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+
+  <h1>Source code for ecoli.library.logging_tools</h1><div class="highlight"><pre>
+<span></span><span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">import</span> <span class="nn">json</span>
+
+<span class="kn">from</span> <span class="nn">vivarium.core.serialize</span> <span class="kn">import</span> <span class="n">serialize_value</span>
+
+
+<div class="viewcode-block" id="make_logging_process">
+<a class="viewcode-back" href="../../../reference/api/ecoli/ecoli.library.logging_tools.html#ecoli.library.logging_tools.make_logging_process">[docs]</a>
+<span class="k">def</span> <span class="nf">make_logging_process</span><span class="p">(</span><span class="n">process_class</span><span class="p">):</span>
+    <span class="k">class</span> <span class="nc">LoggingProcess</span><span class="p">(</span><span class="n">process_class</span><span class="p">):</span>
+        <span class="k">def</span> <span class="nf">ports_schema</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+            <span class="n">ports</span> <span class="o">=</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">ports_schema</span><span class="p">()</span>  <span class="c1"># original port structure</span>
+            <span class="n">ports</span><span class="p">[</span><span class="s2">&quot;log_update&quot;</span><span class="p">]</span> <span class="o">=</span> <span class="p">{</span>
+                <span class="s2">&quot;_default&quot;</span><span class="p">:</span> <span class="p">{},</span>
+                <span class="s2">&quot;_updater&quot;</span><span class="p">:</span> <span class="s2">&quot;set&quot;</span><span class="p">,</span>
+                <span class="s2">&quot;_emit&quot;</span><span class="p">:</span> <span class="kc">True</span><span class="p">,</span>
+            <span class="p">}</span>  <span class="c1"># add a new port</span>
+            <span class="k">return</span> <span class="n">ports</span>
+
+        <span class="k">def</span> <span class="nf">next_update</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">timestep</span><span class="p">,</span> <span class="n">states</span><span class="p">):</span>
+            <span class="n">update</span> <span class="o">=</span> <span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">next_update</span><span class="p">(</span><span class="n">timestep</span><span class="p">,</span> <span class="n">states</span><span class="p">)</span>  <span class="c1"># original update</span>
+            <span class="n">log_update</span> <span class="o">=</span> <span class="p">{</span><span class="s2">&quot;log_update&quot;</span><span class="p">:</span> <span class="n">update</span><span class="p">}</span>  <span class="c1"># log the update</span>
+            <span class="k">return</span> <span class="p">{</span><span class="o">**</span><span class="n">update</span><span class="p">,</span> <span class="o">**</span><span class="n">log_update</span><span class="p">}</span>
+
+    <span class="n">LoggingProcess</span><span class="o">.</span><span class="vm">__name__</span> <span class="o">=</span> <span class="sa">f</span><span class="s2">&quot;Logging_</span><span class="si">{</span><span class="n">process_class</span><span class="o">.</span><span class="vm">__name__</span><span class="si">}</span><span class="s2">&quot;</span>
+    <span class="k">return</span> <span class="n">LoggingProcess</span></div>
+
+
+
+<div class="viewcode-block" id="write_json">
+<a class="viewcode-back" href="../../../reference/api/ecoli/ecoli.library.logging_tools.html#ecoli.library.logging_tools.write_json">[docs]</a>
+<span class="k">def</span> <span class="nf">write_json</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">numpy_dict</span><span class="p">):</span>
+    <span class="n">os</span><span class="o">.</span><span class="n">makedirs</span><span class="p">(</span><span class="n">os</span><span class="o">.</span><span class="n">path</span><span class="o">.</span><span class="n">dirname</span><span class="p">(</span><span class="n">path</span><span class="p">),</span> <span class="n">exist_ok</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
+
+    <span class="k">with</span> <span class="nb">open</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="s2">&quot;w&quot;</span><span class="p">)</span> <span class="k">as</span> <span class="n">outfile</span><span class="p">:</span>
+        <span class="n">json</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">serialize_value</span><span class="p">(</span><span class="n">numpy_dict</span><span class="p">),</span> <span class="n">outfile</span><span class="p">)</span></div>
+
+</pre></div>
+
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