chore: Updated compiled documentation [skip ci]

biosimulators · Sep 17, 2024 · 6ff6945 · 6ff6945
1 parent 9270ab3
commit 6ff6945
Show file tree

Hide file tree

Showing 38 changed files with 343 additions and 364 deletions.
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.1.188',
+    VERSION: '0.1.189',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/about.html b/docs/about.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>About BioSimulators utils &#8212; BioSimulators utils 0.1.188 documentation</title>
+    <title>About BioSimulators utils &#8212; BioSimulators utils 0.1.189 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=ee523f82"></script>
+    <script src="_static/documentation_options.js?v=4a2abb9b"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'about';</script>
@@ -124,8 +124,8 @@
 
 
 
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.188 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.188 documentation - Home"/>`);</script>
+    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.189 documentation - Home"/>
+    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.189 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -469,7 +469,7 @@ <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" t
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.0.2.
     <br/>
   </p>
 </div>

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; BioSimulators utils 0.1.188 documentation</title>
+    <title>Index &#8212; BioSimulators utils 0.1.189 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=ee523f82"></script>
+    <script src="_static/documentation_options.js?v=4a2abb9b"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'genindex';</script>
@@ -121,8 +121,8 @@
 
 
 
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.188 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.188 documentation - Home"/>`);</script>
+    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.189 documentation - Home"/>
+    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.189 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -791,20 +791,6 @@ <h2 id="B">B</h2>
 
       <ul>
         <li><a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl">module</a>
-</li>
-      </ul></li>
-      <li>
-    biosimulators_utils.model_lang.bngl.utils
-
-      <ul>
-        <li><a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl.utils">module</a>
-</li>
-      </ul></li>
-      <li>
-    biosimulators_utils.model_lang.bngl.validation
-
-      <ul>
-        <li><a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl.validation">module</a>
 </li>
       </ul></li>
       <li>
@@ -861,6 +847,20 @@ <h2 id="B">B</h2>
 
       <ul>
         <li><a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba">module</a>
+</li>
+      </ul></li>
+      <li>
+    biosimulators_utils.model_lang.rba.utils
+
+      <ul>
+        <li><a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba.utils">module</a>
+</li>
+      </ul></li>
+      <li>
+    biosimulators_utils.model_lang.rba.validation
+
+      <ul>
+        <li><a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba.validation">module</a>
 </li>
       </ul></li>
       <li>
@@ -1942,10 +1942,10 @@ <h2 id="G">G</h2>
 </li>
       <li><a href="source/biosimulators_utils.model_lang.sbml.html#biosimulators_utils.model_lang.sbml.utils.get_package_namespace">get_package_namespace() (in module biosimulators_utils.model_lang.sbml.utils)</a>
 </li>
-      <li><a href="source/biosimulators_utils.model_lang.bngl.html#biosimulators_utils.model_lang.bngl.utils.get_parameters_variables_outputs_for_simulation">get_parameters_variables_outputs_for_simulation() (in module biosimulators_utils.model_lang.bngl.utils)</a>
+      <li><a href="source/biosimulators_utils.model_lang.cellml.html#biosimulators_utils.model_lang.cellml.utils.get_parameters_variables_outputs_for_simulation">get_parameters_variables_outputs_for_simulation() (in module biosimulators_utils.model_lang.cellml.utils)</a>
 
