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biosimulators · Sep 9, 2024 · 5fcecc2 · 5fcecc2
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diff --git a/bio_compose/__init__.py b/bio_compose/__init__.py
@@ -15,13 +15,12 @@
 
 
 def run_simulation(*args, **kwargs) -> SimulationResult:
-    """
-    Run a simulation with BioCompose.
+    """Run a simulation with BioCompose.
 
-    :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
+    :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
 
     :param kwargs: Keyword arguments
 

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/getting-started.doctree b/documentation/build/doctrees/getting-started.doctree
diff --git a/documentation/build/doctrees/index.doctree b/documentation/build/doctrees/index.doctree
diff --git a/documentation/build/html/_images/bio-compose.png b/documentation/build/html/_images/bio-compose.png
diff --git a/documentation/build/html/_modules/bio_compose.html b/documentation/build/html/_modules/bio_compose.html
@@ -41,9 +41,14 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../getting-started.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../getting-started.html#verification">Verification</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../getting-started.html#simulation-runs">Simulation Runs</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">BioCompose modules</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../modules.html">bio_compose</a></li>
 </ul>
 
@@ -91,13 +96,12 @@ <h1>Source code for bio_compose</h1><div class="highlight"><pre>
 <div class="viewcode-block" id="run_simulation">
 <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="w">    </span><span class="sd">&quot;&quot;&quot;Run a simulation with BioCompose.</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">    :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">    :param kwargs: Keyword arguments</span>
 

diff --git a/documentation/build/html/_modules/index.html b/documentation/build/html/_modules/index.html
@@ -41,9 +41,14 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../getting-started.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../getting-started.html#verification">Verification</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../getting-started.html#simulation-runs">Simulation Runs</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">BioCompose modules</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="../installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="../modules.html">bio_compose</a></li>
 </ul>
 

diff --git a/documentation/build/html/_sources/getting-started.rst.txt b/documentation/build/html/_sources/getting-started.rst.txt
@@ -0,0 +1,87 @@
+Installation
+============
+
+To install `bio-compose`, you can use pip:
+
+.. code-block:: bash
+
+   pip install bio-compose
+
+If you are installing from source, clone the repository and use the following commands:
+
+.. code-block:: bash
+
+   git clone https://github.com/biosimulators/bio-compose.git
+   cd your_project
+   pip install -e .
+
+
+Verification
+============
+
+
+Running a verification with `bio-compose` can be achieved in a few simple steps.
+
+Running a **OMEX verifications**:
+
+.. code-block:: python
+
+    from bio_compose import verify
+
+    filepath = '/path/to/a/valid/omex/file.omex'
+    simulators = ['amici', 'copasi', 'tellurium']
+
+    verification = verify(filepath, simulators)
+
+
+Running **SBML verifications**:
+
+.. code-block:: python
+
+    from bio_compose import verify
+
+    filepath = '/path/to/a/valid/sbml/file.xml'
+    simulators = ['amici', 'copasi', 'tellurium']
+    start_time = 0
+    duration = 100
+    n_steps = 1000
+
+    verification = verify(filepath, start_time, duration, n_steps, simulators)
+
+
+Simulation Runs
+===============
+
+`bio-compose` has a `run_simulation` method that can be used to run either: a Smoldyn simulation **OR** a SBML simulation.
+
+Running a **Smoldyn simulation**:
+
+.. code-block:: python
+
+    from bio_compose import run_simulation
+
+    filepath = '/path/to/a/valid/smoldyn/configuration/txt/file.txt'
+    duration = 10
+    dt = 0.02
+    result = run_simulation(filepath, duration, dt)
+
+
+Running a **SBML simulation**:
+
+.. code-block:: python
+
+    from bio_compose import run_simulation
+
+    filepath = '/path/to/a/valid/sbml/file.xml'
+    simulator = 'copasi'
+    start_time = 0
+    duration = 100
+    n_steps = 1000
+    result = run_simulation(filepath, start_time, duration, n_steps, simulator)
+
+
+
+
+
+
+
diff --git a/documentation/build/html/_sources/index.rst.txt b/documentation/build/html/_sources/index.rst.txt
@@ -7,11 +7,18 @@ BioCompose documentation
 ========================
 Create, execute, and introspect reproducible composite simulations of dynamic biological systems.
 
+.. image:: ./bio-compose.png
+   :alt: BioCompose logo
 
 .. toctree::
    :maxdepth: 2
-   :caption: Contents:
+   :caption: Getting started
+
+   getting-started
+
+.. toctree::
+   :maxdepth: 2
+   :caption: BioCompose modules
 
-   installation
    modules
 
diff --git a/documentation/build/html/bio_compose.html b/documentation/build/html/bio_compose.html
@@ -43,9 +43,14 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="getting-started.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="getting-started.html#verification">Verification</a></li>
+<li class="toctree-l1"><a class="reference internal" href="getting-started.html#simulation-runs">Simulation Runs</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">BioCompose modules</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1 current"><a class="reference internal" href="modules.html">bio_compose</a><ul class="current">
 <li class="toctree-l2 current"><a class="current reference internal" href="#">bio_compose package</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#submodules">Submodules</a></li>
@@ -671,7 +676,7 @@ <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> – Positional arguments
+<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>

diff --git a/documentation/build/html/genindex.html b/documentation/build/html/genindex.html
@@ -41,9 +41,14 @@
   </form>
 </div>
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption" role="heading"><span class="caption-text">Contents:</span></p>
+              <p class="caption" role="heading"><span class="caption-text">Getting started</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="getting-started.html">Installation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="getting-started.html#verification">Verification</a></li>
+<li class="toctree-l1"><a class="reference internal" href="getting-started.html#simulation-runs">Simulation Runs</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">BioCompose modules</span></p>
 <ul>
-<li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">bio_compose</a></li>
 </ul>