Can bbclient module be its own package?

[jkanche]

Hi, I was wondering if it makes sense to separate bbclient module into its own package, definitely reduces the number of dependencies that one would have to install to access resources from bedbase.

[nsheff]

Yeah -- it definitely could be.

Alternatively, we had discussed dividing out the dependencies, so that they would be optional, and the heavier ones could be installed only with optional dependencies. would that work for you?

[jkanche]

that would be perfect, thank you!

My motivation comes from setting up the bioconductor workshop: https://biocpy.github.io/BiocWorkshop2024/tutorials/genomic_ranges.html#load-chip-seq-peaks

[khoroshevskyi]

@jkanche, we just released a new version of geniml.

After this release, all heavy dependencies will no longer be installed by default.

To use bbclient, install geniml version 0.4.2 or higher in the usual way:

pip install geniml>=0.4.2

If you want to use the machine learning modules from geniml, install it this way:

pip install geniml[ml].

These changes will allow users to install geniml with basic requirements quickly, without using additional disk space or time for installing unnecessary dependencies. Let us know about your user experience. Thank you!