Clean up samples

samples/jekyll-template/_config.yml

 source:      .
 destination: ./_site
-plugins:     ./_plugins
+plugin_dir:  ./_plugins
 
-auto:     false
-server:   false
 lsi:      false
 safe:     false
-pygments: true
-markdown: maruku
+highlighter: true
 
-baseurl: ./ #http://ece.uwaterloo.ca/~hdpatel/uwhtml
-root_home: ~hdpatel/uwhtml
+markdown: redcarpet
+redcarpet:
+  extensions: ["no_intra_emphasis", "fenced_code_blocks", "autolink", "strikethrough", "superscript", "with_toc_data", "smart"]
+
+baseurl: ./ 
+root_home: 
 
 permalink: /:year/:month/:day/:title
 exclude:   ["Rakefile", "no-build"]
-title:     Hiren D. Patel
-url:       http://ece.uwaterloo.ca/~hdpatel/uwhtml
+title:     
+url:       
 
 # jekyll-scholar configurations
 scholar:
-  style: _publications/custom-hdp.csl
+  style: publications/customized-jse.csl
   locale: en
-
   sort_by: year
   order: descending
-
-  source: ./_publications
+  source: ./publications
   bibliography: test.bib
   details_dir: ./publications/details
-  details_layout: details.html
-  #query: "@*[public!=no]"
+  query: "@*[public!=no]"
+
+  # Scholar has changed the way it renders bib tags
+  # Need to look at more at the defaults.
+  bibliography_list_tag: "ul"
+
+# jekyll-scholar-extras configurations
+scholar-extras:
+# TODO Options need to be reworked through

samples/jekyll-template/_publications/test.bib

-@book{dragon,
-			Address = {Boston},
-			Author = {Aho, Alfred V., and Lam, Monica S., and Ullman, Jeffrey D.},
-			Booktitle = {Compilers: Principles, Techniques, and Tools},
-			Date-Added = {2010-08-05 09:57:15 +0200},
-			Date-Modified = {2010-08-05 10:06:32 +0200},
-			Edition = {second},
-			Keywords = {compiler, lex, yacc},
-			Publisher = {Addison Wesley},
-			Title = {Compilers: Principles, Techniques, and Tools},
-			Year = {2007},
-      public ={yes}
-}
-		
-@book{python,
-  author={M. Lutz},
-  year={2001},
-  title={Programming Python, Second Edition},
-  publisher={O'Reilly Media, Inc.},
-  address={Sebastopol, CA},
-  pages={1026},
-  pdflink1={./hello/python.pdf},
-  isbn={0596000855}
-}
-
-@book{ruby,
-  abstract  = {Blah blah blah blah blah blah blah blah ... },
-  title     = {The Ruby Programming Language},
-  author    = {Flanagan, David and Matsumoto, Yukihiro},
-  year      = {2008},
-  public    = {yes},
-  publisher = {O'Reilly Media}
-}
-
-@inproceedings{martin:2008klnew,
-  abstract  = {blah blah blah blah blah blah blah blah ... },
-    author = {m. g. f. martin},
-    doi = {10.1111/j.1933-1592.2008.00163.x },
-    booktitle = {philosophy and phenomenological research},
-    keywords = {perception},
-    month = {may},
-    number = {3},
-    pages = {674-681},
-    title = {commentary on action in perception},
-    volume = {76},
-    public    = {yes},
-    year = {2008}}
-
-@article{martin:2008kl,
-  abstract  = {blah blah blah blah blah blah blah blah ... },
-    author = {m. g. f. martin},
-    doi = {10.1111/j.1933-1592.2008.00163.x },
-    journal = {philosophy and phenomenological research},
-    keywords = {perception},
-    month = {may},
-    number = {3},
-    pages = {674-681},
-    title = {commentary on action in perception},
-    volume = {76},
-    public    = {yes},
-    year = {2008}}
-

samples/jekyll-template/index.html

 ---
-layout: default
+layout: default 
 no_sidebar: true
+no_type_sidebar: false
 ---
-{% bibliography_hdp %}
+
+<div class="pure-g-r" id="layout">
+  <div class="pure-u-1-2">
+    <div class="l-left">
+    <h1> Publications</h1>
+    </div>
+  </div>
+
+    <div class="pure-u-1-2">
+      <div class="l-right">
+	<p>
+	  <a class="pure-button" href="{{site.baseurl}}/publications/index.html">By Year</a>
+	  <a class="pure-button" href="{{site.baseurl}}/publications/index_bytype.html">By Type</a>	  
+      </p>
+      </div>
+    </div>
+
+<div class="pure-u-1">
+{% bibliography_year %}
+</div>
+</div>