lab_pages 0.1.0

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data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2018 Caroline Cypranowska
+
+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.

data/README.md

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+# lab_pages
+
+Welcome to the lab_pages Jekyll theme. This theme is designed for academic laboratory pages with multiple team members, projects, and publications to document.
+
+To experiment with this code, add some sample content and run `bundle exec jekyll serve` – this directory is setup just like a Jekyll site!
+
+## Installation
+
+
+## Usage
+
+### _config.yml
+
+Add information about website, webmaster, lab location, and PI contact info in _config.yml. Some information (e.g. `pi_fax` and `lab_fax`) are optional, but PI name, PI email, lab address and city are required. 
+
+### Layouts
+
+There are three layouts with this theme: a homepage (`home`), a default page (`default`), and a papers page (`papers`). A table of papers will be displayed in /papers/index.html and the content will be determined by the .md files in (`/papers/_posts/`). 
+
+### Papers
+
+Each .md file should begin with a date (formatted as `%YYYY-%mm-%dd`) followed by a string. The front matter of each post in `papers/_posts/` should contain the authors names, the paper title, an abbreviated citation, a DOI, and the journal name. The abstract of the paper should be included in the main content. Images can be included in these posts by placing the relevant image in the `/assets/images/` directory and pasting the path in the `-img:` field of the front matter.
+
+### Carousel
+
+The .html file for the homepage carousel is in `_includes/`. Images for the carousel live in the `assets/images/carousel/` directory.
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/isacofflab/lab_pages. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## Development
+
+To set up your environment to develop this theme, run `bundle install`.
+
+Your theme is setup just like a normal Jekyll site! To test your theme, run `bundle exec jekyll serve` and open your browser at `http://localhost:4000`. This starts a Jekyll server using your theme. Add pages, documents, data, etc. like normal to test your theme's contents. As you make modifications to your theme and to your content, your site will regenerate and you should see the changes in the browser after a refresh, just like normal.
+
+When your theme is released, only the files in `_layouts`, `_includes`, `_sass` and `assets` tracked with Git will be bundled.
+To add a custom directory to your theme-gem, please edit the regexp in `lab_pages.gemspec` accordingly.
+
+## License
+
+The theme is available as open source under the terms of the [MIT License](https://opensource.org/licenses/MIT).
+

data/_data/affiliations.yml

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+- name: Affiliated Institution
+  link: http://affiliatedwebsite.edu
+  img: "/assets/images/logo.png"
+  
+- name: Affiliated Grad Program
+  link: http://grad-program.university.edu/
+  
+- name: Different Grad Program
+  link: http://diff-grad.university.edu/

data/_data/alumni.yml

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+- name: Former Grad student
+  position: Postdoc
+  place: New lab
+  link: http://www.linktonewlab.com
+
+- name: Former Postdoc
+  position: Industry scientist
+  place: Fancy corporation 

data/_data/current_lab.yml

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+- name: PI Name
+  position: PI
+  email: pi@institution.edu
+ 
+  
+- name: Grad Student
+  position: Grad Student
+  email: grad@institution.edu
+  github: github_handle
+
+
+- name: Super Postdoc 
+  position: Postdoc
+  email: super_postdoc@institution.edu
+  google_scholar: super_scholar

data/_data/navigation.yml

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+- title: Home
+  url: ./
+- title: Projects
+  url: /projects.html
+- title: Team
+  url: /team.html
+- title: Publications
+  url: /papers/
+- title: Contact
+  url: /contact.html
+- title: Resources
+  url: /resources.html

data/_data/news.yml

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+- date: 2016-05-30
+  description: Grad students graduated this Spring. Congrats to our newly minted PhDs.
+
+- date: 2017-04-02
+  description: Grad student gets NSF Graduate Research Fellowship
+  
+- date: 2017-01-12
+  description: Lab gets BRAIN Initiative grant. Read about it <a href="http://linktograntinfo.com">here</a>

data/_data/projects.yml

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+- title: Really interesting phenomenon
+  description: We use optical and behavioral tools to study really interesting phenomenon. We've made a super <a href="http://paperurl.com">interesting finding</a>
+  img: "../assets/images/carousel/slide-1.png"

data/_data/resources.yml

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+- name: Lab resource
+  link: http://labresource.com
+  
+- name: Lab resource 2
+  link: http://labresource2.com

