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<section id="module-biosimulators_pyneuroml">
<span id="biosimulators-pyneuroml-package"></span><h1>biosimulators_pyneuroml package<a class="headerlink" href="#module-biosimulators_pyneuroml" title="Permalink to this headline">¶</a></h1>
<dl class="py class">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.Simulator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.</span></span><span class="sig-name descname"><span class="pre">Simulator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.Simulator" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">enum.Enum</span></code></p>
<p>A LEMS simulator</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.Simulator.brian2">
<span class="sig-name descname"><span class="pre">brian2</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Brian2'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.Simulator.brian2" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.Simulator.netpyne">
<span class="sig-name descname"><span class="pre">netpyne</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'NetPyNe'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.Simulator.netpyne" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.Simulator.neuron">
<span class="sig-name descname"><span class="pre">neuron</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'NEURON'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.Simulator.neuron" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.Simulator.pyneuroml">
<span class="sig-name descname"><span class="pre">pyneuroml</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'pyNeuroML'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.Simulator.pyneuroml" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.exec_sed_doc">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.</span></span><span class="sig-name descname"><span class="pre">exec_sed_doc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">doc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">working_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_out_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rel_out_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apply_xml_model_changes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pretty_print_modified_xml_models</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">StandardOutputErrorCapturerLevel.c</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.exec_sed_doc" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute the tasks specified in a SED document and generate the specified outputs</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>doc</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocument</span></code> or <code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – SED document or a path to SED-ML file which defines a SED document</p></li>
<li><p><strong>working_dir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – working directory of the SED document (path relative to which models are located)</p></li>
<li><p><strong>base_out_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – <p>path to store the outputs</p>
<ul>
<li><p>CSV: directory in which to save outputs to files
<code class="docutils literal notranslate"><span class="pre">{base_out_path}/{rel_out_path}/{report.id}.csv</span></code></p></li>
<li><p>HDF5: directory in which to save a single HDF5 file (<code class="docutils literal notranslate"><span class="pre">{base_out_path}/reports.h5</span></code>),
with reports at keys <code class="docutils literal notranslate"><span class="pre">{rel_out_path}/{report.id}</span></code> within the HDF5 file</p></li>
</ul>
</p></li>
<li><p><strong>rel_out_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>, optional) – path relative to <code class="xref py py-obj docutils literal notranslate"><span class="pre">base_out_path</span></code> to store the outputs</p></li>
<li><p><strong>apply_xml_model_changes</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – if <code class="xref py py-obj docutils literal notranslate"><span class="pre">True</span></code>, apply any model changes specified in the SED-ML file before
calling <code class="xref py py-obj docutils literal notranslate"><span class="pre">task_executer</span></code>.</p></li>
<li><p><strong>log</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocumentLog</span></code>, optional) – log of the document</p></li>
<li><p><strong>indent</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>, optional) – degree to indent status messages</p></li>
<li><p><strong>pretty_print_modified_xml_models</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – if <code class="xref py py-obj docutils literal notranslate"><span class="pre">True</span></code>, pretty print modified XML models</p></li>
<li><p><strong>log_level</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">StandardOutputErrorCapturerLevel</span></code>, optional) – level at which to log output</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
<li><p><strong>simulator</strong> (<a class="reference internal" href="#biosimulators_pyneuroml.Simulator" title="biosimulators_pyneuroml.Simulator"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code></a>, optional) – simulator</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ReportResults</span></code>: results of each report</p></li>
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocumentLog</span></code>: log of the document</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.exec_sed_task">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.</span></span><span class="sig-name descname"><span class="pre">exec_sed_task</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">preprocessed_task</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.exec_sed_task" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute a task and save its results</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Task</span></code>) – task</p></li>
<li><p><strong>variables</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">Variable</span></code>) – variables that should be recorded</p></li>
