updated package version and new documentation

biosimulators · Oct 22, 2024 · e8bce3a · e8bce3a
1 parent 9c0ec0e
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diff --git a/documentation/build/doctrees/bio_compose.doctree b/documentation/build/doctrees/bio_compose.doctree
diff --git a/documentation/build/doctrees/environment.pickle b/documentation/build/doctrees/environment.pickle
diff --git a/documentation/build/html/_modules/bio_compose/data_model.html b/documentation/build/html/_modules/bio_compose/data_model.html
@@ -103,6 +103,23 @@ <h1>Source code for bio_compose.data_model</h1><div class="highlight"><pre>
         <span class="k">return</span> <span class="n">asdict</span><span class="p">(</span><span class="bp">self</span><span class="p">)</span></div>
 </div>
 
+
+
+<div class="viewcode-block" id="DynamicJson">
+<a class="viewcode-back" href="../../bio_compose.html#bio_compose.data_model.DynamicJson">[docs]</a>
+<span class="k">class</span> <span class="nc">DynamicJson</span><span class="p">:</span>
+    <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">data</span><span class="p">:</span> <span class="n">Dict</span><span class="p">[</span><span class="n">Any</span><span class="p">,</span> <span class="n">Any</span><span class="p">]):</span>
+<span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
+<span class="sd">        Dynamically create a JSON-like object from a dictionary/mapping of any shape.</span>
+<span class="sd">        &quot;&quot;&quot;</span>
+        <span class="k">for</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span> <span class="ow">in</span> <span class="n">data</span><span class="o">.</span><span class="n">items</span><span class="p">():</span>
+            <span class="k">if</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">value</span><span class="p">,</span> <span class="nb">dict</span><span class="p">):</span>
+                <span class="n">value</span> <span class="o">=</span> <span class="n">DynamicData</span><span class="p">(</span><span class="n">value</span><span class="p">)</span>
+            <span class="nb">setattr</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">key</span><span class="p">,</span> <span class="n">value</span><span class="p">)</span>
+
+    <span class="k">def</span> <span class="fm">__repr__</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+        <span class="k">return</span> <span class="sa">f</span><span class="s2">&quot;</span><span class="si">{</span><span class="bp">self</span><span class="o">.</span><span class="vm">__dict__</span><span class="si">}</span><span class="s2">&quot;</span></div>
+
 
 
 <div class="viewcode-block" id="Api">

diff --git a/documentation/build/html/_modules/bio_compose/verifier.html b/documentation/build/html/_modules/bio_compose/verifier.html
@@ -392,7 +392,7 @@ <h1>Source code for bio_compose.verifier</h1><div class="highlight"><pre>
         <span class="n">n_simulators</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">simulators</span><span class="p">)</span>
 
         <span class="c1"># create subplots</span>
-        <span class="n">fig</span><span class="p">,</span> <span class="n">axes</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">nrows</span><span class="o">=</span><span class="n">n_simulators</span><span class="p">,</span> <span class="n">ncols</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">15</span><span class="p">,</span> <span class="mi">5</span> <span class="o">*</span> <span class="n">n_simulators</span><span class="p">))</span>
+        <span class="n">fig</span><span class="p">,</span> <span class="n">axes</span> <span class="o">=</span> <span class="n">plt</span><span class="o">.</span><span class="n">subplots</span><span class="p">(</span><span class="n">nrows</span><span class="o">=</span><span class="n">n_simulators</span><span class="p">,</span> <span class="n">ncols</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">figsize</span><span class="o">=</span><span class="p">(</span><span class="mi">4</span><span class="p">,</span> <span class="mi">3</span> <span class="o">*</span> <span class="n">n_simulators</span><span class="p">))</span>
 
         <span class="c1"># if only one simulator, `axes` won&#39;t be an array, so make it an array</span>
         <span class="k">if</span> <span class="n">n_simulators</span> <span class="o">==</span> <span class="mi">1</span><span class="p">:</span>
@@ -569,9 +569,9 @@ <h1>Source code for bio_compose.verifier</h1><div class="highlight"><pre>
         <span class="bp">self</span><span class="o">.</span><span class="n">job_id</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">data</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;content&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;job_id&#39;</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">verifier</span> <span class="o">=</span> <span class="n">Verifier</span><span class="p">()</span>
 
-<div class="viewcode-block" id="VerificationResult.get_rmse">
-<a class="viewcode-back" href="../../bio_compose.html#bio_compose.verifier.VerificationResult.get_rmse">[docs]</a>
-    <span class="k">def</span> <span class="nf">get_rmse</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">save_dest</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">fig_dimensions</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">color_mapping</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="VerificationResult.get_comparison">
+<a class="viewcode-back" href="../../bio_compose.html#bio_compose.verifier.VerificationResult.get_comparison">[docs]</a>
+    <span class="k">def</span> <span class="nf">get_comparison</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">save_dest</span><span class="p">:</span> <span class="nb">str</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">fig_dimensions</span><span class="p">:</span> <span class="nb">tuple</span><span class="p">[</span><span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">,</span> <span class="n">color_mapping</span><span class="p">:</span> <span class="nb">list</span><span class="p">[</span><span class="nb">str</span><span class="p">]</span> <span class="o">=</span> <span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">&quot;&quot;&quot;</span>
 <span class="sd">        Visualize the root-mean-squared error between simulator verification outputs as a heatmap.</span>