Maintenance fixes

[ordabayevy]

• Deprecated API usages found by TorchFix linter (Use more numerically stable log1p in examples/scanvi/scanvi.py #3397 (comment))
• Remove tests for deprecated torch.triangular_solve
• Replace deep_getattr function with Python's operator.attrgetter

[martinjankowiak]

lgtm thanks!

[kit1980]

You can add TorchFix to the CI to prevent regressions and get future improvements.
It would be very easy if you run flake8, but I see you recently removed flake8 from the CI...

[ordabayevy]

Yes, we moved from flake8 to ruff because it is much faster. Do you plan to support ruff in the future?

[kit1980]

For ruff everything needs to be rewritten completely, in Rust. Maybe someone from ruff community will do that.
TorchFix already uses LibCST as the main library, which is written in Rust, so should be fast already.
Maybe you want to re-enable flake8 just for TorchFix?

Also there is a standalone torchfix script besides the flake8 interface, but currently it doesn't have support for running in CI.

[martinjankowiak]

thanks @kit1980 !

we probably don't want to bring flake8 back into our CI, but i've made an issue to track this in case future versions of torchfix can be brought into our CI more easily: #3399