other cython modules can now use array_wrap_np
add cython function to convert pele::Array into numpy array
remove parallel connect rountines

It's better to do the whole double ended connect in parallel using
pele.concurrant
corrected arguments to AASiteType in pele/angleaxis/aatopology.py
saved symmetry operations as angle-axis rotations as well as matrices in pele/angleaxis/rigidbody.py
added MolecularCluster cluster class and associated minperdist classes/routines
minor reformatting
added simple water cluster test
modified the testing routines
added Molecule class, overloaded various AtomicCluster methods
added water cluster example
Add an SQL index on the minimum and ts energies for the database

This makes searching for minima within an energy range (as is done when
adding a new minimum) a lot faster.  Ditto with transition states.

This change to the dabase will be automatically added to existing
databases.  There is no need to do any database migration
undefer coords in sqlalchemy query in addMinimum

This gives a massive speed up in the addMinimum function.

Minimum.coords (and other non-sql types) are set as deferred, which
means that they are not automatically loaded during a query.  The
following code

    for m in db.session.query(Minimum):
        print m.coords

will access the database once to get the list of mimima, then once for
each iteration to get the coords from the database.  The following code
gets everything at once and is much faster

    from sqlalchemy.orm import undefer
    for m in db.session.query(Minimum).options(undefer("coords")):
        print m.coords

Currently I've only changed it in Database.addMinimum, but we should
think about doing something similar (optionally) for Database.minima()
add a documentation page about database performance
add commit_interval to Database.minimum_adder()

This makes it easy to reduce the frequency that db.session.commit() is
called.  This can make things run faster.  For example, if you set
commit_interval=100 it will only commit every 100 times addMinimum is
called.  Also, the function MinimumAdder.__del__() is overloaded so that
commit will always be called at the end of a run.
fix bug in graph to avoid duplicating edges

Also, add some comments and a function to print graphs.
bug fix to neighbor_iterator.h

fixed uninitialised double in _areneighbors function
newer version of miniconda
more updates to travis

this makes it nearly the same as mcpele
Merge pull request #68 from js850/fix_travis

fix travis error to do with miniconda