Merge branch 'dev' of ssh://github.com/reproducible-biomedical-modeli…

…ng/Biosimulations_COPASI into dev
biosimulators · Dec 14, 2021 · b8811fc · b8811fc
2 parents 8bbabbd + 5206798
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diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -731,8 +731,9 @@ dl.glossary dt {
 
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diff --git a/docs/_static/css/blank.css b/docs/_static/css/blank.css
@@ -0,0 +1,2 @@
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diff --git a/docs/_static/css/theme.css b/docs/_static/css/theme.css
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diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
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-    VERSION: '0.1.32',
+    VERSION: '0.1.33',
     LANGUAGE: 'en',
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diff --git a/docs/_static/js/index.be7d3bbb2ef33a8344ce.js b/docs/_static/js/index.be7d3bbb2ef33a8344ce.js
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+      for (var iMatch = 0; iMatch != objects[prefix].length; ++iMatch) {
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diff --git a/docs/_static/webpack-macros.html b/docs/_static/webpack-macros.html
@@ -12,14 +12,14 @@
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+  <link href="{{ pathto('_static/css/index.ff1ffe594081f20da1ef19478df9384b.css', 1) }}" rel="stylesheet">
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+  <link rel="preload" as="script" href="{{ pathto('_static/js/index.be7d3bbb2ef33a8344ce.js', 1) }}">
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+  <script src="{{ pathto('_static/js/index.be7d3bbb2ef33a8344ce.js', 1) }}"></script>
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diff --git a/docs/about.html b/docs/about.html
@@ -4,11 +4,12 @@
 <html lang="en">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>About BioSimulators-COPASI &#8212; BioSimulators-COPASI 0.1.32 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>About BioSimulators-COPASI &#8212; BioSimulators-COPASI 0.1.33 documentation</title>
 
-  <link href="_static/css/theme.css" rel="stylesheet" />
-  <link href="_static/css/index.c5995385ac14fb8791e8eb36b4908be2.css" rel="stylesheet" />
+  <link href="_static/css/theme.css" rel="stylesheet">
+  <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
 
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@@ -23,10 +24,10 @@
 
 
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="_static/basic.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/blank.css" />
     <link rel="stylesheet" type="text/css" href="_static/css/biosimulators.css" />
 
-  <link rel="preload" as="script" href="_static/js/index.1c5a1a01449ed65a7b51.js">
+  <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
@@ -38,7 +39,7 @@
     <link rel="next" title="Index" href="genindex.html" />
     <link rel="prev" title="biosimulators_copasi package" href="source/biosimulators_copasi.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="en" />
+    <meta name="docsearch:language" content="en">
 
 
       <link rel="icon" sizes="16x16" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-16x16.png">
@@ -48,6 +49,9 @@
       <link rel="icon" sizes="32x32" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-32x32.png">
 
 
+
+    <!-- Google Analytics -->
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
 
@@ -181,21 +185,21 @@
 
               <div>
 
-  <div class="section" id="about-biosimulators-copasi">
+  <section id="about-biosimulators-copasi">
 <h1>About BioSimulators-COPASI<a class="headerlink" href="#about-biosimulators-copasi" title="Permalink to this headline">¶</a></h1>
-<div class="section" id="license">
+<section id="license">
 <h2>License<a class="headerlink" href="#license" title="Permalink to this headline">¶</a></h2>
 <p>This package is released under the <a class="reference external" href="https://github.com/biosimulators/Biosimulators_COPASI/blob/dev/LICENSE">MIT License</a>. COPASI is released under the <a class="reference external" href="http://copasi.org/Download/License/">Artistic 2.0 License</a>.</p>
-</div>
-<div class="section" id="development-team">
+</section>
+<section id="development-team">
 <h2>Development team<a class="headerlink" href="#development-team" title="Permalink to this headline">¶</a></h2>
 <p>This package was developed by the <a class="reference external" href="https://www.karrlab.org">Karr Lab</a> at the Icahn School of Medicine at Mount Sinai and the <a class="reference external" href="https://health.uconn.edu/cell-analysis-modeling/">Center for Cell Analysis &amp; Modeling</a> at the University of Connecticut as part of the <a class="reference external" href="https://reproduciblebiomodels.org/">Center for Reproducible Biomedical Modeling</a>. COPASI was developed by a <a class="reference external" href="http://copasi.org/About/Team/">team</a> at the University of Connecticut, the University of Heidelberg, and the University of Virginia.</p>
-</div>
-<div class="section" id="questions-and-comments">
+</section>
+<section id="questions-and-comments">
 <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" title="Permalink to this headline">¶</a></h2>
 <p>Please contact the <a class="reference external" href="mailto:info&#37;&#52;&#48;biosimulators&#46;org">BioSimulators Team</a> with any questions or comments about the command-line program or Docker image. Please contact the <a class="reference external" href="http://copasi.org/Support/User_Forum/">COPASI Team</a> with any questions or comments about COPASI.</p>
-</div>
-</div>
+</section>
+</section>
 
