cboettig / labnotebook Goto Github PK

Wait, custom domain names are free on github? And I thought AWS S3 static sites were a good deal. Why host a static website anywhere else?

I wonder how their CDNs compare, etc.

e.g. see https://github.com/davebridges/davebridges.github.com/blob/master/robots.txt

See BootstrapCDN

Any different than simply using Cloudflare?

• The base url should provide the date published.
• Add date-modified to yaml, and add date-modified to post metadata
• Pages should also have a fixed date-published, and update the date-modified.

Trick is to have the metadata handle the case of no modification date successfully (e.g. by copying the date published then instead?)

either prune down category list or just eliminate categories and rely on tags alone

I like your installation instructions; I've followed them, with minor changes, and they seem to work well. The minor changes I made were changes to commands in order to sandbox the installation.

1. I installed everything using RVM. If you're using Ubuntu 12.04, you should be able to install RVM with

   sudo apt-get install ruby-rvm
   

   RVM has nice capabilities for sandboxing Ruby installations, so if someone wants to try out your site, they don't have to mess with their own Ruby installation. To replicate your setup, after installing RVM, you could then do the following:

   rvm install 1.9.1 # Installs a sandboxed version of Ruby 1.9.1; system copy of Ruby still exists
   rvm create gemset carlboettiger_labnotebook # Creates a sandboxed Ruby 1.9.1 install
   # This sandboxed Ruby 1.9.1 installation has its own gems, distinct from RVM's root copy 
   # of Ruby 1.9.1, AND the system Ruby install
   rvm use 1.9.1@carlboettiger_labnotebook
   

   Note that every time you start up your terminal, and you want to use this particular Ruby installation, you'll need to type

   rvm use 1.9.1@carlboettiger_labnotebook
   

   so you select the right Ruby installation; otherwise, it will default to the RVM default. (You can also have RVM use your system Ruby installation via

   rvm use system
   

   See the RVM docs for further details about RVM.)

2. Your gem installation instructions will install gems for multiple users, altering the global configuration. It would be better to replace

   sudo gem install jekyll feedzirra nokogiri twitter octokit pandoc-ruby
   

   with

   gem install jekyll feedzirra nokogiri twitter octokit pandoc-ruby # no sudo!
   

   which will limit the installation to a local, single-user install. It will also make the installation more accessible to users who don't have sudo privileges. (I don't have them at work, for instance.)

Both of these recommendations should make the installation safer for interested users.

place visitors can get a snapshot of my openscience activities, such as participation in science online and other conferences, ropensci project , and links to the most relevant posts in the ropensci tag?

Also

• Add links to the categories and tags page off the main lab-notebook.html
• Resize text/layout on categories page
• Add categories to newer pages?
• move "All categories" list into a second column

acknowledge features:

• Syntax highlighting from Solarized
• Static site generation by Jekyll
• Layout by twitter-bootstrap
• Equations by Mathjax
• Editing in Github-flavored-markdown
• Reproducible code from knitr

Note: Not sure how to keep vita easy to maintain (e.g. markdown) and rdfa information as well. Perhaps will need to be automatically generated like other bibliography entries in posts, e.g. through knitcitations.

Wow, ruby+github+jekyll make the web a different place.

Ruby wrapper for the Google Analytics API
tutorial

A bit of liquid code should give a nice customizable plugin for displaying analytics stats when jekyll builds the site.

0000-0002-1642-628X

The rss & email subscribe buttons for a single disqus thread on a post may be confused with those for the blog as a whole, and should possibly be removed.

Also enable mathjax support in disqus and markdown using a bit of jquery.

Use fonts and icons from the amazing FontAwesome

http://www.carlboettiger.info/openwebanalytics

For some reason I cannot get Jekyll to have my twitter extension correctly source in externally provided credentials, even though it works just fine to do so using require from irb

last commit of twitter_feed code

Also see issue #25

Ideally would graphically capture the idea that categories should be seen as separate leather-bound notebooks on a shelf, and selecting each lists the entries in that category as a table of contents. Might make use of twitter-bootstrap javascript for a dynamic feel.

Could consider some twitter-bootstrap accordion folding for tags list too.

add pingdom public page link on info page? http://stats.pingdom.com/fy1sae94ydyi

add cloudflare acknowledgement? (Currently testing if cloudflare additional performance (beyond CDN) improves site load times).

Also twitter now requires even public search by bots be authenticated, so this had to be added.

e.g. see the javascript-based examples here:
http://www.kryogenix.org/code/browser/sorttable/

See my own answer here: http://stackoverflow.com/questions/13243469/how-can-a-jekyll-page-access-its-filename/13300410#13300410

HTML5 allows tags to be unclosed, e.g. <meta charset="utf-8"> instead of <meta charset="utf-8" /> but this is not valid XML.

See:

• Polyglot/xhtml5 author guide
• Benefits of XML
• W3C XHTML media type
• Optional tags in html5

Note that tags with no content must be closed with /> (like the meta example) while tags with content must get a normal closing (<li> item </li> etc) .

