Beam.update_filling_pattern and Beam.update_distance_between_bunches are now called directly in the __init__ when a bunch_list is given.
Beam.init_bunch_list_mpi is a convenience method to initialize a beam using MPI parallelisation with a Bunch per core.
Add tests for Beam.init_bunch_list_mpi

[Fix] CavityResonator.init_phasor_track and CavityResonator.init_phasor

See merge request !24

Fix monitor flush

See merge request !23

Only print version information for one process.

Normalization by average_beta / local_beta

See merge request !17

**Warning, this fix contains changes which will change the default behavior of core functions:**

* Default behavior of Optics is changed when AT lattice is loaded: now default to optic function to s=0 instead of average ones.
* Default behavior of LongRangeResistiveWall and ImpedanceModel when an AT lattice is loaded is to normalized by average_beta / local_beta
* Adds Optics.average_beta attribute
* Add pytest markers for tests and update .gitlab-ci.yml and pyproject.toml files.

[Fix] Quadrupolar wake potential sign

See merge request !22

Add test suite

See merge request !21

Code modifications:

* [Fix] adts in TransverseMapSector
* ComplexData.name_and_coefficients_table is now a staticmethod.
* Extend WakeField to "mixed" componenets (xydip, yxdip, ...).
* Small fix/improvements for rf.py (CavityResonator for n_bin=1)
* [Fix] WakePotential.check_sampling method.
* [Fix] Sweep.plot method.
* Add Element.track_bunch_if_non_empty decorator.
* Modify Bunch.binning to add a return_full_length optional parameter.
* Modify Mpi.share_distributions for n_bin=1.
* Modify TransverseSpaceCharge to work with track_alive = True.
* Modify WakePotential for n_bin=1 and use track_bunch_if_non_empty decorator.
* [Fix] IntrabeamScattering for nonuniform fills with Beam.mpi_switch == False
* Modify PhysicalModel to return errors if needed.
* Update BeamIonElement

Project management:

* Update pyproject.toml and poetry.lock with pytest-mock
* Add assert_attr_changed test function.

Ions

See merge request !18

The Q wake potential should be of the same sign as the Q wake function. A positive Q wake function/potential is defocusing i.e. a positive angular kick is felt by the test particle (for positive test particule position).
Also fix WakePotential.plot_last_wake for negative wake function.

Intrabeam scattering tracking implementation

See merge request !5

Implementation of IBS effect in mbtrack2 tracking. A new class was added, mbtrack2.tracking.ibs. It implements a simple IBS kick based on an analytical model. Four analytical models are available: Piwinski Standard, Piwinski Modified, Completely Integrated Piwinski model, and Bane high-energy approximation. 

trapz is deprecated from scipy 1.14.0

Optimize boolean indexing in CircularResistiveWall

See merge request !15

Nonlinear chromaticity

See merge request !16

Fix docstrings

Merge branch 'feature-nonlinear-chromaticity' of gitlab.synchrotron-soleil.fr:PA/collective-effects/mbtrack2 into feature-nonlinear-chromaticity

changed chromaticity computation in _compute_chro() of transverse_map_sector_generator(). Now it can compute arbitrary order of chromaticity from AT.

Merge branch 'feature-nonlinear-chromaticity' of gitlab.synchrotron-soleil.fr:PA/collective-effects/mbtrack2 into feature-nonlinear-chromaticity

- moved the above function to be inside the TransverseSectorMap
- changes phase_advance_* variables to tune_advance_* variables where appropriate

- moved the above function to be inside the TransverseSectorMap
- changes phase_advance_* variables to tune_advance_* variables where appropriate

- np.random.normal -> np.random.standard_normal, 10% faster
- N = len(bunch) to compute the number of particles only once

- TransverseMap now inherits from TransverseSectorMap
- chromaticity phase shift is computed in _compute_chromatic_phase_advances()
- some optimisation of the code, (250 ms -> <50 ms) speed up for typical
  simulation