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biosimulators · Sep 11, 2024 · f72de5d · f72de5d
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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/doctrees/verification.doctree b/documentation/build/doctrees/verification.doctree
diff --git a/documentation/build/html/_modules/bio_compose/data_model.html b/documentation/build/html/_modules/bio_compose/data_model.html
@@ -78,6 +78,7 @@ <h1>Source code for bio_compose.data_model</h1><div class="highlight"><pre>
 <span></span><span class="kn">import</span> <span class="nn">asyncio</span>
 <span class="kn">import</span> <span class="nn">time</span> 
 <span class="kn">import</span> <span class="nn">os</span>
+<span class="kn">from</span> <span class="nn">warnings</span> <span class="kn">import</span> <span class="n">warn</span> 
 <span class="kn">from</span> <span class="nn">dataclasses</span> <span class="kn">import</span> <span class="n">asdict</span><span class="p">,</span> <span class="n">dataclass</span>
 <span class="kn">from</span> <span class="nn">functools</span> <span class="kn">import</span> <span class="n">wraps</span>
 <span class="kn">from</span> <span class="nn">typing</span> <span class="kn">import</span> <span class="n">Dict</span><span class="p">,</span> <span class="n">List</span><span class="p">,</span> <span class="n">Union</span><span class="p">,</span> <span class="n">Any</span><span class="p">,</span> <span class="n">Callable</span>
@@ -343,12 +344,16 @@ <h1>Source code for bio_compose.data_model</h1><div class="highlight"><pre>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="nd">@wraps</span><span class="p">(</span><span class="n">func</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">wrapper</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
-        <span class="n">fig</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="n">func</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
-        <span class="n">save_dest</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;save_dest&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
-        <span class="k">if</span> <span class="n">save_dest</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
-            <span class="n">dest</span> <span class="o">=</span> <span class="n">save_dest</span> <span class="o">+</span> <span class="s1">&#39;.pdf&#39;</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">export_plot</span><span class="p">(</span><span class="n">fig</span><span class="o">=</span><span class="n">fig</span><span class="p">,</span> <span class="n">save_dest</span><span class="o">=</span><span class="n">dest</span><span class="p">)</span>
-        <span class="k">return</span> <span class="n">data</span>
+        <span class="k">try</span><span class="p">:</span>
+            <span class="n">fig</span><span class="p">,</span> <span class="n">data</span> <span class="o">=</span> <span class="n">func</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">*</span><span class="n">args</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">)</span>
+            <span class="n">save_dest</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;save_dest&#39;</span><span class="p">,</span> <span class="kc">None</span><span class="p">)</span>
+            <span class="k">if</span> <span class="n">save_dest</span> <span class="ow">is</span> <span class="ow">not</span> <span class="kc">None</span><span class="p">:</span>
+                <span class="n">dest</span> <span class="o">=</span> <span class="n">save_dest</span> <span class="o">+</span> <span class="s1">&#39;.pdf&#39;</span>
+                <span class="bp">self</span><span class="o">.</span><span class="n">export_plot</span><span class="p">(</span><span class="n">fig</span><span class="o">=</span><span class="n">fig</span><span class="p">,</span> <span class="n">save_dest</span><span class="o">=</span><span class="n">dest</span><span class="p">)</span>
+            <span class="k">return</span> <span class="n">data</span>
+        <span class="k">except</span> <span class="ne">ValueError</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>   
+            <span class="n">warn</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">e</span><span class="p">))</span>
+            <span class="k">return</span> <span class="p">{}</span>
 
     <span class="k">return</span> <span class="n">wrapper</span></div>
 

diff --git a/documentation/build/html/_modules/bio_compose/verifier.html b/documentation/build/html/_modules/bio_compose/verifier.html
@@ -295,8 +295,8 @@ <h1>Source code for bio_compose.verifier</h1><div class="highlight"><pre>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="k">try</span><span class="p">:</span>
             <span class="n">output</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_output</span><span class="p">(</span><span class="n">job_id</span><span class="o">=</span><span class="n">job_id</span><span class="p">)</span>
-            <span class="k">return</span> <span class="n">output</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;results&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;rmse&#39;</span><span class="p">)</span> <span class="ow">or</span> <span class="p">{}</span>
-        <span class="k">except</span> <span class="ne">Exception</span> <span class="k">as</span> <span class="n">e</span><span class="p">:</span>
+            <span class="k">return</span> <span class="n">output</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;results&#39;</span><span class="p">)</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">&#39;rmse&#39;</span><span class="p">,</span> <span class="p">{})</span> 
+        <span class="k">except</span><span class="p">:</span>
             <span class="kn">import</span> <span class="nn">traceback</span>
             <span class="n">tb_str</span> <span class="o">=</span> <span class="n">traceback</span><span class="o">.</span><span class="n">format_exc</span><span class="p">()</span>
             <span class="n">error_message</span> <span class="o">=</span> <span class="p">(</span>
@@ -505,19 +505,19 @@ <h1>Source code for bio_compose.verifier</h1><div class="highlight"><pre>
 <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>
 
