Fixed book filename and commandline switch.

dist/about-this-site.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+a.sourceLine:empty { height: 1.2em; position: absolute; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -269,7 +271,7 @@ <h2><span class="header-section-number">14.1</span> Building the site</h2>
 markdown documentation and XSD files.</p>
 <div class="sourceCode" id="cb36"><pre class="sourceCode sh"><code class="sourceCode bash"><a class="sourceLine" id="cb36-1" data-line-number="1">$ <span class="ex">./bin/build_schema_documentation.sh</span></a>
 <a class="sourceLine" id="cb36-2" data-line-number="2">$ <span class="bu">cd</span> docs</a>
-<a class="sourceLine" id="cb36-3" data-line-number="3">$ <span class="ex">R</span> -e <span class="st">&#39;build_book.R&#39;</span></a>
+<a class="sourceLine" id="cb36-3" data-line-number="3">$ <span class="ex">R</span> -f <span class="st">&#39;build_book.R&#39;</span></a>
 <a class="sourceLine" id="cb36-4" data-line-number="4">$ <span class="bu">cd</span> ..</a>
 <a class="sourceLine" id="cb36-5" data-line-number="5">$ <span class="fu">git</span> add dist</a>
 <a class="sourceLine" id="cb36-6" data-line-number="6">$ <span class="fu">git</span> commit</a>
@@ -283,7 +285,7 @@ <h2><span class="header-section-number">14.2</span> Deploying the site</h2>
 <code>gh_pages</code> content to the web is currently handled
 by <a href="https://app.netlify.com/sites/ecometadata/overview">Netlify</a>
 which publishes the site to the custom domain
-<a href="https://eml.ecoinformatics.org">https://eml.ecoinformatics.org</a>. To deploy a new
+<a href="https://eml.ecoinformatics.org" class="uri">https://eml.ecoinformatics.org</a>. To deploy a new
 version of the site, first edit, build, and commit the site to the <code>master</code> branch
 as described in the previous section, and then deploy the site using the provided
 deployment shell script which updates the <code>gh_pages</code> branch for you:</p>
@@ -297,7 +299,7 @@ <h2><span class="header-section-number">14.2</span> Deploying the site</h2>
 <h3> References</h3>
 <div id="refs" class="references">
 <div id="ref-xie2015">
-<p>Xie, Yihui. 2015. <em>Dynamic Documents with R and Knitr</em>. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. <a href="http://yihui.name/knitr/">http://yihui.name/knitr/</a>.</p>
+<p>Xie, Yihui. 2015. <em>Dynamic Documents with R and Knitr</em>. 2nd ed. Boca Raton, Florida: Chapman; Hall/CRC. <a href="http://yihui.name/knitr/" class="uri">http://yihui.name/knitr/</a>.</p>
 </div>
 </div>
             </section>

