simple site replace?

.gitignore

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+_site/
+.sass-cache/
+.jekyll-metadata

FAQs/index.html

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+

Gemfile

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+gem 'github-pages'

License.md

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+To the extent possible under law,
+[Karl Broman](https://github.com/kbroman)
+has waived all copyright and related or neighboring rights to
+“[simple site](https://github.com/kbroman/simple_site)”.
+This work is published from the United States.
+<br/>
+[![CC0](https://i.creativecommons.org/p/zero/1.0/88x31.png)](https://creativecommons.org/publicdomain/zero/1.0/)

README.md

@@ -1,2 +1,18 @@
-# jhbeard.github.io
-first stab at site
+## Simple site: Easy websites with GitHub pages
+
+[Github Pages](https://pages.github.com) provide a simple way to make a
+website using Markdown and git.
+
+This is a minimal tutorial to get started.
+
+View the thing [here](http://kbroman.org/simple_site).
+
+---
+
+To the extent possible under law,
+[Karl Broman](https://github.com/kbroman)
+has waived all copyright and related or neighboring rights to
+“[simple site](https://github.com/kbroman/simple_site)”.
+This work is published from the United States.
+<br/>
+[![CC0](https://i.creativecommons.org/p/zero/1.0/88x31.png)](https://creativecommons.org/publicdomain/zero/1.0/)

