Merge branch 'dev' of ssh://github.com/biosimulators/Biosimulators_MA…

…SSpy into dev
biosimulators · Dec 14, 2021 · 145b90d · 145b90d
2 parents 48f17b4 + ef234fa
commit 145b90d
Show file tree

Hide file tree

Showing 17 changed files with 200 additions and 134 deletions.
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
@@ -731,8 +731,9 @@ dl.glossary dt {
 
 .classifier:before {
     font-style: normal;
-    margin: 0.5em;
+    margin: 0 0.5em;
     content: ":";
+    display: inline-block;
 }
 
 abbr, acronym {

diff --git a/docs/_static/css/blank.css b/docs/_static/css/blank.css
@@ -0,0 +1,2 @@
+/* This file is intentionally left blank to override the stylesheet of the
+parent theme via theme.conf. The parent style we import directly in theme.css */
diff --git a/docs/_static/css/index.ff1ffe594081f20da1ef19478df9384b.css b/docs/_static/css/index.ff1ffe594081f20da1ef19478df9384b.css
diff --git a/docs/_static/css/theme.css b/docs/_static/css/theme.css
@@ -1,3 +1,6 @@
+/* Provided by the Sphinx base theme template at build time */
+@import "../basic.css";
+
 :root {
   /*****************************************************************************
   * Theme config

diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.0.4',
+    VERSION: '0.0.5',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/_static/js/index.be7d3bbb2ef33a8344ce.js b/docs/_static/js/index.be7d3bbb2ef33a8344ce.js
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
@@ -328,7 +328,9 @@ var Search = {
     var results = [];
 
     for (var prefix in objects) {
-      for (var name in objects[prefix]) {
+      for (var iMatch = 0; iMatch != objects[prefix].length; ++iMatch) {
+        var match = objects[prefix][iMatch];
+        var name = match[4];
         var fullname = (prefix ? prefix + '.' : '') + name;
         var fullnameLower = fullname.toLowerCase()
         if (fullnameLower.indexOf(object) > -1) {
@@ -342,7 +344,6 @@ var Search = {
           } else if (parts[parts.length - 1].indexOf(object) > -1) {
             score += Scorer.objPartialMatch;
           }
-          var match = objects[prefix][name];
           var objname = objnames[match[1]][2];
           var title = titles[match[0]];
           // If more than one term searched for, we require other words to be

diff --git a/docs/_static/webpack-macros.html b/docs/_static/webpack-macros.html
@@ -12,14 +12,14 @@
 {% endmacro %}
 
 {% macro head_pre_bootstrap() %}
-  <link href="{{ pathto('_static/css/theme.css', 1) }}" rel="stylesheet" />
-  <link href="{{ pathto('_static/css/index.c5995385ac14fb8791e8eb36b4908be2.css', 1) }}" rel="stylesheet" />
+  <link href="{{ pathto('_static/css/theme.css', 1) }}" rel="stylesheet">
+  <link href="{{ pathto('_static/css/index.ff1ffe594081f20da1ef19478df9384b.css', 1) }}" rel="stylesheet">
 {% endmacro %}
 
 {% macro head_js_preload() %}
-  <link rel="preload" as="script" href="{{ pathto('_static/js/index.1c5a1a01449ed65a7b51.js', 1) }}">
+  <link rel="preload" as="script" href="{{ pathto('_static/js/index.be7d3bbb2ef33a8344ce.js', 1) }}">
 {% endmacro %}
 
 {% macro body_post() %}
-  <script src="{{ pathto('_static/js/index.1c5a1a01449ed65a7b51.js', 1) }}"></script>
+  <script src="{{ pathto('_static/js/index.be7d3bbb2ef33a8344ce.js', 1) }}"></script>
 {% endmacro %}
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-MASSpy &#8212; BioSimulators-MASSpy 0.0.4 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-MASSpy &#8212; BioSimulators-MASSpy 0.0.5 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>
@@ -38,7 +39,7 @@
     <link rel="next" title="Index" href="genindex.html" />
     <link rel="prev" title="biosimulators_masspy package" href="source/biosimulators_masspy.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-masspy">
+  <section id="about-biosimulators-masspy">
 <h1>About BioSimulators-MASSpy<a class="headerlink" href="#about-biosimulators-masspy" 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_MASSpy/blob/dev/LICENSE">MIT License</a>. MASSpy is released under the <a class="reference external" href="https://spdx.org/licenses/MIT.html">MIT</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://reproduciblebiomodels.org/">Center for Reproducible Biomedical Modeling</a>. MASSpy was developed by the <a class="reference external" href="https://systemsbiology.ucsd.edu/">Systems Biology Research Group</a> at the <a class="reference external" href="https://ucsd.edu/">University of California, San Diego</a>.</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 address questions and comments about MASSpy to <a class="reference external" href="mailto:zhaiman&#37;&#52;&#48;eng&#46;ucsd&#46;edu">Zachary Haiman</a>.</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-MASSpy 0.0.4 documentation</title>
+    <title>Index &#8212; BioSimulators-MASSpy 0.0.5 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">
 
@@ -252,14 +255,13 @@ <h2 id="P">P</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-MASSpy documentation &#8212; BioSimulators-MASSpy 0.0.4 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-MASSpy documentation &#8212; BioSimulators-MASSpy 0.0.5 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-masspy-documentation">
+  <section id="biosimulators-masspy-documentation">
 <h1>BioSimulators-MASSpy documentation<a class="headerlink" href="#biosimulators-masspy-documentation" title="Permalink to this headline">¶</a></h1>
 <p>BioSimulators-MASSpy provides a <a class="reference external" href="https://biosimulators.org">BioSimulators</a>-compliant command-line interface to the <a class="reference external" href="https://masspy.readthedocs.io/">MASSpy</a> tool for kinetic simulation of metabolic reaction networks. A Docker image for this package is also available.</p>
 <p>This command-line interface and Docker image enable users to use MASSpy 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 kinetic models of metabolic networks in the <a class="reference external" href="https://masspy.readthedocs.io/en/stable/tutorials/reading_writing_models.html">MASSpy schema</a> for the SBML format.</p>
 <p>A list of the algorithms and algorithm parameters supported by MASSpy is available at <a class="reference external" href="https://biosimulators.org/simulators/masspy">BioSimulators</a>.</p>
 <p>A simple web application and web service for using MASSpy 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>
@@ -206,8 +210,8 @@ <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>
@@ -219,14 +223,13 @@ <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>