<li><p><strong>preprocessed_task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code>, optional) – preprocessed information about the task, including possible
model changes and variables. This can be used to avoid repeatedly executing the same initialization
for repeated calls to this method.</p></li>
<li><p><strong>log</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">TaskLog</span></code>, optional) – log for the task</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
<li><p><strong>simulator</strong> (<a class="reference internal" href="#biosimulators_pyneuroml.Simulator" title="biosimulators_pyneuroml.Simulator"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code></a>, optional) – simulator</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">VariableResults</span></code>: results of variables
<code class="xref py py-obj docutils literal notranslate"><span class="pre">TaskLog</span></code>: log</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>ValueError</strong> – if the task or an aspect of the task is not valid, or the requested output variables
could not be recorded</p></li>
<li><p><strong>NotImplementedError</strong> – if the task is not of a supported type or involves an unsuported feature</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.exec_sedml_docs_in_combine_archive">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.</span></span><span class="sig-name descname"><span class="pre">exec_sedml_docs_in_combine_archive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">archive_filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.exec_sedml_docs_in_combine_archive" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>archive_filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – path to COMBINE/OMEX archive</p></li>
<li><p><strong>out_dir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – <p>path to store the outputs of the archive</p>
<ul>
<li><p>CSV: directory in which to save outputs to files
<code class="docutils literal notranslate"><span class="pre">{</span> <span class="pre">out_dir</span> <span class="pre">}/{</span> <span class="pre">relative-path-to-SED-ML-file-within-archive</span> <span class="pre">}/{</span> <span class="pre">report.id</span> <span class="pre">}.csv</span></code></p></li>
<li><p>HDF5: directory in which to save a single HDF5 file (<code class="docutils literal notranslate"><span class="pre">{</span> <span class="pre">out_dir</span> <span class="pre">}/reports.h5</span></code>),
with reports at keys <code class="docutils literal notranslate"><span class="pre">{</span> <span class="pre">relative-path-to-SED-ML-file-within-archive</span> <span class="pre">}/{</span> <span class="pre">report.id</span> <span class="pre">}</span></code> within the HDF5 file</p></li>
</ul>
</p></li>
<li><p><strong>simulator</strong> (<a class="reference internal" href="#biosimulators_pyneuroml.Simulator" title="biosimulators_pyneuroml.Simulator"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code></a>, optional) – simulator</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocumentResults</span></code>: results</p></li>
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">CombineArchiveLog</span></code>: log</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.preprocess_sed_task">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.</span></span><span class="sig-name descname"><span class="pre">preprocess_sed_task</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/__init__.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.preprocess_sed_task" title="Permalink to this definition">¶</a></dt>
<dd><p>Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
repeatedly initializing tasks on repeated calls of <a class="reference internal" href="#biosimulators_pyneuroml.exec_sed_task" title="biosimulators_pyneuroml.exec_sed_task"><code class="xref py py-obj docutils literal notranslate"><span class="pre">exec_sed_task</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Task</span></code>) – task</p></li>
<li><p><strong>variables</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">Variable</span></code>) – variables that should be recorded</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
<li><p><strong>simulator</strong> (<a class="reference internal" href="#biosimulators_pyneuroml.Simulator" title="biosimulators_pyneuroml.Simulator"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code></a>, optional) – simulator</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>preprocessed information about the task</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code></p>
</dd>
</dl>
</dd></dl>
<section id="subpackages">
<h2>Subpackages<a class="headerlink" href="#subpackages" title="Permalink to this headline">¶</a></h2>
<div class="toctree-wrapper compound">
<ul>
<li class="toctree-l1"><a class="reference internal" href="biosimulators_pyneuroml.api.html">biosimulators_pyneuroml.api package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.api.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.api.html#module-biosimulators_pyneuroml.api.brian2">biosimulators_pyneuroml.api.brian2 module</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.api.html#module-biosimulators_pyneuroml.api.netpyne">biosimulators_pyneuroml.api.netpyne module</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.api.html#module-biosimulators_pyneuroml.api.neuron">biosimulators_pyneuroml.api.neuron module</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.api.html#module-biosimulators_pyneuroml.api.pyneuroml">biosimulators_pyneuroml.api.pyneuroml module</a></li>
</ul>
</li>
<li class="toctree-l1"><a class="reference internal" href="biosimulators_pyneuroml.cli.html">biosimulators_pyneuroml.cli package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.cli.html#submodules">Submodules</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.cli.html#module-biosimulators_pyneuroml.cli.brian2">biosimulators_pyneuroml.cli.brian2 module</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.cli.html#module-biosimulators_pyneuroml.cli.netpyne">biosimulators_pyneuroml.cli.netpyne module</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.cli.html#module-biosimulators_pyneuroml.cli.neuron">biosimulators_pyneuroml.cli.neuron module</a></li>
