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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 44f612956d7e34a502912bd2689273f2
config: c52705603931d7a286e171b358b6bb7c
tags: 645f666f9bcd5a90fca523b33c5a78b7
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 44f612956d7e34a502912bd2689273f2
config: c52705603931d7a286e171b358b6bb7c
tags: 645f666f9bcd5a90fca523b33c5a78b7
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5 changes: 2 additions & 3 deletions 0.10.0/_modules/index.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &mdash; smriprep 0.12.3.dev222 documentation</title>
<title>Overview: module code &mdash; smriprep 0.12.3.dev232 documentation</title>
<link rel="stylesheet" href="../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../_static/banner.css" type="text/css" />
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smriprep
</a>
<div class="version">
0.12.3.dev222
0.12.3.dev232
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
Expand Down Expand Up @@ -159,7 +159,6 @@ <h1>All modules for which code is available</h1>
<dd><a href="../../maint_0.8.x/index.html">maint/0.8.x</a></dd>
<dd><a href="../../maint_0.9.x/index.html">maint/0.9.x</a></dd>
<dd><a href="../../master/index.html">master</a></dd>
<dd><a href="../../rel_0.13.0/index.html">rel/0.13.0</a></dd>
<dd><a href="../../rel_0.8.0rc1/index.html">rel/0.8.0rc1</a></dd>
</dl>
</div>
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15 changes: 8 additions & 7 deletions 0.10.0/_modules/smriprep/cli/run.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>smriprep.cli.run &mdash; smriprep 0.12.3.dev222 documentation</title>
<title>smriprep.cli.run &mdash; smriprep 0.12.3.dev232 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/banner.css" type="text/css" />
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smriprep
</a>
<div class="version">
0.12.3.dev222
0.12.3.dev232
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -545,13 +545,13 @@ <h1>Source code for smriprep.cli.run</h1><div class="highlight"><pre>
<span class="kn">import</span> <span class="nn">warnings</span>
<span class="kn">from</span> <span class="nn">time</span> <span class="kn">import</span> <span class="n">strftime</span>
<span class="kn">from</span> <span class="nn">subprocess</span> <span class="kn">import</span> <span class="n">check_call</span><span class="p">,</span> <span class="n">CalledProcessError</span><span class="p">,</span> <span class="n">TimeoutExpired</span>
<span class="kn">from</span> <span class="nn">pkg_resources</span> <span class="kn">import</span> <span class="n">resource_filename</span> <span class="k">as</span> <span class="n">pkgrf</span>

<span class="kn">import</span> <span class="nn">json</span>
<span class="kn">from</span> <span class="nn">bids</span> <span class="kn">import</span> <span class="n">BIDSLayout</span>
<span class="kn">from</span> <span class="nn">nipype</span> <span class="kn">import</span> <span class="n">logging</span><span class="p">,</span> <span class="n">config</span> <span class="k">as</span> <span class="n">ncfg</span>
<span class="kn">from</span> <span class="nn">niworkflows.utils.bids</span> <span class="kn">import</span> <span class="n">collect_participants</span>
<span class="kn">from</span> <span class="nn">..__about__</span> <span class="kn">import</span> <span class="n">__version__</span>
<span class="kn">from</span> <span class="nn">..data</span> <span class="kn">import</span> <span class="n">load_resource</span>
<span class="kn">from</span> <span class="nn">..workflows.base</span> <span class="kn">import</span> <span class="n">init_smriprep_wf</span>

<span class="n">logger</span> <span class="o">=</span> <span class="n">logging</span><span class="o">.</span><span class="n">getLogger</span><span class="p">(</span><span class="s2">&quot;nipype.workflow&quot;</span><span class="p">)</span>
Expand Down Expand Up @@ -728,12 +728,14 @@ <h1>Source code for smriprep.cli.run</h1><div class="highlight"><pre>
<span class="n">boilerplate</span><span class="p">,</span>
<span class="p">)</span>

<span class="n">boilerplate_bib</span> <span class="o">=</span> <span class="n">load_resource</span><span class="p">(</span><span class="s2">&quot;boilerplate.bib&quot;</span><span class="p">)</span>

