Version 0.5.0

Compared to the last release, the following changes have been made to version 0.5.0:

• Deployed the package to PyPI: https://pypi.org/project/ensemble-md/0.5.0/
• Fixed the bug in updating the replica-space trajectories and exchanging replicas in get_swapping_pattern.
• Renamed the parameter mc_scheme as acceptance.
• Added a new parameter proposal that can be specified in the input YAML file and transferred a part of functionalities of n_ex to it.
• Re-implemented the method of multiple swaps so that the swappable pairs are re-identified whenever an attempted swap is accepted.
• Implemented the method of exhaustive swap in get_swapping_pattern.
• Refactored functions including calc_prob_acc and get_swapping_pattern in ensemble_EXE.py
• Updated the documentation
  • Updated the instruction about installation via PyPI
  • Added a section about the available proposal schemes
• Developed/Refined unit tests for the following modules to improve the code coverage:
  • ensemble_EXE.py
  • gmx_parser.py
  • analyze_matrix.py