Ruby 1.9.3-p392 is now required

[#45015533]

There is a denial of service vulnerability in the JSON parser included with Ruby.Denial of Service and Unsafe Object Creation Vulnerability in JSON (CVE-2013-0269)http://www.ruby-lang.org/en/news/2013/02/22/json-dos-cve-2013-0269/This vulnerability is fixed in the latest patch release of Ruby 1.9.3-p392:http://www.ruby-lang.org/en/news/2013/02/22/ruby-1-9-3-p392-is-released/

I've updated the required Ruby used for lab from 1.9.3-p385 to 1.9.3-p392:To update:1. Pull the latest code in the master branch into your lab working dir2. Close all open terminal windows in lab working dir3. Update to latest stable rvm:  $ rvm get stable  $ rvm reload4. cd to lab working dirYou should see a RVM dialog asking if you want to trust new .rvmrc file:  Do you wish to trust this .rvmrc file? (/Users/stephen/dev/concord/lab/.rvmrc)  y[es], n[o], v[iew], c[ancel]> yes  ruby-1.9.3-p392 is not installed.  To install do: 'rvm install ruby-1.9.3-p392'  Failed to create RVM environment 'ruby-1.9.3-p392@lab'.Install updated ruby manually:  $ rvm install ruby-1.9.3-p3925. Change out of ... and then back into lab working dir. This will recreate the lab gemset for the main working directory:  $ cd ..  $ cd lab6. Change to the server dir to recreate the gemset for the webapp:  $ cd server7. cd to root of lab working dir and rebuild project  $ cd ..  $ make clean; make
Gemfile updates: debugger, bourbon, neat

also guard-sass, thor, kramdown

debugger (in server gemset) updated to 1.3.2 for compatibility with Ruby 1.9.3-p392

update bourbon to 3.1.1

bourbon is a Sass mixin library
http://bourbon.io

see change log here: https://github.com/thoughtbot/bourbon/wiki

- Added new transform-style mixin
- Fixed bug with retina-image addon to load correct 1x asset-pipeline image.
- Fixed bug with hide-text addon
- Removed deprecated box-shadow mixin from the button addon.

Procedure used to update bourbon in Lab repo after updating
Gemfile and running bundle install:

  cd src/sass/
  ../../bin/bourbon update

update neat to 1.2.0

neat is a semantic grid framework built on top of Sass and Bourbon
http://neat.bourbon.io/

see change log here: https://github.com/thoughtbot/neat/blob/master/NEWS.md

- New: Auto-detect table layout when span-columns() is called inside row(table)
- Fix: Make shift() reset context after each nested call

Procedure used to update neat in Lab repo after updating
Gemfile and running bundle install:

  cd src/sass
  ../../bin/neat update

update thor to 1.17.0

see changelog: https://github.com/wycats/thor/blob/master/CHANGELOG.md

update kramdown from 0.13.6 to 0.13.8

see: http://kramdown.rubyforge.org/news.html

debugger v1.3.2
change: viewRefreshInterval => timeStepsPerTick

[#45016019]

There are a set of three MD2D model parameters that control model integration time step, period, and sample rate.

The one that controls model integration period has a very confusing name: viewRefreshInterval.

Change the name to timeStepsPerTick

Updates to code, tests, MML importer, example Interactives,
and documentation.
adjust position of falling obstacle

IS [#44983919]

Now the obstacle hots the bottom at the same time as the
atoms -- at least as close as I can make it.

However this makes clear there is also something
strange going on with obstacles and either gravity or
collisions.

Run this model:

/examples/interactives/embeddable.html#interactives/conversion-tests/gravitational-field-test-property-pulldown.json

23.7 ps: orange obstacle is hitting bottom before atoms
46.2 ps: atoms are about to hit before orange obstacle
46.3 ps: orange obstacle has hit before atoms
Interactive updates using new features …

1. use new layout to clean up example Interactives

basic-examples/area-versus-applied-pressure.son
basic-examples/atom-tracing.json
basic-examples/empty-model.json
basic-examples/one-atom.json
basic-examples/simple-ball-drop.json
conversion-tests/aminino-acids.json

2. Use parameters along with property/value style
pulldowns and radio buttons:

conversion-tests/visible-and-invisible.json
draft: new layout idea for Pressure Equillibrium
clarify: embedding html doesn't work yet