update links to use https to i can close #7

README.md

@@ -3,7 +3,7 @@
 Code for generating my personal blog. This blog would not be possible
 without several awesome open source projects including:
 
-- [Jekyll](http://jekyllrb.com) - static site generator
+- [Jekyll](https://jekyllrb.com) - static site generator
 - [Pandoc](http://pandoc.org) - the markup conversion swiss-army knife
   (indispensable)
 - [jekyll-pandoc](https://github.com/mfenner/jekyll-pandoc) - to make the previous two play nice
@@ -14,7 +14,7 @@ without several awesome open source projects including:
 
 ## Building
 
-See my post [here](http://tamasnagy.com/blog/building-jekyll-site-debian/)
+See my post [here](https://tamasnagy.com/blog/building-jekyll-site-debian/)
 to get it up and running on Debian. Other POSIX compliant systems should
 be similar.
 

_config.yml

@@ -5,7 +5,7 @@ email: your-email@domain.com
 description: > # this means to ignore newlines until "baseurl"
   Bioinformatics graduate student at UCSF. Interested in systems biology, image analysis, math, mountains, photography, and more
 baseurl: "" # the subpath of your site, e.g. /blog/
-url: "http://www.tamasnagy.com" # the base hostname & protocol for your site
+url: "https://tamasnagy.com" # the base hostname & protocol for your site
 twitter_username: tlngy
 github_user: tlnagy
 github_repo: tnsite

_includes/footer.html

@@ -2,10 +2,10 @@
 
   <div class="wrapper">
     <p class="rss-subscribe">Subscribe <a href="{{ "/feed.xml" | prepend: site.baseurl }}">via RSS</a></p>
-      
+
     <p>Powered by <a href="http://jekyllrb.com">Jekyll</a>. Theme based on <a href="http://daryl.andrewlee.name">Daryl</a>.</p>
-      
-    <a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/80x15.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">All content on this website</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="http://www.tamasnagy.com" property="cc:attributionName" rel="cc:attributionURL">Tamas Nagy</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>, unless otherwise noted. The <a href="http://github.com/{{ site.github_user }}/{{ site.github_repo}}/">code</a> itself is MIT licensed.
+
+    <a rel="license" href="http://creativecommons.org/licenses/by/4.0/"><img alt="Creative Commons License" style="border-width:0" src="https://i.creativecommons.org/l/by/4.0/80x15.png" /></a><br /><span xmlns:dct="http://purl.org/dc/terms/" property="dct:title">All content on this website</span> by <a xmlns:cc="http://creativecommons.org/ns#" href="https://tamasnagy.com" property="cc:attributionName" rel="cc:attributionURL">Tamas Nagy</a> is licensed under a <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>, unless otherwise noted. The <a href="https://github.com/{{ site.github_user }}/{{ site.github_repo}}/">code</a> itself is MIT licensed.
 
   </div> <!-- .wrapper -->
 

_includes/header.html

@@ -15,7 +15,7 @@ <h2 class="site-tagline">{{ site.tagline }}</h2>
             <a href="{{ site.baseurl }}/reading/">reading</a>
             <a href="{{ site.baseurl }}/about/">about</a>
             <div class="nav-source">
-            <i class="fa fa-github gh-icon"></i><a href="http://github.com/{{ site.github_user }}/{{ site.github_repo }}/blob/master/{{ page.path }}">source</a>
+            <i class="fa fa-github gh-icon"></i><a href="https://github.com/{{ site.github_user }}/{{ site.github_repo }}/blob/master/{{ page.path }}">source</a>
             </div>
         </nav>
 

blog/_posts/2014-04-05-predicting-drug-candidate-promiscuity.md

@@ -25,10 +25,10 @@ where $N_db$ is the number of set comparisons made while searching the database.
 The full presentation can be found below.
 
 <div class="bigspacer"></div>
-<center><iframe src="http://www.slideshare.net/slideshow/embed_code/33171714" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe></center>
+<center><iframe src="https://www.slideshare.net/slideshow/embed_code/33171714" width="476" height="400" frameborder="0" marginwidth="0" marginheight="0" scrolling="no"></iframe></center>
 <div class="bigspacer"></div>
 
 <script type="text/javascript"
-src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
 ## References

blog/_posts/2016-05-31-precision-recall-julia.md

@@ -187,6 +187,6 @@ Voila, we have Figure 3:
 data is negative.](/assets/images/precision-recall.svg)
 
 <script type="text/javascript"
-src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
 ## References

blog/_posts/2017-09-07-microtubule-vortices.md

@@ -31,6 +31,6 @@ I implemented the code using Python 3, NumPy, SciPy, and Matplotlib and it is av
 ![However, they start to coalesce into a grid of vortices](/assets/images/2017-09-07-microtubule-vortices/mt_vortices.gif)
 
 <script type="text/javascript"
-src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
 
 ## References

cv.md

@@ -13,7 +13,7 @@ San Francisco, CA 94158-9001
 
 Email: tamas [at] tamasnagy.com\
 Twitter: [\@tlngy](https://twitter.com/tlngy)\
-Website: [http://www.tamasnagy.com](www.tamasnagy.com)
+Website: <https://tamasnagy.com>