Rakefile

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+require "rubygems"
+require 'rake'
+require 'yaml'
+require 'time'
+
+SOURCE = "."
+CONFIG = {
+  'version' => "0.3.0",
+  'themes' => File.join(SOURCE, "_includes", "themes"),
+  'layouts' => File.join(SOURCE, "_layouts"),
+  'posts' => File.join(SOURCE, "_posts"),
+  'post_ext' => "md",
+  'theme_package_version' => "0.1.0"
+}
+
+# Path configuration helper
+module JB
+  class Path
+    SOURCE = "."
+    Paths = {
+      :layouts => "_layouts",
+      :themes => "_includes/themes",
+      :theme_assets => "assets/themes",
+      :theme_packages => "_theme_packages",
+      :posts => "_posts"
+    }
+
+    def self.base
+      SOURCE
+    end
+
+    # build a path relative to configured path settings.
+    def self.build(path, opts = {})
+      opts[:root] ||= SOURCE
+      path = "#{opts[:root]}/#{Paths[path.to_sym]}/#{opts[:node]}".split("/")
+      path.compact!
+      File.__send__ :join, path
+    end
+
+  end #Path
+end #JB
+
+# Usage: rake post title="A Title" [date="2012-02-09"] [tags=[tag1, tag2]]
+desc "Begin a new post in #{CONFIG['posts']}"
+task :post do
+  abort("rake aborted: '#{CONFIG['posts']}' directory not found.") unless FileTest.directory?(CONFIG['posts'])
+  title = ENV["title"] || "new-post"
+  tags = ENV["tags"] || "[]"
+  slug = title.downcase.strip.gsub(' ', '-').gsub(/[^\w-]/, '')
+  begin
+    date = (ENV['date'] ? Time.parse(ENV['date']) : Time.now).strftime('%Y-%m-%d')
+  rescue Exception => e
+    puts "Error - date format must be YYYY-MM-DD, please check you typed it correctly!"
+    exit -1
+  end
+  filename = File.join(CONFIG['posts'], "#{date}-#{slug}.#{CONFIG['post_ext']}")
+  if File.exist?(filename)
+    abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'
+  end
+
+  puts "Creating new post: #{filename}"
+  open(filename, 'w') do |post|
+    post.puts "---"
+    post.puts "layout: post"
+    post.puts "title: \"#{title.gsub(/-/,' ')}\""
+    post.puts 'description: ""'
+    post.puts "category: "
+    post.puts "tags: []"
+    post.puts "---"
+    post.puts "{% include JB/setup %}"
+  end
+end # task :post
+
+# Usage: rake page name="about.html"
+# You can also specify a sub-directory path.
+# If you don't specify a file extention we create an index.html at the path specified
+desc "Create a new page."
+task :page do
+  name = ENV["name"] || "new-page.md"
+  filename = File.join(SOURCE, "#{name}")
+  filename = File.join(filename, "index.html") if File.extname(filename) == ""
+  title = File.basename(filename, File.extname(filename)).gsub(/[\W\_]/, " ").gsub(/\b\w/){$&.upcase}
+  if File.exist?(filename)
+    abort("rake aborted!") if ask("#{filename} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'
+  end
+
+  mkdir_p File.dirname(filename)
+  puts "Creating new page: #{filename}"
+  open(filename, 'w') do |post|
+    post.puts "---"
+    post.puts "layout: page"
+    post.puts "title: \"#{title}\""
+    post.puts 'description: ""'
+    post.puts "---"
+    post.puts "{% include JB/setup %}"
+  end
+end # task :page
+
+desc "Launch preview environment"
+task :preview do
+  system "jekyll --auto --server"
+end # task :preview
+
+# Public: Alias - Maintains backwards compatability for theme switching.
+task :switch_theme => "theme:switch"
+
+namespace :theme do
+
+  # Public: Switch from one theme to another for your blog.
+  #
+  # name - String, Required. name of the theme you want to switch to.
+  #        The the theme must be installed into your JB framework.
+  #
+  # Examples
+  #
+  #   rake theme:switch name="the-program"
+  #
+  # Returns Success/failure messages.
+  desc "Switch between Jekyll-bootstrap themes."
+  task :switch do
+    theme_name = ENV["name"].to_s
+    theme_path = File.join(CONFIG['themes'], theme_name)
+    settings_file = File.join(theme_path, "settings.yml")
+    non_layout_files = ["settings.yml"]
+
+    abort("rake aborted: name cannot be blank") if theme_name.empty?
+    abort("rake aborted: '#{theme_path}' directory not found.") unless FileTest.directory?(theme_path)
+    abort("rake aborted: '#{CONFIG['layouts']}' directory not found.") unless FileTest.directory?(CONFIG['layouts'])
+
+    Dir.glob("#{theme_path}/*") do |filename|
+      next if non_layout_files.include?(File.basename(filename).downcase)
+      puts "Generating '#{theme_name}' layout: #{File.basename(filename)}"
+
+      open(File.join(CONFIG['layouts'], File.basename(filename)), 'w') do |page|
+        if File.basename(filename, ".html").downcase == "default"
+          page.puts "---"
+          page.puts File.read(settings_file) if File.exist?(settings_file)
+          page.puts "---"
+        else
+          page.puts "---"
+          page.puts "layout: default"
+          page.puts "---"
+        end 
+        page.puts "{% include JB/setup %}"
+        page.puts "{% include themes/#{theme_name}/#{File.basename(filename)} %}" 
+      end
+    end
+
+    puts "=> Theme successfully switched!"
+    puts "=> Reload your web-page to check it out =)"
+  end # task :switch
+
+  # Public: Install a theme using the theme packager.
+  # Version 0.1.0 simple 1:1 file matching.
+  #
+  # git  - String, Optional path to the git repository of the theme to be installed.
+  # name - String, Optional name of the theme you want to install.
+  #        Passing name requires that the theme package already exist.
+  #
+  # Examples
+  #
+  #   rake theme:install git="https://github.com/jekyllbootstrap/theme-twitter.git"