HTML5 spec is kinda logical since closing is syntax redundant even though not closing is not valid XML, see SO question for discussion.

e.g. from http://www.carlboettiger.info/wordpress/community

Tables are always full width:

http://www.carlboettiger.info/2012/11/09/better-tagging-practices.html
http://www.carlboettiger.info/2012/07/03/notes.html
http://www.carlboettiger.info/2012/05/09/notes.html
http://www.carlboettiger.info/2012/05/16/value-of-information.html

overall smaller tables (smaller fonts too?) might be better.

While I'd rather not clutter my footer, wondering about adding links to my profile on other social networks I frequently use -- in particular, figshare, G+, possibly stackoverflow.

http://fortawesome.github.com/Font-Awesome/

Not urgent since none of the new icons are needed. Icons are even crisper at the defaul 14pt font, and now can enable sub-setting for speed. Also see issue #43 for CDN that includes FontAwesome icons.

• Analytics API for pageviews on each page. Trying to get authentication to work with garb

Also:

• Filter out internal views (from specified IP addresses).
  http://support.google.com/analytics/bin/answer.py?hl=en&answer=1034840

Issues are not preserved as part of the Git repository, so consequently this data is not backed up anywhere else. Would be useful to use the API to generate a markdown file with the issue number and discussion log preserved. Could live in an issues/ directory in the repository.

Effectively integrating these into notebook entries themselves (or a separate page in the notebook for issues logs) is rather another challenge, but also valuable. See http://www.carlboettiger.info/2012/10/05/notes.html

• Consider rss links to reading lists associated with each topic.
• Add Icon-based links to notebook categories/tags and to github repos

Could make for faster load times without needing javascript.

First, I tried the following setup in RVM:

Ruby 1.9.3p362 (2012-12-25 revision 38607) [x86_64-linux]

with the following locally installed gems:

activesupport (3.1.9)
addressable (2.3.2)
builder (3.1.4)
bundler (1.2.3)
classifier (1.3.3)
curb (0.7.18)
directory_watcher (1.4.1)
faraday (0.8.4)
faraday_middleware (0.9.0)
fast-stemmer (1.0.1)
feedzirra (0.1.3)
hashie (1.2.0)
i18n (0.6.1)
jekyll (0.12.0)
json (1.7.6)
kramdown (0.13.8)
liquid (2.4.1)
loofah (1.2.1)
maruku (0.6.1)
multi_json (1.5.0, 1.2.0)
multipart-post (1.1.5)
netrc (0.7.7)
nokogiri (1.5.6)
octokit (1.20.0)
pandoc-ruby (0.6.0)
posix-spawn (0.3.6)
pygments.rb (0.3.7)
rake (10.0.3)
rdoc (3.12)
rubygems-bundler (1.1.0)
rvm (1.11.3.5)
sax-machine (0.1.0)
simple_oauth (0.2.0)
syntax (1.0.0)
twitter (4.4.2)
yajl-ruby (1.1.0)

These gems should be the gems installed when running

gem install jekyll feedzirra nokogiri twitter octokit pandoc-ruby

I got the following error when I built the notebook using Jekyll:

Configuration from " /home/oxberry1/carl_lab_notebook.git/_config.yml
/home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/specification.rb:1637:in raise_if_conflicts': Unable to activate activesupport-3.1.9, because multi_json-1.5.0 conflicts with multi_json (< 1.3, >= 1.0) (Gem::LoadError) from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/specification.rb:746:inactivate'
from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/specification.rb:780:in block in activate_dependencies' from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/specification.rb:766:ineach'
from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/specification.rb:766:in activate_dependencies' from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/specification.rb:750:inactivate'
from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems.rb:212:in rescue in try_activate' from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems.rb:209:intry_activate'
from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:59:in rescue in require' from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:35:inrequire'
from /home/oxberry1/carl_lab_notebook.git/_plugins/jekyll-labnotebook-plugins/mendeley_feed.rb:1:in <top (required)>' from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:36:inrequire'
from /home/oxberry1/.rvm/rubies/ruby-1.9.3-p362/lib/ruby/site_ruby/1.9.1/rubygems/custom_require.rb:36:in require' from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/lib/jekyll/site.rb:78:inblock (2 levels) in setup'
from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/lib/jekyll/site.rb:77:in each' from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/lib/jekyll/site.rb:77:inblock in setup'
from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/lib/jekyll/site.rb:76:in each' from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/lib/jekyll/site.rb:76:insetup'
from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/lib/jekyll/site.rb:31:in initialize' from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/bin/jekyll:238:innew'
from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/gems/jekyll-0.12.0/bin/jekyll:238:in <top (required)>' from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/bin/jekyll:19:inload'
from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/bin/jekyll:19:in <main>' from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/bin/ruby_noexec_wrapper:14:ineval'
from /home/oxberry1/.rvm/gems/ruby-1.9.3-p362@jekyll_0_12_0/bin/ruby_noexec_wrapper:14:in `

So I figured I'd try a second installation in RVM:

Ruby 1.9.1p431 (2011-02-18 revision 30908) [x86_64-linux]

