jekyll-scientific 0.0.1

data/.bundle/install.log

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+# Logfile created on 2013-12-27 22:18:55 +0000 by logger.rb/31641
+I, [2013-12-27T22:18:55.996976 #12444]  INFO -- : 0:  unicode (0.4.4) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/unicode-0.4.4.gemspec
+I, [2013-12-27T22:18:55.997993 #12444]  INFO -- : 0:  latex-decode (0.1.1) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/latex-decode-0.1.1.gemspec
+I, [2013-12-27T22:18:55.997993 #12444]  INFO -- : 0:  multi_json (1.8.2) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/multi_json-1.8.2.gemspec
+I, [2013-12-27T22:18:55.998978 #12444]  INFO -- : 0:  bibtex-ruby (3.0.0) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/bibtex-ruby-3.0.0.gemspec
+I, [2013-12-27T22:18:55.999970 #12444]  INFO -- : 0:  little-plugger (1.1.3) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/little-plugger-1.1.3.gemspec
+I, [2013-12-27T22:18:55.999970 #12444]  INFO -- : 0:  logging (1.8.1) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/logging-1.8.1.gemspec
+I, [2013-12-27T22:18:56.000971 #12444]  INFO -- : 0:  mini_portile (0.5.2) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/mini_portile-0.5.2.gemspec
+I, [2013-12-27T22:18:56.000971 #12444]  INFO -- : 0:  nokogiri (1.6.1) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/nokogiri-1.6.1-x86-mingw32.gemspec
+I, [2013-12-27T22:18:56.001972 #12444]  INFO -- : 0:  citeproc-ruby (0.0.6) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/citeproc-ruby-0.0.6.gemspec
+I, [2013-12-27T22:18:56.026980 #12444]  INFO -- : 0:  jekyll-scientific (0.0.1) from C:/Users/Courtney/Documents/projects/jsc/jsc.gemspec
+I, [2013-12-27T22:18:59.526667 #12444]  INFO -- : 0:  json (1.8.1) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/json-1.8.1.gemspec
+I, [2013-12-27T22:18:59.527667 #12444]  INFO -- : 0:  liquid (2.5.4) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/liquid-2.5.4.gemspec
+I, [2013-12-27T22:19:02.399549 #12444]  INFO -- : 0:  rdoc (4.0.1) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/rdoc-4.0.1.gemspec
+I, [2013-12-27T22:19:02.400550 #12444]  INFO -- : 0:  bundler (1.5.0) from C:/bin/Ruby193/lib/ruby/gems/1.9.1/specifications/bundler-1.5.0.gemspec

data/.gitignore

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+.DS_Store
+sftp-config.json
+*.iml
+.idea/
+rdoc/

data/Gemfile

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+source "https://rubygems.org"
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    jekyll-scientific (0.0.1)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    bibtex-ruby (2.3.4)
+      latex-decode (>= 0.0.6)
+      multi_json (~> 1.3)
+    blankslate (2.1.2.4)
+    citeproc-ruby (0.0.6)
+      logging (~> 1.5)
+      nokogiri (~> 1.5)
+    classifier (1.3.3)
+      fast-stemmer (>= 1.0.0)
+    colorator (0.1)
+    commander (4.1.5)
+      highline (~> 1.6.11)
+    fast-stemmer (1.0.2)
+    ffi (1.9.3-x86-mingw32)
+    highline (1.6.20)
+    jekyll (1.4.2)
+      classifier (~> 1.3)
+      colorator (~> 0.1)
+      commander (~> 4.1.3)
+      liquid (~> 2.5.2)
+      listen (~> 1.3)
+      maruku (~> 0.7.0)
+      pygments.rb (~> 0.5.0)
+      redcarpet (~> 2.3.0)
+      safe_yaml (~> 0.9.7)
+      toml (~> 0.1.0)
+    jekyll-scholar (1.2.3)
+      bibtex-ruby (~> 2.3)
+      citeproc-ruby (~> 0.0.6)
+      jekyll (~> 1.0)
+    json (1.8.1)
+    latex-decode (0.1.1)
+      unicode (~> 0.4)
+    liquid (2.5.4)
+    listen (1.3.1)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+      rb-kqueue (>= 0.2)
+    little-plugger (1.1.3)
+    logging (1.8.1)
+      little-plugger (>= 1.1.3)
+      multi_json (>= 1.3.6)
+    maruku (0.7.0)
+    mini_portile (0.5.2)
+    multi_json (1.8.2)
+    nokogiri (1.6.1-x86-mingw32)
+      mini_portile (~> 0.5.0)
+    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 (0.9.3)
+    rb-inotify (0.9.3)
+      ffi (>= 0.5.0)
+    rb-kqueue (0.2.0)
+      ffi (>= 0.5.0)
+    rdoc (4.0.1)
+      json (~> 1.4)
+    redcarpet (2.3.0)
+    safe_yaml (0.9.7)
+    toml (0.1.0)
+      parslet (~> 1.5.0)
+    unicode (0.4.4)
+    yajl-ruby (1.1.0-x86-mingw32)
+
+PLATFORMS
+  x86-mingw32
+
+DEPENDENCIES
+  jekyll-scholar (~> 1.2.3)
+  jekyll-scientific!
+  liquid (~> 2.5.2)
+  rdoc (> 0)