 
               </div>
@@ -207,14 +211,13 @@ <h2>Questions and comments<a class="headerlink" href="#questions-and-comments" t
       </div>
     </div>
 
-  <script src="_static/js/index.1c5a1a01449ed65a7b51.js"></script>
-
-  <footer class="footer mt-5 mt-md-0">
+  <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
+<footer class="footer mt-5 mt-md-0">
   <div class="container">
 
     <div class="footer-item">
       <p class="copyright">
-    &copy; Copyright 2021, BioSimulators Team.<br/>
+    &copy; Copyright 2021, BioSimulators Team.<br>
 </p>
     </div>
 

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -5,10 +5,10 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; BioSimulators-COPASI 0.1.32 documentation</title>
+    <title>Index &#8212; BioSimulators-COPASI 0.1.33 documentation</title>
 
-  <link href="_static/css/theme.css" rel="stylesheet" />
-  <link href="_static/css/index.c5995385ac14fb8791e8eb36b4908be2.css" rel="stylesheet" />
+  <link href="_static/css/theme.css" rel="stylesheet">
+  <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
 
   <link rel="stylesheet"
@@ -23,10 +23,10 @@
 
 
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="_static/basic.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/blank.css" />
     <link rel="stylesheet" type="text/css" href="_static/css/biosimulators.css" />
 
-  <link rel="preload" as="script" href="_static/js/index.1c5a1a01449ed65a7b51.js">
+  <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
@@ -36,7 +36,7 @@
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="en" />
+    <meta name="docsearch:language" content="en">
 
 
       <link rel="icon" sizes="16x16" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-16x16.png">
@@ -46,6 +46,9 @@
       <link rel="icon" sizes="32x32" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-32x32.png">
 
 
+
+    <!-- Google Analytics -->
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
 
@@ -146,6 +149,7 @@ <h1 id="index">Index</h1>
  | <a href="#C"><strong>C</strong></a>
  | <a href="#D"><strong>D</strong></a>
  | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
  | <a href="#G"><strong>G</strong></a>
  | <a href="#M"><strong>M</strong></a>
  | <a href="#P"><strong>P</strong></a>
@@ -231,6 +235,14 @@ <h2 id="E">E</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="source/biosimulators_copasi.html#biosimulators_copasi.utils.fix_copasi_generated_combine_archive">fix_copasi_generated_combine_archive() (in module biosimulators_copasi.utils)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -305,14 +317,13 @@ <h2 id="U">U</h2>
       </div>
     </div>
 
-  <script src="_static/js/index.1c5a1a01449ed65a7b51.js"></script>
-
-  <footer class="footer mt-5 mt-md-0">
+  <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
+<footer class="footer mt-5 mt-md-0">
   <div class="container">
 
     <div class="footer-item">
       <p class="copyright">
-    &copy; Copyright 2021, BioSimulators Team.<br/>
+    &copy; Copyright 2021, BioSimulators Team.<br>
 </p>
     </div>
 

diff --git a/docs/index.html b/docs/index.html
@@ -4,11 +4,12 @@
 <html lang="en">
   <head>
     <meta charset="utf-8" />
-    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>BioSimulators-COPASI documentation &#8212; BioSimulators-COPASI 0.1.32 documentation</title>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
+
+    <title>BioSimulators-COPASI documentation &#8212; BioSimulators-COPASI 0.1.33 documentation</title>
 
-  <link href="_static/css/theme.css" rel="stylesheet" />
-  <link href="_static/css/index.c5995385ac14fb8791e8eb36b4908be2.css" rel="stylesheet" />
+  <link href="_static/css/theme.css" rel="stylesheet">
+  <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
 
 
   <link rel="stylesheet"
@@ -23,10 +24,10 @@
 
 
     <link rel="stylesheet" type="text/css" href="_static/pygments.css" />
-    <link rel="stylesheet" type="text/css" href="_static/basic.css" />
+    <link rel="stylesheet" type="text/css" href="_static/css/blank.css" />
     <link rel="stylesheet" type="text/css" href="_static/css/biosimulators.css" />
 
