placeholder blog

oicr-softeng · Mar 27, 2015 · 57ba048 · 57ba048
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diff --git a/.CNAME.swp b/.CNAME.swp
diff --git a/._config.yml.swp b/._config.yml.swp
diff --git a/.about.md.swp b/.about.md.swp
diff --git a/.archive.md.swp b/.archive.md.swp
diff --git a/.index.html.swp b/.index.html.swp
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.baseurl }}">Head back home</a> to try finding it again.</p>
+</div>
diff --git a/CNAME b/CNAME
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+simpsonlab.github.io
diff --git a/LICENSE.md b/LICENSE.md
@@ -0,0 +1,9 @@
+# Released under MIT License
+
+Copyright (c) 2013 Mark Otto.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/README.md b/README.md
@@ -0,0 +1,118 @@
+# Hyde
+
+Hyde is a brazen two-column [Jekyll](http://jekyllrb.com) theme that pairs a prominent sidebar with uncomplicated content. It's based on [Poole](http://getpoole.com), the Jekyll butler.
+
+![Hyde screenshot](https://f.cloud.github.com/assets/98681/1831228/42af6c6a-7384-11e3-98fb-e0b923ee0468.png)
+
+
+## Contents
+
+- [Usage](#usage)
+- [Options](#options)
+  - [Sidebar menu](#sidebar-menu)
+  - [Sticky sidebar content](#sticky-sidebar-content)
+  - [Themes](#themes)
+  - [Reverse layout](#reverse-layout)
+- [Development](#development)
+- [Author](#author)
+- [License](#license)
+
+
+## Usage
+
+Hyde is a theme built on top of [Poole](https://github.com/poole/poole), which provides a fully furnished Jekyll setup—just download and start the Jekyll server. See [the Poole usage guidelines](https://github.com/poole/poole#usage) for how to install and use Jekyll.
+
+
+## Options
+
+Hyde includes some customizable options, typically applied via classes on the `<body>` element.
+
+
+### Sidebar menu
+
+Create a list of nav links in the sidebar by assigning each Jekyll page the correct layout in the page's [front-matter](http://jekyllrb.com/docs/frontmatter/).
+
+```
+---
+layout: page
+title: About
+---
+```
+
+**Why require a specific layout?** Jekyll will return *all* pages, including the `atom.xml`, and with an alphabetical sort order. To ensure the first link is *Home*, we exclude the `index.html` page from this list by specifying the `page` layout.
+
+
+### Sticky sidebar content
+
+By default Hyde ships with a sidebar that affixes it's content to the bottom of the sidebar. You can optionally disable this by removing the `.sidebar-sticky` class from the sidebar's `.container`. Sidebar content will then normally flow from top to bottom.
+
+```html
+<!-- Default sidebar -->
+<div class="sidebar">
+  <div class="container sidebar-sticky">
+    ...
+  </div>
+</div>
+
+<!-- Modified sidebar -->
+<div class="sidebar">
+  <div class="container">
+    ...
+  </div>
+</div>
+```
+
+
+### Themes
+
+Hyde ships with eight optional themes based on the [base16 color scheme](https://github.com/chriskempson/base16). Apply a theme to change the color scheme (mostly applies to sidebar and links).
+
+![Hyde in red](https://f.cloud.github.com/assets/98681/1831229/42b0b354-7384-11e3-8462-31b8df193fe5.png)
+
+There are eight themes available at this time.
+
+![Hyde theme classes](https://f.cloud.github.com/assets/98681/1817044/e5b0ec06-6f68-11e3-83d7-acd1942797a1.png)
+
+To use a theme, add anyone of the available theme classes to the `<body>` element in the `default.html` layout, like so:
+
+```html
+<body class="theme-base-08">
+  ...
+</body>
+```
+
+To create your own theme, look to the Themes section of [included CSS file](https://github.com/poole/hyde/blob/master/public/css/hyde.css). Copy any existing theme (they're only a few lines of CSS), rename it, and change the provided colors.
+
+### Reverse layout
+
+![Hyde with reverse layout](https://f.cloud.github.com/assets/98681/1831230/42b0d3ac-7384-11e3-8d54-2065afd03f9e.png)
+
+Hyde's page orientation can be reversed with a single class.
+
+```html
+<body class="layout-reverse">
+  ...
+</body>
+```
+
+
+## Development
+
+Hyde has two branches, but only one is used for active development.
+
+- `master` for development.  **All pull requests should be to submitted against `master`.**
+- `gh-pages` for our hosted site, which includes our analytics tracking code. **Please avoid using this branch.**
+
+
+## Author
+
+**Mark Otto**
+- <https://github.com/mdo>
+- <https://twitter.com/mdo>
+
+
+## License
+
+Open sourced under the [MIT license](LICENSE.md).
