diff --git a/docs/_static/basic.css b/docs/_static/basic.css
index 24a49f0..be19270 100644
--- a/docs/_static/basic.css
+++ b/docs/_static/basic.css
@@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js
index 7d88f80..144884e 100644
--- a/docs/_static/doctools.js
+++ b/docs/_static/doctools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 595fe13..1dd0f7b 100644
--- 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: '0.1.3',
+ VERSION: '0.1.4',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js
index d2b4ee9..0e7dc7e 100644
--- a/docs/_static/language_data.js
+++ b/docs/_static/language_data.js
@@ -5,7 +5,7 @@
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
index 261ecaa..6fc9e7f 100644
--- a/docs/_static/searchtools.js
+++ b/docs/_static/searchtools.js
@@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for the full-text search.
*
- * :copyright: Copyright 2007-2020 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
diff --git a/docs/about.html b/docs/about.html
index e994edf..b7e491e 100644
--- a/docs/about.html
+++ b/docs/about.html
@@ -5,14 +5,13 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
- <title>About BioSimulators-AMICI — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>About BioSimulators-AMICI — BioSimulators-AMICI 0.1.4 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>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<link rel="author" title="About these documents" href="#" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
diff --git a/docs/genindex.html b/docs/genindex.html
index aee185b..fc35a6a 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -5,14 +5,13 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
- <title>Index — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>Index — BioSimulators-AMICI 0.1.4 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>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<link rel="author" title="About these documents" href="about.html" />
<link rel="index" title="Index" href="#" />
<link rel="search" title="Search" href="search.html" />
diff --git a/docs/index.html b/docs/index.html
index 519dc58..0cf0626 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -5,14 +5,13 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
- <title>BioSimulators-AMICI documentation — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>BioSimulators-AMICI documentation — BioSimulators-AMICI 0.1.4 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>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<link rel="author" title="About these documents" href="about.html" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
diff --git a/docs/installation.html b/docs/installation.html
index dae536d..90a0f5a 100644
--- a/docs/installation.html
+++ b/docs/installation.html
@@ -5,14 +5,13 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
- <title>Installation instructions — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>Installation instructions — BioSimulators-AMICI 0.1.4 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>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<link rel="author" title="About these documents" href="about.html" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
diff --git a/docs/py-modindex.html b/docs/py-modindex.html
index c56bafd..1aebe1d 100644
--- a/docs/py-modindex.html
+++ b/docs/py-modindex.html
@@ -5,14 +5,13 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
- <title>Python Module Index — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>Python Module Index — BioSimulators-AMICI 0.1.4 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>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<link rel="author" title="About these documents" href="about.html" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />
diff --git a/docs/search.html b/docs/search.html
index 352a98f..301f151 100644
--- 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 — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>Search — BioSimulators-AMICI 0.1.4 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
@@ -13,8 +13,8 @@
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<script src="_static/searchtools.js"></script>
+ <script src="_static/language_data.js"></script>
<link rel="author" title="About these documents" href="about.html" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="#" />
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 9e0c488..bb608d0 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
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diff --git a/docs/source/biosimulators_amici.html b/docs/source/biosimulators_amici.html
index ded750f..2fa0aed 100644
--- a/docs/source/biosimulators_amici.html
+++ b/docs/source/biosimulators_amici.html
@@ -5,14 +5,13 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
- <title>biosimulators_amici package — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>biosimulators_amici package — BioSimulators-AMICI 0.1.4 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>
<script src="../_static/jquery.js"></script>
<script src="../_static/underscore.js"></script>
<script src="../_static/doctools.js"></script>
- <script src="../_static/language_data.js"></script>
<link rel="author" title="About these documents" href="../about.html" />
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
@@ -155,10 +154,14 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
</ul>
</dd>
<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>solver</p>
+<dd class="field-even"><p><ul class="simple">
+<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">amici.amici.SolverPtr</span></code>: solver</p></li>
+<li><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code>: dictionary of arguments for the solver</p></li>
+</ul>
+</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">amici.amici.SolverPtr</span></code></p>
+<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><ul class="simple">
@@ -171,20 +174,22 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
<dl class="py function">
<dt id="biosimulators_amici.core.exec_sed_task">
-<code class="sig-prename descclassname">biosimulators_amici.core.</code><code class="sig-name descname">exec_sed_task</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">task</span></em>, <em class="sig-param"><span class="n">variables</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_AMICI/blob/dev/biosimulators_amici/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_amici.core.exec_sed_task" title="Permalink to this definition">¶</a></dt>
+<code class="sig-prename descclassname">biosimulators_amici.core.</code><code class="sig-name descname">exec_sed_task</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">task</span></em>, <em class="sig-param"><span class="n">variables</span></em>, <em class="sig-param"><span class="n">log</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_AMICI/blob/dev/biosimulators_amici/core.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_amici.core.exec_sed_task" title="Permalink to this definition">¶</a></dt>
<dd><p>Execute a task and save its results</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>task</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">Task</span></code>) – task</p></li>
<li><p><strong>variables</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">list</span></code> of <code class="xref py py-obj docutils literal notranslate"><span class="pre">DataGeneratorVariable</span></code>) – variables that should be recorded</p></li>
+<li><p><strong>log</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">TaskLog</span></code>, optional) – log for the task</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
-<dd class="field-even"><p>results of variables</p>
+<dd class="field-even"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataGeneratorVariableResults</span></code>: results of variables
+<code class="xref py py-obj docutils literal notranslate"><span class="pre">TaskLog</span></code>: log</p>
</dd>
<dt class="field-odd">Return type</dt>
-<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">DataGeneratorVariableResults</span></code></p>
+<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">tuple</span></code></p>
</dd>
</dl>
</dd></dl>
@@ -211,6 +216,12 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
<li><p><strong>keep_individual_outputs</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">bool</span></code>, optional) – if <code class="xref py py-obj docutils literal notranslate"><span class="pre">True</span></code>, keep individual output files</p></li>
</ul>
</dd>
+<dt class="field-even">Returns</dt>
+<dd class="field-even"><p>log</p>
+</dd>
+<dt class="field-odd">Return type</dt>
+<dd class="field-odd"><p><code class="xref py py-obj docutils literal notranslate"><span class="pre">CombineArchiveLog</span></code></p>
+</dd>
</dl>
</dd></dl>
diff --git a/docs/tutorial.html b/docs/tutorial.html
index 5ed91aa..39198dd 100644
--- a/docs/tutorial.html
+++ b/docs/tutorial.html
@@ -5,14 +5,13 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
- <title>Tutorial — BioSimulators-AMICI 0.1.3 documentation</title>
+ <title>Tutorial — BioSimulators-AMICI 0.1.4 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>
<script src="_static/jquery.js"></script>
<script src="_static/underscore.js"></script>
<script src="_static/doctools.js"></script>
- <script src="_static/language_data.js"></script>
<link rel="author" title="About these documents" href="about.html" />
<link rel="index" title="Index" href="genindex.html" />
<link rel="search" title="Search" href="search.html" />