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.

[0.1.10] - 2026-04-28

Fixed

  • Fix module import issues in CLI and dataset commands

[0.1.9] - 2026-04-27

Added

  • Add dataset summary, status, scan, inputs, and remove workflow commands

  • Add project and MD log links in dataset views

  • Add waiting state handling for SLURM jobs

  • Add membrane analysis support for united-atom and coarse-grained systems

Changed

  • Refactor dataset storage around SQLite-backed projects and MD entries

  • Update dataset behavior to overwrite entries with the same rel_path by default and hide UUIDs in show

  • Improve topology, ligand, and reference handling, including missing bonds, dummy atoms, and lipid/PubChem lookups

  • Improve workflow task naming, task tracking, and error handling across the console

  • Switch PDB trajectory handling to PyTraj to reduce memory usage

Fixed

  • Fix dataset summaries, empty MD inputs, and inconsistent input handling

  • Fix SAS and solvent handling in structure and screenshot generation

  • Fix ligand and reference edge cases, including null Mordred values and missing PubChem mappings

  • Fix runtime robustness issues around retries, timeouts, multiprocessing, and database locking

[0.1.8] - 2025-12-03

Added

  • Add --ssleep flag to skip SSL certificate authentication

Changed

  • Update mordred dependency

  • Update biobb_mem to 5.1.2

  • Add n_jobs option to dataset command

  • Add ignore option for dataset config directories

Fixed

  • Fix clustering cutoff when low RMSD difference

[0.1.7] - 2025-11-28

Added

  • Support for URLs as input files

  • Test for network flag and top_no to CI

  • Ignore bonds flag (-ib) for handling systems without bonds

  • Support for virtual site “pseudo-bonds”

  • Support for command line forced inputs

  • RMSD check per fragment functionality

  • Enhanced InChIKey handling with PubChem CID retrieval

Changed

  • Refactored ligand and lipid references to use InChIKeys (#42)

  • Renamed ligands module for better organization

  • Changed dataset subcommand from status to groups

  • Changed source code license to Apache 2

  • Updated HPC instructions (#30)

  • Sample trajectory (smp) now picks frames along trajectory instead of at start

  • Better function checksums implementation

Fixed

  • Fixed PCA memory inefficiency

  • Patched MDTraj problem in PCA

  • Fixed TM score no anchors problem

  • Safe trajectory download implementation

  • Fixed issues with missing topology support

  • Fixed errors in handling missing bonds throughout codebase

  • Fixed handling of missing bonds when finding PTMs

  • Fixed CG-related issues

  • Improved pdb_to_uniprot function for nucleic acids

Changed

  • Use networkx for cycle detection

[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.