scholarmarkdown 1.0.0

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 99d5b736bcf8777363f16fa6f181b68a42a35bd0
+  data.tar.gz: faf2eb639b266ba9eb082f16d63e8bc7f7f9b10b
+SHA512:
+  metadata.gz: cccbcdcc92710f5b7204862c8c3d49217a0c31055432075aed80da58be2d47e5a6c7c882fb655512a34c61e0756b4a48b7f50bb3519c1964a47e5a33f1bef767
+  data.tar.gz: da1129b6bcf6fdeab5980cd94c57ca12597cd85646436ed4231cf3c671bfaeab263fe9df12ed53e7fcf53d35bf8aeccdf9b2fa0a213c0876f312b6603c037efa

data/Gemfile

@@ -0,0 +1,15 @@
+source 'https://rubygems.org'
+
+# references
+gem 'i18n'
+gem 'bibtex-ruby'
+gem 'latex-decode'
+gem 'citeproc-ruby', '>= 1.1.6'
+gem 'csl-styles'
+gem 'bibmarkdown', '~> 1.3.2'
+
+group :development do
+  # management of this gem
+  gem "bundler", "~> 1.0"
+  gem "juwelier", "~> 2.4.7"
+end

data/Gemfile.lock

@@ -0,0 +1,88 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    addressable (2.5.2)
+      public_suffix (>= 2.0.2, < 4.0)
+    bibmarkdown (1.3.2)
+      citeproc-ruby
+      csl-styles
+    bibtex-ruby (4.4.6)
+      latex-decode (~> 0.0)
+    builder (3.2.3)
+    citeproc (1.0.9)
+      namae (~> 1.0)
+    citeproc-ruby (1.1.10)
+      citeproc (~> 1.0, >= 1.0.9)
+      csl (~> 1.5)
+    concurrent-ruby (1.0.5)
+    csl (1.5.0)
+      namae (~> 1.0)
+    csl-styles (1.0.1.8)
+      csl (~> 1.0)
+    descendants_tracker (0.0.4)
+      thread_safe (~> 0.3, >= 0.3.1)
+    faraday (0.12.2)
+      multipart-post (>= 1.2, < 3)
+    git (1.3.0)
+    github_api (0.18.2)
+      addressable (~> 2.4)
+      descendants_tracker (~> 0.0.4)
+      faraday (~> 0.8)
+      hashie (~> 3.5, >= 3.5.2)
+      oauth2 (~> 1.0)
+    hashie (3.5.7)
+    highline (1.7.10)
+    i18n (0.9.5)
+      concurrent-ruby (~> 1.0)
+    juwelier (2.4.9)
+      builder
+      bundler
+      git
+      github_api
+      highline
+      kamelcase (~> 0)
+      nokogiri
+      psych
+      rake
+      rdoc
+      semver2
+    jwt (1.5.6)
+    kamelcase (0.0.2)
+      semver2 (~> 3)
+    latex-decode (0.3.1)
+    mini_portile2 (2.3.0)
+    multi_json (1.13.1)
+    multi_xml (0.6.0)
+    multipart-post (2.0.0)
+    namae (1.0.1)
+    nokogiri (1.8.2)
+      mini_portile2 (~> 2.3.0)
+    oauth2 (1.4.0)
+      faraday (>= 0.8, < 0.13)
+      jwt (~> 1.0)
+      multi_json (~> 1.3)
+      multi_xml (~> 0.5)
+      rack (>= 1.2, < 3)
+    psych (3.0.2)
+    public_suffix (3.0.2)
+    rack (1.5.5)
+    rake (12.3.0)
+    rdoc (6.0.2)
+    semver2 (3.4.2)
+    thread_safe (0.3.6)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bibmarkdown (~> 1.3.2)
+  bibtex-ruby
+  bundler (~> 1.0)
+  citeproc-ruby (>= 1.1.6)
+  csl-styles
+  i18n
+  juwelier (~> 2.4.7)
+  latex-decode
+
+BUNDLED WITH
+   1.14.6

data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright © 2018 Ruben Taelman, Ruben Verborgh
+
+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.