data/_includes/carousel.html

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+<div class="col-lg-12 col-sm-12 col-xs-12 centered">
+    <div id="carousel-example-generic" class="carousel slide" data-ride="carousel">
+        <!-- Indicators -->
+        <ol class="carousel-indicators">
+            {% for img in layout.carousel %}
+            {% if forloop.first == true %}
+                <li data-target="#carousel-example-generic" data-slide-to="0" class="active">
+                </li>
+            {% else %}
+                <li data-target="#carousel-example-generic" data-slide-to="{{ forloop.index0 }}"></li>
+            {% endif %}
+            {% endfor %}
+        </ol>
+
+        <!-- Wrapper for slides -->
+        <div class="carousel-inner">
+            {% for img in layout.carousel %}
+                {% if forloop.first == true %}
+                    <div class="item active">
+                        <img src="{{ "/assets/images/carousel/" }}{{ img }}" alt="">
+                    </div>
+                {% else %}
+                    <div class="item">
+                        <img src="{{ "/assets/images/carousel/" }}{{ img }}" alt="">
+                    </div>
+                {% endif %}
+            {% endfor %}
+        </div>
+    </div> <!--/Carousel -->
+</div>

data/_layouts/default.html

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+<!DOCTYPE html>
+<html lang="{{ site.lang | default: "en-US" }}">
+  <head>
+    <meta charset='utf-8'>
+    <meta http-equiv="X-UA-Compatible" content="IE=edge">
+    <link rel="stylesheet" href="{{ '/assets/css/style.css?v=' | append: site.github.build_revision | relative_url }}">
+    <link rel="stylesheet" type="text/css" href="{{ '/assets/css/print.css' | relative_url }}" media="print">
+    <!--[if lt IE 9]>
+    <script src="//html5shiv.googlecode.com/svn/trunk/html5.js"></script>
+    <![endif]-->
+
+{% seo %}
+  </head>
+  
+  <nav class="navbar" role="navigation">
+        <ul class="navbar-nav">
+            {% assign links = site.data.navigation %}
+            {% for link in links %}
+                {% assign class = nil %}
+                {% if page.url contains link.url %}
+                    {% assign class = 'active' %}
+                {% endif %}
+                {% if link.sublinks %}
+                    <li class="dropdown {{ class }}">
+                        <a href="{{ site.baseurl }}{{ link.url }}" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-haspopup="true" aria-expanded="false">{{ link.title }} <span class="caret"></span></a>
+                        <ul class="dropdown-menu">
+                            {% for sublink in link.sublinks %}
+                                {% if sublink.title == 'separator' %}
+                                <li role="separator" class="divider"></li>
+                            {% else %}
+                                <li>
+                                    <a href="{{ site.baseurl }}{{ sublink.url }}">{{ sublink.title }}</a>
+                                </li>
+                            {% endif %}
+                        {% endfor %}
+                        </ul>
+                    </li>
+                {% else %}
+                    <li class="{{ class }}">
+                        <a href="{{ site.baseurl }}{{ link.url }}">{{ link.title}}</a>
+                    </li>
+                {% endif %}
+            {% endfor %}
+        </ul>
+    </nav>
+    
+  <body>
+    <div class="container">
+      <div class="inner">
+        <section id="main_content">
+          {{ content }}
+        </section>
+
+        <footer>
+          This page was generated with the <a href="https://github.com/isacofflab/lab_pages">lab_pages</a> Jekyll theme.
+        </footer>
+
+      </div>
+    </div>
+
+    {% if site.google_analytics %}
+      <script>
+        (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+        (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+        m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+        })(window,document,'script','//www.google-analytics.com/analytics.js','ga');
+        ga('create', '{{ site.google_analytics }}', 'auto');
+        ga('send', 'pageview');
+      </script>
+    {% endif %}
+  </body>
+</html>

data/_layouts/home.html

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+---
+layout: default
+carousel:
+  - slide-1.png
+  - slide-2.png
+---
+<script src="{{ site.baseurl }}/assets/javascript/jquery-3.3.1.min.js"></script>
+<script src="{{ site.baseurl }}/assets/javascript/bootstrap.min.js"></script>
+
+    <header>
+        <h1>Welcome to {{ page.title | default: site.title }}</h1>
+        <h2>{{ page.description | default: site.description }}</h2>
+    </header>
+
+<div id="carousel_container">
+    <div class="row">
+        {% include carousel.html %}
+    </div>
+</div>
+
+<div class="spacer"></div>
+<div class="spacer"></div>
+
+<h1>News</h1>
+{% assign sorted = site.data.news | sort: 'date' | reverse %}
+<div class="row">
+{% for entry in sorted limit:4 %}
+    <div class="col-md-3">
+        <h3>{{ entry.date }}</h3>
+        <p style="word-wrap: break-word;">{{ entry.description}}</p>
+    </div>
+{% endfor %}
+</div>
+
+{{ content }}

