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.

[0.1.6] - 2025-10-29

Added

  • Dataset documentation and generate_inputs_yaml method

  • Support for missing bonds in molecular systems

  • Error log handling and clickable links for logs in Jupyter display

  • Dataset subcommand to CLI

  • Status dataset command functionality

Changed

  • Renamed model_workflow to mddb_workflow (#22)

  • Updated to Python 3.11 (#41)

  • Updated CI Python version

  • Added cg_test2 to CI testing

  • Fixed recursive transformer functionality

  • Improved exception handling with standardized JSON support

Fixed

  • Imaging repeated uselessly bug

  • Various bugs in molecular system handling

  • SLURM job path issues

  • Biotite tmscore protein check fixes

  • Logging color removal with -nc flag

[0.1.5] - 2025-10-23

Added

  • License file and proper licensing (#16)

  • Manual API tools for better automation

  • Dummy data for enhanced unit testing

  • Channels analysis functionality

  • Membrane analysis for coarse-grained (CG) systems

  • Plot functions for membrane analysis results

  • InChI key support for ligands

  • SwissLipids names to lipid references

  • Structure classes to documentation

  • Parallel processing for InChI key generation

Changed

  • Updated minimum Python version requirement to >=3.10.0

  • Enhanced type hints and docstring coverage across codebase

  • Improved input file processing to be more task-like

  • Moved comments to docstrings for better documentation

  • Refactored lipid analysis functions to use MDAnalysis Universe directly

  • Changed tmscoring implementation to use biotite

  • Updated FATSLiM compatibility with numpy 1.26

  • Improved structure corrector messages

  • Enhanced interactions logic with automatic detection

Fixed

  • Critical fixes in Gromacs integration

  • Gromacs masses fixer improvements

  • Cached exceptions handling

  • Automatic no-reference (noref) detection bugs

  • Interactions reform with type-critical bug fixes

  • Biotite TM score with non-standard amino acids

  • Input trajectory overwriting issues

  • Topology and trajectory input filepath handling

  • UniProt secure connection failures

  • Various path handling improvements

  • Glucolipids linter fixes

Removed

  • Unnecessary dependencies for improved performance

  • Path filters from release workflow trigger

Security

  • Improved secure connection handling for external APIs

[0.1.4] - 2025-08-11

Changed

  • Fixed version name handling

  • Added GHCR (GitHub Container Registry) support

  • Improved Slack notification system

[0.1.3] - 2025-08-11

Added

  • GitHub Container Registry (GHCR) integration

[0.1.2] - 2025-08-11

Added

  • GitHub Container Registry (GHCR) support

[0.1.1] - 2025-08-11

Added

  • GitHub Container Registry (GHCR) functionality

[0.1.0] - 2025-07-23

This is the first major release of the MDDB workflow package.

Added

  • Core molecular dynamics analysis workflow

  • Support for multiple MD simulation formats

  • Automated topology generation

  • Ligand and lipid reference generation

  • PDB reference handling

  • Metadata generation capabilities

  • Structure correction and validation

  • Interaction type detection

  • Comprehensive testing suite

  • Documentation system

  • CI/CD pipeline

[0.0.2] - 2025-07-21

Changed

  • Simplified version extraction from pyproject.toml

[0.0.1] - 2025-04-14

Added

  • Initial release

  • Basic project structure

  • Core functionality implementation

  • Include subfolders support

Note

This changelog was generated from the git commit history on 2025-10-29. For detailed information about specific changes, please refer to the git commit history.