Use Travis to build documentation from master branch

.travis.yml

@@ -0,0 +1,11 @@
+
+# .travis.yml
+
+script: bundle exec rake travis
+
+env:
+  - secure: "ldxWJXz2Z0hhjYETZ7qW0R3IBvBHCE5ZNLS4CYawEQKCGBPneePA8o5/evw8K8Ra3yQI3Ba/XmRZlPQ3aHxW+GReb7yb/HDhe+9obUKikBXvDXErUKQm/2G0PrhXm518uBxaChfQBj2psq9FjnbrHX6ZcVU7L2JhoQfedOOFt9Q="
+
+branches:
+  only:
+    - master

Gemfile

@@ -0,0 +1,4 @@
+source "https://rubygems.org"
+
+gem 'rake', '~> 10.4.2'
+gem 'jekyll', '~> 2.5.2'

Rakefile

@@ -0,0 +1,49 @@
+require 'fileutils'
+require 'rake'
+require 'tmpdir'
+
+destination = './docs/_site/'
+
+desc 'Builds the website using Jekyll'
+task :build do
+   puts 'Rendering markdown to HTML with Jekyll'
+   sh "cd docs && jekyll build"
+   puts 'Rendering finished- results are in _site'
+end
+
+# From Evan Osenko @ https://evansosenko.com/posts/automatic-publishing-github-pages-travis-ci/
+desc 'Generate deck from Travis CI and publish to GitHub Pages.'
+task :travis do
+  # if this is a pull request, do a simple build of the site and stop
+  if ENV['TRAVIS_PULL_REQUEST'].to_s.to_i > 0
+    puts 'Pull request detected. Executing build only.'
+    sh 'bundle exec rake build'
+    next
+  end
+
+  repo = %x(git config remote.origin.url).gsub(/^git:/, 'https:').strip
+  deploy_url = repo.gsub %r{https://}, "https://#{ENV['GH_TOKEN']}@"
+  deploy_branch = repo.match(/github\.io\.git$/) ? 'master' : 'gh-pages'
+  rev = %x(git rev-parse HEAD).strip
+
+  Dir.mktmpdir do |dir|
+    dir = File.join dir, 'site'
+    sh 'bundle exec rake build'
+    fail "Build failed." unless Dir.exists? destination
+    sh "git clone --branch #{deploy_branch} #{repo} #{dir}"
+    sh %Q(rsync -rt --del --exclude=".git" --exclude=".nojekyll" #{destination} #{dir})
+    Dir.chdir dir do
+      # setup credentials so Travis CI can push to GitHub
+      verbose false do
+        sh "git config user.name '#{ENV['GIT_NAME']}'"
+        sh "git config user.email '#{ENV['GIT_EMAIL']}'"
+      end
+
+      sh 'git add --all'
+      sh "git commit -m 'Built from #{rev}'."
+      verbose false do
+        sh "git push -q #{deploy_url} #{deploy_branch}"
+      end
+    end
+  end
+end

docs/Gemfile

@@ -0,0 +1,2 @@
+source 'https://rubygems.org'
+gem 'github-pages'

docs/Gemfile.lock

@@ -0,0 +1,96 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    RedCloth (4.2.9)
+    activesupport (4.1.1)
+      i18n (~> 0.6, >= 0.6.9)
+      json (~> 1.7, >= 1.7.7)
+      minitest (~> 5.1)
+      thread_safe (~> 0.1)
+      tzinfo (~> 1.1)
+    blankslate (2.1.2.4)
+    classifier (1.3.4)
+      fast-stemmer (>= 1.0.0)
+    colorator (0.1)
+    commander (4.1.6)
+      highline (~> 1.6.11)
+    fast-stemmer (1.0.2)
+    ffi (1.9.3)
+    gemoji (1.5.0)
+    github-pages (19)
+      RedCloth (= 4.2.9)
+      jekyll (= 1.5.1)
+      jekyll-mentions (= 0.0.6)
+      jekyll-redirect-from (= 0.3.1)
+      jekyll-sitemap (= 0.3.0)
+      jemoji (= 0.1.0)
+      kramdown (= 1.3.1)
+      liquid (= 2.5.5)
+      maruku (= 0.7.0)
+      rdiscount (= 2.1.7)
+      redcarpet (= 2.3.0)
+    highline (1.6.21)
+    html-pipeline (1.5.0)
+      activesupport (>= 2)
+      nokogiri (~> 1.4)
+    i18n (0.6.9)
+    jekyll (1.5.1)
+      classifier (~> 1.3)
+      colorator (~> 0.1)
+      commander (~> 4.1.3)
+      liquid (~> 2.5.5)
+      listen (~> 1.3)
+      maruku (= 0.7.0)
+      pygments.rb (~> 0.5.0)
+      redcarpet (~> 2.3.0)
+      safe_yaml (~> 1.0)
+      toml (~> 0.1.0)
+    jekyll-mentions (0.0.6)
+      html-pipeline (~> 1.5.0)
+      jekyll (~> 1.4)
+    jekyll-redirect-from (0.3.1)
+      jekyll (~> 1.4)
+    jekyll-sitemap (0.3.0)
+      jekyll (~> 1.4)
+    jemoji (0.1.0)
+      gemoji (~> 1.5.0)
+      html-pipeline (~> 1.5.0)
+      jekyll (~> 1.4)
+    json (1.8.1)
+    kramdown (1.3.1)
+    liquid (2.5.5)
+    listen (1.3.1)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+      rb-kqueue (>= 0.2)
+    maruku (0.7.0)
+    mini_portile (0.6.0)
+    minitest (5.3.4)
+    nokogiri (1.6.2.1)
+      mini_portile (= 0.6.0)
+    parslet (1.5.0)
+      blankslate (~> 2.0)
+    posix-spawn (0.3.8)
+    pygments.rb (0.5.4)
+      posix-spawn (~> 0.3.6)
+      yajl-ruby (~> 1.1.0)
+    rb-fsevent (0.9.4)
+    rb-inotify (0.9.4)
+      ffi (>= 0.5.0)
+    rb-kqueue (0.2.3)
+      ffi (>= 0.5.0)
+    rdiscount (2.1.7)
+    redcarpet (2.3.0)
+    safe_yaml (1.0.3)
+    thread_safe (0.3.4)
+    toml (0.1.1)
+      parslet (~> 1.5.0)
+    tzinfo (1.2.1)
+      thread_safe (~> 0.1)
+    yajl-ruby (1.1.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  github-pages