<li class="toctree-l2"><a class="reference internal" href="biosimulators_pyneuroml.cli.html#module-biosimulators_pyneuroml.cli.pyneuroml">biosimulators_pyneuroml.cli.pyneuroml module</a></li>
</ul>
</li>
</ul>
</div>
</section>
<section id="submodules">
<h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this headline">¶</a></h2>
</section>
<section id="module-biosimulators_pyneuroml.core">
<span id="biosimulators-pyneuroml-core-module"></span><h2>biosimulators_pyneuroml.core module<a class="headerlink" href="#module-biosimulators_pyneuroml.core" title="Permalink to this headline">¶</a></h2>
<p>Methods for using pyNeuroML to execute SED tasks in COMBINE archives and save their outputs</p>
<dl class="field-list simple">
<dt class="field-odd">Author</dt>
<dd class="field-odd"><p>Jonathan Karr <<a class="reference external" href="mailto:karr%40mssm.edu">karr<span>@</span>mssm<span>.</span>edu</a>></p>
</dd>
<dt class="field-even">Date</dt>
<dd class="field-even"><p>2021-05-28</p>
</dd>
<dt class="field-odd">Copyright</dt>
<dd class="field-odd"><p>2021, Center for Reproducible Biomedical Modeling</p>
</dd>
<dt class="field-even">License</dt>
<dd class="field-even"><p>MIT</p>
</dd>
</dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.core.exec_sed_doc">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.core.</span></span><span class="sig-name descname"><span class="pre">exec_sed_doc</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">doc</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">working_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">base_out_path</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">rel_out_path</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">apply_xml_model_changes</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">indent</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">0</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pretty_print_modified_xml_models</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log_level</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">StandardOutputErrorCapturerLevel.c</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/core.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.core.exec_sed_doc" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute the tasks specified in a SED document and generate the specified outputs</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>doc</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocument</span></code> or <code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – SED document or a path to SED-ML file which defines a SED document</p></li>
<li><p><strong>working_dir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – working directory of the SED document (path relative to which models are located)</p></li>
<li><p><strong>base_out_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – <p>path to store the outputs</p>
<ul>
<li><p>CSV: directory in which to save outputs to files
<code class="docutils literal notranslate"><span class="pre">{base_out_path}/{rel_out_path}/{report.id}.csv</span></code></p></li>
<li><p>HDF5: directory in which to save a single HDF5 file (<code class="docutils literal notranslate"><span class="pre">{base_out_path}/reports.h5</span></code>),
with reports at keys <code class="docutils literal notranslate"><span class="pre">{rel_out_path}/{report.id}</span></code> within the HDF5 file</p></li>
</ul>
</p></li>
<li><p><strong>rel_out_path</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>, optional) – path relative to <code class="xref py py-obj docutils literal notranslate"><span class="pre">base_out_path</span></code> to store the outputs</p></li>
<li><p><strong>apply_xml_model_changes</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – if <code class="xref py py-obj docutils literal notranslate"><span class="pre">True</span></code>, apply any model changes specified in the SED-ML file before
calling <code class="xref py py-obj docutils literal notranslate"><span class="pre">task_executer</span></code>.</p></li>
<li><p><strong>log</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocumentLog</span></code>, optional) – log of the document</p></li>
<li><p><strong>indent</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>, optional) – degree to indent status messages</p></li>
<li><p><strong>pretty_print_modified_xml_models</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – if <code class="xref py py-obj docutils literal notranslate"><span class="pre">True</span></code>, pretty print modified XML models</p></li>
<li><p><strong>log_level</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">StandardOutputErrorCapturerLevel</span></code>, optional) – level at which to log output</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
<li><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>, optional) – simulator</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">ReportResults</span></code>: results of each report</p></li>
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocumentLog</span></code>: log of the document</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.core.exec_sed_task">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.core.</span></span><span class="sig-name descname"><span class="pre">exec_sed_task</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">preprocessed_task</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">log</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/core.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.core.exec_sed_task" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute a task and save its results</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Task</span></code>) – task</p></li>
<li><p><strong>variables</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">Variable</span></code>) – variables that should be recorded</p></li>
<li><p><strong>preprocessed_task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code>, optional) – preprocessed information about the task, including possible
