chore: Updating compiled documentation [skip ci]

biosimulators · Dec 14, 2021 · 3b59e9a · 3b59e9a
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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 = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.1.79',
+    VERSION: '0.1.80',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/about.html b/docs/about.html
@@ -6,7 +6,7 @@
     <meta charset="utf-8" />
     <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 the BioSimulators test suite &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>About the BioSimulators test suite &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
   <link href="_static/css/theme.css" rel="stylesheet">
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diff --git a/docs/genindex.html b/docs/genindex.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Index &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>Index &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">

diff --git a/docs/index.html b/docs/index.html
@@ -6,7 +6,7 @@
     <meta charset="utf-8" />
     <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 test suite documentation &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>BioSimulators test suite documentation &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
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@@ -176,17 +176,17 @@
 
   <section id="biosimulators-test-suite-documentation">
 <h1>BioSimulators test suite documentation<a class="headerlink" href="#biosimulators-test-suite-documentation" title="Permalink to this headline">¶</a></h1>
-<p>The BioSimulators test suite is a tool for validating that biosimulation software tools implement the <a class="reference external" href="https://biosimulators.org/conventions">BioSimulators conventions for biosimulation tools</a>.</p>
+<p>The BioSimulators test suite is a tool for validating that biosimulation software tools implement the <a class="reference external" href="https://docs.biosimulations.org/concepts/conventions/">BioSimulators conventions for biosimulation tools</a>.</p>
 <p>The test suite is composed of two parts:</p>
 <ul>
 <li><p>A collection of example modeling projects. Each project is represented by a single <a class="reference external" href="https://combinearchive.org/">COMBINE/OMEX archive</a> that contains one or more simulation experiments described using the <a class="reference external" href="https://sed-ml.org">Simulation Experiment Description Markup Language (SED-ML)</a> and one or more models described using a format such as the <a class="reference external" href="https://bionetgen.org">BioNetGen Language (BNGL)</a>) or the <a class="reference external" href="http://sbml.org">Systems Biology Markup Language (SBML)</a>.</p></li>
 <li><p>Software for checking that biosimulation tools execute these projects according to the BioSimulators conventions.</p>
 <blockquote>
 <div><ul class="simple">
-<li><p>Simulation tools support the <a class="reference external" href="https://biosimulators.org/conventions/simulator-interfaces">BioSimulators standard command-line arguments</a>.</p></li>
-<li><p>Simulation tools support the <a class="reference external" href="https://biosimulators.org/conventions/simulator-images">BioSimulators conventions for Docker images</a>.</p></li>
-<li><p>Simulation tools follow the <a class="reference external" href="https://biosimulators.org/conventions/simulation-experiments">BioSimulators conventions for executing simulations described by SED-ML files in COMBINE/OMEX archives</a>.</p></li>
-<li><p>Simulation tools support the <a class="reference external" href="https://biosimulators.org/conventions/simulation-reports">BioSimulators conventions for the outputs of SED-ML files in COMBINE/OMEX archives</a>.</p></li>
+<li><p>Simulation tools support the <a class="reference external" href="https://docs.biosimulations.org/concepts/conventions/simulator-interfaces/">BioSimulators standard command-line arguments</a>.</p></li>
+<li><p>Simulation tools support the <a class="reference external" href="https://docs.biosimulations.org/concepts/conventions/simulator-images/">BioSimulators conventions for Docker images</a>.</p></li>
+<li><p>Simulation tools follow the <a class="reference external" href="https://docs.biosimulations.org/concepts/conventions/simulation-experiments/">BioSimulators conventions for executing simulations described by SED-ML files in COMBINE/OMEX archives</a>.</p></li>
+<li><p>Simulation tools support the <a class="reference external" href="https://docs.biosimulations.org/concepts/conventions/simulation-run-reports/">BioSimulators conventions for the outputs of SED-ML files in COMBINE/OMEX archives</a>.</p></li>
 </ul>
 </div></blockquote>
 </li>

diff --git a/docs/installation.html b/docs/installation.html
@@ -6,7 +6,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
-    <title>Installation instructions &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>Installation instructions &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
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diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -5,7 +5,7 @@
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-    <title>Python Module Index &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>Python Module Index &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
   <link href="_static/css/theme.css" rel="stylesheet">
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diff --git a/docs/search.html b/docs/search.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Search &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>Search &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/source/biosimulators_test_suite.html b/docs/source/biosimulators_test_suite.html
diff --git a/docs/source/biosimulators_test_suite.results.html b/docs/source/biosimulators_test_suite.results.html
@@ -6,7 +6,7 @@
     <meta charset="utf-8" />
     <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_test_suite.results package &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>biosimulators_test_suite.results package &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
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   <link href="../_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">
@@ -359,7 +359,7 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
 
 <dl class="py class">
 <dt class="sig sig-object py" id="biosimulators_test_suite.results.data_model.TestResultsReport">
-<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">biosimulators_test_suite.results.data_model.</span></span><span class="sig-name descname"><span class="pre">TestResultsReport</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">test_suite_version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'0.1.79'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">results</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">gh_issue</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">gh_action_run</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_test_suite/blob/dev/biosimulators_test_suite/results/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_test_suite.results.data_model.TestResultsReport" title="Permalink to this definition">¶</a></dt>
+<em class="property"><span class="pre">class</span><span class="w"> </span></em><span class="sig-prename descclassname"><span class="pre">biosimulators_test_suite.results.data_model.</span></span><span class="sig-name descname"><span class="pre">TestResultsReport</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">test_suite_version</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'0.1.80'</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">results</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">gh_issue</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">gh_action_run</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_test_suite/blob/dev/biosimulators_test_suite/results/data_model.py"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#biosimulators_test_suite.results.data_model.TestResultsReport" 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>A report of the results of executing the test suite with a simulation tool</p>
 <dl class="py attribute">

diff --git a/docs/source/biosimulators_test_suite.test_case.html b/docs/source/biosimulators_test_suite.test_case.html
@@ -6,7 +6,7 @@
     <meta charset="utf-8" />
     <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_test_suite.test_case package &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>biosimulators_test_suite.test_case package &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
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diff --git a/docs/tutorial.html b/docs/tutorial.html
@@ -6,7 +6,7 @@
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="generator" content="Docutils 0.17.1: http://docutils.sourceforge.net/" />
 
-    <title>Tutorial &#8212; BioSimulators test suite 0.1.79 documentation</title>
+    <title>Tutorial &#8212; BioSimulators test suite 0.1.80 documentation</title>
 
   <link href="_static/css/theme.css" rel="stylesheet">
   <link href="_static/css/index.ff1ffe594081f20da1ef19478df9384b.css" rel="stylesheet">