From 5b6edf52ff93016fe7a755d720ed3957c853b5ac Mon Sep 17 00:00:00 2001
From: Nathan Muncy <nmuncy@fiu.edu>
Date: Thu, 19 May 2022 09:25:58 -0400
Subject: [PATCH] updated docs for package organization

---
 docs/_build/doctrees/environment.pickle       | Bin 46147 -> 45003 bytes
 docs/_build/doctrees/index.doctree            | Bin 4930 -> 4930 bytes
 docs/_build/doctrees/modules.doctree          | Bin 2646 -> 2631 bytes
 docs/_build/doctrees/setup.doctree            | Bin 2281 -> 0 bytes
 docs/_build/html/_sources/index.rst.txt       |   2 +-
 docs/_build/html/_sources/modules.rst.txt     |   1 -
 docs/_build/html/_sources/setup.rst.txt       |   7 --
 docs/_build/html/func_processing.html         |  13 ++-
 .../html/func_processing.resources.afni.html  |   1 -
 .../html/func_processing.resources.ashs.html  |   1 -
 .../func_processing.resources.fmriprep.html   |   1 -
 .../html/func_processing.resources.html       |   1 -
 .../func_processing.resources.reports.html    |   1 -
 .../_build/html/func_processing.workflow.html |  15 ++-
 docs/_build/html/index.html                   |  13 +--
 docs/_build/html/modules.html                 |   2 -
 docs/_build/html/objects.inv                  | Bin 867 -> 854 bytes
 docs/_build/html/searchindex.js               |   2 +-
 docs/_build/html/setup.html                   | 106 ------------------
 docs/build_docs.txt                           |   7 +-
 docs/index.rst                                |   2 +-
 docs/modules.rst                              |   1 -
 docs/setup.rst                                |   7 --
 23 files changed, 31 insertions(+), 152 deletions(-)
 delete mode 100644 docs/_build/doctrees/setup.doctree
 delete mode 100644 docs/_build/html/_sources/setup.rst.txt
 delete mode 100644 docs/_build/html/setup.html
 delete mode 100644 docs/setup.rst

diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
index 9608bfa951f96c0c48c6b7ec9125b64c7de29fe1..1f0a443b75816aa92538d34db4f371987f18cc06 100644
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diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
index 6205d185b46812e7efd8d8df5164caaa54206a47..9ea033be7e6d16b539994a6fee19a80b4dfd925e 100644
GIT binary patch
delta 14
WcmX@4c1Uf*3>HSF%`;h6@&N!V3<W0u

delta 14
WcmX@4c1Uf*3>HS_%`;h6@&N!V5(Ov#

diff --git a/docs/_build/doctrees/modules.doctree b/docs/_build/doctrees/modules.doctree
index 619b65d93827cdab8136ca07ffe2c19bd82d5c38..a8cecf8a35661014a4b1bd11162328dcf5119aee 100644
GIT binary patch
delta 102
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diff --git a/docs/_build/doctrees/setup.doctree b/docs/_build/doctrees/setup.doctree
deleted file mode 100644
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diff --git a/docs/_build/html/_sources/index.rst.txt b/docs/_build/html/_sources/index.rst.txt
index 7c4780a..1f59b8b 100644
--- a/docs/_build/html/_sources/index.rst.txt
+++ b/docs/_build/html/_sources/index.rst.txt
@@ -7,7 +7,7 @@ Welcome to func_processing's documentation!
 ===========================================
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
    :caption: Package Contents:
 
    modules
diff --git a/docs/_build/html/_sources/modules.rst.txt b/docs/_build/html/_sources/modules.rst.txt
index ff6e27c..77ab9ff 100644
--- a/docs/_build/html/_sources/modules.rst.txt
+++ b/docs/_build/html/_sources/modules.rst.txt
@@ -5,4 +5,3 @@ func_processing
    :maxdepth: 4
 