data/README.md

@@ -0,0 +1,45 @@
+# ScholarMarkdown
+[![scholarmarkdown gem version](https://badge.fury.io/rb/scholarmarkdown.svg)](https://rubygems.org/gems/scholarmarkdown)
+
+ScholarMarkdown is Ruby gem for writing scholarly articles in Markdown/HTML. These articles can be viewed in your browser with rich HTML annotations, and they can be printed to PDF into traditional scientific templates via your browser.
+
+It provides an executable (`generate-scholarmd`) for initializing a [nanoc](https://nanoc.ws/) project
+to generate HTML and PDF versions of articles.
+
+ScholarMarkdown consists of a collection of modules that can be configured in your `Rules` file.
+More information on these modules can be found in the [wiki](https://github.com/rubensworks/ScholarMarkdown/wiki/Modules).
+
+## Quick Start
+
+#### 1. Use RubyGems to install this bundle:
+
+```bash
+$ gem install scholarmarkdown
+```
+
+#### 2. Generate your article
+
+_This will create a directory `my-awesome-article` containing the basic files for a ScholarMarkdown project._
+
+```bash
+$ generate-scholarmarkdown my-awesome-article
+$ cd my-awesome-article
+$ bundle install
+```
+
+#### 3. Compile your article
+
+_This will start a live webserver that will continuously compile your article files upon any change._
+
+```
+$ bundle exec guard
+```
+
+#### 4. View your article
+
+Visit `http://localhost:3000/` in your browser to read your article.
+
+Preview in print-mode to see it in its traditional scientific format.
+
+## License
+This software is released under the [MIT license](http://opensource.org/licenses/MIT).

data/Rakefile

@@ -0,0 +1,24 @@
+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'juwelier'
+Juwelier::Tasks.new do |gem|
+  gem.name = "scholarmarkdown"
+  gem.homepage = "http://github.com/rubensworks/ScholarMarkdown"
+  gem.license = "MIT"
+  gem.summary = "A framework for writing markdown-based scholarly articles."
+  gem.email = "rubensworks@gmail.com"
+  gem.authors = ["Ruben Taelman"]
+  gem.executables = ['generate-scholarmarkdown']
+end
+Juwelier::RubygemsDotOrgTasks.new

data/VERSION

@@ -0,0 +1 @@
+1.0.0

data/bin/generate-scholarmarkdown

@@ -0,0 +1,19 @@
+#!/usr/bin/env ruby
+# Initialize a ScholarMarkdown article project
+
+require 'fileutils'
+templatedir = File.dirname(__FILE__) + '/template'
+
+targetdir = ARGV[0]
+if not targetdir
+  puts 'No target directory name was given'
+  exit(1)
+end
+if File.exists?(targetdir)
+  puts 'The target directory already exists'
+  exit(1)
+end
+
+puts 'Initializing project at ' + targetdir
+Dir.mkdir(targetdir)
+FileUtils.copy_entry(templatedir, targetdir)

data/bin/template/.gitignore

@@ -0,0 +1,9 @@
+.DS_Store
+*.pdf
+
+.sass-cache
+Gemfile.lock
+tmp
+output
+*.log
+*.diff

data/bin/template/Gemfile

@@ -0,0 +1,36 @@
+source 'https://rubygems.org'
+
+gem 'nanoc', '~> 4.7'
+
+gem 'scholarmarkdown'
+
+# text processing
+gem 'kramdown'
+gem 'rubypants'
+
+# stylesheets
+gem 'sass'
+
+# references
+gem 'i18n'
+gem 'latex-decode'
+gem 'unicode_utils'
+gem 'citeproc-ruby', '>= 1.1.6'
+gem 'csl-styles'
+
+group :development do
+  # live view
+  gem 'guard-nanoc', '~> 2.1.2'
+  gem 'guard-process'
+  gem 'guard-livereload'
+  gem 'serve'
+  gem 'thin'
+  gem 'rack-livereload'
+  gem 'wdm', '>= 0.1.0' if Gem.win_platform?
+  gem 'rb-readline'
+end
+
+group :test do
+  # validation
+  gem 'w3c_validators', '~> 1.3.1'
+end

data/bin/template/Guardfile

@@ -0,0 +1,15 @@
+guard :nanoc do
+  watch 'nanoc.yaml'
+  watch 'Rules'
+  watch %r{^(content|layouts|lib)/}
+end
+
+guard :process, name: 'server', command: 'bundle exec serve' do
+  watch 'Gemfile.lock'
+end
+
+guard :livereload do
+  watch(%r{^output/}) { |m| m[0].sub(%r{^output/}, '') }
+end
+
+notification :notifu, :nosound => true

