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codeasmanuscript · Nov 1, 2015 · c7b71d6 · c7b71d6
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diff --git a/.gitignore b/.gitignore
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+## Ignore everything ...
+
+
+## ...But not ignore these files
+
diff --git a/404.html b/404.html
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+---
+layout: default
+title: "404: Page not found"
+permalink: 404.html
+---
+
+<div class="page">
+  <h1 class="page-title">404: Page not found</h1>
+  <p class="lead">Sorry, we've misplaced that URL or it's pointing to something that doesn't exist. <a href="{{ site.github.url }}">Head back home</a> to try finding it again.</p>
+</div>
diff --git a/CNAME b/CNAME
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+codeasmanuscript.org
diff --git a/Makefile b/Makefile
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+##-------------------------------------------------------------------
+# Variables
+site_repo=`basename "$$PWD"`
+
+## List of commands to use for Makefile.
+all :
+	@grep -E '^##' Makefile | sed -e 's/##//g'
+##-------------------------------------------------------------------
+## test_local : Test the site locally before building live version
+test_local :
+	jekyll serve --watch
+
+## build_site : Build the GitHub pages site
+build_site :
+	rsync -a --exclude='.git/' --exclude='.gitignore' ../workshops/ ../${site_repo}/
+	./knitpost.R
+	jekyll build
+	git clean -d -x -f
+
+.PHONY : build_site test_local
+
diff --git a/_config.yml b/_config.yml
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+# Dependencies
+markdown:         kramdown
+highlighter:      pygments
+
+# Permalinks
+permalink: pretty
+relative_permalinks: false
+
+# Setup
+title:               Code As Manuscript
+tagline:             'Change the way you see your code.'
+description:         'Writing your code and analyses as if <i>it</i> was the manuscript.'
+url:                 http://codeasmanuscript.org
+
+author:
+  name:           'Code As Manuscript'
+
+# Custom vars
+version:          2.1.0
+
+github:
+  repo:           https://github.com/codeasmanuscript
+
+lesson-list: [Git, Intro, Plotting, Wrangling, Rmarkdown, Macros, ODS]
+category-list: [R, Git, Macros, ODS, Lessons]
+tag-list: [Lessons, Git, GitHub, Macros, ODS, Assignment, Slides, Cheatsheet]
+
+exclude: ['lessons/template/*', gps/eventListing.md, '*.Rmd',
+         evals/, survey/, lessons/potentials.md, README.md]
+
diff --git a/_includes/head.html b/_includes/head.html
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+<head>
+  <link href="http://gmpg.org/xfn/11" rel="profile">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta http-equiv="content-type" content="text/html; charset=utf-8">
+
+  <!-- Enable responsiveness on mobile devices-->
+  <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1">
+
+  <title>
+    {% if page.title == "Home" %}
+      {{ site.title }} &middot; {{ site.tagline }}
+    {% else %}
+      {{ page.title }} &middot; {{ site.title }}
+    {% endif %}
+  </title>
+
+  <!-- CSS -->
+  <link rel="stylesheet" href="{{ site.github.url }}/public/css/poole.css">
+  <link rel="stylesheet" href="{{ site.github.url }}/public/css/syntax.css">
+  <link rel="stylesheet" href="{{ site.github.url }}/public/css/hyde.css">
+  <link rel="stylesheet" href="http://fonts.googleapis.com/css?family=PT+Sans:400,400italic,700|Abril+Fatface">
+
+  <!-- Icons -->
+  <link rel="apple-touch-icon-precomposed" sizes="144x144" href="{{ site.github.url }}/public/apple-touch-icon-144-precomposed.png">
+                                 <link rel="shortcut icon" href="{{ site.github.url }}/public/favicon.ico">
+
+  <!-- RSS -->
+  <link rel="alternate" type="application/rss+xml" title="RSS" href="/atom.xml">
+</head>
diff --git a/_includes/sidebar.html b/_includes/sidebar.html
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+<div class="sidebar">
+  <div class="container"> <!--sidebar-sticky? I deleted it from here-->
+    <div class="sidebar-about">
+      <h2>
+        <a href="{{ site.github.url }}">
+          {{ site.title }}
+        </a>
+      </h2>
+      <p class="lead">{{ site.description }}</p>
+    </div>
+
+    <nav class="sidebar-nav">
+      <a class="sidebar-nav-item{% if page.url == site.github.url %} active{% endif %}" href="{{ site.github.url }}/">Home</a>
+
+      {% comment %}
+        The code below dynamically generates a sidebar nav of pages with
+        `layout: page` in the front-matter. See readme for usage.