    func_processing
-   setup
diff --git a/docs/_build/html/_sources/setup.rst.txt b/docs/_build/html/_sources/setup.rst.txt
deleted file mode 100644
index 552eb49..0000000
--- a/docs/_build/html/_sources/setup.rst.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-setup module
-============
-
-.. automodule:: setup
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/_build/html/func_processing.html b/docs/_build/html/func_processing.html
index 49f377b..612644d 100644
--- a/docs/_build/html/func_processing.html
+++ b/docs/_build/html/func_processing.html
@@ -37,7 +37,18 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption"><span class="caption-text">Package Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="modules.html">func_processing</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="modules.html">func_processing</a><ul class="current">
+<li class="toctree-l2 current"><a class="current reference internal" href="#">func_processing package</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#subpackages">Subpackages</a><ul>
+<li class="toctree-l4"><a class="reference internal" href="func_processing.resources.html">func_processing.resources package</a></li>
+<li class="toctree-l4"><a class="reference internal" href="func_processing.workflow.html">func_processing.workflow package</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="#module-func_processing">Module contents</a></li>
+</ul>
+</li>
+</ul>
+</li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">func_processing package</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#subpackages">Subpackages</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="func_processing.resources.html">func_processing.resources package</a></li>
diff --git a/docs/_build/html/func_processing.resources.afni.html b/docs/_build/html/func_processing.resources.afni.html
index 8872aff..12075bb 100644
--- a/docs/_build/html/func_processing.resources.afni.html
+++ b/docs/_build/html/func_processing.resources.afni.html
@@ -47,7 +47,6 @@
 <li class="toctree-l3"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="setup.html">setup module</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="reference internal" href="func_processing.html">func_processing package</a><ul class="current">
diff --git a/docs/_build/html/func_processing.resources.ashs.html b/docs/_build/html/func_processing.resources.ashs.html
index 207c060..824cc73 100644
--- a/docs/_build/html/func_processing.resources.ashs.html
+++ b/docs/_build/html/func_processing.resources.ashs.html
@@ -47,7 +47,6 @@
 <li class="toctree-l3"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="setup.html">setup module</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="reference internal" href="func_processing.html">func_processing package</a><ul class="current">
diff --git a/docs/_build/html/func_processing.resources.fmriprep.html b/docs/_build/html/func_processing.resources.fmriprep.html
index f0c8db7..76870ea 100644
--- a/docs/_build/html/func_processing.resources.fmriprep.html
+++ b/docs/_build/html/func_processing.resources.fmriprep.html
@@ -47,7 +47,6 @@
 <li class="toctree-l3"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="setup.html">setup module</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="reference internal" href="func_processing.html">func_processing package</a><ul class="current">
diff --git a/docs/_build/html/func_processing.resources.html b/docs/_build/html/func_processing.resources.html
index 7d51675..2358177 100644
--- a/docs/_build/html/func_processing.resources.html
+++ b/docs/_build/html/func_processing.resources.html
@@ -47,7 +47,6 @@
 <li class="toctree-l3"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="setup.html">setup module</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="reference internal" href="func_processing.html">func_processing package</a><ul class="current">
diff --git a/docs/_build/html/func_processing.resources.reports.html b/docs/_build/html/func_processing.resources.reports.html
index bd053de..75899d6 100644
--- a/docs/_build/html/func_processing.resources.reports.html
+++ b/docs/_build/html/func_processing.resources.reports.html
@@ -47,7 +47,6 @@
 <li class="toctree-l3"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
 </ul>
 </li>
-<li class="toctree-l2"><a class="reference internal" href="setup.html">setup module</a></li>
 </ul>
 </li>
 <li class="toctree-l1 current"><a class="reference internal" href="func_processing.html">func_processing package</a><ul class="current">
diff --git a/docs/_build/html/func_processing.workflow.html b/docs/_build/html/func_processing.workflow.html
index 382e2aa..0277a66 100644
--- a/docs/_build/html/func_processing.workflow.html
+++ b/docs/_build/html/func_processing.workflow.html
@@ -16,7 +16,6 @@
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
-    <link rel="next" title="setup module" href="setup.html" />
     <link rel="prev" title="func_processing.resources.reports package" href="func_processing.resources.reports.html" /> 
 </head>
 