+
+<3
diff --git a/_config.yml b/_config.yml
@@ -0,0 +1,31 @@
+# Dependencies
+markdown:         redcarpet
+highlighter:      pygments
+
+# Permalinks
+permalink:        pretty
+relative_permalinks: true
+
+# Setup
+title:            Simpson Lab Blog
+tagline:          'SimpsonLab blog'
+description:      'A blog for the Simpson Lab at the Ontario Institute for Cancer Research'
+url:              http://hyde.getpoole.com
+baseurl:          /
+
+author:
+  name:           'Jared Simpson'
+  url:            https://twitter.com/jaredtsimpson
+
+paginate:         5
+
+# Custom vars
+version:          1.0
+markdown:         kramdown
+
+pages_list:       
+  About: '/about'
+  Archive: '/archive'
+
+github:
+  repo:           https://github.com/simpsonlab/simpsonlab.github.io
diff --git a/_includes/.head.html.swp b/_includes/.head.html.swp
diff --git a/_includes/head.html b/_includes/head.html
@@ -0,0 +1,32 @@
+<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.baseurl }}public/css/poole.css">
+  <link rel="stylesheet" href="{{ site.baseurl }}public/css/syntax.css">
+  <link rel="stylesheet" href="{{ site.baseurl }}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.baseurl }}public/apple-touch-icon-144-precomposed.png">
+                                 <link rel="shortcut icon" href="{{ site.baseurl }}public/favicon.ico">
+
+  <!-- RSS -->
+  <link rel="alternate" type="application/rss+xml" title="RSS" href="/atom.xml">
+
+  <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+  </script>
+</head>
diff --git a/_includes/sidebar.html b/_includes/sidebar.html
@@ -0,0 +1,36 @@
+<div class="sidebar">
+  <div class="container sidebar-sticky">
+    <div class="sidebar-about">
+      <h1>
+        <a href="{{ site.baseurl }}">
+          {{ site.title }}
+        </a>
+      </h1>
+      <p class="lead">{{ site.description }}</p>
+    </div>
+
+    <nav class="sidebar-nav">
+      <a class="sidebar-nav-item{% if page.url == site.baseurl %} active{% endif %}" href="{{ site.baseurl }}">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.layout == "page" %}
+            <a class="sidebar-nav-item{% if page.url == node.url %} active{% endif %}" href="{{ node.url }}">{{ node.title }}</a>
+          {% endif %}
+        {% endif %}
+      {% endfor %}
+
+      <a class="sidebar-nav-item" href="{{ site.github.repo }}/archive/v{{ site.version }}.zip">Download</a>
+      <a class="sidebar-nav-item" href="{{ site.github.repo }}">GitHub project</a>
+      <span class="sidebar-nav-item">Currently v{{ site.version }}</span>
+    </nav>
+
+    <p>&copy; {{ site.time | date: '%Y' }}. All rights reserved.</p>
+  </div>
+</div>
diff --git a/_layouts/.default.html.swp b/_layouts/.default.html.swp
diff --git a/_layouts/default.html b/_layouts/default.html
@@ -0,0 +1,21 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en-us">
+
+  {% include head.html %}
+  <body>
+
+    <h3 class="masthead-title">
+        <a href="/" title="Home">{{ site.title }}</a>
+
+        {% for page in site.pages_list %}
+          &nbsp;&nbsp;&nbsp;
+          <small><a href="{{ page[1]  }}">{{ page[0] }}</a></small>
+        {% endfor %}
+    </h3>
+
+    <div class="content container">
+      {{ content }}
+    </div>
+
+  </body>
+</html>
diff --git a/_layouts/page.html b/_layouts/page.html
@@ -0,0 +1,8 @@
+---
+layout: default
+---
+
+<div class="page">
+  <h1 class="page-title">{{ page.title }}</h1>
+  {{ content }}
+</div>
diff --git a/_layouts/post.html b/_layouts/post.html
@@ -0,0 +1,25 @@
+---
+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="{{ post.url }}">
+            {{ post.title }}
+            <small>{{ post.date | date_to_string }}</small>
+          </a>
+        </h3>
+      </li>
+    {% endfor %}
+  </ul>
+</div>
diff --git a/_posts/.2015-03-27-test.md.swp b/_posts/.2015-03-27-test.md.swp
diff --git a/_posts/2015-03-27-test.md b/_posts/2015-03-27-test.md
@@ -0,0 +1,6 @@
+---
+layout: post
+title: Placeholder
+---
+
+This is a placeholder until actual content is made.
diff --git a/_site/2015/03/27/test/index.html b/_site/2015/03/27/test/index.html
@@ -0,0 +1,67 @@
+<!DOCTYPE html>
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en-us">
+
+  <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>
+
+      Placeholder &middot; Simpson Lab Blog
+
+  </title>
+
+  <!-- CSS -->
+  <link rel="stylesheet" href="/public/css/poole.css">
+  <link rel="stylesheet" href="/public/css/syntax.css">
+  <link rel="stylesheet" href="/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="/public/apple-touch-icon-144-precomposed.png">
+                                 <link rel="shortcut icon" href="/public/favicon.ico">
+
+  <!-- RSS -->
+  <link rel="alternate" type="application/rss+xml" title="RSS" href="/atom.xml">
+
+  <script type="text/javascript" src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
+  </script>
+</head>
+
+  <body>
+
+    <h3 class="masthead-title">
+        <a href="/" title="Home">Simpson Lab Blog</a>
+
+
+          &nbsp;&nbsp;&nbsp;
+          <small><a href="/about">About</a></small>
+
+          &nbsp;&nbsp;&nbsp;
+          <small><a href="/archive">Archive</a></small>
+
+    </h3>
+
+    <div class="content container">
+      <div class="post">
+  <h1 class="post-title">Placeholder</h1>
+  <span class="post-date">27 Mar 2015</span>
+  <p>This is a placeholder until actual content is made.</p>
+
+</div>
+
+<div class="related">
+  <h2>Related Posts</h2>
+  <ul class="related-posts">
+
+  </ul>
+</div>
+
+    </div>
+
+  </body>
+</html>