field"><th class="field-name">Param:</th><td class="field-body">funcName: function name for which the graph is generated; must be present in knowledge base.</td>
-</tr>
-<tr class="field-even field"><th class="field-name">Param:</th><td class="field-body">inOut: default = None; if specified, must be “input” or “output” string. Specification of this argument enables the generation of the function graph with only input or output variables.</td>
-</tr>
-<tr class="field-odd field"><th class="field-name">Returns:</th><td class="field-body">functionGraph</td>
-</tr>
-</tbody>
-</table>
-</dd></dl>
-
 <dl class="method">
 <dt id="kadmos.knowledgebase.knowledgebase.KnowledgeBase.get_function_graph">
 <code class="descname">get_function_graph</code><span class="sig-paren">(</span><em>funcName</em>, <em>inOut=None</em><span class="sig-paren">)</span><a class="headerlink" href="#kadmos.knowledgebase.knowledgebase.KnowledgeBase.get_function_graph" title="Permalink to this definition">¶</a></dt>
@@ -7339,7 +6905,7 @@ argument is specified, only the input or output of the function will be included
 <li><a class="reference internal" href="#utilities">Utilities</a><ul>
 <li><a class="reference internal" href="#module-kadmos.utilities.general">General</a></li>
 <li><a class="reference internal" href="#module-kadmos.utilities.xml">XML</a></li>
-<li><a class="reference internal" href="#module-kadmos.utilities.strings">Strings</a></li>
+<li><a class="reference internal" href="#strings">Strings</a></li>
 <li><a class="reference internal" href="#module-kadmos.utilities.printing">Printing</a></li>
 </ul>
 </li>
diff --git a/doc/genindex.html b/doc/genindex.html
index a5b2a2235b9bb2f1c77ef824783552d26d5e6731..075c7188b419b462f8d45fe79add2edaa7ff9aa6 100644
--- a/doc/genindex.html
+++ b/doc/genindex.html
@@ -71,18 +71,6 @@
 <h2 id="A">A</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.add_actor">add_actor() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.add_contact">add_contact() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.add_dc_general_info">add_dc_general_info() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.add_dc_performance_info">add_dc_performance_info() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.add_dc_remote_component_info">add_dc_remote_component_info() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.add_dc_verification">add_dc_verification() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.add_default_description">add_default_description() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
@@ -93,6 +81,12 @@
 
       <ul>
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.add_default_name">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
+</li>
+      </ul></li>
+      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.add_edge">add_edge() (kadmos.graph.graph_data.DataGraph method)</a>
+
+      <ul>
+        <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.add_edge">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.add_edges_from">add_edges_from() (kadmos.graph.graph_data.DataGraph method)</a>
@@ -141,7 +135,9 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.add_objective_function_by_nodes">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.add_process">add_process() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
+      <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.add_parallel_process">add_parallel_process() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
+</li>
+      <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.add_simple_sequential_process">add_simple_sequential_process() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.add_weighted_edges_from">add_weighted_edges_from() (kadmos.graph.graph_data.DataGraph method)</a>
 
@@ -173,22 +169,12 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.adjlist_outer_dict_factory">(kadmos.graph.graph_kadmos.KadmosGraph attribute)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.utilities.general.assert_dict_keys">assert_dict_keys() (in module kadmos.utilities.general)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.assert_element_tag">assert_element_tag() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
   </ul></td>
 </tr></table>
 
 <h2 id="C">C</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.change_graph_class">change_graph_class() (kadmos.graph.graph_data.DataGraph method)</a>
-
-      <ul>
-        <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.change_graph_class">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
-</li>
-      </ul></li>
       <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.check">check() (kadmos.cmdows.cmdows.CMDOWS method)</a>
 