<span class="c1"># Generate HTML file resolving citations</span>
<span class="n">cmd</span> <span class="o">=</span> <span class="p">[</span>
<span class="s2">&quot;pandoc&quot;</span><span class="p">,</span>
<span class="s2">&quot;-s&quot;</span><span class="p">,</span>
<span class="s2">&quot;--bibliography&quot;</span><span class="p">,</span>
<span class="n">pkgrf</span><span class="p">(</span><span class="s2">&quot;smriprep&quot;</span><span class="p">,</span> <span class="s2">&quot;data/boilerplate.bib&quot;</span><span class="p">),</span>
<span class="nb">str</span><span class="p">(</span><span class="n">boilerplate_bib</span><span class="p">),</span>
<span class="s2">&quot;--citeproc&quot;</span><span class="p">,</span>
<span class="s2">&quot;--metadata&quot;</span><span class="p">,</span>
<span class="s1">&#39;pagetitle=&quot;sMRIPrep citation boilerplate&quot;&#39;</span><span class="p">,</span>
Expand All @@ -751,7 +753,7 @@ <h1>Source code for smriprep.cli.run</h1><div class="highlight"><pre>
<span class="s2">&quot;pandoc&quot;</span><span class="p">,</span>
<span class="s2">&quot;-s&quot;</span><span class="p">,</span>
<span class="s2">&quot;--bibliography&quot;</span><span class="p">,</span>
<span class="n">pkgrf</span><span class="p">(</span><span class="s2">&quot;smriprep&quot;</span><span class="p">,</span> <span class="s2">&quot;data/boilerplate.bib&quot;</span><span class="p">),</span>
<span class="nb">str</span><span class="p">(</span><span class="n">boilerplate_bib</span><span class="p">),</span>
<span class="s2">&quot;--natbib&quot;</span><span class="p">,</span>
<span class="nb">str</span><span class="p">(</span><span class="n">log_dir</span> <span class="o">/</span> <span class="s2">&quot;CITATION.md&quot;</span><span class="p">),</span>
<span class="s2">&quot;-o&quot;</span><span class="p">,</span>
Expand All @@ -762,7 +764,7 @@ <h1>Source code for smriprep.cli.run</h1><div class="highlight"><pre>
<span class="k">except</span> <span class="p">(</span><span class="ne">FileNotFoundError</span><span class="p">,</span> <span class="n">CalledProcessError</span><span class="p">,</span> <span class="n">TimeoutExpired</span><span class="p">):</span>
<span class="n">logger</span><span class="o">.</span><span class="n">warning</span><span class="p">(</span><span class="s2">&quot;Could not generate CITATION.tex file:</span><span class="se">\n</span><span class="si">%s</span><span class="s2">&quot;</span><span class="p">,</span> <span class="s2">&quot; &quot;</span><span class="o">.</span><span class="n">join</span><span class="p">(</span><span class="n">cmd</span><span class="p">))</span>
<span class="k">else</span><span class="p">:</span>
<span class="n">copyfile</span><span class="p">(</span><span class="n">pkgrf</span><span class="p">(</span><span class="s2">&quot;smriprep&quot;</span><span class="p">,</span> <span class="s2">&quot;data/boilerplate.bib&quot;</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">log_dir</span> <span class="o">/</span> <span class="s2">&quot;CITATION.bib&quot;</span><span class="p">))</span>
<span class="n">copyfile</span><span class="p">(</span><span class="nb">str</span><span class="p">(</span><span class="n">boilerplate_bib</span><span class="p">),</span> <span class="nb">str</span><span class="p">(</span><span class="n">log_dir</span> <span class="o">/</span> <span class="s2">&quot;CITATION.bib&quot;</span><span class="p">))</span>
<span class="k">return</span> <span class="n">retval</span></div>


