Try to fix docs GH pages setup

Follow instructions from these sources: https://www.docslikecode.com/articles/github-pages-python-sphinx/ sphinx-doc/sphinx#3382 (comment)
UW-GAC · Dec 28, 2019 · eb87a91 · eb87a91
1 parent 91f8c70
commit eb87a91
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Showing 40 changed files with 129 additions and 124 deletions.
diff --git a/.gitignore b/.gitignore
@@ -14,5 +14,4 @@ selenium_tests/*.jar
 phenotype_inventory/settings/maintenance_mode_state.txt
 phenotype_inventory/settings/ssl_certs
 trait_browser/source_db_test_data
-doctrees/
-.buildinfo
+doc_source/_build
diff --git a/docs/Makefile → doc_source/Makefile b/docs/Makefile → doc_source/Makefile
@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = sphinx-build
 SOURCEDIR     = .
-BUILDDIR      = .
+BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".
 help:
@@ -16,4 +16,8 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+github:
+	@make html
+	@cp -a _build/html/. ../docs
diff --git a/docs/conf.py → doc_source/conf.py b/docs/conf.py → doc_source/conf.py
diff --git a/doc_source/doctrees/environment.pickle b/doc_source/doctrees/environment.pickle
diff --git a/doc_source/doctrees/index.doctree b/doc_source/doctrees/index.doctree
diff --git a/doc_source/html/.buildinfo b/doc_source/html/.buildinfo
@@ -0,0 +1,4 @@
+# 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: 01bdfb2baec2d69bc8fec951d50a79d4
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/index.rst → doc_source/index.rst b/docs/index.rst → doc_source/index.rst
diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -0,0 +1,4 @@
+# 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: 01bdfb2baec2d69bc8fec951d50a79d4
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/html/.nojekyll → docs/.nojekyll b/docs/html/.nojekyll → docs/.nojekyll
diff --git a/docs/html/_sources/index.rst.txt → docs/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt → docs/_sources/index.rst.txt
diff --git a/docs/html/_static/ajax-loader.gif → docs/_static/ajax-loader.gif b/docs/html/_static/ajax-loader.gif → docs/_static/ajax-loader.gif
diff --git a/docs/html/_static/alabaster.css → docs/_static/alabaster.css b/docs/html/_static/alabaster.css → docs/_static/alabaster.css
diff --git a/docs/html/_static/basic.css → docs/_static/basic.css b/docs/html/_static/basic.css → docs/_static/basic.css
diff --git a/docs/html/_static/comment-bright.png → docs/_static/comment-bright.png b/docs/html/_static/comment-bright.png → docs/_static/comment-bright.png
diff --git a/docs/html/_static/comment-close.png → docs/_static/comment-close.png b/docs/html/_static/comment-close.png → docs/_static/comment-close.png
diff --git a/docs/html/_static/comment.png → docs/_static/comment.png b/docs/html/_static/comment.png → docs/_static/comment.png
diff --git a/docs/html/_static/custom.css → docs/_static/custom.css b/docs/html/_static/custom.css → docs/_static/custom.css
diff --git a/docs/html/_static/doctools.js → docs/_static/doctools.js b/docs/html/_static/doctools.js → docs/_static/doctools.js
diff --git a/docs/html/_static/documentation_options.js → docs/_static/documentation_options.js b/docs/html/_static/documentation_options.js → docs/_static/documentation_options.js
diff --git a/docs/html/_static/down-pressed.png → docs/_static/down-pressed.png b/docs/html/_static/down-pressed.png → docs/_static/down-pressed.png
diff --git a/docs/html/_static/down.png → docs/_static/down.png b/docs/html/_static/down.png → docs/_static/down.png
diff --git a/docs/html/_static/file.png → docs/_static/file.png b/docs/html/_static/file.png → docs/_static/file.png
diff --git a/docs/html/_static/jquery-3.2.1.js → docs/_static/jquery-3.2.1.js b/docs/html/_static/jquery-3.2.1.js → docs/_static/jquery-3.2.1.js
diff --git a/docs/html/_static/jquery.js → docs/_static/jquery.js b/docs/html/_static/jquery.js → docs/_static/jquery.js
diff --git a/docs/html/_static/language_data.js → docs/_static/language_data.js b/docs/html/_static/language_data.js → docs/_static/language_data.js
diff --git a/docs/html/_static/minus.png → docs/_static/minus.png b/docs/html/_static/minus.png → docs/_static/minus.png
diff --git a/docs/html/_static/plus.png → docs/_static/plus.png b/docs/html/_static/plus.png → docs/_static/plus.png
diff --git a/docs/html/_static/pygments.css → docs/_static/pygments.css b/docs/html/_static/pygments.css → docs/_static/pygments.css
diff --git a/docs/html/_static/searchtools.js → docs/_static/searchtools.js b/docs/html/_static/searchtools.js → docs/_static/searchtools.js