data/LICENSE

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+Apache License
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+

data/README.md

@@ -0,0 +1,17 @@
+__J__ekyll __Sc__ientific plugin - JSC
+===
+
+A plugin which extends markdown to include features akin to Latex's that make markdown viable for research write-ups.
+
+## Support
+
+* Adds proper formula via [MathJax](http://www.mathjax.org/)
+* Citation support for bib files [bibtex-ruby](https://github.com/inukshuk/bibtex-ruby), and [CSL](https://github.com/citation-style-language/styles)
+
+### Todo
+
+* Add [pandoc](http://johnmacfarlane.net/pandoc/) support so that Jekyll site can be completely written in LateX or another format and output to HTML and PDF.
+See [pandoc-multiple-formats](https://github.com/fauno/jekyll-pandoc-multiple-formats) or [pandoc-plugin](https://github.com/dsanson/jekyll-pandoc-plugin)
+
+* Git hooks to automatically build the jekyll site see [Git global hooks](http://stackoverflow.com/a/8842663/400048) and  [Githooks](http://githooks.com/)
+

data/VERSION

@@ -0,0 +1 @@
+0.0.1

data/jsc.gemspec

@@ -0,0 +1,22 @@
+Gem::Specification.new do |s|
+  s.name        = 'jekyll-scientific'
+  s.version     = File.open('VERSION').first
+  s.authors     = ['Courtney Robinson']
+  s.email       = ['jsc@crlog.info']
+  s.description = %q{A group of plugins that make Jekyll sites easier for research publications. Includes support for LateX formulas and citations}
+  s.summary     = %q{Adds LateX features to a Jekyll site.}
+  s.homepage    = 'https://github.com/zcourts/jsc'
+  s.license     = 'BSD3'
+
+  s.platform         = Gem::Platform::RUBY
+  s.rubygems_version = %q{1.3.6}
+  s.required_rubygems_version = Gem::Requirement.new(">= 1.3.6") if s.respond_to? :required_rubygems_version=
+
+  s.add_development_dependency('jekyll-scholar', '~> 1.2.3')
+  s.add_development_dependency('liquid', '~> 2.5.2')
+  s.add_development_dependency('rdoc', '> 0')
+
+  s.files         = `git ls-files`.split("\n")
+  s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
+  s.require_paths = ["lib"]
+end

data/lib/JSCRef.rb

@@ -0,0 +1,46 @@
+require 'bibtex'
+require 'citeproc'
+require File.dirname(__FILE__) + '/plugin'
+
+module JSC
+  class JSCRef < Liquid::Tag
+    include JSC::Plugin
+
+    def initialize(tag_name, markup, tokens)
+      super
+      @key    = markup
+      @config = Hash.new
+    end
+
+    def render(ctx)
+      set_ctx ctx
+      ctx['jsc']          ||= {}
+      ctx['jsc']['cited'] ||= []
+      refs                = ctx['jsc']['cited'].uniq.map { |key|
+        entries.detect { |e| e.key == key.to_s.strip }
+      }
+      bibliography        = refs.each_with_index.map { |entry, index|
+        if entry == nil
+          content_tag :li, missing_ref(ctx['jsc']['cited'][index])
+        else
+          citation = CiteProc.process entry.to_citeproc,
+                                      :style  => config['bibtex']['style'],
+                                      :locale => config['bibtex']['locale'],
+                                      :format => config['bibtex']['format']
+
+          reference = config['bibtex']['bib_template'] % {
+              :reference => citation,
+              :key       => entry.key,
+              :type      => entry.type,
+              :index     => index+1
+          }
+
+          #link_to "##{[prefix, key].compact.join('-')}", citation.join
+          content_tag :li, reference
+        end
+      }.join("\n")
+      content_tag :ol, bibliography
+    end
+  end
+end
+Liquid::Template.register_tag('Xrefs', JSC::JSCRef)

