updates to docs

biosimulators · Sep 9, 2024 · 4519790 · 4519790
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diff --git a/bio_compose/__init__.py b/bio_compose/__init__.py
@@ -18,27 +18,15 @@ def run_simulation(*args, **kwargs) -> SimulationResult:
     """
     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
+    :param 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
 
-            5 arguments (sbml simulation only):
-                - sbml filepath
-                - simulation start
-                - simulation end
-                - simulation steps
-                - simulator
+    :param kwargs: Keyword arguments
 
-        **kwargs: Keyword arguments.
-
-    Returns:
-        `SimulationResult` instance of simulation results.
+    :return: instance of simulation results.
+    :rtype: bio_compose.runner.SimulationResult
     """
     # set up submission
     runner = SimulationRunner()

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
@@ -3,7 +3,7 @@
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>bio_compose &mdash; BioCompose 0.3.2 documentation</title>
+  <title>bio_compose &mdash; BioCompose 0.5.4 documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
 
@@ -14,7 +14,7 @@
 
         <script src="../_static/jquery.js?v=5d32c60e"></script>
         <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-        <script src="../_static/documentation_options.js?v=71d9d8e6"></script>
+        <script src="../_static/documentation_options.js?v=e1a677a5"></script>
         <script src="../_static/doctools.js?v=9a2dae69"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
     <script src="../_static/js/theme.js"></script>
@@ -94,27 +94,15 @@ <h1>Source code for bio_compose</h1><div class="highlight"><pre>
 <span class="w">    </span><span class="sd">&quot;&quot;&quot;</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):</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">    :param 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">            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">    :param kwargs: Keyword arguments</span>
 
-<span class="sd">        **kwargs: Keyword arguments.</span>
-
-<span class="sd">    Returns:</span>
-<span class="sd">        `SimulationResult` instance of simulation results.</span>
+<span class="sd">    :return: instance of simulation results.</span>
+<span class="sd">    :rtype: bio_compose.runner.SimulationResult</span>
 <span class="sd">    &quot;&quot;&quot;</span>
     <span class="c1"># set up submission</span>
     <span class="n">runner</span> <span class="o">=</span> <span class="n">SimulationRunner</span><span class="p">()</span>

diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
@@ -671,35 +671,18 @@ <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>*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>
+<li><p><strong>args</strong> – 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</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>
+<dd class="field-even"><p>instance of simulation results.</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p><a class="reference internal" href="#bio_compose.runner.SimulationResult" title="bio_compose.runner.SimulationResult">bio_compose.runner.SimulationResult</a></p>
 </dd>
 </dl>
 </dd></dl>