model changes and variables. This can be used to avoid repeatedly executing the same initialization
for repeated calls to this method.</p></li>
<li><p><strong>log</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">TaskLog</span></code>, optional) – log for the task</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
<li><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>, optional) – simulator</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">VariableResults</span></code>: results of variables
<code class="xref py py-obj docutils literal notranslate"><span class="pre">TaskLog</span></code>: log</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><ul class="simple">
<li><p><strong>ValueError</strong> – if the task or an aspect of the task is not valid, or the requested output variables
could not be recorded</p></li>
<li><p><strong>NotImplementedError</strong> – if the task is not of a supported type or involves an unsuported feature</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.core.exec_sedml_docs_in_combine_archive">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.core.</span></span><span class="sig-name descname"><span class="pre">exec_sedml_docs_in_combine_archive</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">archive_filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out_dir</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/core.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.core.exec_sedml_docs_in_combine_archive" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>archive_filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – path to COMBINE/OMEX archive</p></li>
<li><p><strong>out_dir</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – <p>path to store the outputs of the archive</p>
<ul>
<li><p>CSV: directory in which to save outputs to files
<code class="docutils literal notranslate"><span class="pre">{</span> <span class="pre">out_dir</span> <span class="pre">}/{</span> <span class="pre">relative-path-to-SED-ML-file-within-archive</span> <span class="pre">}/{</span> <span class="pre">report.id</span> <span class="pre">}.csv</span></code></p></li>
<li><p>HDF5: directory in which to save a single HDF5 file (<code class="docutils literal notranslate"><span class="pre">{</span> <span class="pre">out_dir</span> <span class="pre">}/reports.h5</span></code>),
with reports at keys <code class="docutils literal notranslate"><span class="pre">{</span> <span class="pre">relative-path-to-SED-ML-file-within-archive</span> <span class="pre">}/{</span> <span class="pre">report.id</span> <span class="pre">}</span></code> within the HDF5 file</p></li>
</ul>
</p></li>
<li><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>, optional) – simulator</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">SedDocumentResults</span></code>: results</p></li>
<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">CombineArchiveLog</span></code>: log</p></li>
</ul>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.core.preprocess_sed_task">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.core.</span></span><span class="sig-name descname"><span class="pre">preprocess_sed_task</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/core.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.core.preprocess_sed_task" title="Permalink to this definition">¶</a></dt>
<dd><p>Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
repeatedly initializing tasks on repeated calls of <a class="reference internal" href="#biosimulators_pyneuroml.core.exec_sed_task" title="biosimulators_pyneuroml.core.exec_sed_task"><code class="xref py py-obj docutils literal notranslate"><span class="pre">exec_sed_task</span></code></a>.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Task</span></code>) – task</p></li>
<li><p><strong>variables</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">Variable</span></code>) – variables that should be recorded</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
<li><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>, optional) – simulator</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>preprocessed information about the task</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code></p>
</dd>
</dl>
</dd></dl>
</section>
<section id="module-biosimulators_pyneuroml.data_model">
<span id="biosimulators-pyneuroml-data-model-module"></span><h2>biosimulators_pyneuroml.data_model module<a class="headerlink" href="#module-biosimulators_pyneuroml.data_model" title="Permalink to this headline">¶</a></h2>
<p>Data model for pyNeuroML algorithms and their parameters</p>
<dl class="field-list simple">
<dt class="field-odd">Author</dt>
<dd class="field-odd"><p>Jonathan Karr <<a class="reference external" href="mailto:karr%40mssm.edu">karr<span>@</span>mssm<span>.</span>edu</a>></p>
</dd>
<dt class="field-even">Date</dt>
<dd class="field-even"><p>2021-06-02</p>
</dd>
<dt class="field-odd">Copyright</dt>
<dd class="field-odd"><p>2021, Center for Reproducible Biomedical Modeling</p>
</dd>
<dt class="field-even">License</dt>
<dd class="field-even"><p>MIT</p>
</dd>
</dl>
<dl class="py class">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.data_model.</span></span><span class="sig-name descname"><span class="pre">RunLemsOptions</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">paths_to_include</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_processors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_memory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">skip_run</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">no_gui</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">load_saved_data</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">reload_events</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">plot</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">show_plot_already</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exec_in_dir</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">exit_on_fail</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">cleanup</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">only_generate_scripts</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">compile_mods</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">realtime_output</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<p>Options for running a LEMS file</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.paths_to_include">
