Skip to content

Commit

Permalink
Updating compiled documentation
Browse files Browse the repository at this point in the history
  • Loading branch information
biosimulatorsdaemon committed Jan 4, 2021
1 parent 2e13006 commit 4143ce4
Show file tree
Hide file tree
Showing 12 changed files with 53 additions and 15 deletions.
2 changes: 1 addition & 1 deletion docs/_static/documentation_options.js
View file
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '0.1.9',
VERSION: '0.1.10',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
Expand Down
2 changes: 1 addition & 1 deletion docs/about.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>4. About the BioSimulators test suite &#8212; BioSimulators test suite 0.1.9 documentation</title>
<title>4. About the BioSimulators test suite &#8212; BioSimulators test suite 0.1.10 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>
Expand Down
12 changes: 10 additions & 2 deletions docs/genindex.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 0.1.9 documentation</title>
<title>Index &#8212; BioSimulators test suite 0.1.10 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>
Expand Down Expand Up @@ -448,6 +448,8 @@ <h2 id="E">E</h2>
<li><a href="source/biosimulators_test_suite.test_case.html#biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject.eval">(biosimulators_test_suite.test_case.published_project.SimulatorCanExecutePublishedProject method)</a>
</li>
<li><a href="source/biosimulators_test_suite.test_case.html#biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase.eval">(biosimulators_test_suite.test_case.published_project.SyntheticCombineArchiveTestCase method)</a>
</li>
<li><a href="source/biosimulators_test_suite.test_case.html#biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.eval">(biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase method)</a>
</li>
</ul></li>
<li><a href="source/biosimulators_test_suite.html#biosimulators_test_suite.exec_core.SimulatorValidator.eval_case">eval_case() (biosimulators_test_suite.exec_core.SimulatorValidator method)</a>
Expand Down Expand Up @@ -749,10 +751,16 @@ <h2 id="R">R</h2>
</li>
<li><a href="source/biosimulators_test_suite.test_case.html#biosimulators_test_suite.test_case.utils.reduce_array_shape">reduce_array_shape() (in module biosimulators_test_suite.test_case.utils)</a>
</li>
<li><a href="source/biosimulators_test_suite.results.html#biosimulators_test_suite.results.data_model.TestResultsReport.results">results (biosimulators_test_suite.results.data_model.TestResultsReport attribute)</a>
<li><a href="source/biosimulators_test_suite.test_case.html#biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.report_error_as_warning">report_error_as_warning() (biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase property)</a>

<ul>
<li><a href="source/biosimulators_test_suite.test_case.html#biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes.report_error_as_warning">(biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes property)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="source/biosimulators_test_suite.results.html#biosimulators_test_suite.results.data_model.TestResultsReport.results">results (biosimulators_test_suite.results.data_model.TestResultsReport attribute)</a>
</li>
<li><a href="source/biosimulators_test_suite.html#biosimulators_test_suite.exec_core.SimulatorValidator.run">run() (biosimulators_test_suite.exec_core.SimulatorValidator method)</a>

<ul>
Expand Down
2 changes: 1 addition & 1 deletion docs/index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>BioSimulators test suite documentation &#8212; BioSimulators test suite 0.1.9 documentation</title>
<title>BioSimulators test suite documentation &#8212; BioSimulators test suite 0.1.10 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>
Expand Down
2 changes: 1 addition & 1 deletion docs/installation.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 test suite 0.1.9 documentation</title>
<title>1. Installation instructions &#8212; BioSimulators test suite 0.1.10 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>
Expand Down
2 changes: 1 addition & 1 deletion docs/py-modindex.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 test suite 0.1.9 documentation</title>
<title>Python Module Index &#8212; BioSimulators test suite 0.1.10 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>
Expand Down
2 changes: 1 addition & 1 deletion docs/search.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 0.1.9 documentation</title>
<title>Search &#8212; BioSimulators test suite 0.1.10 documentation</title>
<link rel="stylesheet" href="_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="_static/alabaster.css" type="text/css" />