       <ul>
@@ -215,6 +201,22 @@
 </li>
       <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.check_uids">check_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
 </li>
+      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.cleancopy">cleancopy() (kadmos.graph.graph_data.DataGraph method)</a>
+
+      <ul>
+        <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.cleancopy">(kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
+</li>
+        <li><a href="KADMOS.html#kadmos.graph.graph_data.RepositoryConnectivityGraph.cleancopy">(kadmos.graph.graph_data.RepositoryConnectivityGraph method)</a>
+</li>
+        <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.cleancopy">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
+</li>
+        <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.cleancopy">(kadmos.graph.graph_process.MdaoProcessGraph method)</a>
+</li>
+        <li><a href="KADMOS.html#kadmos.graph.graph_process.ProcessGraph.cleancopy">(kadmos.graph.graph_process.ProcessGraph method)</a>
+</li>
+      </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.clear">clear() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
@@ -223,8 +225,6 @@
       </ul></li>
       <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS">CMDOWS (class in kadmos.cmdows.cmdows)</a>
 </li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.utilities.general.color_list">color_list() (in module kadmos.utilities.general)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.connect_nested_iterators">connect_nested_iterators() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
@@ -233,12 +233,6 @@
 
       <ul>
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.copy">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
-</li>
-      </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.copy_as">copy_as() (kadmos.graph.graph_data.DataGraph method)</a>
-
-      <ul>
-        <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.copy_as">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.copy_node_with_suffix">copy_node_with_suffix() (kadmos.graph.graph_data.DataGraph method)</a>
@@ -259,8 +253,6 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.create_dsm">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.RepositoryConnectivityGraph.create_mathematical_problem">create_mathematical_problem() (kadmos.graph.graph_data.RepositoryConnectivityGraph method)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.create_mdg">create_mdg() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.create_mpg">create_mpg() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
@@ -273,28 +265,14 @@
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph">DataGraph (class in kadmos.graph.graph_data)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.deepcopy">deepcopy() (kadmos.graph.graph_data.DataGraph method)</a>
-
-      <ul>
-        <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.deepcopy">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
-</li>
-      </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.deepcopy_as">deepcopy_as() (kadmos.graph.graph_data.DataGraph method)</a>
-
-      <ul>
-        <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.deepcopy_as">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
-</li>
-      </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.degree">degree (kadmos.graph.graph_data.DataGraph attribute)</a>
 
       <ul>
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.degree">(kadmos.graph.graph_kadmos.KadmosGraph attribute)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.utilities.general.dict_to_ord_dict">dict_to_ord_dict() (in module kadmos.utilities.general)</a>
-</li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.disconnect_problematic_variables_from">disconnect_problematic_variables_from() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
@@ -319,17 +297,15 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.edge_subgraph">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.edges">edges (kadmos.graph.graph_data.DataGraph attribute)</a>
 
       <ul>
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.edges">(kadmos.graph.graph_kadmos.KadmosGraph attribute)</a>
 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.utilities.xml.Element">Element() (in module kadmos.utilities.xml)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.ensure_abs_xpath">ensure_abs_xpath() (kadmos.cmdows.cmdows.CMDOWS method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.mixin_equation.EquationMixin">EquationMixin (class in kadmos.graph.mixin_equation)</a>
 </li>
@@ -347,12 +323,10 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.find_all_nodes">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.utilities.general.format_string_for_latex">format_string_for_latex() (in module kadmos.utilities.general)</a>
+      <li><a href="KADMOS.html#kadmos.utilities.general.format_string_for_d3js">format_string_for_d3js() (in module kadmos.utilities.general)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="KADMOS.html#kadmos.utilities.general.format_string_for_vistoms">format_string_for_vistoms() (in module kadmos.utilities.general)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.fresh_copy">fresh_copy() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
@@ -385,9 +359,7 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.get_contracted_graph">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_coupling_matrix">get_coupling_matrix() (kadmos.graph.graph_data.DataGraph method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_design_competences_uids">get_design_competences_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
+      <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.get_coupling_matrix">get_coupling_matrix() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_direct_coupling_nodes">get_direct_coupling_nodes() (kadmos.graph.graph_data.DataGraph method)</a>
 