dist/contributors.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+a.sourceLine:empty { height: 1.2em; position: absolute; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;
@@ -284,37 +286,37 @@ <h2><span class="header-section-number">3.1</span> Current contributors</h2>
 <tr class="odd">
 <td>Matthew Jones</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:jones@nceas.ucsb.edu" class="email">jones@nceas.ucsb.edu</a></td>
+<td><a href="mailto:jones@nceas.ucsb.edu">jones@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="even">
 <td>Mark Schildhauer</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:schild@nceas.ucsb.edu" class="email">schild@nceas.ucsb.edu</a></td>
+<td><a href="mailto:schild@nceas.ucsb.edu">schild@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="odd">
 <td>Chris Jones</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:cjones@nceas.ucsb.edu" class="email">cjones@nceas.ucsb.edu</a></td>
+<td><a href="mailto:cjones@nceas.ucsb.edu">cjones@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="even">
 <td>Corinna Gries</td>
 <td>EDI, UW</td>
-<td><a href="mailto:gries@ecoinformatics.org" class="email">gries@ecoinformatics.org</a></td>
+<td><a href="mailto:gries@ecoinformatics.org">gries@ecoinformatics.org</a></td>
 </tr>
 <tr class="odd">
 <td>Margaret O’Brien</td>
 <td>EDI, UCSB</td>
-<td><a href="mailto:mob@msi.ucsb.edu" class="email">mob@msi.ucsb.edu</a></td>
+<td><a href="mailto:mob@msi.ucsb.edu">mob@msi.ucsb.edu</a></td>
 </tr>
 <tr class="even">
 <td>Bryce Mecum</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:mecum@nceas.ucsb.edu" class="email">mecum@nceas.ucsb.edu</a></td>
+<td><a href="mailto:mecum@nceas.ucsb.edu">mecum@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="odd">
 <td>Carl Boettiger</td>
 <td>Berkeley</td>
-<td><a href="mailto:cboettig@berkeley.edu" class="email">cboettig@berkeley.edu</a></td>
+<td><a href="mailto:cboettig@berkeley.edu">cboettig@berkeley.edu</a></td>
 </tr>
 <tr class="even">
 <td>Mitchell Maier</td>
@@ -324,17 +326,17 @@ <h2><span class="header-section-number">3.1</span> Current contributors</h2>
 <tr class="odd">
 <td>Timothy Whiteaker</td>
 <td></td>
-<td><a href="mailto:whiteaker@utexas.edu" class="email">whiteaker@utexas.edu</a></td>
+<td><a href="mailto:whiteaker@utexas.edu">whiteaker@utexas.edu</a></td>
 </tr>
 <tr class="even">
 <td>Stevan Earl</td>
 <td>LTER, ASU</td>
-<td><a href="mailto:stevan.earl@asu.edu" class="email">stevan.earl@asu.edu</a></td>
+<td><a href="mailto:stevan.earl@asu.edu">stevan.earl@asu.edu</a></td>
 </tr>
 <tr class="odd">
 <td>Steven Chong</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:chong@nceas.ucsb.edu" class="email">chong@nceas.ucsb.edu</a></td>
+<td><a href="mailto:chong@nceas.ucsb.edu">chong@nceas.ucsb.edu</a></td>
 </tr>
 </tbody>
 </table>
@@ -353,72 +355,72 @@ <h2><span class="header-section-number">3.2</span> Past contributors</h2>
 <tr class="odd">
 <td>Chad Berkley</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:berkley@nceas.ucsb.edu" class="email">berkley@nceas.ucsb.edu</a></td>
+<td><a href="mailto:berkley@nceas.ucsb.edu">berkley@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="even">
 <td>Jivka Bojilova</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:bojilova@nceas.ucsb.edu" class="email">bojilova@nceas.ucsb.edu</a></td>
+<td><a href="mailto:bojilova@nceas.ucsb.edu">bojilova@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="odd">
 <td>James Brunt</td>
 <td>LTER, UNM</td>
-<td><a href="mailto:brunt@ecoinformatics.org" class="email">brunt@ecoinformatics.org</a></td>
+<td><a href="mailto:brunt@ecoinformatics.org">brunt@ecoinformatics.org</a></td>
 </tr>
 <tr class="even">
 <td>David Blankman</td>
 <td>LTER-Israel, Ma’arg</td>
-<td><a href="mailto:blankman@ecoinformatics.org" class="email">blankman@ecoinformatics.org</a></td>
+<td><a href="mailto:blankman@ecoinformatics.org">blankman@ecoinformatics.org</a></td>
 </tr>
 <tr class="odd">
 <td>Owen Eddins</td>
 <td>LTER LNO, UNM</td>
-<td><a href="mailto:oeddins@lternet.edu" class="email">oeddins@lternet.edu</a></td>
+<td><a href="mailto:oeddins@lternet.edu">oeddins@lternet.edu</a></td>
 </tr>
 <tr class="even">
 <td>Daniel Higgens</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:higgins@nceas.ucsb.edu" class="email">higgins@nceas.ucsb.edu</a></td>
+<td><a href="mailto:higgins@nceas.ucsb.edu">higgins@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="odd">
 <td>Peter McCartney</td>
 <td>LTER CAP, ASU</td>
-<td><a href="mailto:mccartney@ecoinformatics.org" class="email">mccartney@ecoinformatics.org</a></td>
+<td><a href="mailto:mccartney@ecoinformatics.org">mccartney@ecoinformatics.org</a></td>
 </tr>
 <tr class="even">
 <td>Matthew Brooke</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:brooke@ecoinformatics.org" class="email">brooke@ecoinformatics.org</a></td>
+<td><a href="mailto:brooke@ecoinformatics.org">brooke@ecoinformatics.org</a></td>
 </tr>
 <tr class="odd">
 <td>John Harris</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:harris@nceas.ucsb.edu" class="email">harris@nceas.ucsb.edu</a></td>
+<td><a href="mailto:harris@nceas.ucsb.edu">harris@nceas.ucsb.edu</a></td>
 </tr>
 <tr class="even">
 <td>Scott Chapal</td>
 <td>Jones Ecological Research Center</td>
-<td><a href="mailto:chapal@ecoinformatics.org" class="email">chapal@ecoinformatics.org</a></td>
+<td><a href="mailto:chapal@ecoinformatics.org">chapal@ecoinformatics.org</a></td>
 </tr>
 <tr class="odd">
 <td>Tim Bergsma</td>
 <td>LTER KBS, MSU</td>
-<td><a href="mailto:bergsma@ecoinformatics.org" class="email">bergsma@ecoinformatics.org</a></td>
+<td><a href="mailto:bergsma@ecoinformatics.org">bergsma@ecoinformatics.org</a></td>
 </tr>
 <tr class="even">
 <td>Ken Ramsey</td>
 <td>LTER JRN, NMSU</td>
-<td><a href="mailto:ramsey@ecoinformatics.org" class="email">ramsey@ecoinformatics.org</a></td>
+<td><a href="mailto:ramsey@ecoinformatics.org">ramsey@ecoinformatics.org</a></td>
 </tr>
 <tr class="odd">
 <td>Saurabh Garg</td>
 <td>NCEAS, UCSB</td>
-<td><a href="mailto:sgarg@ecoinformatics.org" class="email">sgarg@ecoinformatics.org</a></td>
+<td><a href="mailto:sgarg@ecoinformatics.org">sgarg@ecoinformatics.org</a></td>
 </tr>
 <tr class="even">
 <td>Mark Servilla</td>
 <td>EDI, UNM</td>
-<td><a href="mailto:servilla@ecoinformatics.org" class="email">servilla@ecoinformatics.org</a></td>
+<td><a href="mailto:servilla@ecoinformatics.org">servilla@ecoinformatics.org</a></td>
 </tr>
 </tbody>
 </table>

