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.
- New CLI for reading input and writing output
- New modular design consisting of "test" and "engine" submodules
- CLI arg --top to the parser so that the output topology would be written to a file (no longer printed to stdout)
- Support for python 3
- New "optimization.pyx" module for faster implementation (in C) of find_bead_pos()
- Fixed genMoleculeSDF() which did not use "sdf" input argument
- Fixed function printBonds() which used undefined "atomPartitioning" object
- Function Substructure() no longer creates then reads "tmp-auto-martini.smi" file
- Function check_additivity() no longer creates then reads "tmp-auto-martini.smi" file
- Undefined objects "hbondA" and "hbondD" in function printAtoms()
- Variable "mad" in function checkAdditivity() was already defined as a function
- Testing scripts that work with pytest
- Method "gen_molecule_smi" in topology module no longer raises an exception when kekulization fails
- CLI arg "mode" replaced with "--mode", defaults to "run"
- Initial value of "attempt" set to 0 (from 1) in function solver.cg_molecule()
- Merged function topology.gen_molecule_smi() with master branch
- Submodule "test" (replaced with pytest scripts)
- Pytest routines and test files for validation
- Conda environment file for easy installation
- Github actions CI
- Versioneer for automated version handling
- Improved exception handling in topology.py
- Mode=test no longer supported by the CLI
- TravisCI and CircleCI config files
- PEP 518 compliance with pyproject.toml
- Conda and pypi packages
- New directory structure
- Poetry build and deployment
- Build ext file:
build_ext.py - Dynamic versioning with poetry-dynamic-versioning
- Replaced bs4 with beautifulsoup4 pkg
- Code format and style complies with PEP8
- Old setup file
setup.py MANIFEST.in- Conda env file
environment.yaml - Versioneer
- Sync optimization.pyx with optimization.py
- Improve handling of vcclab.org connection timeout