<span class="sig-name descname"><span class="pre">paths_to_include</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.paths_to_include" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.num_processors">
<span class="sig-name descname"><span class="pre">num_processors</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.num_processors" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.max_memory">
<span class="sig-name descname"><span class="pre">max_memory</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.max_memory" title="Permalink to this definition">¶</a></dt>
<dd><p>maximum memory in bytes</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.skip_run">
<span class="sig-name descname"><span class="pre">skip_run</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.skip_run" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.no_gui">
<span class="sig-name descname"><span class="pre">no_gui</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.no_gui" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.load_saved_data">
<span class="sig-name descname"><span class="pre">load_saved_data</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.load_saved_data" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.reload_events">
<span class="sig-name descname"><span class="pre">reload_events</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.reload_events" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.plot">
<span class="sig-name descname"><span class="pre">plot</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.plot" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.show_plot_already">
<span class="sig-name descname"><span class="pre">show_plot_already</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.show_plot_already" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.exec_in_dir">
<span class="sig-name descname"><span class="pre">exec_in_dir</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.exec_in_dir" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.verbose">
<span class="sig-name descname"><span class="pre">verbose</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.verbose" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.exit_on_fail">
<span class="sig-name descname"><span class="pre">exit_on_fail</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.exit_on_fail" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.cleanup">
<span class="sig-name descname"><span class="pre">cleanup</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.cleanup" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.only_generate_scripts">
<span class="sig-name descname"><span class="pre">only_generate_scripts</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.only_generate_scripts" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.compile_mods">
<span class="sig-name descname"><span class="pre">compile_mods</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.compile_mods" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.realtime_output">
<span class="sig-name descname"><span class="pre">realtime_output</span></span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.realtime_output" title="Permalink to this definition">¶</a></dt>
<dd><dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py method">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.RunLemsOptions.to_kw_args">
<span class="sig-name descname"><span class="pre">to_kw_args</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">simulator</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.RunLemsOptions.to_kw_args" title="Permalink to this definition">¶</a></dt>
<dd><p>Format options as keyword arguments for a LEMS run method</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>simulator</strong> (<a class="reference internal" href="#biosimulators_pyneuroml.data_model.Simulator" title="biosimulators_pyneuroml.data_model.Simulator"><code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code></a>) – simulator</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>keyword arguments for a LEMS run method</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code></p>
</dd>
</dl>
</dd></dl>
</dd></dl>
<dl class="py class">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.Simulator">
<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.data_model.</span></span><span class="sig-name descname"><span class="pre">Simulator</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">value</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.Simulator" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">str</span></code>, <code class="xref py py-class docutils literal notranslate"><span class="pre">enum.Enum</span></code></p>
<p>A LEMS simulator</p>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.Simulator.brian2">
<span class="sig-name descname"><span class="pre">brian2</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'Brian2'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.Simulator.brian2" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.Simulator.netpyne">
<span class="sig-name descname"><span class="pre">netpyne</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'NetPyNe'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.Simulator.netpyne" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.Simulator.neuron">
<span class="sig-name descname"><span class="pre">neuron</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'NEURON'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.Simulator.neuron" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
<dl class="py attribute">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.data_model.Simulator.pyneuroml">
