Change back invariant name to cs_invariant
Simplify SkewQuadrupole track method

- cs_invariant method in Bunch is renamed to 'action'.
- Action is now saved together with BunchMonitor and can be plotted in plot_bunchdata

Update docstrings
Use pd.DataFrame representation for bunch __repr__
Add the track_alive option for Bunch and Beam.init_beam

1st test, not complete

Remove tools.py to avoid circular import problem with wakefield.py -> merged into wakefield.py
Remove machines folder to save machine data in a seperate git instance
Rework import so the code can be used as independant module mbtrack2

Plotting routines now return figure object.

Rebase test_plot on master
plot_phasespacedata -> only "particles" dataset is plotted
plot_phasespacedata -> mandatory arguments

- total_size and save_every input parameters have been removed.
- only_alive option function has been changed
- Some small corrections on scaling of delta, bunch_charge, bunch_current

- "plot_bunchdata" and "plot_phasespacedata" have been separated from particles module.
- Input prompt has been removed from the code.
- Plotting method for variables in Beam object such as "bunch_current" and "bunch_charge" with respect to bunch number has been added.
- Only alive particles plotting option has been added.

Two plotting methods, "plot_bunchdata" and "plot_phasespacedata", have been added to Beam class.
"getplot" method in Bunch class has been modified and renamed to "long_phasespace".

Phase space plotting method was added

Filling_pattern update should happen before no_empty is used !

- total_size and save_every input parameters have been removed.
- only_alive option function has been changed
- Some small corrections on scaling of delta, bunch_charge, bunch_current

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

- "plot_bunchdata" and "plot_phasespacedata" have been separated from particles module.
- Input prompt has been removed from the code.
- Plotting method for variables in Beam object such as "bunch_current" and "bunch_charge" with respect to bunch number has been added.
- Only alive particles plotting option has been added.

Two plotting methods, "plot_bunchdata" and "plot_phasespacedata", have been added to Beam class.
"getplot" method in Bunch class has been modified and renamed to "long_phasespace".

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

Phase space plotting method was added

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