called from .travis.yml and stop looking at coverage on pypy, since performance
is horrific (4x longer when using coverage).

- Turn on timing for tests to aid in profiling
- Make sure we install coverage and nose-timer packages
- Turn segid test on in general
- Rename several tests
- Fix failure caused when OpenMM is not available

the OS X build into a minimal build with as few packages as possible (this
should save ~10 minutes on the aggregate build time, and we were within 1 minute
of going over the limit, I believe).

This fixes a couple subtle bugs from missing imports and a bunch of other minor
things tagged by pyflakes. It also adds a pyflakes check to the Travis CI script
that will fail if any issues are flagged. However, pyflakes flags a lot of
issues that are not really issues, and are IMO the best way to do something. So
there is a wrapper script around pyflakes that filters out these "OK" failures
(including any failure with 3rd-party libraries that I don't want to modify
heavily).

setup

it locally

Should give faster builds and more memory (!!)

This makes a number of changes:

- numpy is now a hard requirement
- coordinates always has shape (frame, natom, 3)
- you can set coordinates, and it is reshaped to a (frame, natom, 3) ndarray,
  and the first frame's coordinates are assigned to the xx, xy, and xz
  attributes of each atom in the Structure
- did the same thing with the 'box' attribute (which is also always a
  numpy.ndarray now)
- add tests for this new functionality

One of the chamber systems I tested was ~60K atoms. When running 4 instances
of the tests, some would occasionally get killed presumably for blowing Travis
memory limits (since it had to store all of the raw data, all of the data
structures, the OpenMM data structures, and their copies in the running
Context).  They are still useful tests, IMO, since it gets every component of
the CHARMM force field in the chamber files. So add an environment variable
option for disabling large tests, and set it in the Travis environment.

Also, `unittest.skipIf` (and `unittest.SkipTest`) don't exist before Python 2.7,
and ParmEd supports at *least* Python 2.6. So add a hacktastic replacement for
the `skipIf` decorator to test/utils.py that behaves *almost* the same way
(basically, if the test is skipped, the decorator prints a message and returns;
so it still prints "ok" at the end, unlike `unittest.skipIf`).

It can't currently decorate a class... we'll see if that's required.