<span class="sig-name descname"><span class="pre">pyneuroml</span></span><em class="property"><span class="w"> </span><span class="p"><span class="pre">=</span></span><span class="w"> </span><span class="pre">'pyNeuroML'</span></em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.data_model.Simulator.pyneuroml" title="Permalink to this definition">¶</a></dt>
<dd></dd></dl>
</dd></dl>
</section>
<section id="module-biosimulators_pyneuroml.utils">
<span id="biosimulators-pyneuroml-utils-module"></span><h2>biosimulators_pyneuroml.utils module<a class="headerlink" href="#module-biosimulators_pyneuroml.utils" title="Permalink to this headline">¶</a></h2>
<p>Utilities for pyNeuroML</p>
<dl class="field-list simple">
<dt class="field-odd">Author</dt>
<dd class="field-odd"><p>Jonathan Karr <<a class="reference external" href="mailto:karr%40mssm.edu">karr<span>@</span>mssm<span>.</span>edu</a>></p>
</dd>
<dt class="field-even">Date</dt>
<dd class="field-even"><p>2021-06-02</p>
</dd>
<dt class="field-odd">Copyright</dt>
<dd class="field-odd"><p>2021, Center for Reproducible Biomedical Modeling</p>
</dd>
<dt class="field-even">License</dt>
<dd class="field-even"><p>MIT</p>
</dd>
</dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.get_available_memory">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">get_available_memory</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.get_available_memory" title="Permalink to this definition">¶</a></dt>
<dd><p>Get the amount of memory available</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>amount of memory available in bytes</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.get_available_processors">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">get_available_processors</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.get_available_processors" title="Permalink to this definition">¶</a></dt>
<dd><p>Get the amount of processors available</p>
<dl class="field-list simple">
<dt class="field-odd">Returns</dt>
<dd class="field-odd"><p>amount of processors available</p>
</dd>
<dt class="field-even">Return type</dt>
<dd class="field-even"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.get_run_lems_options">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">get_run_lems_options</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">num_processors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_memory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.get_run_lems_options" title="Permalink to this definition">¶</a></dt>
<dd><p>Get options for running a LEMS document</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>num_processors</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>, optional) – number of processors to use (only used with NetPyNe)</p></li>
<li><p><strong>max_memory</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>, optional) – maximum memory to use in bytes</p></li>
<li><p><strong>verbose</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – whether to display extra information about simulation runs</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>options</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">RunLemsOptions</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.get_simulator_run_lems_method">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">get_simulator_run_lems_method</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">simulator</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.get_simulator_run_lems_method" title="Permalink to this definition">¶</a></dt>
<dd><p>Get the LEMS run method for a simulator</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>) – simulator to run the LEMS document</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>run LEMS method</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">types.FunctionType</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.read_lems_output_files_configuration">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">read_lems_output_files_configuration</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">xml_root</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.read_lems_output_files_configuration" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the configuration of the output files of a LEMS document</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>xml_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">lxml.etree._Element</span></code>) – LEMS document</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>configuration of the output files of a LEMS document</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.read_xml_file">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">read_xml_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">remove_blank_text</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.read_xml_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Read an XML file</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – path to an XML file</p></li>
<li><p><strong>remove_blank_text</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – whether to remove
formatting so that the file could be exported pretty-printed</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>root element for the XML file</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">lxml.etree._Element</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.run_lems_xml">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">run_lems_xml</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lems_xml_root</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">working_dirname</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'.'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">lems_filename</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">num_processors</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">max_memory</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">verbose</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">False</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.run_lems_xml" title="Permalink to this definition">¶</a></dt>
<dd><p>Run a LEMS document with a simulator</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>lems_xml_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">lxml.etree._Element</span></code>) – LEMS document</p></li>
