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<h1>Build a model graph</h1>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#define-a-graph">Define a graph</a></li>
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<section id="build-a-model-graph">
<h1>Build a model graph<a class="headerlink" href="#build-a-model-graph" title="Link to this heading">#</a></h1>
<p>A directed acyclic graph (DAG) is a directed graph without any cycles.
The model graphs in <em>mmodel</em> are based on the DAG, where each node represents
an execution step, and each edge represents the data flow from one callable
to another. The DAG structure allows us to create model graphs with nonlinear
nodes.</p>
<section id="define-a-graph">
<h2>Define a graph<a class="headerlink" href="#define-a-graph" title="Link to this heading">#</a></h2>
<p>The <code class="docutils literal notranslate"><span class="pre">Graph</span></code> class is the main graph class to establish a model graph.
The class inherits from <code class="docutils literal notranslate"><span class="pre">networkx.DiGraph</span></code>, which is compatible with all
<em>NetworkX</em> operations
(see <a class="reference external" href="https://networkx.org/documentation/stable/">documentation</a>).
To create and modify the graph,
see the documentation for adding
<a class="reference external" href="https://networkx.org/documentation/stable/tutorial.html#nodes">nodes</a>
and adding <a class="reference external" href="https://networkx.org/documentation/stable/tutorial.html#edges">edges</a>.</p>
<p>Aside from the <em>NetworkX</em> operations,
<em>mmodel</em> provides <code class="docutils literal notranslate"><span class="pre">add_grouped_edge</span></code> and <code class="docutils literal notranslate"><span class="pre">add_grouped_edges_from</span></code> to add edges.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">mmodel</span><span class="w"> </span><span class="kn">import</span> <span class="n">Graph</span><span class="p">,</span> <span class="n">Node</span>
<span class="n">G</span> <span class="o">=</span> <span class="n">Graph</span><span class="p">()</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_grouped_edge</span><span class="p">([</span><span class="s1">'a'</span><span class="p">,</span> <span class="s1">'b'</span><span class="p">],</span> <span class="s1">'c'</span><span class="p">)</span>
<span class="c1"># equivalent to</span>
<span class="c1"># G.add_edge('a', 'b')</span>
<span class="c1"># G.add_edge('a', 'c')</span>
</pre></div>
</div>
<p>Similarly, with multiple grouped edges:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">grouped_edges</span> <span class="o">=</span> <span class="p">[</span>
<span class="p">([</span><span class="s1">'a'</span><span class="p">,</span> <span class="s1">'b'</span><span class="p">],</span> <span class="s1">'c'</span><span class="p">),</span>
<span class="p">(</span><span class="s1">'c'</span><span class="p">,</span> <span class="p">[</span><span class="s1">'d'</span><span class="p">,</span> <span class="s1">'e'</span><span class="p">]),</span>
<span class="p">]</span>
<span class="n">G</span> <span class="o">=</span> <span class="n">Graph</span><span class="p">()</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_grouped_edges_from</span><span class="p">(</span><span class="n">grouped_edges</span><span class="p">)</span>
<span class="o">>>></span> <span class="n">G</span> <span class="c1"># no name is given</span>
<span class="o"><</span><span class="n">mmodel</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">Graph</span><span class="o">></span>
<span class="o">>>></span> <span class="nb">print</span><span class="p">(</span><span class="n">G</span><span class="p">)</span>
<span class="n">Graph</span> <span class="k">with</span> <span class="mi">5</span> <span class="n">nodes</span> <span class="ow">and</span> <span class="mi">4</span> <span class="n">edges</span>
</pre></div>
</div>
<p>For linking the node object to the node, two methods are provided:
<code class="docutils literal notranslate"><span class="pre">add_node_object</span></code> and <code class="docutils literal notranslate"><span class="pre">add_node_objects_from</span></code>.
The latter accepts a list of node objects.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="k">def</span><span class="w"> </span><span class="nf">add</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""The sum of x and y."""</span>
<span class="k">return</span> <span class="n">x</span> <span class="o">+</span> <span class="n">y</span>
<span class="k">def</span><span class="w"> </span><span class="nf">subtract</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""The difference between x and y."""</span>
<span class="k">return</span> <span class="n">x</span> <span class="o">-</span> <span class="n">y</span>
<span class="k">def</span><span class="w"> </span><span class="nf">multiply</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">):</span>
<span class="w"> </span><span class="sd">"""The product of x and y."""</span>
<span class="k">return</span> <span class="n">x</span> <span class="o">*</span> <span class="n">y</span>
<span class="n">G</span> <span class="o">=</span> <span class="n">Graph</span><span class="p">()</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_grouped_edge</span><span class="p">([</span><span class="s1">'a'</span><span class="p">,</span> <span class="s1">'b'</span><span class="p">],</span> <span class="s1">'c'</span><span class="p">)</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_node_object</span><span class="p">(</span><span class="n">Node</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"a"</span><span class="p">,</span> <span class="n">func</span><span class="o">=</span><span class="n">add</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="s2">"z"</span><span class="p">))</span>
</pre></div>
</div>
<p>The node object can be accessed using the <code class="docutils literal notranslate"><span class="pre">get_node_object</span></code> method.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">node_a</span> <span class="o">=</span> <span class="n">G</span><span class="o">.</span><span class="n">get_node_object</span><span class="p">(</span><span class="s2">"a"</span><span class="p">)</span>