Expand Down
2 changes: 1 addition & 1 deletion docs/searchindex.js
View file

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions docs/source/biosimulators_test_suite.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>3. biosimulators_test_suite package &#8212; BioSimulators test suite 0.1.9 documentation</title>
<title>3. biosimulators_test_suite package &#8212; BioSimulators test suite 0.1.10 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>
Expand Down Expand Up @@ -451,7 +451,7 @@ <h2><span class="section-number">3.2. </span>Submodules<a class="headerlink" hre
<dd><p>Bases: <code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></p>
<dl class="py attribute">
<dt id="biosimulators_test_suite.exec_cli.BaseController.Meta.arguments">
<code class="sig-name descname">arguments</code><em class="property"> = [(['specifications'], {'type': &lt;class 'str'&gt;, 'help': 'Path or URL to the specifications of the simulator'}), (['-c', '--combine-case'], {'type': &lt;class 'str'&gt;, 'nargs': '+', 'default': None, 'dest': 'case_ids', 'help': &quot;Ids of test cases of evaluate (e.g., 'sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations'). Default: evaluate all test cases&quot;}), (['-o', '--report'], {'default': None, 'help': 'Path to save a report of the results in JSON format'}), (['--verbose'], {'action': 'store_true', 'help': 'If set, print the stdout and stderr of the execution of the tests in real time.'}), (['-v', '--version'], {'action': 'version', 'version': '0.1.9'})]</em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/exec_cli.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_test_suite.exec_cli.BaseController.Meta.arguments" title="Permalink to this definition"></a></dt>
<code class="sig-name descname">arguments</code><em class="property"> = [(['specifications'], {'type': &lt;class 'str'&gt;, 'help': 'Path or URL to the specifications of the simulator'}), (['-c', '--combine-case'], {'type': &lt;class 'str'&gt;, 'nargs': '+', 'default': None, 'dest': 'case_ids', 'help': &quot;Ids of test cases of evaluate (e.g., 'sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations'). Default: evaluate all test cases&quot;}), (['-o', '--report'], {'default': None, 'help': 'Path to save a report of the results in JSON format'}), (['--verbose'], {'action': 'store_true', 'help': 'If set, print the stdout and stderr of the execution of the tests in real time.'}), (['-v', '--version'], {'action': 'version', 'version': '0.1.10'})]</em><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/exec_cli.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_test_suite.exec_cli.BaseController.Meta.arguments" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

<dl class="py attribute">
Expand Down
4 changes: 2 additions & 2 deletions docs/source/biosimulators_test_suite.results.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>3.1.1. biosimulators_test_suite.results package &#8212; BioSimulators test suite 0.1.9 documentation</title>
<title>3.1.1. biosimulators_test_suite.results package &#8212; BioSimulators test suite 0.1.10 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>
Expand Down Expand Up @@ -263,7 +263,7 @@ <h2><span class="section-number">3.1.1.1. </span>Submodules<a class="headerlink"