@@ -37,7 +36,18 @@
         </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
               <p class="caption"><span class="caption-text">Package Contents:</span></p>
 <ul class="current">
-<li class="toctree-l1"><a class="reference internal" href="modules.html">func_processing</a></li>
+<li class="toctree-l1 current"><a class="reference internal" href="modules.html">func_processing</a><ul class="current">
+<li class="toctree-l2 current"><a class="reference internal" href="func_processing.html">func_processing package</a><ul class="current">
+<li class="toctree-l3 current"><a class="reference internal" href="func_processing.html#subpackages">Subpackages</a><ul class="current">
+<li class="toctree-l4"><a class="reference internal" href="func_processing.resources.html">func_processing.resources package</a></li>
+<li class="toctree-l4 current"><a class="current reference internal" href="#">func_processing.workflow package</a></li>
+</ul>
+</li>
+<li class="toctree-l3"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
+</ul>
+</li>
+</ul>
+</li>
 <li class="toctree-l1 current"><a class="reference internal" href="func_processing.html">func_processing package</a><ul class="current">
 <li class="toctree-l2 current"><a class="reference internal" href="func_processing.html#subpackages">Subpackages</a><ul class="current">
 <li class="toctree-l3"><a class="reference internal" href="func_processing.resources.html">func_processing.resources package</a></li>
@@ -434,7 +444,6 @@ <h2>Submodules<a class="headerlink" href="#submodules" title="Permalink to this
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
         <a href="func_processing.resources.reports.html" class="btn btn-neutral float-left" title="func_processing.resources.reports package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
-        <a href="setup.html" class="btn btn-neutral float-right" title="setup module" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 
   <hr/>
diff --git a/docs/_build/html/index.html b/docs/_build/html/index.html
index 6e0e282..e8b9766 100644
--- a/docs/_build/html/index.html
+++ b/docs/_build/html/index.html
@@ -70,20 +70,11 @@ <h1>Welcome to func_processing’s documentation!<a class="headerlink" href="#we
 <p class="caption"><span class="caption-text">Package Contents:</span></p>
 <ul>
 <li class="toctree-l1"><a class="reference internal" href="modules.html">func_processing</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="func_processing.html">func_processing package</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="func_processing.html#subpackages">Subpackages</a></li>
-<li class="toctree-l3"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
-</ul>
-</li>
-<li class="toctree-l2"><a class="reference internal" href="setup.html">setup module</a></li>
+<li class="toctree-l2"><a class="reference internal" href="func_processing.html">func_processing package</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="func_processing.html">func_processing package</a><ul>
-<li class="toctree-l2"><a class="reference internal" href="func_processing.html#subpackages">Subpackages</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="func_processing.resources.html">func_processing.resources package</a></li>
-<li class="toctree-l3"><a class="reference internal" href="func_processing.workflow.html">func_processing.workflow package</a></li>
-</ul>
-</li>
+<li class="toctree-l2"><a class="reference internal" href="func_processing.html#subpackages">Subpackages</a></li>
 <li class="toctree-l2"><a class="reference internal" href="func_processing.html#module-func_processing">Module contents</a></li>
 </ul>
 </li>
diff --git a/docs/_build/html/modules.html b/docs/_build/html/modules.html
index 6fe1757..a37107d 100644
--- a/docs/_build/html/modules.html
+++ b/docs/_build/html/modules.html
@@ -39,7 +39,6 @@
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-<li class="toctree-l2"><a class="reference internal" href="setup.html">setup module</a></li>
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="func_processing.html">func_processing package</a></li>
@@ -94,7 +93,6 @@ <h1>func_processing<a class="headerlink" href="#func-processing" title="Permalin
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\ No newline at end of file
diff --git a/docs/_build/html/setup.html b/docs/_build/html/setup.html
deleted file mode 100644