Expand Down Expand Up @@ -836,7 +838,6 @@ <h1>Source code for smriprep.cli.run</h1><div class="highlight"><pre>
<dd><a href="../../../../maint_0.8.x/index.html">maint/0.8.x</a></dd>
<dd><a href="../../../../maint_0.9.x/index.html">maint/0.9.x</a></dd>
<dd><a href="../../../../master/index.html">master</a></dd>
<dd><a href="../../../../rel_0.13.0/index.html">rel/0.13.0</a></dd>
<dd><a href="../../../../rel_0.8.0rc1/index.html">rel/0.8.0rc1</a></dd>
</dl>
</div>
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>smriprep.interfaces &mdash; smriprep 0.12.3.dev222 documentation</title>
<title>smriprep.interfaces &mdash; smriprep 0.12.3.dev232 documentation</title>
<link rel="stylesheet" href="../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../_static/banner.css" type="text/css" />
Expand Down Expand Up @@ -33,7 +33,7 @@
smriprep
</a>
<div class="version">
0.12.3.dev222
0.12.3.dev232
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../search.html" method="get">
Expand Down Expand Up @@ -163,7 +163,6 @@ <h1>Source code for smriprep.interfaces</h1><div class="highlight"><pre>
<dd><a href="../../../maint_0.8.x/index.html">maint/0.8.x</a></dd>
<dd><a href="../../../maint_0.9.x/index.html">maint/0.9.x</a></dd>
<dd><a href="../../../master/index.html">master</a></dd>
<dd><a href="../../../rel_0.13.0/index.html">rel/0.13.0</a></dd>
<dd><a href="../../../rel_0.8.0rc1/index.html">rel/0.8.0rc1</a></dd>
</dl>
</div>
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5 changes: 2 additions & 3 deletions 0.10.0/_modules/smriprep/interfaces/freesurfer.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>smriprep.interfaces.freesurfer &mdash; smriprep 0.12.3.dev222 documentation</title>
<title>smriprep.interfaces.freesurfer &mdash; smriprep 0.12.3.dev232 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/banner.css" type="text/css" />
Expand Down Expand Up @@ -33,7 +33,7 @@
smriprep
</a>
<div class="version">
0.12.3.dev222
0.12.3.dev232
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -498,7 +498,6 @@ <h1>Source code for smriprep.interfaces.freesurfer</h1><div class="highlight"><p
<dd><a href="../../../../maint_0.8.x/index.html">maint/0.8.x</a></dd>
<dd><a href="../../../../maint_0.9.x/index.html">maint/0.9.x</a></dd>
<dd><a href="../../../../master/index.html">master</a></dd>
<dd><a href="../../../../rel_0.13.0/index.html">rel/0.13.0</a></dd>
<dd><a href="../../../../rel_0.8.0rc1/index.html">rel/0.8.0rc1</a></dd>
</dl>
</div>
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5 changes: 2 additions & 3 deletions 0.10.0/_modules/smriprep/interfaces/reports.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>smriprep.interfaces.reports &mdash; smriprep 0.12.3.dev222 documentation</title>
<title>smriprep.interfaces.reports &mdash; smriprep 0.12.3.dev232 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/banner.css" type="text/css" />
Expand Down Expand Up @@ -33,7 +33,7 @@
smriprep
</a>
<div class="version">
0.12.3.dev222
0.12.3.dev232
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -369,7 +369,6 @@ <h1>Source code for smriprep.interfaces.reports</h1><div class="highlight"><pre>
<dd><a href="../../../../maint_0.8.x/index.html">maint/0.8.x</a></dd>
<dd><a href="../../../../maint_0.9.x/index.html">maint/0.9.x</a></dd>
<dd><a href="../../../../master/index.html">master</a></dd>
<dd><a href="../../../../rel_0.13.0/index.html">rel/0.13.0</a></dd>
<dd><a href="../../../../rel_0.8.0rc1/index.html">rel/0.8.0rc1</a></dd>
</dl>
</div>
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5 changes: 2 additions & 3 deletions 0.10.0/_modules/smriprep/interfaces/surf.html
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<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>smriprep.interfaces.surf &mdash; smriprep 0.12.3.dev222 documentation</title>
<title>smriprep.interfaces.surf &mdash; smriprep 0.12.3.dev232 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/banner.css" type="text/css" />
Expand Down Expand Up @@ -33,7 +33,7 @@
smriprep
</a>
<div class="version">
0.12.3.dev222
0.12.3.dev232
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -460,7 +460,6 @@ <h1>Source code for smriprep.interfaces.surf</h1><div class="highlight"><pre>
<dd><a href="../../../../maint_0.8.x/index.html">maint/0.8.x</a></dd>
<dd><a href="../../../../maint_0.9.x/index.html">maint/0.9.x</a></dd>
<dd><a href="../../../../master/index.html">master</a></dd>
<dd><a href="../../../../rel_0.13.0/index.html">rel/0.13.0</a></dd>
<dd><a href="../../../../rel_0.8.0rc1/index.html">rel/0.8.0rc1</a></dd>
</dl>
</div>
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5 changes: 2 additions & 3 deletions 0.10.0/_modules/smriprep/interfaces/templateflow.html
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Expand Up @@ -3,7 +3,7 @@
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>smriprep.interfaces.templateflow &mdash; smriprep 0.12.3.dev222 documentation</title>
<title>smriprep.interfaces.templateflow &mdash; smriprep 0.12.3.dev232 documentation</title>
<link rel="stylesheet" href="../../../_static/pygments.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/css/theme.css" type="text/css" />
<link rel="stylesheet" href="../../../_static/banner.css" type="text/css" />
Expand Down Expand Up @@ -33,7 +33,7 @@
smriprep
</a>
<div class="version">
0.12.3.dev222
0.12.3.dev232
</div>
<div role="search">
<form id="rtd-search-form" class="wy-form" action="../../../search.html" method="get">
Expand Down Expand Up @@ -341,7 +341,6 @@ <h1>Source code for smriprep.interfaces.templateflow</h1><div class="highlight">
<dd><a href="../../../../maint_0.8.x/index.html">maint/0.8.x</a></dd>
<dd><a href="../../../../maint_0.9.x/index.html">maint/0.9.x</a></dd>
<dd><a href="../../../../master/index.html">master</a></dd>
<dd><a href="../../../../rel_0.13.0/index.html">rel/0.13.0</a></dd>
<dd><a href="../../../../rel_0.8.0rc1/index.html">rel/0.8.0rc1</a></dd>
</dl>
</div>
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