Restructured site base on Alembic

griffithlab · Mar 31, 2017 · 9db2359 · 9db2359
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diff --git a/.DS_Store b/.DS_Store
diff --git a/404.md b/404.md
@@ -0,0 +1,13 @@
+---
+title: "404"
+excerpt: "Page Not Found"
+permalink: 404.html
+indexing: false
+sitemap: false
+---
+
+Sorry, but the page could not be found.
+
+Are you looking for:
+
+{% include nav-header.html %}
diff --git a/CNAME b/CNAME
@@ -0,0 +1 @@
+griffithlab.github.io/gen-viz-workshop/
diff --git a/Gemfile b/Gemfile
@@ -1,34 +1,2 @@
 source "https://rubygems.org"
-ruby RUBY_VERSION
-
-# Use the github-pages gem to deply jekyll to github
-require 'json'
-require 'open-uri'
-versions = JSON.parse(open('https://pages.github.com/versions.json').read)
-
-gem 'github-pages', versions['github-pages']
-
-# 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", "3.4.3"
-
-# 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]
+gemspec
diff --git a/Gemfile.lock b/Gemfile.lock
@@ -1,75 +1,30 @@
+PATH
+  remote: .
+  specs:
+    alembic-jekyll-theme (1.5.2)
+      jekyll (~> 3.3)
+      jekyll-feed (~> 0.5)
+      jekyll-mentions (~> 1.2)
+      jekyll-paginate (~> 1.1)
+      jekyll-redirect-from (~> 0.11)
+      jekyll-seo-tag (~> 2.0)
+      jekyll-sitemap (~> 0.10)
+      jemoji (~> 0.7)
+
 GEM
   remote: https://rubygems.org/
   specs:
-    activesupport (4.2.7)
+    activesupport (4.2.8)
       i18n (~> 0.7)
-      json (~> 1.7, >= 1.7.7)
       minitest (~> 5.1)
       thread_safe (~> 0.3, >= 0.3.4)
       tzinfo (~> 1.1)
     addressable (2.5.1)
       public_suffix (~> 2.0, >= 2.0.2)
-    coffee-script (2.4.1)
-      coffee-script-source
-      execjs
-    coffee-script-source (1.12.2)
     colorator (1.1.0)
-    ethon (0.10.1)
-      ffi (>= 1.3.0)
-    execjs (2.7.0)
-    faraday (0.11.0)
-      multipart-post (>= 1.2, < 3)
     ffi (1.9.18)
     forwardable-extended (2.6.0)
     gemoji (3.0.0)
-    github-pages (130)
-      activesupport (= 4.2.7)
-      github-pages-health-check (= 1.3.3)
-      jekyll (= 3.4.3)
-      jekyll-avatar (= 0.4.2)
-      jekyll-coffeescript (= 1.0.1)
-      jekyll-default-layout (= 0.1.4)
-      jekyll-feed (= 0.9.1)
-      jekyll-gist (= 1.4.0)
-      jekyll-github-metadata (= 2.3.1)
-      jekyll-mentions (= 1.2.0)
-      jekyll-optional-front-matter (= 0.1.2)
-      jekyll-paginate (= 1.1.0)
-      jekyll-readme-index (= 0.0.4)
-      jekyll-redirect-from (= 0.12.1)
-      jekyll-relative-links (= 0.3.0)
-      jekyll-sass-converter (= 1.5.0)
-      jekyll-seo-tag (= 2.1.0)
-      jekyll-sitemap (= 1.0.0)
-      jekyll-swiss (= 0.4.0)
-      jekyll-theme-architect (= 0.0.3)
-      jekyll-theme-cayman (= 0.0.3)
-      jekyll-theme-dinky (= 0.0.3)
-      jekyll-theme-hacker (= 0.0.3)
-      jekyll-theme-leap-day (= 0.0.3)
-      jekyll-theme-merlot (= 0.0.3)
-      jekyll-theme-midnight (= 0.0.3)
-      jekyll-theme-minimal (= 0.0.3)
-      jekyll-theme-modernist (= 0.0.3)
-      jekyll-theme-primer (= 0.1.7)
-      jekyll-theme-slate (= 0.0.3)
-      jekyll-theme-tactile (= 0.0.3)
-      jekyll-theme-time-machine (= 0.0.3)
-      jekyll-titles-from-headings (= 0.1.4)
-      jemoji (= 0.8.0)
-      kramdown (= 1.13.2)
-      liquid (= 3.0.6)
-      listen (= 3.0.6)
-      mercenary (~> 0.3)
-      minima (= 2.0.0)
-      rouge (= 1.11.1)
-      terminal-table (~> 1.4)
-    github-pages-health-check (1.3.3)
-      addressable (~> 2.3)
-      net-dns (~> 0.8)
-      octokit (~> 4.0)
-      public_suffix (~> 2.0)
-      typhoeus (~> 0.7)
