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biosimulators · Sep 9, 2024 · dfe3b92 · dfe3b92
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diff --git a/bio_compose/__init__.py b/bio_compose/__init__.py
@@ -16,13 +16,26 @@
 
 def run_simulation(*args, **kwargs) -> SimulationResult:
     """
-    Run a simulation with BioCompose
+    Run a simulation with BioCompose.
 
     Args:
-        - **args**: Positional arguments:
-            1 argument(**smoldyn simulation only**): smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
-            3 arguments(**smoldyn simulation only**): smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt
-            5 arguments(**sbml simulation only**): sbml filepath, simulation start, simulation end, simulation steps, simulator.
+        *args: Positional arguments:
+            1 argument (smoldyn simulation only):
+                - smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
+
+            3 arguments (smoldyn simulation only):
+                - smoldyn configuration file
+                - smoldyn simulation duration
+                - smoldyn simulation dt
+
+            5 arguments (sbml simulation only):
+                - sbml filepath
+                - simulation start
+                - simulation end
+                - simulation steps
+                - simulator
+
+        **kwargs: Keyword arguments.
 
     Returns:
         `SimulationResult` instance of simulation results.

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.html b/documentation/build/html/_modules/bio_compose.html
@@ -92,13 +92,26 @@ <h1>Source code for bio_compose</h1><div class="highlight"><pre>
 <a class="viewcode-back" href="../bio_compose.html#bio_compose.run_simulation">[docs]</a>
 <span class="k">def</span> <span class="nf">run_simulation</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="o">-&gt;</span> <span class="n">SimulationResult</span><span class="p">:</span>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</span>
-<span class="sd">    Run a simulation with BioCompose</span>
+<span class="sd">    Run a simulation with BioCompose.</span>
 
 <span class="sd">    Args:</span>
-<span class="sd">        - **args**: Positional arguments:</span>
-<span class="sd">            1 argument(**smoldyn simulation only**): smoldyn simulation configuration in which time parameters (dt, duration) are already defined.</span>
-<span class="sd">            3 arguments(**smoldyn simulation only**): smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt</span>
-<span class="sd">            5 arguments(**sbml simulation only**): sbml filepath, simulation start, simulation end, simulation steps, simulator.</span>
+<span class="sd">        *args: Positional arguments:</span>
+<span class="sd">            1 argument (smoldyn simulation only):</span>
+<span class="sd">                - smoldyn simulation configuration in which time parameters (dt, duration) are already defined.</span>
+
+<span class="sd">            3 arguments (smoldyn simulation only):</span>
+<span class="sd">                - smoldyn configuration file</span>
+<span class="sd">                - smoldyn simulation duration</span>
+<span class="sd">                - smoldyn simulation dt</span>
+
+<span class="sd">            5 arguments (sbml simulation only):</span>
+<span class="sd">                - sbml filepath</span>
+<span class="sd">                - simulation start</span>
+<span class="sd">                - simulation end</span>
+<span class="sd">                - simulation steps</span>
+<span class="sd">                - simulator</span>
+
+<span class="sd">        **kwargs: Keyword arguments.</span>
 
 <span class="sd">    Returns:</span>
 <span class="sd">        `SimulationResult` instance of simulation results.</span>

diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
@@ -662,13 +662,36 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Link to this headi
 <dl class="py function">
 <dt class="sig sig-object py" id="bio_compose.run_simulation">
 <span class="sig-prename descclassname"><span class="pre">bio_compose.</span></span><span class="sig-name descname"><span class="pre">run_simulation</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="o"><span class="pre">*</span></span><span class="n"><span class="pre">args</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span> <span class="sig-return"><span class="sig-return-icon">&#x2192;</span> <span class="sig-return-typehint"><a class="reference internal" href="#bio_compose.runner.SimulationResult" title="bio_compose.runner.SimulationResult"><span class="pre">SimulationResult</span></a></span></span><a class="reference internal" href="_modules/bio_compose.html#run_simulation"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#bio_compose.run_simulation" title="Link to this definition"></a></dt>
-<dd><p>Run a simulation with BioCompose</p>
+<dd><p>Run a simulation with BioCompose.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
-<dd class="field-odd"><p><strong>args</strong> (<em>-</em>) – Positional arguments:
-1 argument(<strong>smoldyn simulation only</strong>): smoldyn simulation configuration in which time parameters (dt, duration) are already defined.
-3 arguments(<strong>smoldyn simulation only</strong>): smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt
-5 arguments(<strong>sbml simulation only</strong>): sbml filepath, simulation start, simulation end, simulation steps, simulator.</p>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>*args</strong> – <p>Positional arguments:
+1 argument (smoldyn simulation only):</p>
+<blockquote>
+<div><ul>
+<li><p>smoldyn simulation configuration in which time parameters (dt, duration) are already defined.</p></li>
+</ul>
+</div></blockquote>
+<dl class="simple">
+<dt>3 arguments (smoldyn simulation only):</dt><dd><ul>
+<li><p>smoldyn configuration file</p></li>
+<li><p>smoldyn simulation duration</p></li>
+<li><p>smoldyn simulation dt</p></li>
+</ul>
+</dd>
+<dt>5 arguments (sbml simulation only):</dt><dd><ul>
+<li><p>sbml filepath</p></li>
+<li><p>simulation start</p></li>
+<li><p>simulation end</p></li>
+<li><p>simulation steps</p></li>
+<li><p>simulator</p></li>
+</ul>
+</dd>
+</dl>
+</p></li>
+<li><p><strong>**kwargs</strong> – Keyword arguments.</p></li>
+</ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
 <dd class="field-even"><p><cite>SimulationResult</cite> instance of simulation results.</p>