-<span class="sd">        Args:</span>
-<span class="sd">            - **job_id**: `str`: verification job id. This value can be easily derived from either of `Verifier`&#39;s `.verify_...` methods.</span>
-<span class="sd">            - **fig_dimensions**: `Tuple[int, int], optional`: The value to use as the `figsize` parameter for a call to `matplotlib.pyplot.figure()`. If `None` is passed, default to (8, 6).</span>
-<span class="sd">            - **color_mapping**: `List[str], optional`: list of colors to use for each simulator in the grid. Defaults to None.</span>
-<span class="sd">            - **save_dest**: `str`: destination at which to save figure. Defaults to `None`.</span>
+<span class="sd">        :param job_id: (`str`) verification job id. This value can be easily derived from either of `Verifier`&#39;s `.verify_...` methods.</span>
+<span class="sd">        :param fig_dimensions: (`Tuple[int, int], optional`) The value to use as the `figsize` parameter for a call to `matplotlib.pyplot.figure()`. If `None` is passed, default to (8, 6).</span>
+<span class="sd">        :param color_mapping: (`List[str], optional`) list of colors to use for each simulator in the grid. Defaults to None.</span>
+<span class="sd">        :param save_dest: `(str`) destination at which to save figure. Defaults to `None`.</span>
 
-<span class="sd">         Returns:</span>
-<span class="sd">            `Tuple[matplotlib.Figure, Dict]` of matplotlib Figure and simulator RMSE scores</span>
+<span class="sd">        :return: matplotlib Figure and simulator RMSE scores</span>
+<span class="sd">        :rtype: `Tuple[matplotlib.Figure, Dict]`</span>
 <span class="sd">        &quot;&quot;&quot;</span>
         <span class="c1"># extract data</span>
         <span class="n">rmse_matrix</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_rmse</span><span class="p">(</span><span class="n">job_id</span><span class="p">)</span>
-        <span class="k">if</span> <span class="s1">&#39;error&#39;</span> <span class="ow">in</span> <span class="n">rmse_matrix</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
-            <span class="k">raise</span> <span class="ne">IOError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;The job for </span><span class="si">{</span><span class="n">job_id</span><span class="si">}</span><span class="s2"> is either not ready or has an error. Please check the output.&quot;</span><span class="p">)</span>
+        <span class="k">if</span> <span class="ow">not</span> <span class="n">rmse_matrix</span> <span class="ow">or</span> <span class="s1">&#39;error&#39;</span> <span class="ow">in</span> <span class="n">rmse_matrix</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
+            <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;The job for </span><span class="si">{</span><span class="n">job_id</span><span class="si">}</span><span class="s2"> is either not ready or has an error in rmse scoring. Please check the output.&quot;</span><span class="p">)</span>
+
         <span class="n">simulators</span> <span class="o">=</span> <span class="nb">list</span><span class="p">(</span><span class="n">rmse_matrix</span><span class="o">.</span><span class="n">keys</span><span class="p">())</span>
         <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>
 

diff --git a/documentation/build/html/_sources/verification.rst.txt b/documentation/build/html/_sources/verification.rst.txt
@@ -14,7 +14,6 @@ Running **OMEX verifications**:
 
     verification = verify(filepath, simulators)
 
-
 Running **SBML verifications**:
 
 .. code-block:: python
@@ -27,4 +26,11 @@ Running **SBML verifications**:
     duration = 100
     n_steps = 1000
 