     html-pipeline (2.5.0)
       activesupport (>= 2)
       nokogiri (>= 1.4)
@@ -85,66 +40,20 @@ GEM
       pathutil (~> 0.9)
       rouge (~> 1.7)
       safe_yaml (~> 1.0)
-    jekyll-avatar (0.4.2)
-      jekyll (~> 3.0)
-    jekyll-coffeescript (1.0.1)
-      coffee-script (~> 2.2)
-    jekyll-default-layout (0.1.4)
-      jekyll (~> 3.0)
-    jekyll-feed (0.9.1)
+    jekyll-feed (0.9.2)
       jekyll (~> 3.3)
-    jekyll-gist (1.4.0)
-      octokit (~> 4.2)
-    jekyll-github-metadata (2.3.1)
-      jekyll (~> 3.1)
-      octokit (~> 4.0, != 4.4.0)
     jekyll-mentions (1.2.0)
       activesupport (~> 4.0)
       html-pipeline (~> 2.3)
       jekyll (~> 3.0)
-    jekyll-optional-front-matter (0.1.2)
-      jekyll (~> 3.0)
     jekyll-paginate (1.1.0)
-    jekyll-readme-index (0.0.4)
-      jekyll (~> 3.0)
     jekyll-redirect-from (0.12.1)
       jekyll (~> 3.3)
-    jekyll-relative-links (0.3.0)
-      jekyll (~> 3.3)
     jekyll-sass-converter (1.5.0)
       sass (~> 3.4)
     jekyll-seo-tag (2.1.0)
       jekyll (~> 3.3)
-    jekyll-sitemap (1.0.0)
-      jekyll (~> 3.3)
-    jekyll-swiss (0.4.0)
-    jekyll-theme-architect (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-cayman (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-dinky (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-hacker (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-leap-day (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-merlot (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-midnight (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-minimal (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-modernist (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-primer (0.1.7)
-      jekyll (~> 3.3)
-    jekyll-theme-slate (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-tactile (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-theme-time-machine (0.0.3)
-      jekyll (~> 3.3)
-    jekyll-titles-from-headings (0.1.4)
+    jekyll-sitemap (0.13.0)
       jekyll (~> 3.3)
     jekyll-watch (1.5.0)
       listen (~> 3.0, < 3.1)
@@ -153,22 +62,16 @@ GEM
       gemoji (~> 3.0)
       html-pipeline (~> 2.2)
       jekyll (>= 3.0)
-    json (1.8.6)
     kramdown (1.13.2)
     liquid (3.0.6)
-    listen (3.0.6)
-      rb-fsevent (>= 0.9.3)
-      rb-inotify (>= 0.9.7)
+    listen (3.0.8)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
     mercenary (0.3.6)
     mini_portile2 (2.1.0)
-    minima (2.0.0)
     minitest (5.10.1)
-    multipart-post (2.0.0)
-    net-dns (0.8.0)
     nokogiri (1.7.1)
       mini_portile2 (~> 2.1.0)
-    octokit (4.6.2)
-      sawyer (~> 0.8.0, >= 0.5.3)
     pathutil (0.14.0)
       forwardable-extended (~> 2.6)
     public_suffix (2.0.5)
@@ -178,31 +81,16 @@ GEM
     rouge (1.11.1)
     safe_yaml (1.0.4)
     sass (3.4.23)
-    sawyer (0.8.1)
-      addressable (>= 2.3.5, < 2.6)
-      faraday (~> 0.8, < 1.0)
-    terminal-table (1.7.3)
-      unicode-display_width (~> 1.1.1)
     thread_safe (0.3.6)
-    typhoeus (0.8.0)
-      ethon (>= 0.8.0)
     tzinfo (1.2.3)
       thread_safe (~> 0.1)
-    unicode-display_width (1.1.3)
 
 PLATFORMS
   ruby
 
 DEPENDENCIES
-  github-pages (= 130)
-  jekyll (= 3.4.3)
-  jekyll-feed (~> 0.6)
-  json
-  minima (~> 2.0)
-  tzinfo-data
-
-RUBY VERSION
-   ruby 2.1.3p242
+  alembic-jekyll-theme!
+  bundler (~> 1.12)
 
 BUNDLED WITH
    1.14.6
diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2016 David Darnes
+
+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