<dl class="py class">
<dt id="biosimulators_test_suite.results.data_model.TestResultsReport">
<em class="property">class </em><code class="sig-prename descclassname">biosimulators_test_suite.results.data_model.</code><code class="sig-name descname">TestResultsReport</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">test_suite_version</span><span class="o">=</span><span class="default_value">'0.1.9'</span></em>, <em class="sig-param"><span class="n">results</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">gh_issue</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">gh_action_run</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_test_suite/blob/dev/biosimulators_test_suite/results/data_model.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_test_suite.results.data_model.TestResultsReport" title="Permalink to this definition"></a></dt>
<em class="property">class </em><code class="sig-prename descclassname">biosimulators_test_suite.results.data_model.</code><code class="sig-name descname">TestResultsReport</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">test_suite_version</span><span class="o">=</span><span class="default_value">'0.1.10'</span></em>, <em class="sig-param"><span class="n">results</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">gh_issue</span><span class="o">=</span><span class="default_value">None</span></em>, <em class="sig-param"><span class="n">gh_action_run</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_test_suite/blob/dev/biosimulators_test_suite/results/data_model.py"><span class="viewcode-link">[source]</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">
Expand Down
32 changes: 31 additions & 1 deletion docs/source/biosimulators_test_suite.test_case.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>3.1.2. biosimulators_test_suite.test_case package &#8212; BioSimulators test suite 0.1.9 documentation</title>
<title>3.1.2. biosimulators_test_suite.test_case package &#8212; BioSimulators test suite 0.1.10 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>
Expand Down Expand Up @@ -1145,6 +1145,26 @@ <h2><span class="section-number">3.1.2.1. </span>Submodules<a class="headerlink"
</dl>
</dd></dl>

<dl class="py method">
<dt id="biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.eval">
<code class="sig-name descname">eval</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">specifications</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/test_case/published_project.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.eval" title="Permalink to this definition"></a></dt>
<dd><p>Evaluate a simulator’s performance on a test case</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>specifications</strong> (<code class="xref py py-obj docutils literal notranslate"><span class="pre">dict</span></code>) – specifications of the simulator to validate</p>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>data returned by <a class="reference internal" href="#biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.eval_outputs" title="biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.eval_outputs"><code class="xref py py-obj docutils literal notranslate"><span class="pre">eval_outputs</span></code></a></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">object</span></code></p>
</dd>
<dt class="field-even">Raises</dt>
<dd class="field-even"><p><strong>Exception</strong> – if the simulator did not pass the test case</p>
</dd>
</dl>
</dd></dl>

<dl class="py method">
<dt id="biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.eval_outputs">
<code class="sig-name descname">eval_outputs</code><span class="sig-paren">(</span><em class="sig-param"><span class="n">specifications</span></em>, <em class="sig-param"><span class="n">synthetic_archive</span></em>, <em class="sig-param"><span class="n">synthetic_sed_docs</span></em>, <em class="sig-param"><span class="n">outputs_dir</span></em><span class="sig-paren">)</span><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/test_case/published_project.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.eval_outputs" title="Permalink to this definition"></a></dt>
Expand Down Expand Up @@ -1193,6 +1213,11 @@ <h2><span class="section-number">3.1.2.1. </span>Submodules<a class="headerlink"
</dl>
</dd></dl>

<dl class="py method">
<dt id="biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.report_error_as_warning">
<em class="property">property </em><code class="sig-name descname">report_error_as_warning</code><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/test_case/published_project.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_test_suite.test_case.published_project.UniformTimeCourseTestCase.report_error_as_warning" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

</dd></dl>

</div>
Expand Down Expand Up @@ -1586,6 +1611,11 @@ <h2><span class="section-number">3.1.2.1. </span>Submodules<a class="headerlink"
</dl>
</dd></dl>

<dl class="py method">
<dt id="biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes.report_error_as_warning">
<em class="property">property </em><code class="sig-name descname">report_error_as_warning</code><a class="reference external" href="https://github.com/biosimulators/Biosimulators_test_suite/blob/dev/biosimulators_test_suite/test_case/sedml.py"><span class="viewcode-link">[source]</span></a><a class="headerlink" href="#biosimulators_test_suite.test_case.sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes.report_error_as_warning" title="Permalink to this definition"></a></dt>
<dd></dd></dl>

</dd></dl>

<dl class="py class">
Expand Down
2 changes: 1 addition & 1 deletion docs/tutorial.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>2. Tutorial &#8212; BioSimulators test suite 0.1.9 documentation</title>
<title>2. Tutorial &#8212; BioSimulators test suite 0.1.10 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>
Expand Down

0 comments on commit 4143ce4

Please sign in to comment.