@@ -404,12 +376,6 @@
       <li><a href="KADMOS.html#kadmos.utilities.xml.get_element_details">get_element_details() (in module kadmos.utilities.xml)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.utilities.general.get_element_dict">get_element_dict() (in module kadmos.utilities.general)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_element_of_uid">get_element_of_uid() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_executable_blocks_uids">get_executable_blocks_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_feedback_info">get_feedback_info() (kadmos.graph.graph_data.DataGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.RepositoryConnectivityGraph.get_fpg_based_on_function_nodes">get_fpg_based_on_function_nodes() (kadmos.graph.graph_data.RepositoryConnectivityGraph method)</a>
 </li>
@@ -420,8 +386,6 @@
       <li><a href="KADMOS.html#kadmos.graph.graph_data.RepositoryConnectivityGraph.get_fpg_by_function_nodes">get_fpg_by_function_nodes() (kadmos.graph.graph_data.RepositoryConnectivityGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.utilities.general.get_friendly_id">get_friendly_id() (in module kadmos.utilities.general)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.knowledgebase.knowledgebase.KnowledgeBase.get_function_dependencies">get_function_dependencies() (kadmos.knowledgebase.knowledgebase.KnowledgeBase method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_function_graph">get_function_graph() (kadmos.graph.graph_data.DataGraph method)</a>
 
@@ -451,15 +415,9 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.get_graph_properties">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_inputs_uids">get_inputs_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.knowledgebase.knowledgebase.KnowledgeBase.get_kb_graphs">get_kb_graphs() (kadmos.knowledgebase.knowledgebase.KnowledgeBase method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.utilities.general.get_list_entries">get_list_entries() (in module kadmos.utilities.general)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.get_lowest_psn">get_lowest_psn() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_mathematical_functions_uids">get_mathematical_functions_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.utilities.general.get_mdao_setup">get_mdao_setup() (in module kadmos.utilities.general)</a>
 </li>
@@ -470,6 +428,8 @@
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.get_mpg">get_mpg() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
+</li>
+      <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.get_nested_process_ordering">get_nested_process_ordering() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_node_attributes">get_node_attributes() (kadmos.graph.graph_data.DataGraph method)</a>
 
@@ -515,12 +475,6 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.get_number_of_couplings">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.get_ordered_cycles">get_ordered_cycles() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_outputs_uids">get_outputs_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_parameters_uids">get_parameters_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_partitioned_graph">get_partitioned_graph() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
@@ -528,21 +482,11 @@
 </li>
       </ul></li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.RepositoryConnectivityGraph.get_path_combinations">get_path_combinations() (kadmos.graph.graph_data.RepositoryConnectivityGraph method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_possible_function_order">get_possible_function_order() (kadmos.graph.graph_data.DataGraph method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.get_process_hierarchy">get_process_hierarchy() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph.get_process_list">get_process_list() (kadmos.graph.graph_process.MdaoProcessGraph method)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.knowledgebase.knowledgebase.KnowledgeBase.get_rcg">get_rcg() (kadmos.knowledgebase.knowledgebase.KnowledgeBase method)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_same_graph_class">get_same_graph_class() (kadmos.graph.graph_data.DataGraph method)</a>
-
-      <ul>
-        <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.get_same_graph_class">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
-</li>
-      </ul></li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.get_sources">get_sources() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
@@ -568,14 +512,10 @@
 </li>
       </ul></li>
       <li><a href="KADMOS.html#kadmos.utilities.general.get_uid">get_uid() (in module kadmos.utilities.general)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.utilities.xml.get_uid_search_xpath">get_uid_search_xpath() (in module kadmos.utilities.xml)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.utilities.general.get_unique_friendly_id">get_unique_friendly_id() (in module kadmos.utilities.general)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_used_parameter_uids">get_used_parameter_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.get_xpath_of_uid">get_xpath_of_uid() (kadmos.cmdows.cmdows.CMDOWS method)</a>
+      <li><a href="KADMOS.html#kadmos.utilities.xml.get_xpath_from_uxpath">get_xpath_from_uxpath() (in module kadmos.utilities.xml)</a>
 </li>
   </ul></td>
 </tr></table>
@@ -685,8 +625,6 @@
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="KADMOS.html#module-kadmos.utilities.strings">kadmos.utilities.strings (module)</a>
-</li>
       <li><a href="KADMOS.html#module-kadmos.utilities.xml">kadmos.utilities.xml (module)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph">KadmosGraph (class in kadmos.graph.graph_kadmos)</a>
@@ -711,22 +649,18 @@
 </li>
       <li><a href="KADMOS.html#kadmos.utilities.general.make_singular">make_singular() (in module kadmos.utilities.general)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.mark_as_constraint">mark_as_constraint() (kadmos.graph.graph_data.DataGraph method)</a>
+      <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_constraint">mark_as_constraint() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.mark_as_constraints">mark_as_constraints() (kadmos.graph.graph_data.DataGraph method)</a>
+      <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_design_variable">mark_as_design_variable() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.mark_as_design_variable">mark_as_design_variable() (kadmos.graph.graph_data.DataGraph method)</a>
+      <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_objective">mark_as_objective() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.mark_as_design_variables">mark_as_design_variables() (kadmos.graph.graph_data.DataGraph method)</a>
+      <li><a href="KADMOS.html#kadmos.graph.graph_data.FundamentalProblemGraph.mark_as_qoi">mark_as_qoi() (kadmos.graph.graph_data.FundamentalProblemGraph method)</a>
 </li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.mark_as_objective">mark_as_objective() (kadmos.graph.graph_data.DataGraph method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.mark_as_qois">mark_as_qois() (kadmos.graph.graph_data.DataGraph method)</a>
+      <li><a href="KADMOS.html#kadmos.graph.mixin_mdao.MdaoMixin">MdaoMixin (class in kadmos.graph.mixin_mdao)</a>
 </li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="KADMOS.html#kadmos.graph.mixin_mdao.MdaoMixin">MdaoMixin (class in kadmos.graph.mixin_mdao)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_process.MdaoProcessGraph">MdaoProcessGraph (class in kadmos.graph.graph_process)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.utilities.xml.merge">merge() (in module kadmos.utilities.xml)</a>
@@ -755,8 +689,6 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.merge_sequential_functions">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.minimize_feedback">minimize_feedback() (kadmos.graph.graph_data.DataGraph method)</a>
-</li>
   </ul></td>
 </tr></table>
 