-    verification = verify(filepath, start_time, duration, n_steps, simulators)
+    verification = verify(filepath, start_time, duration, n_steps, simulators)
+
+Visualizing verifications:
+
+.. code-block:: python
+    
+    verification.observables()  # visualize observables
+    verification.rmse(save_dest='/my/save/path/for/observables')  # visualize root-mean-square error scores for all simulators involved in the verification.
diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
@@ -642,17 +642,18 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
-<li><p><strong>job_id</strong> (<em>-</em>) – <cite>str</cite>: verification job id. This value can be easily derived from either of <cite>Verifier</cite>’s <cite>.verify_…</cite> methods.</p></li>
-<li><p><strong>fig_dimensions</strong> (<em>-</em>) – <cite>Tuple[int, int], optional</cite>: The value to use as the <cite>figsize</cite> parameter for a call to <cite>matplotlib.pyplot.figure()</cite>. If <cite>None</cite> is passed, default to (8, 6).</p></li>
-<li><p><strong>color_mapping</strong> (<em>-</em>) – <cite>List[str], optional</cite>: list of colors to use for each simulator in the grid. Defaults to None.</p></li>
-<li><p><strong>save_dest</strong> (<em>-</em>) – <p><cite>str</cite>: destination at which to save figure. Defaults to <cite>None</cite>.</p>
-<dl class="simple">
-<dt>Returns:</dt><dd><p><cite>Tuple[matplotlib.Figure, Dict]</cite> of matplotlib Figure and simulator RMSE scores</p>
-</dd>
-</dl>
-</p></li>
+<li><p><strong>job_id</strong> – (<cite>str</cite>) verification job id. This value can be easily derived from either of <cite>Verifier</cite>’s <cite>.verify_…</cite> methods.</p></li>
+<li><p><strong>fig_dimensions</strong> – (<cite>Tuple[int, int], optional</cite>) The value to use as the <cite>figsize</cite> parameter for a call to <cite>matplotlib.pyplot.figure()</cite>. If <cite>None</cite> is passed, default to (8, 6).</p></li>
+<li><p><strong>color_mapping</strong> – (<cite>List[str], optional</cite>) list of colors to use for each simulator in the grid. Defaults to None.</p></li>
+<li><p><strong>save_dest</strong> – <cite>(str</cite>) destination at which to save figure. Defaults to <cite>None</cite>.</p></li>
 </ul>
 </dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>matplotlib Figure and simulator RMSE scores</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><cite>Tuple[matplotlib.Figure, Dict]</cite></p>
+</dd>
 </dl>
 </dd></dl>
 

diff --git a/documentation/build/html/searchindex.js b/documentation/build/html/searchindex.js
diff --git a/documentation/build/html/verification.html b/documentation/build/html/verification.html
@@ -100,6 +100,11 @@ <h1>Verification<a class="headerlink" href="#verification" title="Link to this h
 <span class="n">verification</span> <span class="o">=</span> <span class="n">verify</span><span class="p">(</span><span class="n">filepath</span><span class="p">,</span> <span class="n">start_time</span><span class="p">,</span> <span class="n">duration</span><span class="p">,</span> <span class="n">n_steps</span><span class="p">,</span> <span class="n">simulators</span><span class="p">)</span>
 </pre></div>
 </div>
+<p>Visualizing verifications:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">verification</span><span class="o">.</span><span class="n">observables</span><span class="p">()</span>  <span class="c1"># visualize observables</span>
+<span class="n">verification</span><span class="o">.</span><span class="n">rmse</span><span class="p">(</span><span class="n">save_dest</span><span class="o">=</span><span class="s1">&#39;/my/save/path/for/observables&#39;</span><span class="p">)</span>  <span class="c1"># visualize root-mean-square error scores for all simulators involved in the verification.</span>
+</pre></div>
+</div>
 </section>
 
 

diff --git a/documentation/source/verification.rst b/documentation/source/verification.rst
@@ -14,15 +14,6 @@ Running **OMEX verifications**:
 
     verification = verify(filepath, simulators)
 
-Visualizing verifications:
-
-.. code-block:: python
-    # visualize observables
-    verification.observables()
-
-    # visualize root-mean-square error scores for all simulators involved in the verification.
-    verification.rmse(save_dest='/my/save/path/for/observables')
-
 Running **SBML verifications**:
 
 .. code-block:: python
@@ -35,4 +26,11 @@ Running **SBML verifications**:
     duration = 100
     n_steps = 1000
 
-    verification = verify(filepath, start_time, duration, n_steps, simulators)
+    verification = verify(filepath, start_time, duration, n_steps, simulators)
+
+Visualizing verifications:
+
+.. code-block:: python
+    
+    verification.observables()  # visualize observables
+    verification.rmse(save_dest='/my/save/path/for/observables')  # visualize root-mean-square error scores for all simulators involved in the verification.