Revamp website with new home page

Merges #7
Closes #4 (permalinks to headers)
Closes #5 (creates new favicon)
Closes #6 (centers landing page)

Revamps or creates homepage /about /explore /studies /software /media /hnep.
Adopt Jekyll for templating pages
/repurpose and /disease-genes imported verbatim from previous version

.gitignore

@@ -1,2 +1,6 @@
+_site
+.sass-cache
+.jekyll-metadata
+
 ### Linux ###
 *~

Gemfile

@@ -0,0 +1,30 @@
+source "https://rubygems.org"
+
+# Hello! This is where you manage which Jekyll version is used to run.
+# When you want to use a different version, change it below, save the
+# file and run `bundle install`. Run Jekyll with `bundle exec`, like so:
+#
+# bundle exec jekyll serve
+#
+# This will help ensure the proper Jekyll version is running.
+# Happy Jekylling!
+gem "jekyll", "~> 3.8.5"
+
+# This is the default theme for new Jekyll sites. You may change this to anything you like.
+gem "minima", "~> 2.0"
+
+# If you want to use GitHub Pages, remove the "gem "jekyll"" above and
+# uncomment the line below. To upgrade, run `bundle update github-pages`.
+# gem "github-pages", group: :jekyll_plugins
+
+# If you have any plugins, put them here!
+group :jekyll_plugins do
+ gem "jekyll-feed", "~> 0.6"
+end
+
+# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
+gem "tzinfo-data", platforms: [:mingw, :mswin, :x64_mingw, :jruby]
+
+# Performance-booster for watching directories on Windows
+gem "wdm", "~> 0.1.0" if Gem.win_platform?
+

Gemfile.lock

@@ -0,0 +1,74 @@
+GEM
+ remote: https://rubygems.org/
+ specs:
+ addressable (2.6.0)
+ public_suffix (>= 2.0.2, < 4.0)
+ colorator (1.1.0)
+ concurrent-ruby (1.1.5)
+ em-websocket (0.5.1)
+ eventmachine (>= 0.12.9)
+ http_parser.rb (~> 0.6.0)
+ eventmachine (1.2.7)
+ ffi (1.11.1)
+ forwardable-extended (2.6.0)
+ http_parser.rb (0.6.0)
+ i18n (0.9.5)
+ concurrent-ruby (~> 1.0)
+ jekyll (3.8.5)
+ addressable (~> 2.4)
+ colorator (~> 1.0)
+ em-websocket (~> 0.5)
+ i18n (~> 0.7)
+ jekyll-sass-converter (~> 1.0)
+ jekyll-watch (~> 2.0)
+ kramdown (~> 1.14)
+ liquid (~> 4.0)
+ mercenary (~> 0.3.3)
+ pathutil (~> 0.9)
+ rouge (>= 1.7, < 4)
+ safe_yaml (~> 1.0)
+ jekyll-feed (0.12.1)
+ jekyll (>= 3.7, < 5.0)
+ jekyll-sass-converter (1.5.2)
+ sass (~> 3.4)
+ jekyll-seo-tag (2.6.1)
+ jekyll (>= 3.3, < 5.0)
+ jekyll-watch (2.2.1)
+ listen (~> 3.0)
+ kramdown (1.17.0)
+ liquid (4.0.3)
+ listen (3.1.5)
+ rb-fsevent (~> 0.9, >= 0.9.4)
+ rb-inotify (~> 0.9, >= 0.9.7)
+ ruby_dep (~> 1.2)
+ mercenary (0.3.6)
+ minima (2.5.0)
+ jekyll (~> 3.5)
+ jekyll-feed (~> 0.9)
+ jekyll-seo-tag (~> 2.1)
+ pathutil (0.16.2)
+ forwardable-extended (~> 2.6)
+ public_suffix (3.1.0)
+ rb-fsevent (0.10.3)
+ rb-inotify (0.10.0)
+ ffi (~> 1.0)
+ rouge (3.4.1)
+ ruby_dep (1.5.0)
+ safe_yaml (1.0.5)
+ sass (3.7.4)
+ sass-listen (~> 4.0.0)
+ sass-listen (4.0.0)
+ rb-fsevent (~> 0.9, >= 0.9.4)
+ rb-inotify (~> 0.9, >= 0.9.7)
+
+PLATFORMS
+ ruby
+
+DEPENDENCIES
+ jekyll (~> 3.8.5)
+ jekyll-feed (~> 0.6)
+ minima (~> 2.0)
+ tzinfo-data
+
+BUNDLED WITH
+ 2.0.2

_includes/footer.html

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+<footer>
+ <a href="../about#acknowledgements">Greene Lab, Baranzini Lab, et al</a><br />
+ <a
+ href="https://creativecommons.org/licenses/by/4.0/"
+ title="Creative Commons Attribution 4.0 International"
+ ><i class="fab fa-creative-commons-by" style="margin-right: 5px"></i>CC BY
+ 4.0</a
+ >
+</footer>

_includes/header.html

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+<header data-deep>
+ <a href=".." class="logo_button">
+ <img src="../logo.svg" />
+ </a>
+ {% include nav.html %}
+</header>

