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

ImpedanceModel -> new method to compute beam and bunch energy loss
beam_loss_factor -> drop 0 from data only if it is there, avoid bug if it is not

Fig bug for ProfileMonitor if dimension is not in list

Changes in loss_factor to use frequency instead of omega
Read_CST forces to have positive real part of longitudinal impedances
New functions : Gaussian_bunch_spectrum, beam_spectrum, beam_loss_factor
ImpedanceModel.plot_area in GHz

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".

to be used with getplot method in Bunch class, particles module

Phase space plotting method was added

Filling_pattern update should happen before no_empty is used !

Bugfix on ComplexData addition : sort data before interpolation
Wakefield class : Add static method to add wakefields
ImpedanceModel class : add methods to handle more easily the wakefields. Maybe can be improved more by using a single Wakefield of each type ?
ImpedanceModel class : add plot_area and summary. summary to be improved more

Add Yokoya_elliptic function to compute Yokoya factors for an elliptic shape.
Add an option to divide by value in read_CST
Add docstrings to read_CST and read_IW2D

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

Add a ImpedanceModel object which derives from Element and is used to sum up different Wakefield elements
Fix uppercase module in resistive_wall.py

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

Circular and rectangular tapers
Correct module name in tools.py
Add kick factor calculation for quadrupolar wakes (similar to dipolar ones)

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

CircularAperture, ElipticalAperture and RectangularAperture elements are added

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

Test OK, to improve

ring.L instead of ring.L0

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