Refactor file I/O to use context managers and fix bare excepts

[avinxshKD]

I've been digging through mkconcore.py and concore.py, and I noticed we're opening a lot of files without context managers (with statements). While CPython's GC usually handles cleanup, it's not guaranteed and can lead to file descriptor leaks, especially during complex I/O operations or if the script crashes.

Also, there are several except: blocks that catch everything (including KeyboardInterrupt and SystemExit). This makes debugging a pain because you can't easily kill the process if it hangs in a loop, and it masks actual errors we might want to see.

I'd like to refactor these file operations to use with open(...) as f: and narrow down the exception handling to specific errors like IOError or FileNotFoundError. It's a bit of housekeeping but will make the codebase much more robust.

[avinxshKD]

@pradeeban @Rahuljagwani Let me know if this makes sense, ill raise a PR. Thanks

[avinxshKD]

Hi, @pradeeban @Rahuljagwani

Just wanted to ask if there are any community calls or project meets around the org. Would be so nice to join if something like that happens.

Hve been working on the project for around 5–6 weeks now. Still learning, but improving with each PR. Got a bunch merged, a few closed too, BUT learned from all of it. Hoping to keep doing better.

Lastly Thanks for all the work you put into maintaining the org.

[pradeeban]

@avinxshKD sure, you can go ahead. The project was largely done by GSoC contributors from 4 years: 2021 (1 contributor as part of Emory-BMI), 2022 (2 contributors as part of Emory-BMI), 2023 (3 contributors as part of Emory-BMI), and 2025 (1 contributor as part of Alaska). So it makes sense some of these issues were overlooked as we focused on features. Good to fix these.

We do not have meetings at this point. But once we have an accepted contributor, we will have weekly meetings that last an hour.

[pradeeban]

Also, @avinxshKD, make sure to fix the critical mistakes and bugs in the concore repository. concore-lite is just a minimal tutorial repository. We must fix the breaking issues here. Other than that, we can choose to live with many bugs here, as we otherwise will be essentially maintaining two separate repositories and cherrypicking the fixes between the repositories. Not an efficient use of time.

[avinxshKD]

hey thanks for the context @pradeeban

Understood our priority, I'll focus on fixing critical issues in the main concore repository first. This refactor in concore-lite is straightforward, so I'll knock it out quickly and then shift attention to identifying and fixing breaking bugs in the primary repo.

Appreciate the heads-up on the project history. Makes sense why some of these housekeeping items slipped through when features were the main focus.

I'll have the PR up shortly for this one and start auditing concore for more serious issues. Already fixed some issues from main today, do check when free,

Also wanted to ask you the prefrred date for the proposal as im already working on it, thanks again🌸