Update environment and documentation (#81)

This build is based on ec186c2. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/manubot-rootstock/builds/295841617 https://travis-ci.org/greenelab/manubot-rootstock/jobs/295841618 [ci skip] The full commit message that triggered this build is copied below: Update environment and documentation (#81) Pandoc upgraded to v2.0.0.1 Swap anaconda packages to conda-forge Update build.sh for pandoc 2.0 WeasyPrint was not renderring MathJax, so use --webtex to convert equations to SVGs for PDF output. See Kozea/WeasyPrint#59
manubot · Nov 1, 2017 · 0460e84 · 0460e84
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diff --git a/README.md b/README.md
@@ -15,4 +15,4 @@ This directory contains the following files, which are mostly ignored on the `ma
 ## Source
 
 The manuscripts in this directory were built from
-[`38effe877efc7bd6c6de338f306db2a2a33a5df1`](https://github.com/greenelab/manubot-rootstock/commit/38effe877efc7bd6c6de338f306db2a2a33a5df1).
+[`ec186c275c972411e027a4fdbc6a6cf1f611a003`](https://github.com/greenelab/manubot-rootstock/commit/ec186c275c972411e027a4fdbc6a6cf1f611a003).
diff --git a/index.html b/index.html
@@ -1,15 +1,20 @@
 <!DOCTYPE html>
-<html>
+<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
 <head>
-  <meta charset="utf-8">
-  <meta name="generator" content="pandoc">
-  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
-  <meta name="author" content="John Doe">
-  <meta name="author" content="Jane Roe">
-  <meta name="dcterms.date" content="2017-10-09">
-  <meta name="keywords" content="markdown, publishing, manubot">
+  <meta charset="utf-8" />
+  <meta name="generator" content="pandoc" />
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
+  <meta name="author" content="John Doe" />
+  <meta name="author" content="Jane Roe" />
+  <meta name="dcterms.date" content="2017-11-01" />
+  <meta name="keywords" content="markdown, publishing, manubot" />
   <title>Manubot Rootstock: Manuscript Title</title>
-  <style type="text/css">code{white-space: pre;}</style>
+  <style type="text/css">
+      code{white-space: pre-wrap;}
+      .smallcaps{font-variant: small-caps;}
+      .line-block{white-space: pre-line;}
+      .column{display: inline-block;}
+  </style>
   <link rel="stylesheet" href="github-pandoc.css">
   <!--[if lt IE 9]>
     <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
@@ -23,7 +28,7 @@
 <header>
 <h1 class="title">Manubot Rootstock: Manuscript Title</h1>
 </header>
-<p><small><em> This manuscript was automatically generated from <a href="https://github.com/greenelab/manubot-rootstock/tree/38effe877efc7bd6c6de338f306db2a2a33a5df1">greenelab/manubot-rootstock@38effe8</a> on October 9, 2017. </em></small></p>
+<p><small><em> This manuscript was automatically generated from <a href="https://github.com/greenelab/manubot-rootstock/tree/ec186c275c972411e027a4fdbc6a6cf1f611a003">greenelab/manubot-rootstock@ec186c2</a> on November 1, 2017. </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
 <li><p><strong>John Doe</strong><br> <img src="images/orcid.svg" alt="ORCID icon" width="13" height="13" /> <a href="https://orcid.org/XXXX-XXXX-XXXX-XXXX">XXXX-XXXX-XXXX-XXXX</a> · <img src="images/github.svg" alt="GitHub icon" width="13" height="13" /> <a href="https://github.com/johndoe">johndoe</a> · <img src="images/twitter.svg" alt="Twitter icon" width="13" height="13" /> <a href="https://twitter.com/johndoe">johndoe</a><br> <small> Department of Something, University of Whatever · Funded by Grant XXXXXXXX </small></p></li>
@@ -50,7 +55,7 @@ <h2 id="references" class="page_break_before">References</h2>
 <div id="ref-WiyRG9Qh">
 <p>2. <strong>Sci-Hub provides access to nearly all scholarly literature</strong><br />
 Daniel S Himmelstein, Ariel R Romero, Stephen R McLaughlin, Bastian Greshake Tzovaras, Casey S Greene<br />
-<em>PeerJ Preprints</em> (2017-07-20) <a href="https://doi.org/10.7287/peerj.preprints.3100" class="uri">https://doi.org/10.7287/peerj.preprints.3100</a></p>
+<em>PeerJ Preprints</em> (2017-10-12) <a href="https://doi.org/10.7287/peerj.preprints.3100" class="uri">https://doi.org/10.7287/peerj.preprints.3100</a></p>
 </div>
 <div id="ref-15nwuvjrA">
 <p>3. <strong>Vagelos Report Summer 2017</strong><br />

diff --git a/index.html.ots b/index.html.ots
diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/manuscript.pdf.ots b/manuscript.pdf.ots