dist/data-structure-modules.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+a.sourceLine:empty { height: 1.2em; position: absolute; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;

dist/discovery-and-interpretation-modules.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+a.sourceLine:empty { height: 1.2em; position: absolute; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;

dist/eml-ecological-metadata-language.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+a.sourceLine:empty { height: 1.2em; position: absolute; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;

dist/eml-schema.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+a.sourceLine:empty { height: 1.2em; position: absolute; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;

dist/features.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
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+a.sourceLine:empty { height: 1.2em; position: absolute; }
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 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
     -ms-user-select: none; user-select: none;

dist/index.html

@@ -51,7 +51,7 @@
 <style type="text/css">
 a.sourceLine { display: inline-block; line-height: 1.25; }
 a.sourceLine { pointer-events: none; color: inherit; text-decoration: inherit; }
-a.sourceLine:empty { height: 1.2em; }
+a.sourceLine:empty { height: 1.2em; position: absolute; }
 .sourceCode { overflow: visible; }
 code.sourceCode { white-space: pre; position: relative; }
 pre.sourceCode { margin: 0; }
@@ -63,11 +63,13 @@
 a.sourceLine { text-indent: -1em; padding-left: 1em; }
 }
 pre.numberSource a.sourceLine
-  { position: relative; left: -4em; }
+  { position: relative; }
+pre.numberSource a.sourceLine:empty
+  { position: absolute; }
 pre.numberSource a.sourceLine::before
   { content: attr(data-line-number);
-    position: relative; left: -1em; text-align: right; vertical-align: baseline;
-    border: none; pointer-events: all; display: inline-block;
+    position: absolute; left: -5em; text-align: right; vertical-align: baseline;
+    border: none; pointer-events: all;
     -webkit-touch-callout: none; -webkit-user-select: none;
     -khtml-user-select: none; -moz-user-select: none;
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