jekyll-scientific 0.0.1 → 0.0.2

data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    jekyll-scientific (0.0.1)
+    jekyll-scientific (0.0.2)
 
 GEM
   remote: https://rubygems.org/

data/README.md

@@ -3,7 +3,20 @@ __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
+# How to use it
+
+In your Jekyll _config.yaml file add a gems array and add jsc to it as in
+gems : [jsc]
+
+On the command line run
+
+``` bash
+   gem install jekyll-scientific
+```
+
+That's it, plugin specific config options are included below.
+
+## What it supports 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)
@@ -13,5 +26,68 @@ A plugin which extends markdown to include features akin to Latex's that make ma
 * 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/)
+* Unfortunately you can't run custom plugins with GitHub pages (for obv. reasons). So JSC sites need to be built locally and their _site directory pushed to GitHub.
+One the list of things to do is use git hooks to automatically build the jekyll site see [Git global hooks](http://stackoverflow.com/a/8842663/400048) and  [Githooks](http://githooks.com/)
+
+# Configuration
+
+Various config options are available for each plugin included.
+
+## Citations
+
+Citations are provided by [jekyll-scholar](https://github.com/inukshuk/jekyll-scholar/).
+Visit the link for detailed covered of available options and usage.
+In summary the following options are available to configure how citations work
+
+``` yaml
+   scholar:
+     style: apa
+     locale: en
+
+     sort_by: none
+     order: ascending
+
+     source: bibtex #says refereces.bib stored in bibtex folder
+     bibliography: references #says a file called bibtex/references.bib is the main bib file
+     bibliography_template: "%{reference}"
+
+     details_dir:    bibliography
+     details_layout: bibtex.html
+     details_link:   Details
+
+     query: "@*"
+```
+To cite a work from the main bib fileuse the cite tag as in:
+e.g. {% cite kirsch2006distance %} would cite the entry with the given name.
+To append a list of references at the bottom of the page or post use the references tag as in:
+{% bibliography -c %},-c tells it to only include citations used on the current page or post without -c all entries from the bibliography file will be listed
+
+
+## LateX math / Formulas
+
+Formulas are done using the MathJax library. There are two tags available for adding math.
+
+1. {% m %} and {% em %}  pairs are used to add math inline i.e. within a sentence
+
+2. {% math %} and {% endmath %} pairs are used to add math in a centered block as is typical in LateX documents.
+
+For e.g.
+
+``` latex
+
+{% m %}
+	e = mc^2
+{% em %}
+
+{% math %}
+\mathbf{V}_1 \times \mathbf{V}_2 =  \begin{vmatrix}
+\mathbf{i} & \mathbf{j} & \mathbf{k} \\
+\frac{\partial X}{\partial u} &  \frac{\partial Y}{\partial u} & 0 \\
+\frac{\partial X}{\partial v} &  \frac{\partial Y}{\partial v} & 0
+\end{vmatrix}
+{% endmath %}
+
+```
+### todo
 
+Formulas are currently not as configurable as they could be. MathJax has a lot of config options that could be added.

data/VERSION

@@ -1 +1 @@
-0.0.1
+0.0.2

data/bin/jsc

@@ -0,0 +1,4 @@
+#!/usr/bin/env ruby
+spec       = Gem::Specification.find_by_name('jekyll-scientific')
+shell_path = File.join(spec.gem_dir, 'bin', 'jsc_shell.sh')
+exec("sh #{shell_path} " + ARGV.join( ' ' ))

data/bin/jsc_publish.sh

@@ -0,0 +1,41 @@
+#!/bin/sh
+# get publish message to use
+message=$1
+if [ -z "$1" ]
+then #if argument is empty
+   #get the last commit message from this branch and use it as the commit to publish the site
+   message=$(git log -n 1 --format="%s %n %n %b")
+fi
+# generate - just to make sure latest changes have been built
+jekyll build --trace
+#push the current branch to remote
+git push
+# get branch name into $branch -http://git-blame.blogspot.co.uk/2013/06/checking-current-branch-programatically.html
+branch=$(git symbolic-ref --short -q HEAD)
+tmp_d="/tmp/jsc"
+#remove /tmp/jsc
+rm -rf ${tmp_d}
+mkdir ${tmp_d}
+cp -r _site/. ${tmp_d}/
+#checkout gh-pages
+git checkout gh-pages
+current_branch=$(git symbolic-ref --short -q HEAD)
+if [[ "$current_branch" == *gh-pages* ]]
+then
+	#copy /tmp/jsc/* to current dir, replacing existing files
+	cp -rv ${tmp_d}/. ./.
+	# commit changes with message from command line or last commit msg
+	git add -u
+	git add .
+	git commit -a -m ${message}
+	# push gh-pages branch
+	git push
+	# checkout $branch
+	git checkout ${branch}
+else
+  red='\e[0;31m' #red - http://stackoverflow.com/a/5947802/400048
+  NC='\e[0m' # No Color
+  echo -e "${red}Failed to checkout gh-pages branch, site not published!${NC}"
+fi
+# remove /tmp/jsc
+rm -rf ${tmp_d}

data/bin/jsc_shell.sh

@@ -0,0 +1,10 @@
+#!/bin/sh
+action=$1
+cur_dir="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+
+if [ -z "$1" ]
+then #if argument is empty default to publish
+   action="publish"
+fi
+shift #effectively get rid of first argument (the action)
+sh ${cur_dir}/jsc_${action}.sh "$@"

data/jsc.gemspec

@@ -19,4 +19,5 @@ Gem::Specification.new do |s|
   s.files         = `git ls-files`.split("\n")
   s.test_files    = `git ls-files -- {test,spec,features}/*`.split("\n")
   s.require_paths = ["lib"]
+  s.executables << 'jsc'
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: jekyll-scientific
 version: !ruby/object:Gem::Version
-  version: 0.0.1
+  version: 0.0.2
   prerelease: 
 platform: ruby
 authors:
@@ -63,7 +63,8 @@ description: A group of plugins that make Jekyll sites easier for research publi
   Includes support for LateX formulas and citations
 email:
 - jsc@crlog.info
-executables: []
+executables:
+- jsc
 extensions: []
 extra_rdoc_files: []
 files:
@@ -74,6 +75,9 @@ files:
 - LICENSE
 - README.md
 - VERSION
+- bin/jsc
+- bin/jsc_publish.sh
+- bin/jsc_shell.sh
 - jekyll-scientific-0.0.1.gem
 - jsc.gemspec
 - lib/JSCRef.rb