Cleanup package for dependency in scib-metrics

[adamgayoso]

Hello, I'm interested in using these metrics in the package we are building:

https://github.com/YosefLab/scib-metrics

which contains reimplementations of the scib metrics mostly using jax. I think it would be cool to include the balanced ari/ami here, but this package currently seems to contain superfluous and restricted dependencies (e.g., jupyterlab, and tight restrictions on numpy etc). Furthermore, there is some cython code that can make things complicated. However, it does look straightforward to reimplement that one function using numba for example.

Is there any interest in including these two changes (removing unnecessary dependencies and porting to use numba) here?

[adamgayoso]

If you wanted, you could also refactor this package to use https://github.com/scverse/cookiecutter-scverse

[hsmaan]

Hi @adamgayoso, I'm glad to see that your team has an interest in adding these metrics. We'd be happy to refactor the code to try to include the balanced ARI and AMI in scib-metrics.

I've removed the restricted and unnecessary dependencies, as well as the notebooks which use them in the scib_metrics branch. For the cython code, I'm a little less sure as I do not have experience with numba. If I can work with a member of your team on that aspect, that would help move things along a bit quicker. Otherwise, I can look into things and try to port it.