       <ul>
-        <li><a href="source/biosimulators_utils.model_lang.cellml.html#biosimulators_utils.model_lang.cellml.utils.get_parameters_variables_outputs_for_simulation">(in module biosimulators_utils.model_lang.cellml.utils)</a>
+        <li><a href="source/biosimulators_utils.model_lang.rba.html#biosimulators_utils.model_lang.rba.utils.get_parameters_variables_outputs_for_simulation">(in module biosimulators_utils.model_lang.rba.utils)</a>
 </li>
         <li><a href="source/biosimulators_utils.model_lang.sbml.html#biosimulators_utils.model_lang.sbml.utils.get_parameters_variables_outputs_for_simulation">(in module biosimulators_utils.model_lang.sbml.utils)</a>
 </li>
@@ -2729,10 +2729,6 @@ <h2 id="M">M</h2>
         <li><a href="source/biosimulators_utils.model_lang.html#module-biosimulators_utils.model_lang">biosimulators_utils.model_lang</a>
 </li>
         <li><a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl">biosimulators_utils.model_lang.bngl</a>
-</li>
-        <li><a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl.utils">biosimulators_utils.model_lang.bngl.utils</a>
-</li>
-        <li><a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl.validation">biosimulators_utils.model_lang.bngl.validation</a>
 </li>
         <li><a href="source/biosimulators_utils.model_lang.cellml.html#module-biosimulators_utils.model_lang.cellml">biosimulators_utils.model_lang.cellml</a>
 </li>
@@ -2749,6 +2745,10 @@ <h2 id="M">M</h2>
         <li><a href="source/biosimulators_utils.model_lang.neuroml.html#module-biosimulators_utils.model_lang.neuroml.validation">biosimulators_utils.model_lang.neuroml.validation</a>
 </li>
         <li><a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba">biosimulators_utils.model_lang.rba</a>
+</li>
+        <li><a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba.utils">biosimulators_utils.model_lang.rba.utils</a>
+</li>
+        <li><a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba.validation">biosimulators_utils.model_lang.rba.validation</a>
 </li>
         <li><a href="source/biosimulators_utils.model_lang.sbml.html#module-biosimulators_utils.model_lang.sbml">biosimulators_utils.model_lang.sbml</a>
 </li>
@@ -3466,8 +3466,6 @@ <h2 id="R">R</h2>
       <li><a href="source/biosimulators_utils.viz.vega.escher.html#biosimulators_utils.viz.vega.escher.core.read_escher_map_config">read_escher_map_config() (in module biosimulators_utils.viz.vega.escher.core)</a>
 </li>
       <li><a href="source/biosimulators_utils.combine.html#biosimulators_utils.combine.io.CombineArchiveReader.read_manifest">read_manifest() (biosimulators_utils.combine.io.CombineArchiveReader method)</a>
-</li>
-      <li><a href="source/biosimulators_utils.model_lang.bngl.html#biosimulators_utils.model_lang.bngl.validation.read_model">read_model() (in module biosimulators_utils.model_lang.bngl.validation)</a>
 </li>
       <li><a href="source/biosimulators_utils.model_lang.smoldyn.html#biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter.read_model_output_dataframe">read_model_output_dataframe() (biosimulators_utils.model_lang.smoldyn.simularium_converter.SmoldynDataConverter method)</a>
 </li>
@@ -4161,14 +4159,14 @@ <h2 id="V">V</h2>
 </li>
       <li><a href="source/biosimulators_utils.html#biosimulators_utils.config.Config.VALIDATE_IMPORTED_MODEL_FILES">VALIDATE_IMPORTED_MODEL_FILES (biosimulators_utils.config.Config attribute)</a>
 </li>
-      <li><a href="source/biosimulators_utils.model_lang.bngl.html#biosimulators_utils.model_lang.bngl.validation.validate_model">validate_model() (in module biosimulators_utils.model_lang.bngl.validation)</a>
+      <li><a href="source/biosimulators_utils.model_lang.cellml.html#biosimulators_utils.model_lang.cellml.validation.validate_model">validate_model() (in module biosimulators_utils.model_lang.cellml.validation)</a>
 
       <ul>
-        <li><a href="source/biosimulators_utils.model_lang.cellml.html#biosimulators_utils.model_lang.cellml.validation.validate_model">(in module biosimulators_utils.model_lang.cellml.validation)</a>
-</li>
         <li><a href="source/biosimulators_utils.model_lang.lems.html#biosimulators_utils.model_lang.lems.validation.validate_model">(in module biosimulators_utils.model_lang.lems.validation)</a>
 </li>
         <li><a href="source/biosimulators_utils.model_lang.neuroml.html#biosimulators_utils.model_lang.neuroml.validation.validate_model">(in module biosimulators_utils.model_lang.neuroml.validation)</a>
+</li>
+        <li><a href="source/biosimulators_utils.model_lang.rba.html#biosimulators_utils.model_lang.rba.validation.validate_model">(in module biosimulators_utils.model_lang.rba.validation)</a>
 </li>
         <li><a href="source/biosimulators_utils.model_lang.sbml.html#biosimulators_utils.model_lang.sbml.validation.validate_model">(in module biosimulators_utils.model_lang.sbml.validation)</a>
 </li>
@@ -4542,7 +4540,7 @@ <h2 id="Z">Z</h2>
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.0.2.
     <br/>
   </p>
 </div>

diff --git a/docs/index.html b/docs/index.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>BioSimulators utils documentation &#8212; BioSimulators utils 0.1.188 documentation</title>
+    <title>BioSimulators utils documentation &#8212; BioSimulators utils 0.1.189 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=ee523f82"></script>
+    <script src="_static/documentation_options.js?v=4a2abb9b"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'index';</script>
@@ -123,8 +123,8 @@
 
