Hidden Assumptions in Codebase Causing Frequent Errors

[ChuanyuXue]

There are multiple hidden assumptions in the codebase that are not well-documented. This leads to frequent errors when users run the tool, especially related to common functions used in utils folder, such as input file parsing (#32) and saving result files.

This type of assumptions should be either removed or have clear documentation.

TODO:

• Identify and document all hidden assumptions in the repo that could cause similar errors.
• Either modify the code to handle these cases and provide meaningful error messages with suggested fixes.
• Clearly list all assumptions cannot be fixed in the documentation, like a dedicated “Known Issues” section.