*** LOCAL GEMS ***

activesupport (3.1.9)
addressable (2.3.2)
builder (3.1.4)
bundler (1.2.3)
classifier (1.3.3)
curb (0.7.18)
directory_watcher (1.4.1)
faraday (0.8.4)
faraday_middleware (0.9.0)
fast-stemmer (1.0.1)
feedzirra (0.1.3)
hashie (1.2.0)
i18n (0.6.1)
jekyll (0.12.0)
json (1.7.6)
kramdown (0.13.8)
liquid (2.4.1)
loofah (1.2.1)
maruku (0.6.1)
multi_json (1.5.0, 1.2.0)
multipart-post (1.1.5)
netrc (0.7.7)
nokogiri (1.5.6)
octokit (1.20.0)
pandoc-ruby (0.6.0)
posix-spawn (0.3.6)
pygments.rb (0.3.7)
rake (10.0.3)
rdoc (3.12)
rubygems-bundler (1.1.0)
rvm (1.11.3.5)
sax-machine (0.1.0)
simple_oauth (0.2.0)
syntax (1.0.0)
twitter (4.4.2)
yajl-ruby (1.1.0)

Again, these gems should be installed when running the command

gem install jekyll feedzirra nokogiri twitter octokit pandoc-ruby

I got the following error when building the notebook in Jekyll:

Configuration from /home/oxberry1/carl_lab_notebook.git/_config.yml
Building site: /home/oxberry1/carl_lab_notebook.git -> /home/oxberry1/carl_lab_notebook.git/_site
YAML Exception reading 2010-02-09-Comparative-Phylogenetics-Notebook-(from-OWW).markdown: syntax error on line 2, col 22: tags: [model-choice, ]' YAML Exception reading 2010-02-16-Comparative-Phylogenetics-Notebook-(from-OWW).markdown: syntax error on line 2, col 22:tags: [model-choice, ]'
YAML Exception reading 2010-03-04-Comparative-Phylogenetics-Notebook-(from-OWW).markdown: syntax error on line 2, col 21: `tags: [code-tricks, ]'

Liquid Exception: undefined method sort_by!' for #<Array:0x000000052fdf50> in tags.html /home/oxberry1/carl_lab_notebook.git/_plugins/tag-cloud.rb:75:inrender'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/liquid-2.4.1/lib/liquid/block.rb:94:in block in render_all' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/liquid-2.4.1/lib/liquid/block.rb:92:incollect'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/liquid-2.4.1/lib/liquid/block.rb:92:in render_all' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/liquid-2.4.1/lib/liquid/block.rb:82:inrender'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/liquid-2.4.1/lib/liquid/template.rb:124:in render' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/liquid-2.4.1/lib/liquid/template.rb:132:inrender!'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/jekyll-0.12.0/lib/jekyll/convertible.rb:79:in do_layout' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/jekyll-0.12.0/lib/jekyll/page.rb:100:inrender'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/jekyll-0.12.0/lib/jekyll/site.rb:204:in block in render' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/jekyll-0.12.0/lib/jekyll/site.rb:203:ineach'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/jekyll-0.12.0/lib/jekyll/site.rb:203:in render' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/jekyll-0.12.0/lib/jekyll/site.rb:41:inprocess'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/gems/jekyll-0.12.0/bin/jekyll:264:in <top (required)>' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/bin/jekyll:19:inload'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/bin/jekyll:19:in <main>' /home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/bin/ruby_noexec_wrapper:14:ineval'
/home/oxberry1/.rvm/gems/ruby-1.9.1-p431@carl_notebook/bin/ruby_noexec_wrapper:14:in `

As a test, I built the Jekyll-bootstrap site (cloned from its canonical Git repo today) using the two configurations above. The build worked flawlessly with the first configuration, and completed with minor HTML rendering errors in the second configuration. Any suggestions as to what might be going on?

My host OS is Fedora 17-x86_64, in case that matters. You should be able to use RVM and the gem lists above to replicate at least the Ruby part of my configuration.

Generating graphs that work well in both light and dark themes for the notebook is quite tricky. Using solarized colors for the graphs is the natural solution.

Should allow custom url and custom formatting.

• Should these be set in _config.yml variables?
• Easier to just edit module for custom layout?
• Add CSS controlled markup to feeds
• Review writing liquid extensions, consider choice of function types
• Consider creating as separate repository

Consider white or light grey (github-like?) navbar?

Post latest open & closed issues, github activity

Use octokit, has access to the full v3 API.

Does require I actually learn some Ruby. This intro seems to hit my basic needs (i.e. mostly array handling, also see this SO question )

placed pdfs of my study sheets for the final are in assets/files/pbg-core-notes.

Ideally this would let me support CiTO ontology and other relevant ontologies.

http://webmasters.stackexchange.com/questions/35625/serve-up-syntactic-xhtml5-using-the-text-html-mime-type

http://www.carlboettiger.info/2011/05/08/building-a-semantic-notebook.html#comment-679639088

Consider locally indexed search using indextank
or tipue search.

Otherwise it won't track visitors probably (at least, for me). See ketch@338d784 .

• Description should more closely match postdoctoral work.
• Separate description of thesis work, with links to Alan & CSGF

Or a short description that better/more accurately unifies post-doc and grad work.