data/bin/template/README.md

@@ -0,0 +1,15 @@
+# My Scholarly Article
+
+## Build
+```
+bundle install
+bundle exec nanoc compile
+```
+
+## Development mode
+```
+bundle install
+bundle exec guard
+```
+
+View on http://localhost:3000/

data/bin/template/Rules

@@ -0,0 +1,51 @@
+#!/usr/bin/env ruby
+
+require 'scholarmarkdown/snippets'
+require 'scholarmarkdown/filter/acronym'
+require 'scholarmarkdown/filter/citation'
+require 'scholarmarkdown/filter/hyphenate_iri'
+require 'scholarmarkdown/filter/include_code'
+require 'scholarmarkdown/filter/labelify'
+require 'scholarmarkdown/filter/references_to_footer'
+require 'scholarmarkdown/filter/headerids_to_section'
+
+Encoding.default_external = "UTF-8"
+
+compile '/index.*' do
+  filter :erb
+  filter :scholar_citation, bibfile: items['/references.bib'],
+                            style: 'lncs-custom'
+  filter :kramdown
+  filter :scholar_hyphenate_iri
+  filter :scholar_include_code
+  filter :scholar_labelify
+  filter :scholar_references_to_footer
+  filter :scholar_headerids_to_section
+  filter :rubypants
+  layout '/default.*'
+end
+
+ignore '/*.md'
+ignore '/*.bib'
+ignore '/*.csv'
+
+route '/**/*.{html,md}*' do
+  if item.identifier =~ '/index.*'
+    '/index.html'
+  else
+    item.identifier.without_ext + '/index.html'
+  end
+end
+
+compile '/**/{screen,print}.scss' do
+  filter :sass, syntax: :scss,
+                style: :compressed
+  write item.identifier.without_ext + '.css'
+end
+ignore '/**/*.scss'
+
+compile '/**/*' do
+  write item.identifier.to_s
+end
+
+layout '/**/*', :erb

data/bin/template/config.ru

@@ -0,0 +1,11 @@
+#\ -p 3000
+require 'serve'
+require 'serve/rack'
+require 'rack-livereload'
+use Rack::LiveReload, no_swf: true
+
+root = File.dirname(__FILE__) + '/output'
+run Rack::Cascade.new [
+  Serve::RackAdapter.new(root),
+  Rack::Directory.new(root),
+]

data/bin/template/content/abstract.md

@@ -0,0 +1,15 @@
+## Abstract
+<!-- Context      -->
+Lorem ipsum dolor sit amet, consectetur adipiscing elit.
+<!-- Need         -->
+Vestibulum finibus dignissim augue, id pellentesque est facilisis non.
+<!-- Task         -->
+Donec fringilla dolor non neque iaculis blandit.
+<!-- Object       -->
+Praesent aliquet eleifend iaculis.
+<!-- Findings     -->
+Quisque pellentesque at odio ac bibendum.
+<!-- Conclusion   -->
+Pellentesque imperdiet felis urna, quis facilisis lacus gravida non.
+<!-- Perspectives -->
+Donec quis lectus eget sem tempor tristique pellentesque in dolor.

data/bin/template/content/index.md.erb

@@ -0,0 +1,21 @@
+---
+title: "My Awesome Article"
+---
+<header markdown="1">
+# <%= @item[:title] %>
+
+{:#authors}
+- <%= person 'John Doe', 'http://www.example.org/', 'http://www.example.org/#me' %>
+
+{:#affiliations}
+- {:#myaffiliation} Awesome Inc.
+
+<%= section 'abstract' %>
+</header>
+
+<main>
+  <!-- Add sections by specifying their file name, excluding the '.md' suffix. -->
+  <%= section 'introduction'  %>
+</main>
+
+<footer></footer>

data/bin/template/content/introduction.md

@@ -0,0 +1,4 @@
+## Introduction
+{:#introduction}
+
+This is a great article on the [Semantic Web](cite:cites semanticweb), written in Markdown.

data/bin/template/content/references.bib

@@ -0,0 +1,10 @@
+@article{semanticweb,
+  title = {The semantic web},
+  author = {Berners-Lee, Tim and Hendler, James and Lassila, Ora and others},
+  journal = {Scientific American},
+  volume = {284},
+  number = {5},
+  pages = {28--37},
+  year = {2001},
+  publisher = {New York, NY, USA:}
+}