Add cs_invariant to plot_beamdata, plot_bunchdata and streak_beamdata

Add n_bin optional parameter for CavityResonator used only if mpi is false.
Various docstring improvements.

Add Courant Snyder invariant monitoring in BeamMonitor
Add a bunch_cs method to Beam

Set hdf5 file to "a" mode fix an issue where the ProfileMonitor in MPI mode hung when writing data.
Remove flushing in ProfileMonitor.write() to avoid hung issuse in MPI mode.

Fix Monitor.track_bunch_data method to check that only the bunch which bunch_num is specified can write on the file
Modify the behaviour of BunchMonitor, PhaseSpaceMonitor, ProfileMonitor
Make the same modification within WakePotentialMonitor.
Style change to BunchSpectrumMonitor

Remove ipynb file from gitignore

move down init

Add requirements.txt for pip install
Update mbtrack2.yml to add accelerator-toolbox dependency for lattice import

Fix plot_phasespacedata and plot_profiledata
Change color map for streak plots for plot_profiledata, plot_wakedata, plot_cavitydata

Add utilities and instability folders
Change folder name from collective_effects to impedance

Remove untested code
Rename BeamLoadingVlasov to BeamLoadingEquilibrium

Change wake function in CircularResistiveWall to enforce fundamental theorem of beam loading.
Rework Resonator class to set manually time and frequency arrays and enforce fundamental theorem of beam loading.
Change to WakeField.impedance_components and WakeField.wake_components to allow methods begining by W or Z in WakeField subclasses.

Multiple hdf5 file can now be made without having to use MPI. This is achieved by clearing the file name storage every time the monitor is closed.

Changing Ncav after initialization now change the total shunt impedance Rs

Change beam_equilibrium to allow to minimize center of mass offset instead of energy balance.

New LongRangeResistiveWall class to deal with multi-bunch and multi-turn wakes from resistive wall.
Add Mpi.share_means method to share bunch means using MPI.

Allow to plot detuning, tuning angle and powers from tracking.

Add Ncav parameter and Rs_per_cavity attribute to remove ambiguity about what should be used
Add attributes and methods to compute Pc, Pb and Pr.
Add method to set optimal coupling value.

Correct typo in ion_frequency

Fix error on plot_beamdata.
Add option to specify ylim to streak_bunchspectrum and to streak_beamspectrum.

Fix TD calculation for transverse dipolar wakes due to sign change in the 31/08/2021 commit.