data/lib/JSCite.rb

@@ -0,0 +1,42 @@
+require 'bibtex'
+require 'citeproc'
+require File.dirname(__FILE__) + '/plugin'
+
+module JSC
+  class JSCite < Liquid::Tag
+    include JSC::Plugin
+
+    def initialize(tag_name, markup, tokens)
+      super
+      @key    = markup
+      @config = Hash.new
+    end
+
+    def render(ctx)
+      set_ctx ctx
+      ctx['jsc']          ||= {}
+      ctx['jsc']['cited'] ||= []
+      ctx['jsc']['cited'] << key
+      entry = bib[key.to_s.strip]
+      if entry == nil
+        missing_ref key
+      else
+        puts 'entry'
+        puts entry
+        puts 'citeproc'
+        puts entry.to_citeproc
+        puts 'key'
+        puts entry.key
+        citation = CiteProc.process entry.to_citeproc,
+                                    :style  => config['bibtex']['style'],
+                                    :locale => config['bibtex']['locale'],
+                                    :format => config['bibtex']['format'],
+                                    :mode   => :citation
+        puts 'citation'
+        puts citation
+        link_to "##{[prefix, key].compact.join('-')}", citation.join
+      end
+    end
+  end
+end
+Liquid::Template.register_tag('Xcite', JSC::JSCite)

data/lib/jsc.rb

@@ -0,0 +1,3 @@
+require 'jekyll/scholar'
+
+require File.dirname(__FILE__) + '/math_jax'

data/lib/math_jax.rb

@@ -0,0 +1,29 @@
+require File.dirname(__FILE__) + '/plugin'
+module JSC
+  class MathJaxBlock < Liquid::Tag
+    include JSC::Plugin
+
+    def render(ctx)
+      set_ctx ctx
+      math_jax + '<script type="math/tex; mode=display">'
+    end
+  end
+  class MathJaxInline < Liquid::Tag
+    include JSC::Plugin
+
+    def render(ctx)
+      set_ctx ctx
+      math_jax + '<script type="math/tex">'
+    end
+  end
+  class MathJaxEnd < Liquid::Tag
+    def render(ctx)
+      '</script>'
+    end
+  end
+end
+
+Liquid::Template.register_tag('math', JSC::MathJaxBlock)
+Liquid::Template.register_tag('m', JSC::MathJaxInline)
+Liquid::Template.register_tag('endmath', JSC::MathJaxEnd)
+Liquid::Template.register_tag('em', JSC::MathJaxEnd)

data/lib/plugin.rb

@@ -0,0 +1,44 @@
+module JSC
+  module Plugin
+    attr_reader :site, :ctx
+
+    def config
+      @config                              ||= Hash.new
+      @config['match_jax']                 ||= Hash.new
+      @config['match_jax']['config']       ||= 'default.js'
+      @config['match_jax']['local_config'] ||= ''
+      @config['match_jax']['url']          ||= ''
+      @config
+    end
+
+    def set_ctx(ctx)
+      @ctx, @site, = ctx, ctx.registers[:site]
+      @config      = @site.config['jsc'] || {}
+      ctx['jsc']   ||= {}
+    end
+
+    def mj_config
+      config['match_jax']['config']
+    end
+
+    def mj_local?
+      !config['match_jax']['local_config'].empty?
+    end
+
+    def mj_local
+      mj_local? ? ',' + config['match_jax']['config'] : ''
+    end
+
+    def mj_url
+      config['match_jax']['url'].empty? ? 'http://cdn.mathjax.org/mathjax/latest/MathJax.js' : config['match_jax']['url']
+    end
+
+    def math_jax
+      r                         = !ctx['jsc']['mj_injected'] ?
+          "<script type=\"text/javascript\" src=\"#{mj_url}?config=#{mj_config}#{mj_local}\"></script>" : ''
+      ctx['jsc']['mj_injected'] ||= true
+      r
+      #todo need to modify   loadComplete     http://docs.mathjax.org/en/latest/configuration.html#local-config-files
+    end
+  end
+end

metadata

@@ -0,0 +1,109 @@
+--- !ruby/object:Gem::Specification
+name: jekyll-scientific
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+  prerelease: 
+platform: ruby
+authors:
+- Courtney Robinson
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2013-12-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: jekyll-scholar
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.3
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.2.3
+- !ruby/object:Gem::Dependency
+  name: liquid
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.5.2
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 2.5.2
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    none: false
+    requirements:
+    - - ! '>'
+      - !ruby/object:Gem::Version
+        version: '0'
+description: A group of plugins that make Jekyll sites easier for research publications.
+  Includes support for LateX formulas and citations
+email:
+- jsc@crlog.info
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- .bundle/install.log
+- .gitignore
+- Gemfile
+- Gemfile.lock
+- LICENSE
+- README.md
+- VERSION
+- jekyll-scientific-0.0.1.gem
+- jsc.gemspec
+- lib/JSCRef.rb
+- lib/JSCite.rb
+- lib/jsc.rb
+- lib/math_jax.rb
+- lib/plugin.rb
+homepage: https://github.com/zcourts/jsc
+licenses:
+- BSD3
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  none: false
+  requirements:
+  - - ! '>='
+    - !ruby/object:Gem::Version
+      version: 1.3.6
+requirements: []
+rubyforge_project: 
+rubygems_version: 1.8.24
+signing_key: 
+specification_version: 3
+summary: Adds LateX features to a Jekyll site.
+test_files: []