@@ -935,12 +867,6 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.relabel_function_nodes">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_children_of">remove_children_of() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_contact">remove_contact() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_data_graph_element">remove_data_graph_element() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.remove_edge">remove_edge() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
@@ -953,23 +879,15 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.remove_edges_from">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_element_based_on_uid">remove_element_based_on_uid() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_element_based_on_xpath">remove_element_based_on_xpath() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.remove_function_nodes">remove_function_nodes() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.remove_function_nodes">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.utilities.general.remove_if_exists">remove_if_exists() (in module kadmos.utilities.general)</a>
-</li>
   </ul></td>
   <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_in_and_outputs">remove_in_and_outputs() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_inputs">remove_inputs() (kadmos.cmdows.cmdows.CMDOWS method)</a>
+      <li><a href="KADMOS.html#kadmos.utilities.general.remove_if_exists">remove_if_exists() (in module kadmos.utilities.general)</a>
 </li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.remove_node">remove_node() (kadmos.graph.graph_data.DataGraph method)</a>
 
@@ -985,18 +903,6 @@
         <li><a href="KADMOS.html#kadmos.graph.graph_kadmos.KadmosGraph.remove_nodes_from">(kadmos.graph.graph_kadmos.KadmosGraph method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_outputs">remove_outputs() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_parameter">remove_parameter() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_parameters">remove_parameters() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_parameters_element">remove_parameters_element() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_process_graph_element">remove_process_graph_element() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
-      <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.remove_workflow_element">remove_workflow_element() (kadmos.cmdows.cmdows.CMDOWS method)</a>
-</li>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.RepositoryConnectivityGraph">RepositoryConnectivityGraph (class in kadmos.graph.graph_data)</a>
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       <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.resolve_uids">resolve_uids() (kadmos.cmdows.cmdows.CMDOWS method)</a>
@@ -1035,16 +941,14 @@
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       <li><a href="KADMOS.html#kadmos.cmdows.cmdows.CMDOWS.simplify_equations">simplify_equations() (kadmos.cmdows.cmdows.CMDOWS method)</a>
 </li>
+  </ul></td>
+  <td style="width: 33%; vertical-align: top;"><ul>
       <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.size">size() (kadmos.graph.graph_data.DataGraph method)</a>
 