-  <link rel="preload" as="script" href="_static/js/index.1c5a1a01449ed65a7b51.js">
+  <link rel="preload" as="script" href="_static/js/index.be7d3bbb2ef33a8344ce.js">
 
     <script data-url_root="./" id="documentation_options" src="_static/documentation_options.js"></script>
     <script src="_static/jquery.js"></script>
@@ -37,7 +38,7 @@
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="Installation instructions" href="installation.html" />
     <meta name="viewport" content="width=device-width, initial-scale=1" />
-    <meta name="docsearch:language" content="en" />
+    <meta name="docsearch:language" content="en">
 
 
       <link rel="icon" sizes="16x16" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-16x16.png">
@@ -47,6 +48,9 @@
       <link rel="icon" sizes="32x32" href="https://github.com/biosimulations/biosimulations/raw/dev/libs/shared/assets/src/assets/icons/favicon-32x32.png">
 
 
+
+    <!-- Google Analytics -->
+
   </head>
   <body data-spy="scroll" data-target="#bd-toc-nav" data-offset="80">
 
@@ -170,13 +174,13 @@
 
               <div>
 
-  <div class="section" id="biosimulators-copasi-documentation">
+  <section id="biosimulators-copasi-documentation">
 <h1>BioSimulators-COPASI documentation<a class="headerlink" href="#biosimulators-copasi-documentation" title="Permalink to this headline">¶</a></h1>
 <p>BioSimulators-COPASI provides a <a class="reference external" href="https://biosimulators.org">BioSimulators</a>-compliant command-line interface to the <a class="reference external" href="http://copasi.org">COPASI</a> biological simulation tool. A Docker image for this package is also available.</p>
 <p>This command-line interface and Docker image enable users to use COPASI to execute <a class="reference external" href="https://combinearchive.org/">COMBINE/OMEX archives</a> that describe one or more simulation experiments (in <a class="reference external" href="https://sed-ml.org">SED-ML format</a>) of one or more models (in <a class="reference external" href="http://sbml.org">SBML format</a>).</p>
 <p>A list of the algorithms and algorithm parameters supported by COPASI is available at <a class="reference external" href="https://biosimulators.org/simulators/copasi">BioSimulators</a>.</p>
 <p>A simple web application and web service for using COPASI to execute COMBINE/OMEX archives is also available at <a class="reference external" href="https://run.biosimulations.org">runBioSimulations</a>.</p>
-<div class="section" id="contents">
+<section id="contents">
 <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this headline">¶</a></h2>
 <div class="toctree-wrapper compound">
 <ul>
@@ -187,8 +191,9 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 </li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">Tutorial</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="tutorial.html#creating-combine-omex-archives-and-encoding-simulation-experiments-into-sed-ml">Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML</a></li>
-<li class="toctree-l2"><a class="reference internal" href="tutorial.html#command-line-program">Command-line program</a></li>
+<li class="toctree-l2"><a class="reference internal" href="tutorial.html#command-line-program-for-executing-combine-omex-archives">Command-line program for executing COMBINE/OMEX archives</a></li>
 <li class="toctree-l2"><a class="reference internal" href="tutorial.html#docker-image-with-a-command-line-entrypoint">Docker image with a command-line entrypoint</a></li>
+<li class="toctree-l2"><a class="reference internal" href="tutorial.html#command-line-program-for-correcting-combine-omex-archives-created-by-copasi">Command-line program for correcting COMBINE/OMEX archives created by COPASI</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="source/biosimulators_copasi.html">API documentation</a><ul>
@@ -207,8 +212,8 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
 <li class="toctree-l1"><a class="reference internal" href="genindex.html">Index</a></li>
 </ul>
 </div>
-</div>
-</div>
+</section>
+</section>
 
 
               </div>
@@ -220,14 +225,13 @@ <h2>Contents<a class="headerlink" href="#contents" title="Permalink to this head
       </div>
     </div>
 
-  <script src="_static/js/index.1c5a1a01449ed65a7b51.js"></script>
-
-  <footer class="footer mt-5 mt-md-0">
+  <script src="_static/js/index.be7d3bbb2ef33a8344ce.js"></script>
+<footer class="footer mt-5 mt-md-0">
   <div class="container">
 
     <div class="footer-item">
       <p class="copyright">
-    &copy; Copyright 2021, BioSimulators Team.<br/>
+    &copy; Copyright 2021, BioSimulators Team.<br>
 </p>
     </div>
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		@@ -0,0 +1,2 @@
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