 
 
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.188 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.188 documentation - Home"/>`);</script>
+    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.189 documentation - Home"/>
+    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.189 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -452,7 +452,7 @@ <h2>Contents<a class="headerlink" href="#contents" title="Link to this heading">
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.0.2.
     <br/>
   </p>
 </div>

diff --git a/docs/installation.html b/docs/installation.html
@@ -8,7 +8,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
-    <title>Installation instructions &#8212; BioSimulators utils 0.1.188 documentation</title>
+    <title>Installation instructions &#8212; BioSimulators utils 0.1.189 documentation</title>
 
 
 
@@ -36,7 +36,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=ee523f82"></script>
+    <script src="_static/documentation_options.js?v=4a2abb9b"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'installation';</script>
@@ -124,8 +124,8 @@
 
 
 
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.188 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.188 documentation - Home"/>`);</script>
+    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.189 documentation - Home"/>
+    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.189 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -531,7 +531,7 @@ <h2>Dockerfile and Docker image<a class="headerlink" href="#dockerfile-and-docke
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.0.2.
     <br/>
   </p>
 </div>

diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -7,7 +7,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; BioSimulators utils 0.1.188 documentation</title>
+    <title>Python Module Index &#8212; BioSimulators utils 0.1.189 documentation</title>
 
 
 
@@ -35,7 +35,7 @@
 <link rel="preload" as="script" href="_static/scripts/pydata-sphinx-theme.js?digest=dfe6caa3a7d634c4db9b" />
   <script src="_static/vendor/fontawesome/6.5.2/js/all.min.js?digest=dfe6caa3a7d634c4db9b"></script>
 
-    <script src="_static/documentation_options.js?v=ee523f82"></script>
+    <script src="_static/documentation_options.js?v=4a2abb9b"></script>
     <script src="_static/doctools.js?v=9a2dae69"></script>
     <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
     <script>DOCUMENTATION_OPTIONS.pagename = 'py-modindex';</script>
@@ -124,8 +124,8 @@
 
 
 
-    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.188 documentation - Home"/>
-    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.188 documentation - Home"/>`);</script>
+    <img src="_static/biosimulators-logo.svg" class="logo__image only-light" alt="BioSimulators utils 0.1.189 documentation - Home"/>
+    <script>document.write(`<img src="_static/biosimulators-logo.svg" class="logo__image only-dark" alt="BioSimulators utils 0.1.189 documentation - Home"/>`);</script>
 
 
 </a></div>
@@ -504,16 +504,6 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl"><code class="xref">biosimulators_utils.model_lang.bngl</code></a></td><td>
        <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl.utils"><code class="xref">biosimulators_utils.model_lang.bngl.utils</code></a></td><td>
-       <em></em></td></tr>
-     <tr class="cg-1">
-       <td></td>
-       <td>&#160;&#160;&#160;
-       <a href="source/biosimulators_utils.model_lang.bngl.html#module-biosimulators_utils.model_lang.bngl.validation"><code class="xref">biosimulators_utils.model_lang.bngl.validation</code></a></td><td>
-       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -554,6 +544,16 @@ <h1>Python Module Index</h1>
        <td>&#160;&#160;&#160;
        <a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba"><code class="xref">biosimulators_utils.model_lang.rba</code></a></td><td>
        <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba.utils"><code class="xref">biosimulators_utils.model_lang.rba.utils</code></a></td><td>
+       <em></em></td></tr>
+     <tr class="cg-1">
+       <td></td>
+       <td>&#160;&#160;&#160;
+       <a href="source/biosimulators_utils.model_lang.rba.html#module-biosimulators_utils.model_lang.rba.validation"><code class="xref">biosimulators_utils.model_lang.rba.validation</code></a></td><td>
+       <em></em></td></tr>
      <tr class="cg-1">
        <td></td>
        <td>&#160;&#160;&#160;
@@ -924,7 +924,7 @@ <h1>Python Module Index</h1>
         <div class="footer-item">
 
   <p class="sphinx-version">
-    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.4.7.
+    Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 8.0.2.
     <br/>
   </p>
 </div>