Changelog

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

[Unreleased]

Granular solution output modes, providing clearer labeling for optimal and sub-optimal repairs.

Unified solution selection logic under a single --sol argument (replacing internal --single-sol and --sub-opt flags).
Updated README and documentation to reflect the new command-line interface.

Variable names are now quoted in generated logic programs for ASP compliance.
Replaced the -v/--verbose flag with the more specific -f/--format implementation.
Refined internal configuration names and progress output terminology for consistency.

Fixed a bug where providing multiple observation-updater pairs would only process the last one.

Added .csv format support as a proposal for observation files.
Option to write and export repaired model files under a new unified parser module.
Full model.zginml support with unified parsing of Boolean expressions.
Added vertex node support.
Fully functioning asp_reader with example files and pytest integration.
Replaced custom shell test scripts (run_tests.sh) with native pytest testing (test_model_files.py).
Extensively populated the examples/ directory for test automation.
Introduced a standard logging system, including a specific debug mode for updaters.
Support for multiple observation files of the same topology in a single run.

Readers have been redesigned as polymorphic Parsers (parser_ginml.py, parser_bnet.py, parser_asp.py), capable of both read() and write() operations.
The BNET parser now evaluates functions comprehensively using Quine-McCluskey logic reduction, dropping degenerate regulators, and assuming monotonicity (defaulting to positive).
Repaired GINsim networks now retain their original .ginml XML layout styling and preserve the inner files of .zginml zip archives.
Edge signs are explicitly displayed in function repair proposals.
Significant refactoring of the repair engine, and simplified dynamic loading of updater classes.
Changed configuration class structures, now utilizing elegant pythonic @property getters and setters.
Migrated all command-line interface arguments to argparse.
Cleaned up unneeded dependencies such as asp_helper and consolidated the code.