<li><p><strong>working_dirname</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>, optional) – working directory for the LEMS document</p></li>
<li><p><strong>lems_filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>, optional) – path to file for the LEMS document</p></li>
<li><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>, optional) – simulator to run the LEMS document</p></li>
<li><p><strong>num_processors</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>, optional) – number of processors to use (only used with NetPyNe)</p></li>
<li><p><strong>max_memory</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">int</span></code>, optional) – maximum memory to use in bytes</p></li>
<li><p><strong>verbose</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – whether to display extra information about simulation runs</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><dl class="simple">
<dt>dictionary that maps the id of each output file</dt><dd><p>to a Pandas data frame with its value</p>
</dd>
</dl>
</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code> => <code class="xref py py-obj docutils literal notranslate"><span class="pre">pandas.DataFrame</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.set_sim_in_lems_xml">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">set_sim_in_lems_xml</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">simulation_xml</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">task</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">Simulator.pyneuroml</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.set_sim_in_lems_xml" title="Permalink to this definition">¶</a></dt>
<dd><p>Set the simulation in a LEMS document</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>simulation_xml</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">lxml.etree._Element</span></code>) – LEMS simulation</p></li>
<li><p><strong>task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Task</span></code>) – task</p></li>
<li><p><strong>variables</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">Variable</span></code>) – variables to record</p></li>
<li><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>, optional) – simulator to run the LEMS document</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.validate_lems_document">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">validate_lems_document</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">lems_xml_root</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.validate_lems_document" title="Permalink to this definition">¶</a></dt>
<dd><p>Validate LEMS document</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>lems_xml_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">lxml.etree._Element</span></code>) – LEMS document</p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.validate_task">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">validate_task</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">task</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">variables</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">simulator</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">config</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.validate_task" title="Permalink to this definition">¶</a></dt>
<dd><p>Validate a task</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Task</span></code>) – task</p></li>
<li><p><strong>variables</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">Variable</span></code>) – variables</p></li>
<li><p><strong>simulator</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Simulator</span></code>) – simulator</p></li>
<li><p><strong>config</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Config</span></code>, optional) – BioSimulators common configuration</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>KiSAO id for a possibly alternative simulation algorithm</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code></p>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.write_lems_output_files_configuration">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">write_lems_output_files_configuration</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">xml_root</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">output_file_configs</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.write_lems_output_files_configuration" title="Permalink to this definition">¶</a></dt>
<dd><p>Read the configuration of the output files of a LEMS document</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>xml_root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">lxml.etree._Element</span></code>) – LEMS document</p></li>
<li><p><strong>output_file_configs</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code>) – configuration of the output files of a LEMS document</p></li>
</ul>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="biosimulators_pyneuroml.utils.write_xml_file">
<span class="sig-prename descclassname"><span class="pre">biosimulators_pyneuroml.utils.</span></span><span class="sig-name descname"><span class="pre">write_xml_file</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">root</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">filename</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">pretty_print</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">True</span></span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_pyNeuroML/blob/dev/biosimulators_pyneuroml/utils.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_pyneuroml.utils.write_xml_file" title="Permalink to this definition">¶</a></dt>
<dd><p>Write an XML file</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>root</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">lxml.etree._Element</span></code>) – root element for the XML file</p></li>
<li><p><strong>filename</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – path to an XML file</p></li>
<li><p><strong>pretty_print</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – whether to pretty-print the file (required for NeuroML)</p></li>
</ul>
</dd>
</dl>
</dd></dl>