Updates to setup.py to correct incorrect information.  Changed version number to 0.1.0.
Updated doctests in yank.py.  Note that 'coordinates' has changed to 'positions' in all cases to match openmm convention.
Had to remove automated version writing to netcdf file because I couldn't get this to work; will have to fix later.
Moved analyze-dataset.py to scripts/, where it belongs.
Removed outdated tests.
oldrepex now passes doctests.
Removed velocity assignment code, since this is now built-in for Context.
repex nose test now works.
Deleted test_repex_mpi, since there is little chance of getting it working.
Increased coverage of yank tests.
Turned off verbose output from weave.
Merge pull request #33 from jchodera/master

More updates to fix doctests.  Still one travis-ci failure due to unsuppressed weave output, but will fix that later.