Pygran

Added
- Versioneer for automated code versioning
- Improved code structure
- Support for python 3.10
- Separated analysis, sim, and params into separate packages.
- New params module to replace pygran_params pkg

Changed
- Improved code quality and compliance with PEP8
- Made mpi4py an optional requirement
- Switched to lower-case module names
- Support for pygran_analysis vx.x.x
- Support for pygran_sim vx.x.x
- Improved liggghts compilation progress bar

Removed
- Old versioning system
- Support for python 3.7

Changed
- Fixed bug with analysis.core.computeIntensitySegregation: 'self.types'

Added
- New interface for user-defined functions used in multisphere particles
- version, author, and email available from __init__ module
- New keyword 'psd_style' for specifying particle distribution
- New polydisperse example for DEM simulation
- Support for multiple VTK file formats (vtp, vtu)
- Documentation for Mesh class in Analysis section

Changed
- Fixed bugs in intensitySegergation routines in analysis.core.py*
- Improved docstrings in analysis.core.py* and analysis.equilibrium.py
- Renamed Particles.molecules to Particles.Molecules
- Fixed typo in compaction.html file (missing quotes for wallZ)
- Moved simulation.generator submodule to analysis
- Fixed bug in simulation.models with cylindrical boxes

Removed
- Method computeGCOM() in analysis.core.py*
- Attribute 'length' for Particles.molecule

Added
- A random prime number generator for LIGGGHTS (in engine_ligggghts.py)
- Support for polydisperse systems (normal psd, lognormal psd, and discrete distribution)
- PyGran.simulation version printed to pygran.log file

Changed
- Fixed bug in Particles._goto() method

Added
- New `configure' function for specifying which LIGGGHTS version to use
- New `increment' option for System frame propagation. Certain frames can now be skipped when reading multiple traj files.
- Cell and point attributes are exposed separately via: Mesh.points.attr and Mesh.cells.attr
- New version navigation
- Online documentation based on Sphinx
- Pytest scripts for validation

Removed
- Manual in pdf format

Changed
- SubSystem objects are now constructed only once (factory) and thus retain the same memory address from frame to frame
- Mesh SubSystem now takes the optional arg `avgCellData' which transforms cell arrays to their weighted-avg values
- System can now be constructed with additional arguments passed for each SubSystem type
- System rewinds itself after the last frame is reached and it starts reading frame 1 when it is looped over.
- Fixed bug with System frame propagation when both Particles and Mesh were stored
- Fixed bug in SSMP mode when the slave processors did not produce any output
- Fixed bug with user-created scripts importing themselves (leading to double execution)
- Renamed method `add_viscous' to `addViscous' in engine_liggghts and dem modules
- DEM engine config files are stored in ~/.config/engine_name.ini
- System method 'units' always applies to the currently loaded frame
- System method 'units' always returns current unit system (str)

Added

- New dynamic contact model module for the LIGGGHTS-PUBLIC engine. Currently this module supports only contact models derived from the spring-dashpot model.
- Support for dynamic keyword parsing in the LIGGGHTS-PUBLIC engine.
- New tutorial for installing PyGran/LIGGGHTS on Ubuntu 18.04 LTS.

Changed
- Renamed Simulator, Analyzer, and Material modules to simulation, analysis, and params, respectively.
- Fixed bug in the contact duraction computation of the numerical solver in the simulation module.