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

Fig bug for ProfileMonitor if dimension is not in list

Add ProfileMonitor to save bunch profile
Add a track_bunch_data to Monitor class to group the code of track methods from BunchMonitor and PhaseSpaceMonitor
Implement BeamMonitor for the case without mpi
Remove hard coded h=416 ! in BeamMonitor

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 !

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

Class to store physical parameters
TODO: add up/down and right/left distinction for apperture

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

The HDF5 is now open only once on all the cores to be able to write in parallel in the same file. The file must be closed at the end of the tracking.
BeamMonitor is used to save global statistics of all bunches
Add docstrings
TODO : Adding a flush() call at some point might be needed !

Add a monitor module to save tracking data based on h5py
Bunch Monitor is used to get statistics from a specific bunch
PhaseSpaceMonitor is used to save the phase space of a specific bunch
For now the .hdf5 file is opened and closed at each write operation, this seems to cause some problems for mpi.

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