<span class="o">>>></span> <span class="nb">print</span><span class="p">(</span><span class="n">node_a</span><span class="p">)</span>
<span class="n">a</span>
<span class="n">add</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="k">return</span><span class="p">:</span> <span class="n">z</span>
<span class="n">functype</span><span class="p">:</span> <span class="n">function</span>
<span class="n">The</span> <span class="nb">sum</span> <span class="n">of</span> <span class="n">x</span> <span class="ow">and</span> <span class="n">y</span><span class="o">.</span>
<span class="c1"># or with multiple node objects</span>
<span class="c1"># both nodes add input values but output to different parameters</span>
<span class="n">node_objects</span> <span class="o">=</span> <span class="p">[</span>
<span class="n">Node</span><span class="p">(</span><span class="s2">"a"</span><span class="p">,</span> <span class="n">add</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="s2">"z"</span><span class="p">),</span>
<span class="n">Node</span><span class="p">(</span><span class="s2">"b"</span><span class="p">,</span> <span class="n">subtract</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="s2">"m"</span><span class="p">),</span>
<span class="n">Node</span><span class="p">(</span><span class="s2">"c"</span><span class="p">,</span> <span class="n">multiply</span><span class="p">,</span> <span class="n">output</span><span class="o">=</span><span class="s2">"n"</span><span class="p">,</span> <span class="n">inputs</span><span class="o">=</span><span class="p">[</span><span class="s2">"z"</span><span class="p">,</span> <span class="s2">"m"</span><span class="p">]),</span>
<span class="p">]</span>
<span class="n">G</span><span class="o">.</span><span class="n">add_node_objects_from</span><span class="p">(</span><span class="n">node_objects</span><span class="p">)</span>
<span class="o">>>></span> <span class="n">node_b</span> <span class="o">=</span> <span class="n">G</span><span class="o">.</span><span class="n">get_node_object</span><span class="p">(</span><span class="s2">"b"</span><span class="p">)</span>
<span class="o">>>></span> <span class="nb">print</span><span class="p">(</span><span class="n">node_b</span><span class="p">)</span>
<span class="n">b</span>
<span class="n">subtract</span><span class="p">(</span><span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">)</span>
<span class="k">return</span><span class="p">:</span> <span class="n">m</span>
<span class="n">functype</span><span class="p">:</span> <span class="n">function</span>
<span class="n">The</span> <span class="n">difference</span> <span class="n">between</span> <span class="n">x</span> <span class="ow">and</span> <span class="n">y</span><span class="o">.</span>
</pre></div>
</div>
<p>The object is stored as a node attribute, and the function signature
(<code class="docutils literal notranslate"><span class="pre">inspect.Signature</span></code>) is stored. The parameter values are converted
to signature objects.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The node output parameter needs to be unique.</p>
</div>
</section>
<section id="graph-visualization">
<h2>Graph visualization<a class="headerlink" href="#graph-visualization" title="Link to this heading">#</a></h2>
<p>The graph can be visualized or saved using the <code class="docutils literal notranslate"><span class="pre">visualize</span></code> method.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">G</span><span class="o">.</span><span class="n">visualize</span><span class="p">()</span>
<span class="c1"># or with a filename</span>
<span class="n">G</span><span class="o">.</span><span class="n">visualize</span><span class="p">(</span><span class="n">outfile</span><span class="o">=</span><span class="s2">"graph.png"</span><span class="p">)</span>
</pre></div>
</div>
</section>
<section id="name-and-docstring">
<h2>Name and docstring<a class="headerlink" href="#name-and-docstring" title="Link to this heading">#</a></h2>
<p>The name and graph string behave as the <em>networkx</em> graphs. To add the name to the graph:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># during graph definition</span>
<span class="n">G</span> <span class="o">=</span> <span class="n">Graph</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">"Graph Example"</span><span class="p">)</span>
<span class="c1"># after definition</span>
<span class="c1"># G.graph['name'] = 'ModelGraph Example'</span>
<span class="o">>>></span> <span class="n">G</span>
<span class="o"><</span><span class="n">mmodel</span><span class="o">.</span><span class="n">graph</span><span class="o">.</span><span class="n">Graph</span> <span class="s1">'Graph Example'</span><span class="o">></span>
<span class="o">>>></span> <span class="nb">print</span><span class="p">(</span><span class="n">G</span><span class="p">)</span>
<span class="n">Graph</span> <span class="n">named</span> <span class="s1">'Graph Example'</span> <span class="k">with</span> <span class="mi">0</span> <span class="n">nodes</span> <span class="ow">and</span> <span class="mi">0</span> <span class="n">edges</span>
</pre></div>
</div>
</section>
<section id="mutability">
<h2>Mutability<a class="headerlink" href="#mutability" title="Link to this heading">#</a></h2>
<p>A graph object is mutable. A shallow or deepcopy is needed to create a copy
of the graph.</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">G</span><span class="o">.</span><span class="n">copy</span><span class="p">()</span> <span class="c1"># shallow copy</span>
<span class="n">G</span><span class="o">.</span><span class="n">deepcopy</span><span class="p">()</span> <span class="c1"># deep copy</span>
</pre></div>
</div>
<p>For more ways to interact with <code class="docutils literal notranslate"><span class="pre">Graph</span></code> and <code class="docutils literal notranslate"><span class="pre">networkx.DiGraph</span></code>, see
<a class="reference internal" href="ref_graph.html"><span class="doc">graph reference</span></a>.</p>
</section>
</section>
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