_includes/nav.html

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+<nav>
+ <a
+ href="{% if page.topLevel != true %}../{% endif %}about"
+ class="nav_button"
+ title="Learn more about the network"
+ data-active="{% if page.category == 'about' %}true{% endif %}"
+ >About{% if page.icons %}<i class="fas fa-book-open fa-sm" data-right></i>{%
+ endif %}</a
+ >
+ <a
+ href="{% if page.topLevel != true %}../{% endif %}explore"
+ class="nav_button"
+ title="View, search, and play with the network"
+ data-active="{% if page.category == 'explore' %}true{% endif %}"
+ >Explore{% if page.icons %}<i class="fas fa-search fa-sm" data-right></i>{%
+ endif %}</a
+ >
+ <a
+ href="{% if page.topLevel != true %}../{% endif %}studies"
+ class="nav_button"
+ title="Analyses and papers related to the network"
+ data-active="{% if page.category == 'studies' %}true{% endif %}"
+ >Studies{% if page.icons %}<i class="fas fa-microscope fa-sm" data-right></i
+ >{% endif %}</a
+ >
+ <a
+ href="{% if page.topLevel != true %}../{% endif %}software"
+ class="nav_button"
+ title="Tools used to make the network"
+ data-active="{% if page.category == 'software' %}true{% endif %}"
+ >Software{% if page.icons %}<i class="fas fa-code fa-sm" data-right></i>{%
+ endif %}</a
+ >
+ <a
+ href="{% if page.topLevel != true %}../{% endif %}media"
+ class="nav_button"
+ title="Publications, articles, and other related media"
+ data-active="{% if page.category == 'media' %}true{% endif %}"
+ >Media{% if page.icons %}<i class="fas fa-feather-alt fa-sm" data-right></i
+ >{% endif %}</a
+ >
+</nav>

_layouts/default.html

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+<html>
+ <head>
+ <!-- metatags - https://metatags.io/ -->
+ <title>Hetionet - {{ page.title }}</title>
+ <meta name="viewport" content="width=device-width, initial-scale=1" />
+ <meta
+ name="title"
+ property="og:title"
+ content="Hetionet - {{ page.title }}"
+ />
+ <meta property="og:type" content="website" />
+
+ <!-- global styles -->
+ <link href="../global.css" rel="stylesheet" />
+
+ <!-- page styles -->
+ <link href="page.css" rel="stylesheet" />
+
+ <!-- scripts -->
+ <script src="../scripts.js"></script>
+ </head>
+ <body>
+ {% include header.html %}
+ <main>
+ <section class="title_section">
+ <div class="section">
+ <h2>
+ {{ page.title }}<i class="{{ page.icon }} fa-sm" data-right></i>
+ </h2>
+ </div>
+ </section>
+ {{ content }}
+ </main>
+ {% include footer.html %}
+
+ <!-- Matomo -->
+ <script type="text/javascript">
+ var _paq = window._paq || [];
+ /* tracker methods like "setCustomDimension" should be called before "trackPageView" */
+ _paq.push(['setCookieDomain', '*.het.io']);
+ _paq.push(['trackPageView']);
+ _paq.push(['enableLinkTracking']);
+ (function() {
+ var u = 'https://piwik.dhimmel.com/';
+ _paq.push(['setTrackerUrl', u + 'matomo.php']);
+ _paq.push(['setSiteId', '3']);
+ var d = document,
+ g = d.createElement('script'),
+ s = d.getElementsByTagName('script')[0];
+ g.type = 'text/javascript';
+ g.async = true;
+ g.defer = true;
+ g.src = u + 'matomo.js';
+ s.parentNode.insertBefore(g, s);
+ })();
+ </script>
+ <noscript
+ ><p>
+ <img
+ src="https://piwik.dhimmel.com/matomo.php?idsite=3&amp;rec=1"
+ style="border:0;"
+ alt=""
+ /></p
+ ></noscript>
+ <!-- End Matomo Code -->
+ </body>
+</html>

_layouts/landing.html

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+<html>
+ <head>
+ <!-- metatags - https://metatags.io/ -->
+ <title>{{ page.title }}</title>
+ <meta name="viewport" content="width=device-width, initial-scale=1" />
+ <meta name="title" property="og:title" content="{{ page.title }}" />
+ <meta
+ name="description"
+ property="og:description"
+ content="{{ page.description }}"
+ />
+ <meta name="keywords" content="{{ page.keywords }}" />
+ <meta property="og:type" content="website" />
+ <meta property="og:url" content="https://het.io/" />
+
+ <!-- global styles -->
+ <link href="global.css" rel="stylesheet" />
+
+ <!-- page styles -->
+ <link href="page.css" rel="stylesheet" />
+
+ <!-- scripts -->
+ <script src="scripts.js"></script>
+
+ <!-- favicons - https://realfavicongenerator.net/ -->
+ <link rel="apple-touch-icon" sizes="180x180" href="apple-touch-icon.png" />
+ <link
+ rel="icon"
+ type="image/png"
+ sizes="192x192"
+ href="favicon-192x192.png"
+ />
+ <link rel="manifest" href="site.webmanifest" />
+ <link rel="mask-icon" href="safari-pinned-tab.svg" color="#02b3e4" />
+ <meta name="msapplication-TileColor" content="#02b3e4" />
+ <meta name="theme-color" content="#02b3e4" />
+ <meta property="og:image" content="share-thumbnail.png" />
+ </head>
+ <body>
+ <canvas></canvas>
+ {{ content }}
+ <script src="deep-field.js"></script>
+ </body>
+</html>