Dependencies

[suhrig]

Hi Jon,

Thank you for this rich and easy-to-use package!

I am currently facing a technical issue where I want to install the package alongside some other in-house python package in the same poetry project. There is a conflict between the in-house package and mepylome: the former needs plotly > 6.3.2, the latter needs plotly < 6.0.0. Is there a necessity to pin the version of plotly below version 6 for mepylome to work? I just hacked a copy of mepylome to use plotly 6.5.2 and the CNV plot worked without (obvious) issues. Would it be possible to upgrade the dependency?

Likewise, mepylome is bound to setuptools < 82.0.0, because of its dependency on the deprecated package pkg_resources. Is there any chance this dependency can be lifted?

Best regards,
Sebastian

[brj0]

Hi Sebastian,

I pinned plotly as there was a serious bug (with 6.0.x) that made CNV-plots impossible. I just unpinned it (only the github version; I will update the pypi version a bit later), as it seems that this bug is now fixed. The dependency on the deprecated package pkg_resources comes from the package pyranges (this is used for the CNV plots). It looks like pyranges will be updated soon (some API will change as well) to a better version (only for python 3.12 though). I’ll wait for that release and then adapt the code accordingly.

Regards,
Jon