Update cosolvkit towards v0.6.0

[mallanos]

This pull request introduces several improvements and updates to the documentation and the code. The main focus is on improving usability, configuration clarity, and logging, as well as updating default parameters and correcting inconsistencies. Several new features were included in the analysis pipeline as well. Below are the most important changes, grouped by theme:

Documentation and Configuration Updates:

• Updated the README.md to reflect new configuration parameter names and defaults, clarified instructions, fixed typos, and improved example usage. Notable changes include renaming parameters (e.g., radius → box_size, output → output_dir), updating cosolvent and repulsive force parameter names, and correcting SMILES strings. [1] [2] [3] [4] [5] [6]

CLI Script Improvements:

• Added logging throughout the create_cosolvent_system.py script using a new setup_logging utility, providing clearer runtime feedback and error reporting. [1] [2] [3]
• Updated argument and configuration handling: replaced deprecated or ambiguous parameters (e.g., radius → box_size), updated default simulation steps to 25000000, added new arguments for temperature, and improved error checking for configuration consistency. [1] [2]
• Improved protein variant assignment logic and error handling, and clarified the logic for building systems with or without a receptor.
• Enhanced handling of repulsive forces: renamed parameters, improved consistency checks, and ensured repulsive forces are only applied when using the OpenMM engine. [1] [2]

Simulation and Output Handling:

• Standardized file naming and output directory usage throughout the script, ensuring all outputs and logs are saved in the specified output_dir.
• Updated the MD simulation invocation to use new parameter names and improved error handling for unsupported formats.

These changes collectively improve the reliability, clarity, and usability of the cosolvkit setup and simulation workflow.