+      {% endcomment %}
+
+      {% assign pages_list = site.pages %}
+      {% for node in pages_list %}
+        {% if node.title != null %}
+          {% if node.sidebar == true %}
+            {% if node.layout == "page" %}
+              <a class="sidebar-nav-item{% if page.url == node.url %} active{% endif %}" href="{{ site.github.url }}{{ node.url }}">{{ node.title }}</a>
+            {% endif %}
+          {% endif %}
+        {% endif %}
+      {% endfor %}
+
+      <a class="sidebar-nav-item" href="{{ site.github.repo }}">GitHub</a>
+    </nav>
+
+    <p>&copy; {{ site.time | date: '%Y' }}. All rights reserved.</p>
+  </div>
+</div>
diff --git a/_layouts/default.html b/_layouts/default.html
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+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en-us">
+
+  {% include head.html %}
+
+  <body class="theme-base-0d">
+
+    {% include sidebar.html %}
+
+    <div class="content container">
+      {{ content }}
+    </div>
+
+  </body>
+</html>
diff --git a/_layouts/page.html b/_layouts/page.html
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+---
+layout: default
+---
+
+<div class="page">
+  <h1 class="page-title">{{ page.title }}</h1>
+  {{ content }}
+</div>
diff --git a/_layouts/post.html b/_layouts/post.html
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+---
+layout: default
+---
+
+<div class="post">
+  <h1 class="post-title">{{ page.title }}</h1>
+  <span class="post-date">{{ page.date | date_to_string }}</span>
+  {{ content }}
+</div>
+
+<div class="related">
+  <h2>Related Posts</h2>
+  <ul class="related-posts">
+    {% for post in site.related_posts limit:3 %}
+      <li>
+        <h3>
+          <a href="{{ site.github.url }}{{ post.url }}">
+            {{ post.title }}
+            <small>{{ post.date | date_to_string }}</small>
+          </a>
+        </h3>
+      </li>
+    {% endfor %}
+  </ul>
+</div>
diff --git a/atom.xml b/atom.xml
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+---
+layout: null
+---
+
+<?xml version="1.0" encoding="utf-8"?>
+<feed xmlns="http://www.w3.org/2005/Atom">
+
+ <title>{{ site.title }}</title>
+ <link href="{{ site.url }}/atom.xml" rel="self"/>
+ <link href="{{ site.url }}/"/>
+ <updated>{{ site.time | date_to_xmlschema }}</updated>
+ <id>{{ site.url }}</id>
+ <author>
+   <name>{{ site.author.name }}</name>
+   <email>{{ site.author.email }}</email>
+ </author>
+
+ {% for post in site.posts %}
+ <entry>
+   <title>{{ post.title }}</title>
+   <link href="{{ site.url }}{{ post.url }}"/>
+   <updated>{{ post.date | date_to_xmlschema }}</updated>
+   <id>{{ site.url }}{{ post.id }}</id>
+   <content type="html">{{ post.content | xml_escape }}</content>
+ </entry>
+ {% endfor %}
+
+</feed>
diff --git a/knitpost.R b/knitpost.R
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+#!/usr/bin/Rscript --vanilla
+
+# Taken and modified from
+# http://varianceexplained.org/pages/workflow.html
+
+# compiles all .Rmd files in _R directory into .md files in the _posts
+# directory, if the input file is older than the output file.
+
+# run ./knitpages.R to update all knitr files that need to be updated.
+
+KnitPost <- function(input, outfile, base.url = '/') {
+    # this function is a modified version of an example here:
+    # http://jfisher-usgs.github.com/r/2012/07/03/knitr-jekyll/
+    knitr::opts_knit$set(base.url = base.url)
+    knitr::opts_chunk$set(fig.path = 'images/',
+                          collapse = TRUE)
+    knitr::render_jekyll()
+    knitr::knit(input, outfile, envir = parent.frame())
+    txt <- sub('^published: false', 'published: true',
+               readLines(outfile))
+    writeLines(txt, outfile)
+}
+
+for (infile in list.files(pattern="*.Rmd", full.names=TRUE, recursive = TRUE)) {
+    outfile <- paste0(sub("\\.Rmd$", ".md", infile))
+
+    # knit only if the input file is the last one modified
+    if (!file.exists(outfile) |
+        file.info(infile)$mtime > file.info(outfile)$mtime) {
+        KnitPost(infile, outfile)
+    }
+}
+
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		## Ignore everything ...


		## ...But not ignore these files