Output all run-time information into files

[adamjohnwright]

Currently the output from running the model is being printed to standard out. It is possible to create a log file for this output. It would also be good to output the model into a file as well. And then a third file for run-time parameters.

[Shruthii7]

Hello, @adamjohnwright

I was exploring this issue and observed that output is currently handled through scattered print statements across different parts of the codebase (Python, R, and Julia), with no centralised or structured logging mechanism.

Additionally, there does not appear to be a consistent way to persist runtime outputs, model results, or execution parameters into files.

I would like to work on enhancing this by:

• Introducing structured runtime logging with timestamps
• Saving model outputs into structured files (e.g., CSV)
• Recording run-time parameters separately for reproducibility
• Organizing outputs into a consistent directory structure

This would improve usability, debugging, and reproducibility when running MP-BioPath on multiple datasets.

Please let me know if this approach aligns with the intended direction, or if there are specific parts of the codebase I should focus on.

Thank you!