Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

The sample script plot_HH.py has been replaced for specific examples on how to plot data post-processed with pyMBE: plot_branched_polyampholyte.py, plot_peptide.py, and plot_peptide_mixture_grxmc_ideal.py. (#95)
Sample scripts now take the pH as an argparse input instead of looping over several pH values. This enables paralization of the sample scripts and avoids conflicts with the current post-processing pipeline. (#95)
Switched from os.makedirs to Path().mkdir() to prevent ocasional failure of the scripts when running them in paralel. (#91)
pmb.set_reduced_units() now redefines the reduced units instead of creating a new instance of pint.UnitRegistry. Therefore, the user can do operations between objects defining before and after changing the set of reduced units without getting a ValueError (#89)
pmb.set_reduced_units() now checks that the arguments provided by the user have the right dimensionality. (#89)
The constants stored as attributes in pyMBE.pymbe_library are now using their values stabilished in the 2019 SI. The value is taken directly from scipy.constants instead of being a hard-coded constant. (#86)
Switched to Ctest for testing, allowing to run the tests on paralel (#87)

Code of conduct of our community CODE_OF_CONDUCT.md, adhering to the Contributor Covenant v2.1 (#104)
New optional argument backbone_vector enabling to build molecules along an input vector using pmb.create_molecule and pmb.create_pmb_object (#99)
Unit testing for reaction methods (#86)
New boolean flag --ideal as argparse argument of samples/globular_protein.py enabling to run the script without setting up interactions.
Unit tests for pmb.create_protein, pmb.enable_motion_of_rigid_object, pmb.protein_sequence_parser, pmb.define_protein, pmb.read_protein_vtf_in_df (#101)
Library lattice.py, a general builder for crystaline lattices. This library is part of on-going project to support hydrogels in pyMBE. (#93)
New sample script showing how to use the analysis tools in pyMBE for post-processing time series from the sample scripts analyze_time_series.py (#95)
A new optional argument ignore_files for lib.analysis.analyze_time_series, enabling to provide a list of files to be ignored for post-processing of time series. (#95)
Functional testing for all sample scripts. (#95)
Unit testing for reaction methods. (#86)

Wrong parsing in pmb.protein_sequence_parser of input sequences provided as a list of aminoacids using the three letter code. (#101)
Wrong setup of the rigid object in pmb.enable_motion_of_rigid_object, leading to crashes in samples/globular_protein.py when enabling the protein motion. (#101)
The argparse argument --move_protein of samples/globular_protein.py is now a boolean flag instead of taking arbitrary float values. (#101)
lib.analysis.get_dt now raises a ValueError if the two first two rows of the dataframe have the same values for the time, which break the subsequent code. (#95)
Removed global state variables, instead they are now created by the constructor of pyMBE.pymbe_library. This prevents two instances of the pyMBE library to share the same memory address for their attributes. (#89)
Required Python dependency versions compatible with ESPResSo 4.2 (#84)
NumPy 2, Pandas 2 and the development version of ESPResSo are now fully supported. (#106)
Fixed several deprecated paths and function names in tutorials/pyMBE_tutorial.ipynb. (#77, #78, #79, #80, #81)