Update environment and documentation (#81)

dhimmel · dhimmel · commit 868a80d107a3 · 2017-11-01T16:49:45.000Z
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
diff --git a/manuscript.html b/manuscript.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/manuscript.md b/manuscript.md
@@ -2,11 +2,12 @@
 author-meta:
 - John Doe
 - Jane Roe
-date-meta: '2017-10-09'
+date-meta: '2017-11-01'
 keywords:
 - markdown
 - publishing
 - manubot
+lang: en-US
 title: 'Manubot Rootstock: Manuscript Title'
 ...
 
@@ -17,8 +18,8 @@ title: 'Manubot Rootstock: Manuscript Title'
 
 <small><em>
 This manuscript was automatically generated
-from [greenelab/manubot-rootstock@38effe8](https://github.com/greenelab/manubot-rootstock/tree/38effe877efc7bd6c6de338f306db2a2a33a5df1)
-on October  9, 2017.
+from [greenelab/manubot-rootstock@ec186c2](https://github.com/greenelab/manubot-rootstock/tree/ec186c275c972411e027a4fdbc6a6cf1f611a003)
+on November  1, 2017.
 </em></small>
 
 ## Authors
diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/references.json b/references.json
@@ -4,12 +4,12 @@
       "date-parts": [
         [
           2017,
-          8,
-          11
+          10,
+          19
         ]
       ],
-      "date-time": "2017-08-11T15:31:27Z",
-      "timestamp": 1502465487706
+      "date-time": "2017-10-19T20:42:14Z",
+      "timestamp": 1508445734214
     },
     "posted": {
       "date-parts": [
@@ -51,7 +51,7 @@
       "timestamp": 1496034615000
     },
     "source": "Crossref",
-    "is-referenced-by-count": 0,
+    "is-referenced-by-count": 1,
     "title": "Opportunities And Obstacles For Deep Learning In Biology And Medicine",
     "prefix": "10.1101",
     "author": [
@@ -303,6 +303,7 @@
     },
     "abstract": "Report detailing work done in the Greene Lab at the University of Pennsylvania for the Summer of 2017. Sparse matrix implementation of degree-weighted path count (DWPC) over a heterogeneous network of biomedical information. Summer research conducted as part of the Penn Vagelos Scholars Program in Molecular Life Science (MLS).",
     "DOI": "10.6084/m9.figshare.5346577",
+    "page": "-",
     "publisher": "Figshare",
     "title": "Vagelos Report Summer 2017",
     "URL": "https://doi.org/10.6084/m9.figshare.5346577",
@@ -338,17 +339,18 @@
       "date-parts": [
         [
           2017,
-          7,
-          20
+          10,
+          12
         ]
       ]
     },
-    "abstract": "The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent of Sci-Hub's coverage was unclear. As of March 2017, we find that Sci-Hub's database contains 68.9% of all 81.6 million scholarly articles, which rises to 85.2% for those published in closed access journals. Furthermore, Sci-Hub contains 77.0% of the 5.2 million articles published by inactive journals. Coverage varies by discipline, with 92.8% coverage of articles in chemistry journals compared to 76.3% for computer science. Coverage also varies by publisher, with the coverage of the largest publisher, Elsevier, at 97.3%. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. Finally, we estimate that over a six-month period in 2015–2016, Sci-Hub provided access for 99.3% of valid incoming requests. Hence, the scope of this resource suggests the subscription publishing model is becoming unsustainable. For the first time, the overwhelming majority of scholarly literature is available gratis to anyone with an Internet connection.",
+    "abstract": "The website Sci-Hub provides access to scholarly literature via full text PDF downloads. The site enables users to access articles that would otherwise be paywalled. Since its creation in 2011, Sci-Hub has grown rapidly in popularity. However, until now, the extent of Sci-Hub’s coverage was unclear. As of March 2017, we find that Sci-Hub’s database contains 68.9% of all 81.6 million scholarly articles, which rises to 85.2% for those published in toll access journals. Coverage varies by discipline, with 92.8% coverage of articles in chemistry journals compared to 76.3% for computer science. Coverage also varies by publisher, with the coverage of the largest publisher, Elsevier, at 97.3%. Our interactive browser at https://greenelab.github.io/scihub allows users to explore these findings in more detail. We find Sci-Hub preferentially covers popular, paywalled content, containing 96.2% of citations to toll access journals since 2015. For recently requested articles by Unpaywall users, oaDOI provided access to 48.8% whereas Sci-Hub contained 81.5%. Together, oaDOI and Sci-Hub covered 94.1%, demonstrating that gaps in Sci-Hub’s coverage, especially for open access articles, can be filled using licit services. For the first time, nearly all scholarly literature is available gratis to anyone with an Internet connection. Sci-Hub’s scope suggests the subscription publishing model is becoming unsustainable.",
     "DOI": "10.7287/peerj.preprints.3100",
+    "page": "-",
     "publisher": "PeerJ Preprints",
     "title": "Sci-Hub provides access to nearly all scholarly literature",
+    "version": "2",
     "URL": "https://doi.org/10.7287/peerj.preprints.3100",
-    "version": "1",
     "short_url": "https://doi.org/b9s5"
   }
 ]
diff --git a/variables.json b/variables.json
@@ -1,5 +1,5 @@
 {
-  "date": "October  9, 2017",
+  "date": "November  1, 2017",
   "authors": [
     {
       "github": "johndoe",
@@ -22,7 +22,7 @@
   ],
   "ci_source": {
     "repo_slug": "greenelab/manubot-rootstock",
-    "commit": "38effe877efc7bd6c6de338f306db2a2a33a5df1"
+    "commit": "ec186c275c972411e027a4fdbc6a6cf1f611a003"
   },
   "manuscript_stats": {
     "reference_counts": {