diff --git a/docs/html/_static/underscore-1.3.1.js → docs/_static/underscore-1.3.1.js b/docs/html/_static/underscore-1.3.1.js → docs/_static/underscore-1.3.1.js
diff --git a/docs/html/_static/underscore.js → docs/_static/underscore.js b/docs/html/_static/underscore.js → docs/_static/underscore.js
diff --git a/docs/html/_static/up-pressed.png → docs/_static/up-pressed.png b/docs/html/_static/up-pressed.png → docs/_static/up-pressed.png
diff --git a/docs/html/_static/up.png → docs/_static/up.png b/docs/html/_static/up.png → docs/_static/up.png
diff --git a/docs/html/_static/websupport.js → docs/_static/websupport.js b/docs/html/_static/websupport.js → docs/_static/websupport.js
diff --git a/docs/html/genindex.html → docs/genindex.html b/docs/html/genindex.html → docs/genindex.html
diff --git a/docs/html/index.html b/docs/html/index.html
diff --git a/docs/index.html b/docs/index.html
@@ -1,6 +1,114 @@
-<html>
-    <head>
-        <meta http-equiv="refresh" content="0; url=html/index.html" />
-    </head>
-    <body></body>
-</html>
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+  "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml">
+  <head>
+    <meta http-equiv="X-UA-Compatible" content="IE=Edge" />
+    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+    <title>Welcome to PIE’s documentation! &#8212; PIE 2.13 documentation</title>
+    <link rel="stylesheet" href="_static/alabaster.css" type="text/css" />
+    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
+    <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
+    <script type="text/javascript" src="_static/jquery.js"></script>
+    <script type="text/javascript" src="_static/underscore.js"></script>
+    <script type="text/javascript" src="_static/doctools.js"></script>
+    <script type="text/javascript" src="_static/language_data.js"></script>
+    <link rel="index" title="Index" href="genindex.html" />
+    <link rel="search" title="Search" href="search.html" />
+
+  <link rel="stylesheet" href="_static/custom.css" type="text/css" />
+
+
+  <meta name="viewport" content="width=device-width, initial-scale=0.9, maximum-scale=0.9" />
+
+  </head><body>
+
+
+    <div class="document">
+      <div class="documentwrapper">
+        <div class="bodywrapper">
+
+
+          <div class="body" role="main">
+
+  <div class="section" id="welcome-to-pie-s-documentation">
+<h1>Welcome to PIE’s documentation!<a class="headerlink" href="#welcome-to-pie-s-documentation" title="Permalink to this headline">¶</a></h1>
+<div class="toctree-wrapper compound">
+</div>
+</div>
+<div class="section" id="indices-and-tables">
+<h1>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h1>
+<ul class="simple">
+<li><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></li>
+<li><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></li>
+<li><a class="reference internal" href="search.html"><span class="std std-ref">Search Page</span></a></li>
+</ul>
+</div>
+
+
+          </div>
+
+        </div>
+      </div>
+      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
+        <div class="sphinxsidebarwrapper">
+<h1 class="logo"><a href="#">PIE</a></h1>
+
+
+
+
+
+
+
+
+<h3>Navigation</h3>
+
+<div class="relations">
+<h3>Related Topics</h3>
+<ul>
+  <li><a href="#">Documentation overview</a><ul>
+  </ul></li>
+</ul>
+</div>
+<div id="searchbox" style="display: none" role="search">
+  <h3>Quick search</h3>
+    <div class="searchformwrapper">
+    <form class="search" action="search.html" method="get">
+      <input type="text" name="q" />
+      <input type="submit" value="Go" />
+      <input type="hidden" name="check_keywords" value="yes" />
+      <input type="hidden" name="area" value="default" />
+    </form>
+    </div>
+</div>
+<script type="text/javascript">$('#searchbox').show(0);</script>
+
+
+
+
+
+
+
+
+        </div>
+      </div>
+      <div class="clearer"></div>
+    </div>
+    <div class="footer">
+      &copy;2019, Leslie S. Emery, Adrienne Stilp.
+
+      |
+      Powered by <a href="http://sphinx-doc.org/">Sphinx 1.8.5</a>
+      &amp; <a href="https://github.com/bitprophet/alabaster">Alabaster 0.7.12</a>
+
+      |
+      <a href="_sources/index.rst.txt"
+          rel="nofollow">Page source</a>
+    </div>
+
+
+
+
+  </body>
+</html>
diff --git a/docs/html/objects.inv → docs/objects.inv b/docs/html/objects.inv → docs/objects.inv
diff --git a/docs/html/search.html → docs/search.html b/docs/html/search.html → docs/search.html
diff --git a/docs/html/searchindex.js → docs/searchindex.js b/docs/html/searchindex.js → docs/searchindex.js