docs/_config.yml

@@ -0,0 +1,48 @@
+plugins:     ./_plugins
+layouts:     ./_layouts
+include:     ['.htaccess']
+exclude:     []
+keep_files:  ['.git','.svn']
+gems:        []
+timezone:    nil
+encoding:    utf-8
+
+future:      true
+show_drafts: nil
+limit_posts: 0
+highlighter: pygments
+
+relative_permalinks: true
+
+permalink:     date
+paginate_path: 'page:num'
+paginate:      nil
+
+markdown:      kramdown
+markdown_ext:  markdown,mkdown,mkdn,mkd,md
+textile_ext:   textile
+
+excerpt_separator: "\n\n"
+
+defaults:
+    -
+        scope:
+            path: ""
+        values:
+            layout: "page"
+
+kramdown:
+  auto_ids: true
+  footnote_nr: 1
+  entity_output: as_char
+  toc_levels: 1..6
+  smart_quotes: lsquo,rsquo,ldquo,rdquo
+  use_coderay: false
+
+  coderay:
+    coderay_wrap: div
+    coderay_line_numbers: inline
+    coderay_line_numbers_start: 1
+    coderay_tab_width: 4
+    coderay_bold_every: 10
+    coderay_css: style

docs/_layouts/page.html

@@ -0,0 +1,49 @@
+<!DOCTYPE html>
+<html>
+
+    <head>
+        <meta charset='utf-8' />
+        <meta http-equiv="X-UA-Compatible" content="chrome=1" />
+        <meta name="description" content="Preprocessed Connectomes Project" />
+        <link rel="stylesheet" href="stylesheets/bib-publication-list.css"/>
+        <link rel="stylesheet" type="text/css" media="screen" href="stylesheets/stylesheet.css">
+	    <script src="http://code.jquery.com/jquery-latest.min.js" type="text/javascript"></script>
+        <script src="javascripts/menu_script.js"></script>
+        <title>PCP Quality Assessment Protocol</title>
+    </head>
+
+    <body>
+
+        <div id="container">
+
+        <!-- HEADER -->
+            <header>
+                <!--<a id="forkme_banner" href="https://github.com/ccraddock/abide_preproc">View on GitHub</a>-->
+
+                <h1 id="project_title">PCP Quality Assessment Protocol</h1><br>
+  		        <div id='cssmenu'>
+  		            <ul>
+  		                <li><a href='index.html'>Overview</a></li>
+                        <li class='active'><a href='publications.html'>Publications</a></li>
+                        <li class='active'><a href='https://groups.google.com/d/forum/pcp_forum' target="_blank">Forum</a></li>
+                        <li class='active'><a href='https://preprocessed-connectomes-project.github.io' target="_blank">PCP</a></li>
+  		                <li class='active'><a href='https://github.com/preprocessed-connectomes-project/quality-assessment-protocol' target="_blank">View on Github</a></li>
+
+  		            </ul>
+  		        </div>
+            </header>
+
+                <div id="main_content_wrap" class="outer">
+                    <section id="main_content" class="inner">
+                        {{ content }}
+                    </section>
+                </div>
+
+            <!-- FOOTER  -->
+            <footer class="inner">
+                <p>Published with <a href="http://pages.github.com">GitHub Pages</a></p>
+            </footer>
+
+        </div>  
+    </body>
+</html>