Perform IBI on bond and angle potentials

v0.3.0

State and Pair API changes:
- Creating a State object will automatically handle the creation of a states directory and a corresponding directory for each state.
- The add_state function of pair.py now has a calculate_target_rdf option, so that the target RDF can be determined from the trajectory passed into the State object. The user can still manually pass into target_rdf (either a text file or np array).
- The MSIBI object that is created first gets passed into each State created. This is to ensure that the rdf related parameters are available when using calculate_target_rdf=True . I couldn't really think of a better way to do this.
- Added calcualte_rdf.py to the utils dir. This has a function called state_pair_rdf using freud (via cmeutils). This is what is used when calcualte_target_rdf=True in Pair.add_state() This function could probably just be moved into state.py. I wasn't sure if there would be more involved that might warrant having an rdf related file in utils

Other changes:
- The hoomd system loaded in the HOOMD2_HEADER starts from frame 0 of the trajectory rather than the last frame.
- The same rdf function above is used in the compute_current_rdf() function during iterations.

- Freud used for RDFs instead of mdtraj

- fix setup

- blacked and isorted

- switched logging for prints
- allow reading in from gsd
- add tutorial notebook
- added/updated docstrings