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

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [0.3] - [2026-08-xx]
### Added

* **Reaction Progression:** Multi-stage reaction template generation to handle multi stage reaction progressions, copolymerizations and small molecules which needs few templates for the polymerization reactions.
* **Looping Control:** A new loop control parameter in the input file to prevent the explosion of unnecessary reactions. Defaults to `5` loops, but can be optimized by setting `loop: <int>` or disabled entirely with `loop: False`.
* **Advanced Detection:** Index-based functional group detection and index-based reaction detection to accurately identify reacting atoms post-first reaction.
* **Pathway Deduplication:** NetworkX-based deduplication detection to actively filter redundant reaction pathways.
* **Reaction Libraries:** Robust library modules for various polymer chemistries, including Epoxies, Polyamides, Polyesters, Polycarbonates, Polysiloxanes, Polyureas, Polyurethanes, and Vinyl polymers.
* **Force Field Parameters:** PCFF force field additions, specifically including new `s_m` sulfone parameters.

### Changed

* **Library Organization:** Centralized the reaction libraries into dedicated modules to improve maintainability and expandability.
* **Structure Generation:** Improved 3D molecule embedding to better handle highly congested polymer structures.

### Removed

* **Legacy Code:** Removed legacy compatibility shims (`_compat.py`).

### Fixed

* Addressed various stability and progression issues tracked in recent bug reports.
* Improved Error handling when no reaction instances are found for the specified monomer combinations.

## [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.