Change Log

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.

[0.2.3] - [2026-06-24]

Added

  • Added a new Session class to centralize session-based input/output handling across the entire package.

  • Added a new ARXCLI module to provide a streamlined Command-Line Interface for running the AutoREACTER workflow with a single command.

    • The CLI supports input file parsing, session management, and orchestrating the end-to-end workflow.

Changed

  • Centralized state management across the entire package. The Session object is now the single source of truth. All modules and functions have been refactored to use the Session for accessing inputs, outputs, and configuration.

  • Centralized the versioning system to dynamically pull from the package’s __version__ attribute.

  • Updated all documentation, examples, and CI configuration to reflect the new API and workflow changes.

[0.2.2] - 2026-06-09

Added

  • Added a new PyPI-ready version of AutoREACTER.

  • Added new reactions to the reaction library.

  • Added the ARXSession module for centralized session-based input/output handling.

  • Added unit tests for the LUNAR API wrapper.

  • Added MANIFEST.in to support packaging of required non-Python files.

  • Added outputs save direction same as the input file directory.

Changed

  • Refactored cache and staging logic to use temporary/session-based directories instead of manually managed base_dir paths.

  • Updated .frc file handling to use package-included force field files.

  • Moved frc_files inside the AutoREACTER package for more reliable access after installation.

  • Improved PCFF .frc directory discovery to be more robust against repository layout changes.

  • Updated prepare_reactions.py, molecule_3d_preparation.py, REACTER_files_builder.py, and lunar_api_wrapper.py to use session-based inputs.

  • Updated documentation, examples, CI configuration, and getting-started instructions.

Deprecated

  • Deprecated direct base_dir-style path handling in favor of ARXSession-based workflow management.

Removed

  • Removed older manual cache directory resolution logic.

  • Removed temporary/editor backup files from the repository.

  • Removed outdated path-resolution behavior that depended on repository-relative assumptions.

  • Removed the old dated folder output method.

Fixed

  • Fixed .frc file path resolution issues when running AutoREACTER from different locations.

  • Improved error messages for missing or unresolved .frc files.

Security

  • No security-related changes in this release.

[0.2.1] - 2026-05-04

Fixed

  • Fixed issue where cache/00_cache was not cleared when initiating a new AutoREACTER run.

  • Improved cache handling to prevent bugs caused by deleting cache files in the middle of a run.

  • Added a warning message when the --cleanup command is used to delete all cached runs, to prevent accidental data loss.

[0.2.0] - 2026-05-01

Breaking

  • Migrated to a class-based architecture (not backward compatible).

  • Updated input schema: explicit density and temperature per replica required.

  • Replaced RDKit atom map numbers with isotope-based tracking.

  • Changed output structure to dated run directories.

  • Introduced library-driven workflow for reactions and functional groups.

Added

  • CLI interface (AutoREACTER.py) with –help and –cleanup support.

  • Jupyter-based interactive visualization tools.

  • Support for string-based LAMMPS atom types (e.g., PCFF).

  • Force field selection via input.json.

  • Retention cleanup utility for managing old runs.

  • Modular detectors and libraries for workflow stages.

  • Control over non-reactive species retention.

Changed

  • Refactored core workflow into modular classes.

  • Improved atom mapping robustness using isotopes.

  • Optimized input generation to reduce unnecessary LAMMPS files.

Fixed

  • Enforced strict validation of external tool paths.

[0.1.0] - 2026-02-17

Added

  • Initial release of AutoREACTER as a script-based workflow for polymer simulation preparation.

  • Support for Jupyter Notebook–based interactive execution.

  • Functional group detection using SMARTS-based pattern matching (step-growth monomers only).

  • Library-driven workflow with structured definitions for functional groups and reactions.

  • Deterministic reindexing for consistent reaction templates and mapping files.

  • Generation of REACTER-compatible LAMMPS input files using integer-based atom typing.

  • Unified input parsing via a single structured input file for simulation configuration.