data/_layouts/paper.html

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+---
+layout: default
+---
+<div class="row">
+    <div class="col-md-12">
+        {% if page.image %}
+        <img src="{{ page.image }}">
+        {% endif %}
+        <div>
+            <h2>{{ page.title }}</h2>
+        </div>
+        <p>
+            <div>
+                {{ page.authors }} {{ page.year }}, {{ page.journal}}
+            </div>
+        </p>
+    </div>
+</div>
+
+<div class="row">
+    <div class="col-md-3">
+        {% if page.doi %}
+        <i class="fa fa-external-link fa-fw"></i>
+        <a href="http://dx.doi.org/{{ page.doi }}">{{ page. doi }}</a>
+        {% endif %}
+    </div>
+</div>
+
+{{ content }}

data/_sass/_bootstrap.scss

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+/*!
+ * Bootstrap v3.3.7 (http://getbootstrap.com)
+ * Copyright 2011-2016 Twitter, Inc.
+ * Licensed under MIT (https://github.com/twbs/bootstrap/blob/master/LICENSE)
+ */
+
+// Core variables and mixins
+@import "bootstrap/variables";
+@import "bootstrap/mixins";
+
+// Reset and dependencies
+@import "bootstrap/normalize";
+@import "bootstrap/print";
+@import "bootstrap/glyphicons";
+
+// Core CSS
+@import "bootstrap/scaffolding";
+@import "bootstrap/type";
+@import "bootstrap/code";
+@import "bootstrap/grid";
+@import "bootstrap/tables";
+@import "bootstrap/forms";
+@import "bootstrap/buttons";
+
+// Components
+@import "bootstrap/component-animations";
+@import "bootstrap/dropdowns";
+@import "bootstrap/button-groups";
+@import "bootstrap/input-groups";
+@import "bootstrap/navs";
+@import "bootstrap/navbar";
+@import "bootstrap/breadcrumbs";
+@import "bootstrap/pagination";
+@import "bootstrap/pager";
+@import "bootstrap/labels";
+@import "bootstrap/badges";
+@import "bootstrap/jumbotron";
+@import "bootstrap/thumbnails";
+@import "bootstrap/alerts";
+@import "bootstrap/progress-bars";
+@import "bootstrap/media";
+@import "bootstrap/list-group";
+@import "bootstrap/panels";
+@import "bootstrap/responsive-embed";
+@import "bootstrap/wells";
+@import "bootstrap/close";
+
+// Components w/ JavaScript
+@import "bootstrap/modals";
+@import "bootstrap/tooltip";
+@import "bootstrap/popovers";
+@import "bootstrap/carousel";
+
+// Utility classes
+@import "bootstrap/utilities";
+@import "bootstrap/responsive-utilities";

data/_sass/bootstrap/_alerts.scss

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+//
+// Alerts
+// --------------------------------------------------
+
+
+// Base styles
+// -------------------------
+
+.alert {
+  padding: $alert-padding;
+  margin-bottom: $line-height-computed;
+  border: 1px solid transparent;
+  border-radius: $alert-border-radius;
+
+  // Headings for larger alerts
+  h4 {
+    margin-top: 0;
+    // Specified for the h4 to prevent conflicts of changing $headings-color
+    color: inherit;
+  }
+
+  // Provide class for links that match alerts
+  .alert-link {
+    font-weight: $alert-link-font-weight;
+  }
+
+  // Improve alignment and spacing of inner content
+  > p,
+  > ul {
+    margin-bottom: 0;
+  }
+
+  > p + p {
+    margin-top: 5px;
+  }
+}
+
+// Dismissible alerts
+//
+// Expand the right padding and account for the close button's positioning.
+
+.alert-dismissable, // The misspelled .alert-dismissable was deprecated in 3.2.0.
+.alert-dismissible {
+  padding-right: ($alert-padding + 20);
+
+  // Adjust close link position
+  .close {
+    position: relative;
+    top: -2px;
+    right: -21px;
+    color: inherit;
+  }
+}
+
+// Alternate styles
+//
+// Generate contextual modifier classes for colorizing the alert.
+
+.alert-success {
+  @include alert-variant($alert-success-bg, $alert-success-border, $alert-success-text);
+}
+
+.alert-info {
+  @include alert-variant($alert-info-bg, $alert-info-border, $alert-info-text);
+}
+
+.alert-warning {
+  @include alert-variant($alert-warning-bg, $alert-warning-border, $alert-warning-text);
+}
+
+.alert-danger {
+  @include alert-variant($alert-danger-bg, $alert-danger-border, $alert-danger-text);
+}