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

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biosimulators · Dec 23, 2020 · ec57b46 · ec57b46
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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: '0.1.17',
+    VERSION: '0.1.18',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',

diff --git a/docs/about.html b/docs/about.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>3. About BioSimulators utils &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>3. About BioSimulators utils &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>

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 utils 0.1.17 documentation</title>
+    <title>Index &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>

diff --git a/docs/index.html b/docs/index.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>BioSimulators utils documentation &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>BioSimulators utils documentation &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
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diff --git a/docs/installation.html b/docs/installation.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>1. Installation instructions &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>1. Installation instructions &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
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diff --git a/docs/py-modindex.html b/docs/py-modindex.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>Python Module Index &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>Python Module Index &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
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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 utils 0.1.17 documentation</title>
+    <title>Search &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
 

diff --git a/docs/searchindex.js b/docs/searchindex.js
diff --git a/docs/source/biosimulators_utils.archive.html b/docs/source/biosimulators_utils.archive.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.1. biosimulators_utils.archive package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.1. biosimulators_utils.archive package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.biosimulations.html b/docs/source/biosimulators_utils.biosimulations.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.2. biosimulators_utils.biosimulations package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.2. biosimulators_utils.biosimulations package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.combine.html b/docs/source/biosimulators_utils.combine.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.3. biosimulators_utils.combine package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.3. biosimulators_utils.combine package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.gh_action.html b/docs/source/biosimulators_utils.gh_action.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.4. biosimulators_utils.gh_action package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.4. biosimulators_utils.gh_action package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>

diff --git a/docs/source/biosimulators_utils.html b/docs/source/biosimulators_utils.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2. biosimulators_utils package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2. biosimulators_utils package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>

diff --git a/docs/source/biosimulators_utils.kisao.html b/docs/source/biosimulators_utils.kisao.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.5. biosimulators_utils.kisao package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.5. biosimulators_utils.kisao package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>

diff --git a/docs/source/biosimulators_utils.plot.html b/docs/source/biosimulators_utils.plot.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.6. biosimulators_utils.plot package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.6. biosimulators_utils.plot package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.report.html b/docs/source/biosimulators_utils.report.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.7. biosimulators_utils.report package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.7. biosimulators_utils.report package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.sedml.html b/docs/source/biosimulators_utils.sedml.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.8. biosimulators_utils.sedml package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.8. biosimulators_utils.sedml package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.simulator.html b/docs/source/biosimulators_utils.simulator.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.9. biosimulators_utils.simulator package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.9. biosimulators_utils.simulator package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
     <script id="documentation_options" data-url_root="../" src="../_static/documentation_options.js"></script>
@@ -340,11 +340,14 @@ <h2><span class="section-number">2.1.9.1. </span>Submodules<a class="headerlink"
 </dl>
 <dl class="py function">
 <dt id="biosimulators_utils.simulator.io.read_simulator_specs">
-<code class="sig-prename descclassname">biosimulators_utils.simulator.io.</code><code class="sig-name descname">read_simulator_specs</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_or_url</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_utils/blob/dev/biosimulators_utils/simulator/io.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_utils.simulator.io.read_simulator_specs" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">biosimulators_utils.simulator.io.</code><code class="sig-name descname">read_simulator_specs</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">path_or_url</span></em>, <em class="sig-param"><span class="n">patch</span><span class="o">=</span><span class="default_value">None</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_utils/blob/dev/biosimulators_utils/simulator/io.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_utils.simulator.io.read_simulator_specs" title="Permalink to this definition">¶</a></dt>
 <dd><p>Read the specifications of a simulator</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters</dt>
-<dd class="field-odd"><p><strong>path_or_url</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – file path or URL for the specifications of a simulator</p>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>path_or_url</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">str</span></code>) – file path or URL for the specifications of a simulator</p></li>
+<li><p><strong>patch</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code>, optional) – values of properties to supersede those in <code class="xref py py-obj docutils literal notranslate"><span class="pre">path_or_url</span></code></p></li>
+</ul>
 </dd>
 <dt class="field-even">Returns</dt>
 <dd class="field-even"><p>specifications of a simulator</p>

diff --git a/docs/source/biosimulators_utils.simulator_registry.html b/docs/source/biosimulators_utils.simulator_registry.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.10. biosimulators_utils.simulator_registry package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.10. biosimulators_utils.simulator_registry package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.utils.html b/docs/source/biosimulators_utils.utils.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.11. biosimulators_utils.utils package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.11. biosimulators_utils.utils package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
     <link rel="stylesheet" href="../_static/alabaster.css" type="text/css" />
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diff --git a/docs/source/biosimulators_utils.xml.html b/docs/source/biosimulators_utils.xml.html
@@ -5,7 +5,7 @@
   <head>
     <meta charset="utf-8" />
     <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-    <title>2.1.12. biosimulators_utils.xml package &#8212; BioSimulators utils 0.1.17 documentation</title>
+    <title>2.1.12. biosimulators_utils.xml package &#8212; BioSimulators utils 0.1.18 documentation</title>
     <link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
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