+  #   rake theme:install name="cool-theme"
+  #
+  # Returns Success/failure messages.
+  desc "Install theme"
+  task :install do
+    if ENV["git"]
+      manifest = theme_from_git_url(ENV["git"])
+      name = manifest["name"]
+    else
+      name = ENV["name"].to_s.downcase
+    end
+
+    packaged_theme_path = JB::Path.build(:theme_packages, :node => name)
+
+    abort("rake aborted!
+      => ERROR: 'name' cannot be blank") if name.empty?
+    abort("rake aborted! 
+      => ERROR: '#{packaged_theme_path}' directory not found.
+      => Installable themes can be added via git. You can find some here: http://github.com/jekyllbootstrap
+      => To download+install run: `rake theme:install git='[PUBLIC-CLONE-URL]'`
+      => example : rake theme:install git='git@github.com:jekyllbootstrap/theme-the-program.git'
+    ") unless FileTest.directory?(packaged_theme_path)
+
+    manifest = verify_manifest(packaged_theme_path)
+
+    # Get relative paths to packaged theme files
+    # Exclude directories as they'll be recursively created. Exclude meta-data files.
+    packaged_theme_files = []
+    FileUtils.cd(packaged_theme_path) {
+      Dir.glob("**/*.*") { |f| 
+        next if ( FileTest.directory?(f) || f =~ /^(manifest|readme|packager)/i )
+        packaged_theme_files << f 
+      }
+    }
+
+    # Mirror each file into the framework making sure to prompt if already exists.
+    packaged_theme_files.each do |filename|
+      file_install_path = File.join(JB::Path.base, filename)
+      if File.exist? file_install_path and ask("#{file_install_path} already exists. Do you want to overwrite?", ['y', 'n']) == 'n'
+        next
+      else
+        mkdir_p File.dirname(file_install_path)
+        cp_r File.join(packaged_theme_path, filename), file_install_path
+      end
+    end
+
+    puts "=> #{name} theme has been installed!"
+    puts "=> ---"
+    if ask("=> Want to switch themes now?", ['y', 'n']) == 'y'
+      system("rake switch_theme name='#{name}'")
+    end
+  end
+
+  # Public: Package a theme using the theme packager.
+  # The theme must be structured using valid JB API.
+  # In other words packaging is essentially the reverse of installing.
+  #
+  # name - String, Required name of the theme you want to package.
+  #        
+  # Examples
+  #
+  #   rake theme:package name="twitter"
+  #
+  # Returns Success/failure messages.
+  desc "Package theme"
+  task :package do
+    name = ENV["name"].to_s.downcase
+    theme_path = JB::Path.build(:themes, :node => name)
+    asset_path = JB::Path.build(:theme_assets, :node => name)
+
+    abort("rake aborted: name cannot be blank") if name.empty?
+    abort("rake aborted: '#{theme_path}' directory not found.") unless FileTest.directory?(theme_path)
+    abort("rake aborted: '#{asset_path}' directory not found.") unless FileTest.directory?(asset_path)
+
+    ## Mirror theme's template directory (_includes)
+    packaged_theme_path = JB::Path.build(:themes, :root => JB::Path.build(:theme_packages, :node => name))
+    mkdir_p packaged_theme_path
+    cp_r theme_path, packaged_theme_path
+
+    ## Mirror theme's asset directory
+    packaged_theme_assets_path = JB::Path.build(:theme_assets, :root => JB::Path.build(:theme_packages, :node => name))
+    mkdir_p packaged_theme_assets_path
+    cp_r asset_path, packaged_theme_assets_path
+
+    ## Log packager version
+    packager = {"packager" => {"version" => CONFIG["theme_package_version"].to_s } }
+    open(JB::Path.build(:theme_packages, :node => "#{name}/packager.yml"), "w") do |page|
+      page.puts packager.to_yaml
+    end
+
+    puts "=> '#{name}' theme is packaged and available at: #{JB::Path.build(:theme_packages, :node => name)}"
+  end
+
+end # end namespace :theme
+
+# Internal: Download and process a theme from a git url.
+# Notice we don't know the name of the theme until we look it up in the manifest.
+# So we'll have to change the folder name once we get the name.
+#
+# url - String, Required url to git repository.
+#        
+# Returns theme manifest hash
+def theme_from_git_url(url)
+  tmp_path = JB::Path.build(:theme_packages, :node => "_tmp")
+  abort("rake aborted: system call to git clone failed") if !system("git clone #{url} #{tmp_path}")
+  manifest = verify_manifest(tmp_path)
+  new_path = JB::Path.build(:theme_packages, :node => manifest["name"])
+  if File.exist?(new_path) && ask("=> #{new_path} theme package already exists. Override?", ['y', 'n']) == 'n'
+    remove_dir(tmp_path)
+    abort("rake aborted: '#{manifest["name"]}' already exists as theme package.")
+  end
+
+  remove_dir(new_path) if File.exist?(new_path)
+  mv(tmp_path, new_path)
+  manifest
+end
+
+# Internal: Process theme package manifest file.
+#
+# theme_path - String, Required. File path to theme package.
+#        
+# Returns theme manifest hash
+def verify_manifest(theme_path)
+  manifest_path = File.join(theme_path, "manifest.yml")
+  manifest_file = File.open( manifest_path )
+  abort("rake aborted: repo must contain valid manifest.yml") unless File.exist? manifest_file
+  manifest = YAML.load( manifest_file )
+  manifest_file.close
+  manifest
+end
+
+def ask(message, valid_options)
+  if valid_options
+    answer = get_stdin("#{message} #{valid_options.to_s.gsub(/"/, '').gsub(/, /,'/')} ") while !valid_options.include?(answer)
+  else
+    answer = get_stdin(message)
+  end
+  answer
+end
+
+def get_stdin(message)
+  print message
+  STDIN.gets.chomp
+end
+
+#Load custom rake scripts
+Dir['_rake/*.rake'].each { |r| load r }