       <ul>
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 </li>
       </ul></li>
-  </ul></td>
-  <td style="width: 33%; vertical-align: top;"><ul>
-      <li><a href="KADMOS.html#kadmos.graph.graph_data.DataGraph.sort_non_coupled_nodes">sort_non_coupled_nodes() (kadmos.graph.graph_data.DataGraph method)</a>
-</li>
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@@ -1119,8 +1023,6 @@
 
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-</li>
-        <li><a href="KADMOS.html#kadmos.graph.mixin_vistoms.VistomsMixin.vistoms_add">(kadmos.graph.mixin_vistoms.VistomsMixin method)</a>
 </li>
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   </ul></td>
@@ -1129,12 +1031,8 @@
 
       <ul>
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-</li>
-        <li><a href="KADMOS.html#kadmos.graph.mixin_vistoms.VistomsMixin.vistoms_create">(kadmos.graph.mixin_vistoms.VistomsMixin method)</a>
 </li>
       </ul></li>
-      <li><a href="KADMOS.html#kadmos.graph.mixin_vistoms.VistomsMixin">VistomsMixin (class in kadmos.graph.mixin_vistoms)</a>
-</li>
   </ul></td>
 </tr></table>
 
diff --git a/doc/objects.inv b/doc/objects.inv
index 4dad1c2a908d2c6a0acb952bb471b2215c342cd2..807edb0c20ed1703f19b5a3a1d7193da45c9c7ad 100644
Binary files a/doc/objects.inv and b/doc/objects.inv differ
diff --git a/doc/py-modindex.html b/doc/py-modindex.html
index 70a8d21e6da329ba2fa671a99e891db813ec6cd7..70e1cee3d31021da2e1c589bac397f23ae09ab36 100644
--- a/doc/py-modindex.html
+++ b/doc/py-modindex.html
@@ -73,11 +73,6 @@
        <td>&#160;&#160;&#160;
        <a href="KADMOS.html#module-kadmos.utilities.printing"><code class="xref">kadmos.utilities.printing</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="KADMOS.html#module-kadmos.utilities.strings"><code class="xref">kadmos.utilities.strings</code></a></td><td>
-       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 87891cd2bcffa94175c61d0cbb2e27c15055bfb3..b9ebc829b366a3427c3e6bceb463c8b0abde0018 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/kadmos/__init__.py b/kadmos/__init__.py
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..ab55bb1afcfc57eae20afec76d516c55dcd2be7a 100644
--- a/kadmos/__init__.py
+++ b/kadmos/__init__.py
@@ -0,0 +1 @@
+__version__ = "0.7.5"
diff --git a/setup.py b/setup.py
index edc6eb90734b7c1d6ab921d910efc0dc89aca031..88562a1b98bcbc53b577818d12e764abcaf7c785 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,7 @@ setup(name='kadmos',
             'flask',
             'matplotlib',
             'matlab',
-            'networkx',
+            'networkx>=2.0',
             'numpy',
             'progressbar2'
       ],
diff --git a/submit.md b/submit.md
index f9e75f53f3971aba8c1b51e8ad0635b80feecc6b..902bac6e8ef38eb991db55d11ec8f1dae8366bc0 100644
--- a/submit.md
+++ b/submit.md
@@ -3,6 +3,8 @@ Instructions for submitting a new version of KADMOS to PyPi
 
 - Adapt the version in the setup.py file (for versions that are published to PyPi it should be just something like '0.6', the next intermediate version which is not published would be '0.7dev'.
 
+- Adapt the version in the __init__.py file
+
 - Adapt the changelog in the [readme.md](readme.md) file.
 
 - Adapt the [MANIFEST.in](MANIFEST.in) file (this file specifies what should be included in the distribution, by default only .py or .pyc files are included in the distribution). Normally you only need to adapt the included visualization packages here.