New features:

- Trajectory actions in Cython

- Trajectory generators (MD, minimization) run as a background task
  provide access to their current state in a thread-safe way.

- New method atomIterator() complements atomList() and may become
  more efficient in future versions.


New examples:

- MDintegrator (a simple Velocity Verlet written in Cython)

- Visualization/additional_objects.py

Improvements:

- Documentation updated, completed, and built with Sphinx.

- Universe description string in trajectories made unambiguous.

- Cython replaces Pyrex everywhere in MMTK.

- Name conflicts in the database cause a warning to be printed.


Bug fixes:

- Memory leak in trajectory output removed.

- The force contribution from bond terms was NaN at zero bond length.

- Elastic Network Model force fields now work correctly with subsets.

- A universe is marked as updated when the mass of one of its atoms changes.

- Subspace.RigidMotionSubspace was wrong for linked rigid bodies.

- Internal coordinate objects detected cyclic bond structures in cases
  where there are none.

- Opening a trajectory whose universe contains named objects could fail.