index 6b13c91..0000000
--- a/docs/_build/html/setup.html
+++ /dev/null
@@ -1,106 +0,0 @@
-<!DOCTYPE html>
-<html class="writer-html5" lang="en" >
-<head>
-  <meta charset="utf-8" />
-  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>setup module &mdash; func_processing 1.0 documentation</title><link rel="stylesheet" href="_static/css/theme.css" type="text/css" />
-    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
-  <!--[if lt IE 9]>
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-  <script id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
-        <script src="_static/jquery.js"></script>
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-    <script src="_static/js/theme.js"></script>
-    <link rel="index" title="Index" href="genindex.html" />
-    <link rel="search" title="Search" href="search.html" />
-    <link rel="prev" title="func_processing.workflow package" href="func_processing.workflow.html" /> 
-</head>
-
-<body class="wy-body-for-nav"> 
-  <div class="wy-grid-for-nav">
-    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
-      <div class="wy-side-scroll">
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-<div role="search">
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-    <input type="text" name="q" placeholder="Search docs" />
-    <input type="hidden" name="check_keywords" value="yes" />
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-        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
-              <p class="caption"><span class="caption-text">Package Contents:</span></p>
-<ul class="current">
-<li class="toctree-l1 current"><a class="reference internal" href="modules.html">func_processing</a><ul class="current">
-<li class="toctree-l2"><a class="reference internal" href="func_processing.html">func_processing package</a></li>
-<li class="toctree-l2 current"><a class="current reference internal" href="#">setup module</a></li>
-</ul>
-</li>
-<li class="toctree-l1"><a class="reference internal" href="func_processing.html">func_processing package</a></li>
-</ul>
-
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-            <a href="_sources/setup.rst.txt" rel="nofollow"> View page source</a>
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-</div>
-          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
-           <div itemprop="articleBody">
-             
-  <div class="section" id="setup-module">
-<h1>setup module<a class="headerlink" href="#setup-module" title="Permalink to this headline">¶</a></h1>
-</div>
-
-
-           </div>
-          </div>
-          <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="func_processing.workflow.html" class="btn btn-neutral float-left" title="func_processing.workflow package" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
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-
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-    <p>&#169; Copyright 2022, Nathan Muncy.</p>
-  </div>
-
-  Built with <a href="https://www.sphinx-doc.org/">Sphinx</a> using a
-    <a href="https://github.com/readthedocs/sphinx_rtd_theme">theme</a>
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diff --git a/docs/build_docs.txt b/docs/build_docs.txt
index 1d88971..5dc7375 100644
--- a/docs/build_docs.txt
+++ b/docs/build_docs.txt
@@ -44,10 +44,7 @@ Edit index.rst - add modules
 		:caption: Package Contents:
 
 		modules
-		workflow
-		resources
-
-# $ sphinx-apidoc -o . .. --ext-autodoc
-$ sphinx-apidoc -f -o . ..
+		func_processing
 
+$ sphinx-apidoc -f -o . ../func_processing
 $ make html
diff --git a/docs/index.rst b/docs/index.rst
index 7c4780a..1f59b8b 100644
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -7,7 +7,7 @@ Welcome to func_processing's documentation!
 ===========================================
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
    :caption: Package Contents:
 
    modules
diff --git a/docs/modules.rst b/docs/modules.rst
index ff6e27c..77ab9ff 100644
--- a/docs/modules.rst
+++ b/docs/modules.rst
@@ -5,4 +5,3 @@ func_processing
    :maxdepth: 4
 
    func_processing
-   setup
diff --git a/docs/setup.rst b/docs/setup.rst
deleted file mode 100644
index 552eb49..0000000
--- a/docs/setup.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-setup module
-============
-
-.. automodule:: setup
-   :members:
-   :undoc-members:
-   :show-inheritance: