dependency on deprecated pkg_resources

[diekhans]

ncls produces the below warning that will become an error.

However, given the lack of activity, it seems like this package is dead.
Unfortunate, because it is very useful.

The pyranges is not a good alternative, as it has a heavy-weight dependency on Pandas.

.../python3.12/site-packages/ncls/__init__.py:2:
UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
  import pkg_resources

[endrebak]

Hi. I am sure I can fix this but if you want the world's fastest overlap operations in any language you should have a look at https://github.com/pyranges/ruranges/blob/master/ruranges/__init__.py#L69

It even supports groups (like chromosomes or transcripts or whatever) and is just a rust library with a Python wrapper.

[endrebak]

It also includes other operations like subtract and nearest.

[endrebak]

I'll update the README for this library with a ruranges link and a smol readme for ruranges.

[endrebak]

And update NCLS so it will continue working.

[diekhans]

Thank you for the update. Will you be so kind as to update bioconda? flair is distribute in bioconda, so it needs all the dependencies in bioconda :-( Oh, I didn't know about ruranges. This looks awesome. I am not sure it is the right tool for this application, where we just need a simple range dictionary. However, I will spread the word about ruranges! I know about pyranges, but any project because of the pandas heavy-weight dependence. If Pandas is not the right tool for the job, having it as a dependency is painful. It looks like ruranges is a excellent alternative. endrebak ***@***.***> writes:

…

endrebak left a comment (pyranges/ncls#59) Hi. I am sure I can fix this but if you want the world's fastest overlap operations in any language you should have a look at https://github.com/pyranges/ruranges/blob/master/ruranges/__init__.py#L69 It even supports groups (like chromosomes or transcripts or whatever) and is just a rust library with a Python wrapper. -- Reply to this email directly or view it on GitHub: #59 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>