Phase space plotting method was added

Filling_pattern update should happen before no_empty is used !

Add T1 = RF period to synchrotron object
Add binning and plot_profile to Bunch object // plot_profile to improve
Modify beam.filling_pattern to store the array instead of computing it every time
Add distance_between_bunches method to Beam object
Modify not_empty method of Beam to use filling_pattern

Optic functions as arrays
Uses PyAT lattice for import
Adapt other files for the change

Update machines/__init__.py, machines/soleil.py, tracking/__init__.py, tracking/aperture.py, tracking/element.py, tracking/optics.py, tracking/parallel.py, tracking/particles.py, tracking/rf.py, tracking/synchrotron.py files

To be PEP8 complient:
Lowercase folders
Extended docstrings
Rename and divide some files

Add synchrotron radiation in transverse plane
Fix a mistake in the transverse one turn map

New parallel module to handle Mpi class which is used in Beam

Add bunch_X properties to Beam class
Add a generator over "not empty" bunches to Beam class
Modify Bunch class in order to have mean, std and emit as property and not method

Empty bunches are now not None any more but represented by Bunch class with 1 mp set to dead
Change init_beam to reflect the change

Empty bunches are now not None any more but represented by Bunch class with 1 mp set to dead
Change init_beam to reflect the change

Use pandas DF to hold data in Bunch class instead of numpy masked array -> better behaviour and allows to set to alive particles only